REVIEW | doi:10.20944/preprints202009.0513.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: PIP2; membrane dynamics; disease; actin dynamics; phosphoinositides; signaling
Online: 22 September 2020 (09:04:28 CEST)
In this review we summarize the recent development in understanding the role of PIP2 in cellular function and signaling. We first discuss the effect of PIP2 on actin binding proteins addressing the mechanism of the actin cytoskeletal dynamics such as polymerization or depolymerization of the filamentous network or the coupling to membrane to generate forces. Next, we outline the role of PIP2 in membrane dynamics. We summarized how the membrane organization depends upon PIP2 in the presence of ions or transmembrane proteins that are sensitive to membrane curvature. We discuss how clathrin coated pits interact with adaptor proteins during the endocytosis process, which is facilitated by PIP2. Finally, we discuss the role of PIP2 in cell signaling and diseases.
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Aurora-A; Molecular dynamics simulation; Activation loop; Conformational dynamics
Online: 25 February 2021 (11:20:09 CET)
The conformational state of the activation loop (A-loop) is pivotal for the activation of most protein kinases. Hence, the characterization of the conformational dynamics of the A-loop is important to increase our understanding of the molecular processes related to diseases and to support the discovery of small molecule kinase inhibitors. Here, we carry out a combination of Molecular Dynamics (MD) and Essential Dynamics (ED) analyses to fully map the effects of phosphorylation, ADP, and conformation disrupting (CD) inhibitors (i.e., CD532 and MLN8054) on the dynamics of the A-loop of Aurora-A. MD revealed that the stability of the A-loop in an open conformation is enhanced by single phospho-Thr-288, while paradoxically, the presence of second phosphorylation at Thr-287 decreases such stability and renders the A-loop more fluctuant in time and space. Moreover, we found that such post-translational modification has a significant effect on the direction of A-loop motions. ED analysis suggests that the presence of the phosphate moiety induces the dynamics of Aurora-A to sample two distinct energy minima, instead of a single large minimum, as in unphosphorylated Aurora-A states. This suggests that the conformational distributions of Aurora-A with both single and double phospho-threonine modifications are remarkably different from the unphosphorylated state. In the closed states, binding of CD532 and MLN8054 inhibitors has the effect of increasing the distance of the N- and C-lobes of the kinase domain of Aurora-A, and the angle analysis between those two lobes during MD simulations showed that the N- and C-lobes are kept more open in presence of CD532, compared to MLN8054. As the A-loop is a common feature of Aurora protein kinases, our studies provide a general description of the conformational dynamics of this structure upon phosphorylation and different ligands binding.
REVIEW | doi:10.20944/preprints201810.0329.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: protein dynamics; coarse-grained simulation; Monte-Carlo dynamics; structural flexibility; large-scale dynamics; elastic network model;
Online: 15 October 2018 (17:10:57 CEST)
Fluctuations of protein three-dimensional structures and large-scale conformational transitions are crucial for the biological function of proteins and their complexes. Experimental studies of such phenomena remain very challenging and therefore molecular modeling can be a good alternative or a valuable supporting tool for the investigation of large molecular systems and long-time events. In this mini-review, we present two alternative approaches to the coarse-grained (CG) modeling of dynamic properties of protein systems. We discuss two CG representations of polypeptide chains used for Monte Carlo dynamics simulations of protein local dynamics and conformational transitions and, on other hand, highly simplified structure-based Elastic Network Models of protein flexibility. In contrast to classical Molecular Dynamics the modeling strategies discussed here allow quite accurate modeling of much larger systems and longer time dynamic phenomena. We briefly describe the main features of these models and outline some of their applications, including modeling of near-native structure fluctuations, sampling of large regions of the protein conformational space, or possible support for the structure prediction of large proteins and their complexes.
SHORT NOTE | doi:10.20944/preprints202202.0168.v1
Online: 14 February 2022 (07:25:28 CET)
Newton's second law, sometimes called the fundamental principle of dynamics, although considered as an irreducible axiom of mechanics based on and validated by experience, might paradoxically depend on the energetic content of our cosmos, through the existence of a dynamical form of aether appearing, in the ancient theory of Fatio de Duillier and Lesage, as an explanation of gravitational forces. In such a framework, Newton's theory is an approximation valid for small velocities as it was the case in special relativity theory.
REVIEW | doi:10.20944/preprints201810.0360.v1
Subject: Chemistry And Materials Science, Medicinal Chemistry Keywords: Molecular Dynamics, CoSolvent Molecular Dynamics, Drug design, Fragment Screening, Docking
Online: 16 October 2018 (12:15:17 CEST)
Molecular dynamics(MD) simulations are playing an increasingly important role in structure-based drug discovery (SBDD). Here we review the use of MD for proteins in aqueous solvation, organic/aqueous mixed solvents (MDmix) and with small ligands, to the classic SBDD problems: binding mode and binding free energy predictions. The simulation of proteins in their condensed state reveals the solvent structure and preferential interaction sites (hot spots) on the protein surface. This information is largely transferable across all classes of protein ligands (from water to drugs) and can be used very effectively to understand ligand recognition and improve the predictive capability of well-established methods such as molecular docking. MD simulations for protein and drug or drug-like compounds are now being used but are still computationally expensive and can only be applied to specific cases. On the other hand, MDmix simulations can now be used in SBDD and we will describe the latest developments and implementations. We expect to see an increase in the application of these techniques to a plethora of protein targets to identify new drug candidates with the advent of new tools and faster computers.
ARTICLE | doi:10.20944/preprints202207.0284.v1
Subject: Physical Sciences, Applied Physics Keywords: two-level transition; electron dynamics; spin dynamics; spin angular momentum perturbation
Online: 19 July 2022 (09:53:58 CEST)
State transition in the multiple-levels system has the great potential applications in the quantum technology. In this article we employ a deterministic approach in complex space to analyze the dynamics of the 1s-2p electron transition in the hydrogen atom. The electron’s spin motion is embodied in the framework of quantum Hamilton mechanics that allows us to examine the transition dynamics more precisely. The transition is driven by an oscillating electric field in the z-direction. The electron’s transition process can be visualized by monitoring its motion in the complex space. The quantum potential and the total energy proposed in this paper provide new indices to observe the dynamic changes of electrons in the transition process.
REVIEW | doi:10.20944/preprints201811.0079.v1
Subject: Physical Sciences, Applied Physics Keywords: interpersonal coordination; competition; dynamical systems; discrete dynamics; continuous dynamics; sporting activity
Online: 5 November 2018 (03:30:07 CET)
Complex human behavior, including interlimb and interpersonal coordination, has been studied from a dynamical system perspective. We review the applications of a dynamical system approach to a sporting activity, which includes continuous, discrete, and switching dynamics. Continuous dynamics identified switching between in- and anti-phase synchronization, controlled by an interpersonal distance of 0.1 m during expert kendo matches, using a relative phase analysis. As discrete dynamics, return map analysis was applied to the time series of movements during kendo matches, and six coordination patterns were classified. Furthermore, state transition probabilities were calculated based on the two states, which clarified the coordination patterns and switching behavior. We introduced switching dynamics with temporal inputs to clarify the simple rules underlying the complex behavior corresponding to switching inputs in a striking action as a non-autonomous system. As a result, we determined that the time evolution of the striking action was characterized as fractal-like movement patterns generated by a simple Cantor set rule with rotation. Finally, we propose a switching hybrid dynamics to understand both court-net sports, as strongly coupled interpersonal competition, and weakly coupled sports, such as martial arts.
Subject: Computer Science And Mathematics, Computer Science Keywords: icosahedron; dynamics; equivariant map
Online: 15 December 2019 (13:31:39 CET)
Drawing inspiration from a recent construction of a polyhedral structure associated with an icosahedrally-symmetric map on the Riemann sphere, the article shows how to build such "dynamical polyhedra" for other icosahedral maps. First, icosahedral algebra is used to determine a special family of maps with 60 periodic critical points. The topological behavior of each map is worked out and results in a geometric algorithm that constructs a system of edges---the dynamical polyhedron---in natural correspondence to a map's topology. It turns out that the maps' descriptions fall into classes the presentation of which concludes the paper.
ARTICLE | doi:10.20944/preprints201810.0645.v1
Subject: Computer Science And Mathematics, Logic Keywords: adaptive dynamics; evolution; cooperation
Online: 29 October 2018 (02:15:33 CET)
Evolution of cooperation has traditionally been studied by assuming that individuals adopt either of two pure strategies, to cooperate or defect. Recent work have considered continuous cooperative investments, turning full cooperation and full defection into two opposing ends of a spectrum and sometimes allowing for the emergence of the traditionally-studied pure strategies through evolutionary diversification. These studies have typically assumed a well-mixed population in which individuals are encountered with equal probability, Here, we allow for the possibility of assortative interactions by assuming that, with specified probabilities, an individual interacts with one or more other individuals of the same strategy. A closely related assumption has previously been made in evolutionary game theory and has been interpreted in terms of relatedness. We systematically study the effect of relatedness and find, among other conclusions, that the scope for evolutionary branching is reduced by either higher average degree of, or higher uncertainty in, relatedness with interaction partners. We also determine how different types of non-linear dependencies of benefits and costs constrain the types of evolutionary outcomes that can occur. While our results overall corroborate the conclusions of earlier studies, that higher relatedness promotes the evolution of cooperation, our investigation gives a comprehensive picture of how relatedness affects the evolution of cooperation with continuous investments.
ARTICLE | doi:10.20944/preprints202112.0266.v1
Subject: Chemistry And Materials Science, Nanotechnology Keywords: Density Functional Theory; Molecular Dynamics; Umbrella Sampling; Brownian Dynamics; Multiscale; Nanoparticle; Aggregation; Clustering
Online: 16 December 2021 (10:51:29 CET)
Titanium dioxide nanoparticles have risen concerns about their possible toxicity and the European Food Safety Authority recently banned the use of TiO2 nano-additive in food products. Following the intent of relating nanomaterials atomic structure with their toxicity without having to conduct large scale experiments on living organisms, we investigate the aggregation of titanium dioxide nanoparticles using a multi-scale technique: starting from ab initio Density Functional Theory to get an accurate determination of the energetics and electronic structure, we switch to classical Molecular Dynamics simulations to calculate the Potential of Mean Force for the connection of two identical nanoparticles in water; the fitting of the latter by a set of mathematical equations is the key for the upscale. Lastly, we perform Brownian Dynamics simulations where each nanoparticle is a spherical bead. This coarsening strategy allows studying the aggregation of a few thousand nanoparticles. Applying this novel procedure, we find three new molecular descriptors, namely, the aggregation free energy and two numerical parameters used to correct the observed deviation from the aggregation kinetic described by the Smoluchowski theory. Molecular descriptors can be fed into QSAR models to predict the toxicity of a material knowing its physicochemical properties, without having to conduct large scale experiments on living organisms.
ARTICLE | doi:10.20944/preprints202105.0307.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Clonorchis sinensis; cathepsin D; aspartic peptidase; molecular dynamics simulation; pH effect; flap dynamics
Online: 13 May 2021 (14:03:32 CEST)
Cathepsin D (CatD; EC 184.108.40.206) family peptidases of parasitic organisms are regarded as potential drug targets as they play critical roles in the physiology and pathobiology of parasites. Previously, we characterized the biochemical features of cathepsin D isozyme 2 (CatD2) in the carcinogenic liver fluke Clonorchis sinensis (CsCatD2). In this study, we performed all-atomic molecular dynamics simulations by applying different systems for the ligand-free/bound forms under neutral and acidic conditions to investigate the pH-dependent structural alterations and associated functional changes in CsCatD2. CsCatD2 showed several distinctive characteristics as follows: 1) CsCatD2-inhibitor complex formed more hydrogen bonds; 2) acidic pH caused major conformational transitions from open to closed state in this enzyme; 3) neutral pH induced displacement of the N-terminal part to hinder the accessibility of the active site and open allosteric site of this enzyme; and 4) the flap dynamics metrics, including distance (d1), TriCα angles (θ1 and θ2), and dihedral angle (ϕ), account for the asymmetrical twisting motion of the active site of this enzyme. These findings provide an in-depth understanding of the pH-dependent structural dynamics of CsCatD2 and basic information for the rational design of an inhibitor as a drug targeting CsCatD2.
ARTICLE | doi:10.20944/preprints201910.0309.v1
Subject: Computer Science And Mathematics, Computational Mathematics Keywords: fluid dynamics Android app; compressible flows; isentropic flows; Android app for gas dynamics
Online: 27 October 2019 (15:30:45 CET)
The computing power of smartphones has not received considerable attention in the mainstream education system. Most of the education-oriented smartphone applications (apps) are limited to general purpose services like Massive Open Online Courses (MOOCs), language learning, and calculators (performing basic mathematical calculations). Greater potential of smartphones lies in educators and researchers developing their customized apps for learners in highly specific domains. In line with this, we present Fluid Dynamics, a highly accurate Android application for measuring flow properties in compressible flows. This app can determine properties across the stationary normal and oblique shock, moving normal shock and across Prandtl $-$ Meyer expansion fan. This app can also measure isentropic flows, Fanno flows, and Rayleigh flows. The functionality of this app is also extended to calculate properties in the atmosphere by assuming the International Standard Atmosphere (ISA) relations and also flows across the Pitot tube. Such measurements are complicated and time-consuming since the relations are implicit and hence require the use of numerical methods, which give rise to repetitive calculations. The app is an efficient semi-implicit solver for gas dynamics formulations and uses underlying numerical methods for the computations in a graphical user interface (GUI), thereby easing and quickening the learning of concerned users. The app is designed for the Android operating system, the most ubiquitous and capable surveillance platform, and its calculations are based on JAVA based code methodology. In order to check its accuracy, the app's results are validated against the existing data given in the literature.
ARTICLE | doi:10.20944/preprints202307.0197.v1
Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: molecular dynamics; polymorph; thermal decomposition
Online: 4 July 2023 (11:34:06 CEST)
A self-consistent charge density-functional tight-binding method combined with molecular dynamics simulations is employed to reveal the effect of polymorph on the thermal decomposition stability of 1,1-Diamino-2,2-Dinitroethylene (FOX-7). Two types of heating, constant temperature heating and temperature-programmed heating, are adopted. Potential evolution indicates that γ-FOX-7 possesses the lowest thermal stability, as it is closer to the decomposition state. Crystal form has an important influence on the thermal decomposition of FOX-7, resulting in different decomposition rates and initial reactions. In general, β- and γ-FOX-7 always decompose more completely than α-FOX-7. This work emphases the importance of polymorph dependent initial decay of an energetic polymorphic compound once heated in a volume constrained condition.
ARTICLE | doi:10.20944/preprints202305.0603.v1
Online: 9 May 2023 (08:29:43 CEST)
We study the synchronous dynamics of three diffusively coupled erbium-doped fiber lasers (EDLFs) in the unidirectional ring configuration without external pump modulation. The dynamical behavior of the system is analyzed using time series, Fourier spectra, Poincaré sections, bifurcation diagrams, and Lyapunov exponents for different values of the coupling strength. For weak coupling, we observe a well-known route to chaos from a stable equilibrium through a Hopf bifurcation and a series of torus bifurcations as the coupling strength is increased. An interesting result is found for large values of the coupling strength, where the phase locking is close to zero. This allows a significant increase in the peak energy of the EDFLs pulses, i.e., above the coupling strength the lasers switch to a Q-switching mode with large-amplitude short pulses. This result allows us to propose a new method for increasing the laser pulse energy based on the control of the bistability by the rotating wave in the array of three unidirectionally ring-coupled EDFLs as a function of the coupling strength. In our system, we were able to increase the peak laser power by almost 20 times more than a continuous single EDFL.
ARTICLE | doi:10.20944/preprints202204.0187.v1
Subject: Environmental And Earth Sciences, Space And Planetary Science Keywords: Dynamics; Solar System; Global Warming
Online: 20 April 2022 (08:53:55 CEST)
Global warming is one of the problems of human civilization and decarbonization policy is the main solution to this problem. In this work, we propose an alternative method of using the gravity-assist by the asteroids to increase the orbital distance of the Earth from the Sun. We can manipulate the orbit of asteroids in the asteroid belt by solar sailing and propulsion engines to guide them towards the Mars orbit and a gravitational scattering can put asteroids in a favorable direction to provide an energy loss scattering from the Earth. The result would be increasing the orbital distance of the earth and consequently cooling down the Earth’s temperature. We calculate the increase in the orbital distance of the earth for each scattering and investigate the feasibility of performing this project.
ARTICLE | doi:10.20944/preprints202112.0169.v1
Subject: Environmental And Earth Sciences, Geophysics And Geology Keywords: Plumes; dynamics; resistivity; contamination; groundwater
Online: 10 December 2021 (11:28:20 CET)
The contamination of areas around solid urban waste dumps is a global challenge for the maintenance of environmental quality in large urban centres in developing countries. This study applied geophysical methods (electrical resistivity) to identify leachate contamina-tion plumes in the subsoil and groundwater, as well as to describe their temporal (2020 and 2021) dynamics in the lithology and groundwater around the Hulene - B waste dump, Maputo, Mozambique. Geophysical methods (electrical resistivity) were applied to identify possible groundwater contamination plumes, their dynamics, mechanisms of their enrichment and dispersion. Eight 400 m electrical resistivity profiles were performed, four profiles in January 2020 and four profiles in May 2021, overlapped, and the data were inverted with RES2D software. The electrical resistivity models indicate an E - W move-ment of large contamination plumes that dilute superficially into the natural surface wa-ter receiving basin and groundwater, creating zones of resistive anomalies. The thickness of the plumes in the subsurface environment was shown to be extensive in summer for profiles 1a and 2b and we associate it with the higher leachate production and migration mechanisms, which are intense in the hot and rainy season. Profile 4b showed the prop-agation of anomalous surface and subsurface areas, which was associated with higher leachate production and migration process in the new deposition zone (west). The spatial distribution of contamination plumes at both stations reduced significantly as we moved further away from the waste deposit, revealing the attenuating effect of groundwater and lithological substrate (Profile 3 a, b, and fig.7).
ARTICLE | doi:10.20944/preprints202111.0406.v1
Online: 22 November 2021 (14:22:59 CET)
We research the interaction between six representative carbon-based nanoparticles (CBNs) and 20 standard amino acids through all-atom molecular dynamics simulations. The six carbon-based nanoparticles are fullerene(C60), CNT55L3, CNT1010L3, CNT1515L3, CNT2020L3, and two-dimensional-graphene(Graphene33). Their curvatures decrease sequentially, and all of CNT are single-walled carbon nanotubes. We have observed that as the curvature of CBNs decreases, the adsorption effect of 20 amino acids with them has an increasing trend. In addition, we also used multi-dimensional clustering to analyze the adsorption effects of 20 amino acids on six carbon-based nanoparticles. We observed that the π-π interaction still plays an extremely important role in the adsorption of amino acids on carbon-based nanoparticles. Individual long-chain amino acids and “Benzene-like” Pro also have a strong adsorption effect with carbon-based nanoparticles.
REVIEW | doi:10.20944/preprints202002.0417.v1
Subject: Biology And Life Sciences, Biophysics Keywords: chromatin; mechanics; nucleosomes; dynamics; epigenetics
Online: 28 February 2020 (02:27:13 CET)
The nucleus has been studied for well over 100 years, and chromatin has been the intense focus of experiments for decades. In this review, we focus on an understudied aspect of chromatin biology, namely the chromatin fiber polymer's mechanical properties. In recent years, innovative work deploying interdisciplinary approaches including computational modeling, in vitro manipulations of purified and native chromatin have resulted in deep mechanistic insights into how the mechanics of chromatin might contribute to its function. The picture that emerges is one of a nucleus that is shaped as much by external forces pressing down upon it, as internal forces pushing outwards from the chromatin. These properties may have evolved to afford the cell a dynamic and reversible force-induced communication highway which allows rapid coordination between external cues and internal genomic function.
ARTICLE | doi:10.20944/preprints201909.0111.v1
Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: Li2MnO3; Molecular dynamics; diffusion; delithiation
Online: 10 September 2019 (15:41:27 CEST)
Li2MnO3 is critical component in the well-studied Li-excess cathode materials xLi2MnO3•(1- x)LiMO2 for achieving high lithium storage capacity. In this article, the diffusion of Li ions in Li2MnO3 is studied using molecular dynamics (MD) simulation with well-behaved empirical force fields obtained by fitting against the crystal structure from experiment and phonons calculated using Density Function Theory (DFT). We have found two possible tetrahedral hopping channels, 0-TM and 1-TM(Mn4+) channel, which are differentiated by the face sharing octahedral cations. Simulation results show that the 0-TM channel is active for Li hopping, while 1-TM(Mn4+) channel is inactive. During the delithiation process, the Li ions in the TM layered are firstly removed, then those in the Li layer. However, the Li ions will be trapped in the tetrahedral 0-TM channels as long as the four face sharing octahedral sites are cleared. Up to x=1.0 for Li2-xMnO3, almost all the Li ions are located at the tetrahedral sites, forming a regular array along a axis. The de-intercalation of tetrahedral Li ions requires a high voltage (>5.2 V vs. Li/Li+), limiting the practical capacities measured in lab. The diffusion of Mn ions into the Li layers is observed in a deeper delithiated structure (x=1.2 for Li2-xMnO3), indicating an initial phase transformation to a spinel-like structure. However, the Mn ions are mainly trapped in the tetrahedral sites in the Li layer, instead of the octahedral sites fin spinel-like structure. A few of Mn ions diffusing into the octahedral sites in Li layers have no face sharing tetrahedral Li ions, revealing a further Li de-intercalation is imperative for the complete phase transformation. Our model is not stable for x≥1.4 in Li2-xMnO3. Other charge compensation mechanism should be considered in this high delithiation stage, eg. oxygen release.
ARTICLE | doi:10.20944/preprints201809.0137.v1
Subject: Environmental And Earth Sciences, Oceanography Keywords: particle dynamics; optical properties; Sediment;
Online: 7 September 2018 (13:14:39 CEST)
Measurements of optical properties have been used for decades to study particle distributions in the ocean. They have been found useful to constrain suspended mass concentration as well as particle-related properties such as size, composition, packing (particle porosity or density) and settling velocity. Optical properties, however, provide measurements that are biased, as certain particles (based on size, composition, shape or packing) contribute to a specific property more than others. Here we study this issue both theoretically as well as by contrasting different optical properties collected simultaneously in a bottom boundary layer, to highlight the utility of such measurements as well as the biases we are likely to encounter using different optical properties to study suspended particles. In particular, we investigate the possibility to infer settling velocity from vertical profiles of optical measurements, finding that the effects of aggregation dynamics can seldom be ignored.
ARTICLE | doi:10.20944/preprints201806.0034.v1
Subject: Physical Sciences, Quantum Science And Technology Keywords: quantum information; quantum dynamics; entanglement
Online: 4 June 2018 (11:03:21 CEST)
Quantum Computation, in the gate array version, uses logical gates adopting convenient forms for computational algorithms based on those of classical computation. There, two-level quantum systems are the basic elements connecting the binary nature of classical computation with the settlement of quantum processing. Despite, their design depends on specific quantum systems and physical interactions involved, exacerbating the dynamics analysis. Predictable and controllable manipulation should be addressed to control the quantum states, but resources are restricted to limitations imposed by the physical settlement. This work presents a formalism to decompose the quantum information dynamics in SU(22d) for 2d-partite two-level systems into 22d-1 SU(2) quantum subsystems. Decomposition lets to set control procedures, to generate large entangled states and to design specialized dedicated quantum gates. There, easy and traditional operations proposed by quantum computation are recovered for more complex and large systems. Alternating the parameters of local and non-local interactions, the procedure states a universal exchange semantics on the generalized Bell states basis. It could be understood as a momentary splitting of the 2d information channels into 22d-1 pairs of 2 level quantum information subsystems and a settlement of the quantum information manipulation free of the imposed restrictions by the underlying physical system.
ARTICLE | doi:10.20944/preprints202012.0262.v2
Subject: Physical Sciences, Acoustics Keywords: Fluid-Structure interactions; Topological fluid dynamics; General fluid mechanics; Mathematical fluid dynamics; Applied mathematics
Online: 25 January 2021 (10:32:15 CET)
This article objectively assesses, the hypothesis of the streamline's shape theory and its formulated equation. The deduction of proof uses algebra rather than first-order partial differential equations to address the specific hypothesis of "Streamline's shape theory" from the fundamental perspective of applied mathematics and scientifically derives mathematical relations of the axioms and corollaries in the field of fluid dynamics. The algebraic methods employed provide progressively more distinct and precise solutions compared to first-order partial differential equations. The foremost objective of this work is to evaluate if the formulations of the streamline's shape theory can have solutions for inviscid-incompressible and viscid-compressible flows of Newtonian fluids and to identify their nature. Secondly, to understand how the topology of the body and the free-stream conditions affect these solutions with due regards to the shape and size of the body interacting with the fluid flow. Finally, to explore the possibility of this theory to develop a CFD solver for streamline simulation to reduce the experimentation in the analysis of flow-structure interactions of Newtonian fluids and also to identify its scope of applications and limitations.
ARTICLE | doi:10.20944/preprints201810.0740.v2
Subject: Social Sciences, Decision Sciences Keywords: political polarization; echo-chambers; social networks; binary voter model; discussion dynamics; opinion dynamics model
Online: 17 December 2018 (10:11:31 CET)
Polarization in online social networks has gathered a significant amount of attention in the research community and in the public sphere due to stark disagreements with millions of participants in topics surrounding politics, climate, the economy and other areas where an agreement is required. There are multiple approaches to investigating the scenarios in which polarization occurs and given that polarization is not a new phenomenon but that its virality may be supported by the low cost and latency messaging offered by online social media platforms; an investigation into the intrinsic dynamics of online opinion evolution is presented for complete networks. Extending a model which utilizes the Binary Voter Model (BVM) to examine the effect of the degree of freedom for selecting contacts based upon homophily, simulations show that different opinions are reinforced for a period of time when users have a greater range of choice for association. The facility of discussion threads and groups formed upon common views further delays the rate in which a consensus can form between all members of the network. This can temporarily incubate members from interacting with those who can present an alternative opinion where a voter model would then proceed to produce a homogeneous opinion based upon pairwise interactions.
Subject: Engineering, Control And Systems Engineering Keywords: flexible robot arm; robust-adaptive control, sliding mode variable structure control; actuator dynamics; zero dynamics
Online: 15 September 2021 (10:22:41 CEST)
Modelling errors, robust stabilization/tracking problems under parameter and model uncertainties complicate the control of the flexible underactuated systems. Chattering-free sliding-mode based input-output control law realizes robustness against the structured and unstructured uncertainties in the system dynamics and avoids excitation of unmodeled dynamics. The main purpose is to propose a robust adaptive solution for stabilizing and tracking direct-drive (DD) flexible robot arms under parameter and model uncertainties, as well as external disturbances. A lightweight robot arm subject to external and internal dynamic effects was taken into consideration. The challenges are compensating actuator dynamics with the inverter switching effects and torque ripples, stabilizing the zero dynamics under parameter/model uncertainties and disturbances while precisely track the predefined reference position. The precise control of this kind of system demands an accurate system model and knowledge of all sources that excite unmodeled dynamics. For this purpose, equations of motion for a flexible robot arm were derived and formulated for the large motion via Lagrange’s method. The goals were determined to achieve high-speed, precise position control, and satisfied accuracy by compensating the unwanted torque ripple and friction that degrades performance through an adaptive robust control approach. The actuator dynamics and their effect on the torque output were investigated due to the transmitted torque to the load side. The high-performance goals, precision&robustness issues, and stability concerns were satisfied by using robust-adaptive input-output linearization-based control law combining chattering-free sliding mode control (SMC) while avoiding the excitation of unmodeled dynamics.
ARTICLE | doi:10.20944/preprints202011.0469.v1
Subject: Physical Sciences, Particle And Field Physics Keywords: Cabibbo angle; fermion mixing; charged current interactions; nonlinear dynamics and chaos; complex dynamics; Feigenbaum’s constant
Online: 18 November 2020 (11:05:33 CET)
Our earlier work has tentatively shown that the hierarchy of fermion masses and mixing angles follows from the universal behavior of nonlinear dynamics. In this brief sequel we survey a similar scenario in which the Cabibbo angle arises from the nonlinear dynamics of charged-current interactions.
REVIEW | doi:10.20944/preprints201912.0131.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: single nucleotide polymorphism; docking; molecular dynamics; in-silico studies; protein dynamics; missense; prediction algorithm; mutation
Online: 10 December 2019 (07:56:43 CET)
Single nucleotide polymorphisms (SNP) are associated with diseases and drug response variabilities in humans. Elucidating the damaging and disease-associated SNPs using wet-laboratory approaches can be challenging and resource-demanding due to the large number of SNPs in the human genome. Due to the growth in the field of computational biology and bioinformatics, algorithms have been developed to help screen and filter out the most deleterious SNPs that are worth considering for wet-laboratory studies. Here we review the existing in-silico based methods used to predict and characterize the effects of SNPs on protein structure and function. This cutting-edge approach will facilitate the search for novel therapeutics, help understand the etiology of diseases and fast-track the personalized medicine agenda.
REVIEW | doi:10.20944/preprints201902.0122.v6
Subject: Biology And Life Sciences, Biophysics Keywords: Leishmania; Trypanosoma; Molecular Dynamics; Theoretical Chemistry
Online: 22 September 2023 (11:07:35 CEST)
This review presents an updated overview of research concerning Leishmania protein structures, primarily sourced from the Protein Data Bank (PDB), that play a role in the metabolic pathways of the Leishmania parasite. Furthermore, we assess the current progress in the identification and development of bioactive chemical agents aimed at addressing this substantially overlooked tropical disease. We have analyzed experimental data obtained from in vitro, in vivo and in silico sources. This data has been categorized into four main areas: a) vector taxonomy and geographic distribution; b) parasite taxonomy and geographic distribution; c) enzymatic functions of proteins engaged in parasite/host interactions throughout various developmental stages (such as oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases, and cytokines); and d) established and experimental treatments employing bioactive chemical compounds. Our objective is to establish a foundational point of reference for research efforts concentrating on the elucidation of interaction mechanisms and the processes of ligand-protein activation/inactivation, specifically linked to Leishmania infections. Consequently, we emphasize enzymes recognized for their involvement in the biochemical pathways incited during Leishmania infection episodes. This review encapsulates the current understanding, offering insights to inform and direct future explorations aimed at targeting proteins and pathways to enhance the management of Leishmania-related diseases.
ARTICLE | doi:10.20944/preprints202305.0234.v1
Subject: Engineering, Mechanical Engineering Keywords: Molecular dynamics; LAMMPS; displacement cascade; defects
Online: 4 May 2023 (08:27:04 CEST)
Zirconium nitride (Zr-N) is a candidate material for inert matric fuel elements in breeder reactors. They have shown exceptional resistance to radiative corrosive environments. They have shown excellent resistance to radiation stability at operational conditions in current generation reactors. But being a candidate nuclear fuel material in generation reactors, their radiation stability at higher temperature conditions observed has not been reported. We have employed molecular dynamics simulations to study the damage cascades and radiation stability of ZrN at 600K. The process of primary damage evolution by considering varying overlapping cascades with 10, 20 keV incident PKA’s reported here. The defects interface interaction and diffusion mechanism at the interface are reported.
ARTICLE | doi:10.20944/preprints202304.0948.v1
Subject: Chemistry And Materials Science, Metals, Alloys And Metallurgy Keywords: Aluminum electrolysis; Molecular Dynamics; Viscosity; Conductivity
Online: 26 April 2023 (03:46:16 CEST)
The analysis of high-temperature physicochemical properties of theK3AlF6-Na3AlF6-AlF3 molten salt system is crucial for practical production of electrolytic aluminum. In this paper, the physicochemical properties of the K3AlF6-Na3AlF6-AlF3 molten salt electrolyte system at 1173 K and standard atmospheric pressure were simulated using molecular dynamics calculations. The effects of Zr、B、C、W、Ti、Hf、Nb、and Ta on the radial distribution function, coordination number, viscosity and conductivity of the electrolyte system are discussed in detail. The simulation results show that the coordination number between Al-F and the conductivity is decreasing as the content of B2- increases. And the coordination number between Al-F and the viscosity is decreasing as the content of Zr4+ increases. With the addition of impurity elements such as C, W, Ti, Hf, Nb, and Ta, the data show that C has no significant effect on this electrolyte system, while the presence of W will decrease the coordination number between Al-F in the system. The presence of Ti, Hf, Nb, and Ta may intensify the decomposition reaction between one of the Al-F ligands, which increases the coordination number between Al-F and the number of ions in the electrolyte. This work provides theoretical support for the subsequent study of inert anodes containing Zr, B, Ti, Hf, Nb, and Ta.
ARTICLE | doi:10.20944/preprints202302.0484.v2
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Passive dynamics; equine; forelimb; head; neck; lameness
Online: 28 February 2023 (06:06:24 CET)
Passive dynamics is an aspect of locomotion which is entirely dependent on the mechanical configuration and linkages of adjacent body segments. Tension distribution along mechanical linkages enables execution of movement patterns with reduced need for complex neurological pathways and may play a role in reestablishing postural stability following external disturbances. Here we demonstrate a uni-directional mechanical relationship between the equine forelimb, head and neck, which may have implications for balance and forelimb loading in the horse. These observations suggest that forelimb, head and neck movement coordination (observed in the horse during unrestrained locomotion) is largely controlled by the mechanical linkages between body segments, rather than being entirely dependent on neurological input as previously thought. This highlights the potential significance of research directed at investigating passively induced movements in understanding common locomotory patterns. Additionally, it suggests a mode of postural control which may provide instantaneous adjustments to postural disturbances, thus promoting rapid and efficient locomotion.
ARTICLE | doi:10.20944/preprints202210.0261.v1
Subject: Social Sciences, Education Keywords: System dynamics; Education; Teaching; Learning; Systemsthinking
Online: 19 October 2022 (02:13:49 CEST)
This article addresses a challenge modeling novices face in model conceptualization: the recognition of behavior modes. Despite behavior modes being at the heart of system dynamics modeling, there is no unifying taxonomy for them, making them harder to learn for beginners. The article proposes criteria a taxonomy should satisfy, critically reviews previous taxonomies in the literature, and then introduces a new consistent taxonomy based on slope and curvature with mode names that refer only to visual cues and free of references to prior mathematical or domain-specific knowledge. Evidence from an exploratory experiment suggests that novices actually have difficulties classifying curves when using previous taxonomies. Links from these elementary modes to analogous terms in other taxonomies in diverse disciplines allow this taxonomy to be related to other ones. The article concludes by mentioning relevant limitations and future steps.
ARTICLE | doi:10.20944/preprints202205.0377.v1
Subject: Engineering, Energy And Fuel Technology Keywords: detonation; super-knock; CSP; explosive dynamics
Online: 27 May 2022 (09:48:29 CEST)
The occurrence and intensity of the detonation phenomenon at spark-ignition (SI) engine conditions is investigated, with the objective to successfully predict super-knock and to elucidate the effect of kinetics and transport at the ignition front. The computational singular perturbation (CSP) framework is employed in order to investigate the chemical and transport mechanisms of deflagration and detonation cases in the context of 2D high-fidelity numerical simulations. The analysis revealed that the detonation development is characterized by: (i) stronger explosive dynamics and (ii) enhanced role of convection. The role of chemistry was also found to be pivotal to the detonation development which explained the stronger explosive character of the system, the latter being an indication of the system's reactivity. The role of convection was found to be enhanced at the edge of the detonating front, thereby suggesting that it is the result and not the cause of the detonation onset. Moreover, the increased contribution of convection was found to be related mainly to heat convection. Remarkably, the detonation front was mainly characterized by dissipative and not explosive dynamics. Finally, diffusion was found to have negligible role to both examined cases.
ARTICLE | doi:10.20944/preprints202205.0137.v1
Online: 10 May 2022 (10:11:48 CEST)
Two modal decomposition techniques, including proper orthogonal decomposition (POD) and dynamic mode decomposition (DMD), are used to identify the wake patterns past single and two crossing cylinders in 60° and 90° arrangements with gap ratio G = 4. The flow is simulated using direct numerical simulations (DNS) for Reynolds numbers Re = 100. The spatial scale of flow decreases with increasing modal frequency from the modal analysis. Two main modes are identified in the wake of the cylinders, namely spatially antisymmetric and symmetric modes. Antisymmetric and symmetric modes are related to cylinders’ vortex shedding and shedding vortices’ shift motion, respectively, whose frequencies are odd and even multiples of cylinders’ lift force frequency. In addition, a low-frequency mode concerning the shadowing effect of the downstream cylinder (DC) in 90° arrangement is found in the wake of the DC centre.
REVIEW | doi:10.20944/preprints202202.0257.v1
Subject: Engineering, Industrial And Manufacturing Engineering Keywords: Biodiesel; Microreactor; Transesterification; Computational Fluid Dynamics
Online: 21 February 2022 (14:53:11 CET)
Microfluidic devices or microdevices refer to systems with a characteristic length in the micrometer range. Systems in this size allow handling small quantities of reagents and samples, with reduced residence time, better control of chemical species concentration, high heat and mass transfers, and high surface/volume ratio. These characteristics led to the application of these microdevices in several areas, such as biological systems, energy, liquid-liquid extraction, food, agricultural sectors, pharmaceuticals, flow chemistry, microreactors, and biodiesel synthesis. Microreactors are devices that have interconnected microchannels, in which small amounts of reagents are manipulated and react for a certain period of time. The traditional characteristics of microreactors are less quantities of reagents and samples, high surface area in relation to volume (10000 m2 m-3), reduction of resistance to heat and mass transfer, reduced reaction times, and narrower residence time distributions. In recent years, several studies have been carried out on biodiesel production in microreactors that explore the influence of operating conditions, mixing and reaction yield, numbering, and especially the microdevices design. Despite all the advantages of microreactors, the literature shows that there are only a few applications on an industrial scale. Two main reasons that hinder the adoption of this technology are the scale-up to a large enough volume to deliver the necessary production capacity and the costs related to industrial manufacturing microreactors. It is often stated that large-scale production of microreactors can be easily achieved by numbering-up. However, researches show that an incredibly high number of microdevices would be needed, which results in a technical unfeasibility and a strong impact on the construction costs of the industrial system. The present review aims to show whether microreactors can replace conventional biodiesel production processes and how this replacement technology could be carried out. The current chapter was divided into the following sections: Introduction, Synthesis and Purification of Biodiesel in Microreactors, Fundamentals of CFD, and Fundamentals of Scale-up. Finally, conclusions and future perspectives are exposed.
ARTICLE | doi:10.20944/preprints202111.0381.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Multi-scale molecular dynamics； IBI； CBNs
Online: 22 November 2021 (11:08:58 CET)
Our work uses Iterative Boltzmann Inversion (IBI) to study the coarse-grained interaction between 20 amino acids and the representative carbon nanotube CNT55L3. IBI is a multi-scale simulation method that has attracted the attention of many researchers in recent years. It can effectively modify the coarse-grained model derived from the Potential of Mean Force (PMF). IBI is based on the distribution result obtained by All-Atom molecular dynamics simulation, that is, the target distribution function, the PMF potential energy is extracted, and then the initial potential energy extracted by the PMF is used to perform simulation iterations using IBI. Our research results have gone through more than 100 iterations, and finally, the distribution obtained by coarse-grained molecular simulation (CGMD) can effectively overlap with the results of all-atom molecular dynamics simulation (AAMD). In addition, our work lays the foundation for the study of force fields for the simulation of the coarse-graining of super-large proteins and other important nanoparticles.
ARTICLE | doi:10.20944/preprints202104.0699.v1
Subject: Physical Sciences, Acoustics Keywords: Molecular Dynamics; Graphene oxide; Simultaneous Detection
Online: 27 April 2021 (10:07:51 CEST)
The selectivity in the simultaneous detection of ascorbic acid (AA), dopamine (DA), and uric acid (UA) has been an open problem in the biosensing field. Many surface modification methods were carried out for glassy carbon electrodes (GCE), including the use of graphene oxide and amino acids as a selective layer. In this work, molecular dynamics (MD) simulations were performed to investigate the role of serine oligomers on the selectivity of the AA, DA, UA analytes. Our models consisted of a graphene oxide (GO) sheet under a solvent environment. Serine tetramers were added into the simulation box and were adsorbed on the GO surface. Then, the adsorption of each analyte on the mixed surface was monitored from MD trajectories. It was found that the adsorption of AA was preferred by serine oligomers due to the largest number of hydrogen-bond forming functional groups of AA, while UA was the least preferred due to its highest aromaticity. Finally, the role of hydrogen bonds on the electron transfer selectivity of biosensors was discussed with some previous studies.
ARTICLE | doi:10.20944/preprints202104.0006.v1
Subject: Physical Sciences, Acoustics Keywords: Colloids; Confinement; Ordering; Locomotion; Brownian Dynamics
Online: 1 April 2021 (10:19:02 CEST)
Confinement can induce substantial changes in the physical properties of macromolecules in suspension. Soft confinement is a particular class of restriction where the boundaries that constraint the particles in a region of the space are not well-defined. This scenario leads to a broader structural and dynamical behavior than the observed in systems enclosed between rigid walls. In this contribution, we study the ordering and diffusive properties of a two-dimensional colloidal model system subjected to a one-dimensional parabolic trap. Increasing the trap strength makes it possible to go through weak to strong confinement, allowing a dimensional transition from two- to one-dimension. The non-monotonic response of the static and dynamical properties to the gradual dimensionality change affects the system phase behavior. We find that the particle dynamics is connected with the structural transitions induced by the parabolic trap. In particular, at low and intermediate confinement regimes, complex structural and dynamical scenarios arise, where the softness of the external potential induces melting and freezing, resulting in faster and slower particle diffusion, respectively. Besides, at strong confinements, colloids move basically along one direction, and the whole system behaves structurally and dynamically similar to a one-dimensional colloidal system.
ARTICLE | doi:10.20944/preprints202012.0671.v1
Subject: Medicine And Pharmacology, Immunology And Allergy Keywords: HPV; E7; variants; molecular dynamics simulation
Online: 25 December 2020 (16:05:04 CET)
The oncogenic potential of high-risk HPVs is focused on producing the E6 and E7 oncoproteins responsible for disrupting the control of the cell cycle. Epidemiological studies propose the presence of the N29S and H51N variants of the HPV16 E7 protein as a significant association with cervical cancer. It has been suggested that changes in the amino acid sequence of E7 variants may affect the oncoprotein 3D structure; however, this remains unknown. Analysis of the structural differences of the HPV16 E7 protein and its variants (N29S and H51N) was performed through homology modeling and structural refinement by molecular dynamics simulation. We propose for the first time a 3D structure of the E7 reference protein and two of its variants (N29S and H51N) and conclude that the mutations induced by the variants in N29S and H51N have a significant influence on the 3D structure of the E7 protein of HPV16, which could be related to the oncogenic capacity of this protein.
ARTICLE | doi:10.20944/preprints202005.0450.v1
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: epidemiology; transmission dynamics; isolated population; Spain
Online: 27 May 2020 (09:05:14 CEST)
Background: Since March 2020, Spain is severely hit by the ongoing pandemic of coronavirus disease 19 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Understanding and disrupting the early transmission dynamics of the infection is crucial for impeding sustained transmission. Methods: We recorded all COVID-19 cases and traced their contacts in an isolated rural community. We also sampled 10 households, 6 public service sites and the wastewater from the village sewage for environmental SARS-CoV-2 RNA. Results: The first village patient diagnosed with COVID-19-compatible symptoms occurred on March 3, 2020, twelve days before lockdown. A peak of 39 cases occurred on March 30. By May 15, the accumulated number of symptomatic cases was 53 (6% of the population), of which only 22 (41%) had been tested and confirmed by RT-PCR as SARS-CoV-2 infected, including 16 hospitalized patients. Contacts (n=144) were six times more likely to develop symptoms. Environmental sampling detected SARS-CoV-2 RNA in two households with known active cases and in two public service sites: the petrol station and the pharmacy. Samples from other sites and the wastewater tested negative. Conclusions: The low proportion of patients tested by RT-PCR calls for urgent changes in disease management. We propose that early testing of all cases and their close contacts would reduce infection spread, reducing the disease burden and fatalities. In a context of restricted testing, environmental RNA surveillance might prove useful for early warning and to identify high-risk settings enabling a targeted resource deployment.
ARTICLE | doi:10.20944/preprints201912.0247.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: anthrax; lead compounds; molecular dynamics; docking
Online: 19 December 2019 (07:06:38 CET)
There has recently been interest in the development of small-molecule inhibitors of the oligomerization of Bacillus anthracis protective antigen for therapeutic use. Some of the proposed lead compounds have, however, unfavorable solubility in aqueous medium, which prevents their clinical use. In this computational work, we have designed several hundreds of derivatives with progressively higher hydrosolubility and tested their ability to dock the relevant binding cavity. The highest-ranking docking hits were then subjected to 125 ns-long simulations to ascertain the stability of the binding modes. Several of the potential candidates performed quite disappointingly , but two molecules showed very stable binding modes throughout the complete simulations. Besides the identification of these two promising leads, these molecular dynamics simulations allowed the discovery of several insights that shall prove useful in the further improvement of these candidate towards higher potency and stability.
ARTICLE | doi:10.20944/preprints201905.0152.v1
Subject: Engineering, Mechanical Engineering Keywords: friction dynamics; stick-slip; brake materials
Online: 13 May 2019 (10:11:49 CEST)
This contribution addresses dry sliding friction of a “Non-Asbestos Organic” friction material (pad) rubbed against a pearlitic grey cast iron disc. This configuration is commonly used in brakes in US, Europe and Asia. The initial stage of friction is of particular interest when addressing “creep-groan” phenomena occurring in passenger and sport utility vehicles with automatic transmissions. The custom built Universal Friction Tester allowing the variation of sliding speed, test temperature, normal load, stiffness and humidity of the system was used in this experiment in combination with surface analysis by polarized light microscopy, scanning electron microscopy and stylus profilometry. The obtained results indicate that the “stick” phase in the so-called “stick-slip” phenomenon does not really exist. The surfaces of pad and disc are in continuous relative movement. The complexity of surfaces does not allow for a definitive description of exact mechanisms responsible for the detected changes of friction forces. The observed friction process can be rather described as a stretching with possible localized relaxations causing the jerky behavior in the stretching phase, followed by slip between two materials in contact. Understanding of factors contributing to the stretching at different scale levels of friction system is necessary for development of proper models. An accurate friction model should also incorporate the vibrational element introduced by phenomena occurring at the friction surfaces. The absence of heterogeneous regions on the friction surface and “evenly distributed friction level” can help when mitigating creep-groan in the investigated brake system. Understanding of factors on different scales of friction is also required when developing the improved brakes.
ARTICLE | doi:10.20944/preprints201805.0021.v1
Subject: Chemistry And Materials Science, Biomaterials Keywords: capsaicin; chitosan; lecithin; dissipative particle dynamics
Online: 2 May 2018 (11:07:01 CEST)
Transport of hydrophobic drugs in the human body exhibits complications due to the low solubility of these compounds. With the purpose of enhancing the bioavailability and biodistribution of such drugs, recent studies have reported the use of amphiphilic molecules, such as phospholipids, for synthesis of nanoparticles or nanocapsules. Given that phospholipids can self–assemble in liposomes or micellar structures, they are ideal candidates to function as vehicles of hydrophobic molecules. In this work, we report mesoscopic simulations of nanoliposomes, constituted by lecithin and coated with a shell of chitosan. The stability of such structure and the efficiency of encapsulation of capsaicin, as well as the internal and superficial distribution of capsaicin and chitosan inside the nanoliposome were analyzed. The characterization of the system was carried out through density maps and the potentials of mean force for the lecithin–capsaicin, lecithin–chitosan and capsaicin–chitosan interactions. The results of these simulations show that chitosan is deposited on the surface of the nanoliposome, as has been reported in some experimental works. It was also observed that a nanoliposome of approximately 18 nm in diameter is stable during the simulation. The deposition behavior was found to be influenced by pattern of N-acetylation of chitosan.
ARTICLE | doi:10.20944/preprints202007.0332.v1
Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: Car-Parrinello molecular dynamics; ab-initio molecular dynamics; sum-frequency generation spectroscopy; maximally localized Wannier orbitals
Online: 15 July 2020 (10:25:31 CEST)
In the present work, we provide an electronic structure based method for the “on-the-fly” deter- mination of vibrational sum frequency generation (v-SFG) spectra. The predictive power of this scheme is demonstrated at the air-water interface. While the instantaneous fluctuations in dipole moment are obtained using the maximally localized Wannier functions, the fluctuations in polar- izability are approximated to be proportional to the second moment of Wannier functions. The spectrum henceforth obtained captures the signatures of hydrogen bond stretching, bending, as well as low-frequency librational modes.
ARTICLE | doi:10.20944/preprints201707.0080.v2
Subject: Public Health And Healthcare, Health Policy And Services Keywords: implementation; adoption; health interventions; community prevention; obesity prevention interventions; system dynamics; systems thinking; endogenous dynamics; qualitative modeling; case studies
Online: 27 July 2017 (17:54:29 CEST)
In this study, we present case studies to explore the dynamics of implementation and maintenance of health interventions. We analyze how specific interventions are built and eroded, how the building and erosion mechanisms are interconnected, and why we can see significantly different erosion rates across otherwise similar organizations. We use multiple comparative obesity prevention case studies to provide empirical information on the mechanisms of interest, and use qualitative systems modeling to integrate our evolving understanding into an internally consistent and transparent theory of the phenomenon. Our preliminary results identify reinforcing feedback mechanisms, including design of organizational processes, motivation of stakeholders, and communication among stakeholders, which influence implementation and maintenance of intervention components. Over time, these feedback mechanisms may drive a wedge between otherwise similar organizations, leading to distinct configurations of implementation and maintenance processes.
ARTICLE | doi:10.20944/preprints202204.0193.v1
Subject: Physical Sciences, Astronomy And Astrophysics Keywords: event-universe; dendrograms; hierarchic relational representation; dendrogramic dynamics; shape dynamics; stability of event-universe; arrow of time
Online: 21 April 2022 (07:56:21 CEST)
Recently we started the development of Holographic Dendrogramic Theory (DH-theory). It is based on the novel mathematical representation of the relational event universe (in the spirit of (Smolin, Barbour, Rovelli). Elementary events are represented by branches of dendrograms, finite trees, which are generated from data with clustering algorithms. In this note we study the dynamics of the event-universe generated by the appearance of a new event. Generally, each new event can generate the complete reconstruction of the whole dendrogramic universe. However, we found (via numerical simulation) unexpected stability of this universe. Its events are coupled via the hierarchic relational structure which is relatively stable with respect even random generation of new events. We also observe the regularity patterns in location of new events on dendrograms. In the curse of evolution, the dendrogram’s complexity increases and determine the arrow of time the event universe. We use the complexity measure from particle shape dynamics which was shown to be increase in both direction away from a Janus point and thus determine the arrow of time in symmetrical manner away from a Janus point. The particle shape dynamics theory is a relational theory with close ideological resemblance to DH-theory as both relays on Mach’s principle and Leibniz’s relationalism and his principles. By using the complexity measure on dendrograms and its p-adic string representation, we demonstrate the emergence of time arrow from the p-adic zero-dimensional field, where space and time are absent.
ARTICLE | doi:10.20944/preprints202309.1995.v1
Subject: Physical Sciences, Condensed Matter Physics Keywords: Casimir effect; Actuation dynamics; MEMS; NEMS; Stiction
Online: 28 September 2023 (11:48:45 CEST)
Here, we investigate the actuation dynamics of a micro device with different intervening liquids between the actuating components under the influence of Casimir and dissipative hydrodynamic forces. This is enabled via phase space portraits, which demonstrate that by increasing the dielectric response of the intervening layer the device may not come into stiction due to the decreasing in magnitude Casmir force. Moreover, it is feasible to expand area of motion using intervening liquids with lower dynamic viscosity or increasing the slip length of the intervening fluid. Finally, under the influence of an external driven force, which is the realistic case for possible applications, the system can reach stable oscillation at larger separations with an amplitude higher for the liquid that lead to lower Casimir and hydrodynamic forces.
ARTICLE | doi:10.20944/preprints202309.1024.v1
Subject: Engineering, Mechanical Engineering Keywords: inducer; centrifugal pump; cavitation; computational fluid dynamics
Online: 15 September 2023 (05:31:12 CEST)
An inducer is one of the most important components of centrifugal pumps, whose presence will result in a significant increase in hydraulic performance and pump efficiency. The primary function of the inducer, however, is to delay the destructive phenomenon of cavitation, which has presented a considerable design challenge. Nevertheless, the amount of improvement and increase in inducer performance in both cavitation and non-cavitation modes depends critically on the radial laxity of the blade tip. As part of this study, the performance of the inducer in the cavitation state has been simulated and compared with the experimental data, which are in good agreement. This paper examines the effect of blade tip lagging on cavitation, and the results indicate that this will improve cavitation and delay this destructive phenomenon but will negatively affect the non-cavitation performance. With the increase in clearance, the range of the return current will increase at the tip of the inducer blade as well.
ARTICLE | doi:10.20944/preprints202308.1258.v1
Subject: Engineering, Control And Systems Engineering Keywords: cutting system; cutting dynamics; regenerative effect; vibrations
Online: 17 August 2023 (13:00:44 CEST)
The article is devoted to the issues of assessing the impact of changes in the delay value in the feed direction, what determines the regenerative nature of self-excitation of the cutting system, on the dynamics of metal processing on metal-cutting machines. It is this interconnected model of the cutting system that allows to identify the main dynamic effects that occur in the cutting system, including the effect of vibrations regeneration when cutting along the track. The article also has a section dedicated to the experiment on a real metalworking machine, on which vibrations of the top of the cutting wedge of the tool were measured and based on these data, a real calculation of the delay time and the magnitude of the change in the area of the cut layer was carried out, due to variations in the real feed. The conducted studies have shown that in addition to the vibrations of the cutting tool in the direction of feeding, the vibration activity of the tool in the direction of cutting plays an essential role in ensuring the regenerative effect. The delay time constant of the operator is formed, which determines the real value of the feed during cutting.
ARTICLE | doi:10.20944/preprints202308.0385.v1
Subject: Physical Sciences, Astronomy And Astrophysics Keywords: Jupiter; Atmosphere; Spectroscopy; Atmosphere dynamics; Doppler velocimetry
Online: 4 August 2023 (08:26:10 CEST)
We present a new study of Jupiter atmosphere’s dynamics using for the first time the extremely high resolution capabilities of VLT/ESPRESSO to retrieve wind velocities in Jupiter’s troposphere, with a dedicated ground-based Doppler velocimetry method. These results are complemented by a deeper analysis of Cassini data during its flyby of Jupiter in December 2000, performing cloud tracking at visible wavelengths, obtaining a more comprehensive dynamical interpretation. We explore the effectiveness of this new method to measure winds in Jupiter, using high resolution spectroscopy data obtained from ESPRESSO observations performed in July 2019, with a Doppler velocimetry method based on back scattered solar radiation in the visible range. Coupled with our ground based results, we retrieved a latitudinal and longitudinal profile of Jupiter’s winds along select bands of the atmosphere. Comparing the results between cloud tracking methods, based on previous reference observations, and our new Doppler velocimetry approach we found a good agreement between them, demonstrating the eectiveness of this technique. The winds obtained in this exploratory study have a two-fold relevance: they contribute for the temporal and spatial variability study of Jupiter troposphere’s dynamics, and also the results presented here validate this Doppler technique to study the dynamics of Jupiter’s atmosphere and pave the way for further exploration of a broader region of Jupiter’s disk for a more comprehensive retrieval of winds and to evaluate their spatial and temporal variability.
Subject: Social Sciences, Geography, Planning And Development Keywords: Geographies; Geopolitics; Territoriality; Power dynamics; Global affairs
Online: 10 July 2023 (10:28:51 CEST)
This book review addresses the contribution of Tim Marshall’s “The Power of Geography”. The purpose of this essay is to highlight the significant role of geography in shaping political landscapes, alliances, and global affairs through the book review. What is new about this essay is its accessible presentation of complex geopolitical concepts, making it a valuable resource for students of geography and readers interested in global politics. Through the analysis of case studies and historical background, the book illuminates the interplay between physical landscapes, territoriality, and power dynamics. The findings highlight the continuing influence of geography on nations, regional identities, and the evolving global order.
REVIEW | doi:10.20944/preprints202306.0162.v1
Subject: Public Health And Healthcare, Public Health And Health Services Keywords: Viral Encephalitis; Transmission Dynamics; Epidemiology; One Health
Online: 2 June 2023 (08:57:30 CEST)
Viral Encephalitis is a significant public health concern globally, especially west Africa. There are more than 500 known arboviruses with over 100 of them identified to cause encephalitic diseases in humans and animals, giving rise to a tremendous burden of the diseases, and socioeconomic strains in tropical and subtropical regions worldwide. Despite their importance, few effective preventive and control measures in form of vaccines and therapeutics are available and where they are, usage is limited. These limitations are largely hinged on the paucity of information about the molecular epidemiology and transmission patterns of VE in west Africa. Here, we reviewed the transmission dynamics, ecological drivers, and molecular epidemiology of VE in the region. Collectively, timely and accurate interventions are essential for encephalitic viral disease control. Moreover, the integrated health system approach, combining surveillance, vaccination, vector control, and community engagement could be effective in preventing viral encephalitis globally.
REVIEW | doi:10.20944/preprints202305.2112.v1
Subject: Biology And Life Sciences, Aging Keywords: ATP production; mitochondrial network; mitochondria dynamics, MCU
Online: 30 May 2023 (10:32:39 CEST)
Exercise produces oxidants from a variety of intracellular sources, including NADPH oxidases (NOX) and mitochondria. Exercise-derived ROS are beneficial, and the amount and location of these ROS are important to avoid muscle damage associated with oxidative stress. We discuss here some of the evidence that involves ROS production associated with skeletal muscle contraction and the potential oxidative stress associated with muscle contraction. We also discuss the potential role of H2O2 produced after NOX activation in the regulation of glucose transport in skeletal muscle. Finally, we propose a model based on evidence for the role of different populations of mitochondria in skeletal muscle in the regulation of ATP production upon exercise. The sub-sarcolemmal population of mitochondria has the enzymatic and metabolic components to establish a high mitochondrial membrane potential when fissioned at rest but lacks the capacity to produce ATP; calcium entry to the mitochondria will further increase the metabolic input. Upon exercise, sub-sarcolemmal mitochondria will fuse to intermyofibrillar mitochondria and will transfer the membrane potential to them. These mitochondria are rich in ATP synthase and will subsequentially produce the ATP needed for muscle contraction in long-term exercise. These events will optimize energy use and minimize mitochondria ROS production.
ARTICLE | doi:10.20944/preprints202305.1717.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Ecological networks, bioengineering, synthetic biology, invasion dynamics
Online: 25 May 2023 (03:05:45 CEST)
The possibility of abrupt transitions threatens to poise ecosystems into irreversibly degraded states. Recently, it has been proposed the use of engineered microbiomes in endangered ecosystems to prevent them to cross tipping points and avoid collapse. Potential targets for such interventions include some of the most prominent life-support systems in the biosphere: drylands and coral reefs. Since engineering can require the introduction of microorganisms not present in resident communities, how can we weight the potential outcomes? One way is to use general models of species interactions where the "synthetic" strain is incorporated into a standard multispecies model. Here we follow this approach by modelling a resource-consumer community where one of the species is a modified one that acts by preserving some key resource. We show how the indirect effect of damping the decay of shared resources results in biodiversity increase, and last but not less, the successful incorporation of the synthetic within the ecological network. Further extensions and implications for future restoration and terraformation strategies are discussed.
ARTICLE | doi:10.20944/preprints202305.0447.v1
Subject: Engineering, Mechanical Engineering Keywords: polyimide; Molecular dynamics simulation; tribology; graphene oxide
Online: 8 May 2023 (04:53:07 CEST)
To improve the wear resistance of polyimide (PI), surface modification was developed. In this study, the tribological properties of graphene (GN), graphene oxide (GO), and KH550-grafted graphene oxide (K5-GO) modified PI were evaluated by molecular dynamics (MD) at the atomic level. The findings indicated that the addition of nanomaterials can significantly enhance the friction performance of PI. The friction coefficient of PI composites decreased from 0.253 to 0.232, 0.136, and 0.079 after coating GN, GO and K5-GO, respectively. Among them, the K5-GO/PI exhibited the best surface wear resistance. Importantly, the mechanism behind the modification of PI was thoroughly revealed by observing the wear state, analyzing the changes of interfacial interactions, interfacial temperature, and relative concentration.
ARTICLE | doi:10.20944/preprints202305.0162.v1
Subject: Engineering, Mechanical Engineering Keywords: Catamaran sailing; drag; hydrofoils; fluid dynamics; optimizaton
Online: 4 May 2023 (02:38:48 CEST)
Catamaran hulls have always been associated with smaller vessels in naval engineering and construction. However, recent research results have shown that by considering specific criteria based on materiality, structure and functionality, they can be designed for a more complex industry, such as hydrofoil design. Among the challenges in this type of vessel, one of the most difficult variables is estimating the resistance to the advance in the function of the degree of uncertainty generated. This research focuses on optimising the drag of a sport sailing catamaran by implementing hydrofoils, through the application of computational fluid dynamics (CFD), at different speeds to demonstrate that it is possible to modify and improve the current appendages of this vessel.
ARTICLE | doi:10.20944/preprints202305.0059.v1
Subject: Computer Science And Mathematics, Computational Mathematics Keywords: Breakwater; Simulation; Fluids Dynamics; H-FEM; PDE
Online: 2 May 2023 (05:14:15 CEST)
A wave is an energy that can propagate with a medium, the propagation of a wave moves with respect to time by carrying energy that moves with velocity per unit of time. Sea waves are one of the propagating wave problems that are broken down to produce wave propagation with a relatively inhomogeneous minimum amplitude and speed of sea waves which have their own difficulties in solving them numerically. This study aims to analyze the stability of wave propagation of submerged breakwaters using the Boundary Element Method. This research will approximate the boundary discretization of the breakwater domain and then combine it with the Finite Element Method in determining the moving elements of the velocity of fluid flow through a porous submerged breakwater. This study varies the magnitude of the incoming propagation velocity and the influence of the breakwater distance. The results of this study indicate that the resulting minimal wave assuming v = 1 m/s and the breakwater distance of s = 20 m gives a wave reflection with a minimum wave speed and amplitude of 0.12515 m
ARTICLE | doi:10.20944/preprints202304.0169.v1
Subject: Physical Sciences, Theoretical Physics Keywords: Squeezing; Quantum Dynamics; Integrable Systems; Exact Solutions
Online: 10 April 2023 (10:27:15 CEST)
Quantum squeezing, an intriguing phenomenon that amplifies the uncertainty of one variable while diminishing that of its conjugate, may be studied as a time-dependent process, with exact solutions frequently derived from frameworks grounded in adiabatic invariants. Remarkably, we reveal that exact solutions can be ascertained in the presence of time-variant elastic forces, eschewing dependence on invariants or frozen eigenstates formalism. Delving into these solutions as an inverse problem unveils their direct connection to the design of elastic fields, responsible for inducing squeezing transformations onto canonical variables. Of particular note, the dynamic transformations under investigation belong to a class of gentle quantum operations, distinguished by their delicate manipulation of particles, thereby circumventing the abrupt energy surges commonplace in conventional control protocols.
ARTICLE | doi:10.20944/preprints202302.0349.v1
Subject: Chemistry And Materials Science, Physical Chemistry Keywords: Confined colloids; waterlike anomalies; Molecular Dynamics simulation
Online: 21 February 2023 (03:49:27 CET)
The interaction between hard-core soft-shell colloids are characterized by having two characteristic distances: one associated with the penetrable, soft corona and another one corresponding to the impenetrable core. Isotropic core-softened potentials with two characteristic length scales have long been applied to understand the properties of such colloids. Those potentials usually show waterlike anomalies, and recent findings have indicated the existence of multiple anomalous regions in the 2D limit under compression, while in 3D only one anomalous region is observed. In this direction, we perform Molecular Dynamics simulations to unveil the details about the structural behavior in the quasi-2D limit of a core-softened colloid. The fluid was confined between highly repulsive solvophobic walls, and the behavior at distinct wall separation and colloid density was analyzed. Our results indicated a straight relation between the 2D or 3D-like behavior and the layers separation. We can relate that if the system behaves as independent 2D-layers, it will have a 2D-like behavior. However, for some separations the layers are connected, with colloids hopping from one layer to another – having then a 3D-like structural behavior. Those findings fill the gap in the depiction of the anomalous behavior from 2D to 3D.
ARTICLE | doi:10.20944/preprints202210.0419.v2
Subject: Physical Sciences, Other Keywords: Swarm dynamics; Criticality; Ising Model; Collective behavior
Online: 7 November 2022 (02:40:22 CET)
Social insects, such as honey bees exhibit complex behavioral patterns and their inconspicuous coordination enables decision-making on the colony level. It is thus proposed, that a high-level description of their collective behavior might share commonalities with neural processes in the brains. At the same time, recent research concerning overarching features of neural activity implies that brains are poised at the edge of the critical phase transition and that such a state is enabling maximal computational power and adaptability. In our research, we applied some tools developed in the computational neuroscience field to the dataset of bee trajectories recorded within the hive, during the course of many days. Our results imply that certain characteristics of the system are remarkably similar to the Ising model when it operates at critical temperature and also shares some of the features with the human brain at the resting state
ARTICLE | doi:10.20944/preprints202202.0339.v1
Subject: Engineering, Mechanical Engineering Keywords: Wave; Energy; Dynamics; Modeling; Generator; Converter; linear
Online: 25 February 2022 (13:53:54 CET)
Recently, most countries suffering from global warming due to the waste gases coming out of the combustion engines used to generate electric power by traditional methods. Therefore, many countries are currently trying to find alternative solutions to this problem by using renewable energies such as solar energy, wind energy, and energy generated from the waves of the ocean and sea to overcome pollution problems. The waves of the seas and oceans have enormous and largely untapped energy, so this work presents an efficient way to use the energy of sea waves to generate electricity. And also, trying to be a way to produce electricity from wave energy in the future. The best suitable places along the shores of Jizan city were inspected to install the buoy system to revenue advantage of the wave supreme height to achieve the height amount of electrical energy. A mathematical model was made to analyze the wave energy and convert it into energy extracted by mechanical force. The mathematical analyzes used the data collected from satellite maps of the numerous severe waves in the Red sea of the Jazan area, and the data published in previous research along that area. It was found that the beach of the Al Shuqaiq area is the greatest for installing the buoy and obtaining the highest electrical energy due to the presence of the highest wave intensity, followed by the beach of the Baysh and Al Morgan area. Also, one of the objectives of this research is to study the design of a device powered by a buoy to use the waves of the Red Sea to generate electric power. The influence of the buoy system design parameters such as the buoy diameter, length of the cylinder, and the length of the connecting rod on the electrical energy generation from wave energy was investigated. The current device is designed with a gearbox to produce continuous power with a single electric generator. A floating mooring device uses the rise and fall of bulges to convert sea wave energy into electrical energy. The device consists of a float, arm, two wheels of different diameters, a gear set, and an electric generator. The effect of the design of several factors on the performance of the device for converting the sea waves energy into electrical energy, including the length of the buoy arm, the wave height by changing the cam diameter, and the conversion ratios between the gear set, to optimize the output power of the wave energy.
ARTICLE | doi:10.20944/preprints202112.0318.v1
Subject: Engineering, Mechanical Engineering Keywords: Wheelchair; climbing stairs; dynamics of movement; sensors
Online: 21 December 2021 (08:59:36 CET)
The article presents the stages of modeling and simulation of a new design of a wheelchair with the option of moving up and down stairs. These analyzes were aimed at the synthesis of the de-sign parameters and parameters of the sensor and control systems. The simulation results were verified by experimentally testing the prototype.
ARTICLE | doi:10.20944/preprints202111.0088.v1
Subject: Chemistry And Materials Science, Surfaces, Coatings And Films Keywords: Liquids; Confinement; Stress Relaxation; Molecular Dynamics; Hysteresis
Online: 3 November 2021 (14:56:25 CET)
When liquids are confined into nanometer-scale slit, the induced layering-like film structure allows the liquid to sustain non-isotropic stresses and thus being load-bearing. Such anisotropic characteristics of liquid under confinement arise naturally from the liquids’ wave number dependent compressibility that does not need solidification to take place as a prerequisite. In other words, liquids under confinement can still remain fluidity with molecules being (sub-)diffusive. However, the extensively prolonged structural relaxation time can cause hysteresis of stress relaxation of confined molecules in response to the motions of confining walls and thereby yield the quasi-static stress tensor history-dependent. In this work, by means of molecule dynamics, the discrepancy of stress tensor of a highly confined key base-oil component, i.e. 1-decene trimer, is captured after its relaxation from being compressed and decompressed. The results indicate that among the effects (e.g. confinement, molecular structure, and film density) that can potentially affect confined stress tensor, the ordering status of the confined molecules plays a predominant role.
ARTICLE | doi:10.20944/preprints202005.0332.v2
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: coronavirus; substitution rate; positive selection; demographic dynamics
Online: 21 June 2020 (16:10:26 CEST)
A new form of coronavirus called severe acute respiratory disease coronavirus type 2 (SARS-CoV-2) is currently causing a pandemic. A six-month evolutionary history of SARS-CoV-2 is witnessed by characterising the total genome of 821 samples using comparative phylogenomic approaches. Our analyses produced striking inclusive results that may guide scientists/professionals for the past/future of pandemic. Phylogenetic and time estimation analyses suggest the proximate origin of pandemic strain as Guangdong and the origin time as first half of September 2019, not Wuhan and December 2019, respectively. The viral genome experienced a substitution rate similar to other RNA viruses, but it is particularly high in some of the peptides encoding sequences such as leader protein, E gene, orf8, orf10, nsp10, N gene, S gene and M gene and nsp4, while low in nsp11, orf7a, 3C-like proteinase, nsp9, nsp8 and endoRNase. Most strikingly, the divergence rate of amino acid sequences is high proportional to nucleotide divergence. Additionally, specific non-synonymous mutations in nsp3 and nsp6 evolved under positive selection. The exponential growth rate (r), doubling time (Td) and R0 were estimated to be 47.43 per year, 5.39 days and 2.72, respectively. Comparison of synapomorphies distinguishing the SARS-CoV-2 and the candidate ancestor bat coronavirus indicates that mutation pattern in nsp3 and S gene enabled the new strain to invade human and become a pandemic strain. We arrive at the following main conclusions: (i) six months evolution of viral genome is nearly neutral, (ii) origin of pandemic is not Wuhan and predates formal reports, (iii) although viral population is ongoing an exponential growth, the doubling time is evolving towards shortening, and (iv) divergence rate of total genome is similar to other RNA viruses, but it is prominently high in some genes while low in some others and evolution in these genes should be closely monitored as their protein products intervening to pathogenicity, virulence and immune response.
ARTICLE | doi:10.20944/preprints202004.0193.v2
Subject: Computer Science And Mathematics, Computational Mathematics Keywords: COVID-19; lockdown; sensitivity analysis; epidemic dynamics
Online: 23 May 2020 (10:47:33 CEST)
In the promptness of the COVID-19 outbreak, it would be very important to observe and estimate the pattern of diseases to reduce the contagious infection. To study this effect, we developed a COVID-19 analytical epidemic framework that combines with isolation and lockdown effect by incorporating five various groups of individuals. Then we analyze the model by evaluating the equilibrium points and analyzing their stability as well as determining the basic reproduction number. The extensive numerical simulations show the dynamics of a different group of the population over time. Thus, our findings based on the sensitivity analysis and the reproduction number highlight the role of outbreak of the virus that can be useful to avoid a massive collapse in Bangladesh and rest of the world. The outcome of this study concludes that outbreak will be in control which ensures the social and economic stability.
REVIEW | doi:10.20944/preprints202002.0203.v1
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: Alzheimer’s disease; biomarkers dynamics; interaction; time order
Online: 15 February 2020 (15:06:18 CET)
The Aβ cascade and alternations of biomarkers in neuro-inflammation, synaptic dysfunction and neuronal injury followed by Aβ have progressed. But the question is how to use the biomarkers. Here, we examine the evidence and pathogenic implications of protein interactions and the time order of alternation. After the deposition of Aβ, the change of tau, NfL and NG is the main alternation and connection to others. The neuro-inflammation, synaptic dysfunction and neuronal injury function is exhibited prior the structural and metabolic changes in the brain following Aβ deposition. The time order of such biomarkers compared to the tau protein is not clear. Despite the close relationship between biomarkers and plaque Aβ deposition, several factors favor one or the other. There is an interaction between the proteins that CSF SNAP-25, VILIP-1 and YKL-40 can predict the brain amyloid burden. The Aβ cascade hypothesis could be the pathway, but not all subjects are converted to AD, even with very high elevated Aβ. The interaction of biomarkers and the time order of change require further research to identify the right subjects and right molecular target for precision medicine therapies.
REVIEW | doi:10.20944/preprints201812.0015.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: microtubule dynamics; mitosis; spindle; molecular motor protein
Online: 3 December 2018 (09:06:22 CET)
Proper regulation of microtubules (MTs) is critical for the execution of diverse cellular processes, including mitotic spindle assembly and chromosome segregation. There are a multitude of cellular factors that regulate the dynamicity of MTs and play critical roles in mitosis. Members of the Kinesin-8 family of motor proteins act as MT-destabilizing factors to control MT length in a spatially and temporally regulated manner. In this review, we focus on recent advances in our understanding of the structure and function of the Kinesin-8 motor domain, and the emerging contributions of the C-terminal tail of Kinesin-8 proteins to regulate motor activity and localization.
REVIEW | doi:10.20944/preprints201811.0024.v1
Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: mitochondria; mitochondrial dynamics; fusion; fission; pluripotency; differentiation
Online: 2 November 2018 (06:05:44 CET)
Mitochondria are highly dynamic organelles that continuously change their shape. Their main function is ATP production; however, they are additionally involved in a variety of cellular phenomena, such as apoptosis, cell cycle, proliferation, differentiation, reprogramming, and aging. The change in mitochondrial morphology is closely related to the functionality of mitochondria. Normal mitochondrial dynamics are critical for cellular function, embryonic development, and tissue formation. Thus, defect in proteins involved in mitochondrial dynamics that control mitochondrial fusion and fission can affect cellular differentiation, proliferation, cellular reprogramming, and aging. Here we review the processes and proteins involved in mitochondrial dynamics and its various associated cellular phenomena.
ARTICLE | doi:10.20944/preprints201807.0327.v1
Subject: Physical Sciences, Fluids And Plasmas Physics Keywords: rarefied gas dynamics; modelling evaporation; R13-equations
Online: 18 July 2018 (09:55:45 CEST)
Due to failure of the continuum hypothesis for higher Knudsen numbers, rarefied gases and microflows of gases are particularly difficult to model. Macroscopic transport equations compete with particle methods, such as DSMC to find accurate solutions in the rarefied gas regime. Due to growing interest in micro flow applications, such as micro fuel cells, it is important to model and understand evaporation in this flow regime. Here, evaporation boundary conditions for the R13 equations, which are macroscopic transport equations with applicability in the rarefied gas regime, are derived. The new equations utilize Onsager relations, linear relations between thermodynamic fluxes and forces, with constant coefficients, that need to be determined. For this, the boundary conditions are fitted to DSMC data and compared to other R13 boundary conditions from kinetic theory and Navier-Stokes-Fourier (NSF) solutions for two one-dimensional steady-state problems. Overall, the suggested fittings of the new phenomenological boundary conditions show better agreement to DSMC than the alternative kinetic theory evaporation boundary conditions for R13. Furthermore, the new evaporation boundary conditions for R13 are implemented in a code for the numerical solution of complex, two-dimensional geometries and compared to NSF solutions. Different flow patterns between R13 and NSF for higher Knudsen numbers are observed.
ARTICLE | doi:10.20944/preprints201711.0085.v1
Subject: Computer Science And Mathematics, Robotics Keywords: rectilinear; PID; friction; spring-mass system; dynamics
Online: 14 November 2017 (05:23:06 CET)
This paper deals with the analytical modeling and control of rectilinear snake robots. During recent times snake robots have created much interest among researchers. The rectilinear pattern gait is one of the four biological snake locomotion modes. Rectilinear snakes have been widely used in rescue operations especially in rough terrains especially in narrow spaces where human intervention is not easy. Computational analysis of rectilinear motion is done using MATLAB.
ARTICLE | doi:10.20944/preprints201710.0162.v1
Subject: Chemistry And Materials Science, Polymers And Plastics Keywords: hydrogel; thermal conductivity; 3ω method; molecular dynamics
Online: 25 October 2017 (03:54:39 CEST)
As the interface between human and machine becomes blurred, hydrogel incorporated electronics and devices have emerged to be a new class of flexible/stretchable electronic and ionic devices due to their extraordinary properties, such as soft, mechanically robust and biocompatible. However, heat dissipation in these devices could be a critical issue and remains unexplored. Here, we report the experimental measurements and equilibrium molecular dynamics simulations of thermal conduction in polyacrylamide (PAAm) hydrogels. The thermal conductivity of PAAm hydrogels can be modulated by both the crosslinking density and water content in hydrogels. The crosslinking density dependent thermal conductivity in hydrogels varies from 0.33 to 0.51 Wm-1K-1, giving a 54% enhancement. We attribute the crosslinking effect to the competition between the increased conduction pathways and the enhanced phonon scattering effect. Moreover，water content can act as filler in polymers which lead to nearly 40% enhancement in thermal conductivity in PAAm hydrogels with water content vary from 23 to 88 wt%. Furthermore，we find the thermal conductivity of PAAm hydrogel is insensitive to temperature in the range of 25 oC – 40 oC. Our study offers fundamental understanding of thermal transport in soft materials and provides design guidance for hydrogel-based devices.
ARTICLE | doi:10.20944/preprints201709.0030.v2
Subject: Physical Sciences, Condensed Matter Physics Keywords: dynamical equation; crystal; period vectors; periodic structure; period dynamics; pressure; stress; many-body interaction; molecular dynamics; periodic boundary conditions
Online: 9 August 2018 (08:36:53 CEST)
Since crystals are made of periodic structures in space, predicting their three period vectors starting from any values based on the inside interactions is a basic theoretical physics problem. For the general situation where crystals are under constant external stress, we derived dynamical equations of the period vectors in the framework of Newtonian dynamics, for pair potentials recently (doi:/10.1139/cjp-2014-0518). The derived dynamical equations show that the period vectors are driven by the imbalance between the internal and external stresses. This presents a physical process where when the external stress changes, the crystal structure changes accordingly, since the original internal stress can not balance the external stress. The internal stress has both a full kinetic energy term and a full interaction term. It is extended to many-body interactions in this paper. As a result, all conclusions in the pair-potential case also apply for many-body potentials.
ARTICLE | doi:10.20944/preprints202309.0233.v1
Subject: Physical Sciences, Condensed Matter Physics Keywords: low density lipoproteins; hemoperfusion; azobenzene; adsorption; molecular dynamics
Online: 6 September 2023 (15:11:39 CEST)
One of the strategies to reduce the contents of the low density lipoproteins (LDLs) in a blood is a hemoperfusion, in which case they are selectively retracted from plasma by an adsorber located outside the patient body. Recently, a photo-controllable smart surface was developed for this purpose characterised by high selectivity and reusability [C.Guo et al., ACS Applied Materials & Interfaces 2022, DOI:10.1021/acsami.2c07193]. We present a mesoscopic model for such a setup involving the azobenzene-containing polymer brush and the model LDL particles. The latter comprise an uniform spherical core covered by a shell of elongated particles representing phospholipids. The system is studied using the coarse-grained molecular dynamics simulation. We examined the dependences of the binding energy on both the length of polymer chains and the grafting density of a brush, and established optimal conditions for the adsorption. These are explained by a competition between the concentration of azobenzenes and phospholipids in the same spatial region, flexibility of polymer chains, and excluded volume effects.
Subject: Chemistry And Materials Science, Materials Science And Technology Keywords: carbon; atomic structure; electron-dynamics; potential energy; force-exertion; atomic binding
Online: 17 May 2019 (08:36:23 CEST)
Many studies discuss carbon-based materials because of the versatility of its element. They include different opinions for scientific problems and discuss fairly at convincing and compelling levels within the scope and application. A gas-state carbon atom converts into various states depending on its conditions of processing. The electron transfer mechanism in the gas-state carbon atom is responsible to convert it into various states, namely, graphite, nanotube, fullerene, diamond, lonsdaleite and graphene. The shape of ‘energy trajectory’ enables transferring electrons from the left- and right-sides of an atom is like a parabola. That ‘energy trajectory’ is linked to states (filled state and suitable nearby unfilled state) where force-exertion along the poles of transferring electrons is remained balance. So, the mechanism of originating different states of a gas-state carbon atom is under the involvement of energy first. This is not the case for atoms executing confined inter-state electron-dynamics as the force is involved first. Graphite-, nanotube- and fullerene-state atoms ‘partially evolve partially develop’ (form) their structures. These possess one-dimensional, two-dimensional and four-dimensional ordering of atoms, respectively. Their structural formation also comprises ‘energy curve’ having a shape-like parabola. Transferring suitable filled state electron to suitable nearby unfilled state is under a balance force exerting along the poles. The graphite structure under only attained-dynamics of atoms can also be formed but in two-dimension. Here, binding energy between graphite-state carbon atoms is for a small difference of exerting forces along their opposite poles. Structural formation in diamond, lonsdaleite and graphene atoms involve energy to gain required infinitesimal displacements of electrons through which they maintain orientationally-controlled exerting forces along dedicated poles. In this study, the growth of diamond is found to be south to east-west (ground) where atoms bound ground to south. Thus, diamond atoms merge for a tetra-electron ground to south topological structure. Lonsdaleite atoms merge for a bi-electron ground to just-south topological structure. The growth of graphene is found to be north to ground where atoms bound ground to north. Thus, graphene atoms merge for a tetra-electron ground to north topological structure. Glassy carbon exhibits layered-topological structure where, tri-layers of gas-, graphite- and lonsdaleite-state atoms successively bind in repetitive order. Nanoscale hardness is also sketched based on different force-energy behaviors of different state carbon atoms. Here, structure evolution in each carbon state atom explores its own science.
ARTICLE | doi:10.20944/preprints202307.1711.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: competition; scale insects; mutualism; temporal dynamics; xerophytic shrubland
Online: 25 July 2023 (11:12:59 CEST)
Interspecific competition between herbivorous insects is a major selection pressure affecting the distribution, abundance, and structure of their populations. Facilitator-mediated interactions, such as mutualism, can influence competition. Furthermore, the temporal dynamics of competitive relationships affect the interaction’s outcome. Here, we re-evaluated the data on the competition for space between two herbivorous insects commonly known as scales (Toumeyella martinezae and Opuntiaspis philococcus) in either the presence or absence of Liometopum apiculatum (a mutualistic species of T. martinezae) and its variations over time. We selected 27 Myrtillocactus geometrizans plants on which the studied insects were present; the plants were classified into one of five different conditions: either of the scale species were present on the plant, without its competitor; T. martinezae with neither its mutualistic species nor the competitor; and both scale species competing in either presence or absence of the mutualistic species. We kept a photographic record of each condition, measured the size of (as an indicator of the development stage) and area occupied by the individual scales, estimated the total coverage of each scale species, and assessed their relative occupation of space and their competitive intensity. We found temporal variations in competitive intensity. T. martinezae occupied more space during the first months, whereas O. philococcus did so towards the end of the study period. The population structure changed over time and between species, affecting the competitive interactions. In conclusion, the dynamics of competition change over time, and the mutualistic species has a positive effect on T. martinezae when the scales are in competition. However, temporal variations resulting from changes in the life cycle of the scales allow the two competitors to coexist in the same place at the same time.
ARTICLE | doi:10.20944/preprints202307.1164.v1
Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: Norepinephrine, Norepinephrine transporter, molecular dynamics, efflux, Gβγ subunit.
Online: 18 July 2023 (09:13:37 CEST)
Norepinephrine (NE) uptake through the NE transporter (NET) is the primary mechanism to ter-minate the action of this neurotransmitter. Dysregulation of brain NE levels is associated with various conditions, including attention deficits, depression, and Alzheimer's disease. Recently, we identified an interaction between the related dopamine (DA) transporter (DAT) and G protein βγ subunits. Activation of Gβγ in cells and brain slices leads to DA efflux through DAT. However, the potential interaction between Gβγ and NET has not been reported. Here, we used a combina-tion of molecular modeling approaches to elucidate the structural details of the NET/Gβγ inter-action, supported by experimental evidence. Through 1.5µs of molecular dynamic simulation, we observed a favorable NET/Gβγ interaction mediated by the intracellular carboxy terminus of NET. As a consequence, the binding energy of NE for NET also changes resulting in alterations of the electrostatic profile of NET. We propose that these changes mediate the NE efflux effect. Fi-nally, we provide experimental evidence demonstrating that Gβγ physically interacts with NET and that the Gβγ activator mSIRK induces NE efflux through the transporter. These findings identified a novel interaction between Gβγ and NET and highlighted its potential implications in the regulation of NE neurotransmission and associated disorders.
ARTICLE | doi:10.20944/preprints202306.0665.v1
Subject: Chemistry And Materials Science, Polymers And Plastics Keywords: Molecular Dynamics; polyelectrolytes; , polymerization; , self-assembly; graph theory
Online: 9 June 2023 (04:20:41 CEST)
The chemical feedback between building blocks in templated polymerization of diblock copolymers and their consecutive micellization was studied for the first time by means of coarse-grained molecular dynamics simulations. Using a stochastic polymerization model, we were able to reproduce the experimental findings on the effect of chemical feedback on the polymerization rates at low and high solution concentrations. The size and shape of micelles were computed using a newly development software in python conjugated with graph theory. In full agreement with the experiments, our simulations revealed that micelles formed by the templated micellization are more spherical and have lower radius of gyration than those formed by the traditional two-step micellization method. Understanding the underlying mechanisms in templated reaction/assembly of polymers will help for rational design of new synthetic supramolecular materials.
ARTICLE | doi:10.20944/preprints202305.2151.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Population dynamics; age structure; entropy; Maximum Entropy Principle
Online: 30 May 2023 (13:20:58 CEST)
Models with age as a variable but actual dynamics invariant under age structure allow use of MaxEnt to predict uniform age structure. Interpretations include a major role for accepting randomness as a causal principle in ecology (in the face of ignorance, in a further interpretative stance).
ARTICLE | doi:10.20944/preprints202305.1609.v1
Subject: Engineering, Control And Systems Engineering Keywords: neural dynamics; neural oscillation; bio-inspiration; artificial intelligence
Online: 23 May 2023 (08:05:36 CEST)
This paper investigates the dynamic properties of artificial neural networks using differential equations and explores the influence of parameters on stability and neural oscillations. By analyzing the equilibrium point of the differential equations, we identify conditions for asymptotic stability and criteria for oscillation in artificial neural networks. Furthermore, we demonstrate how adjusting synaptic weights between neurons can effectively control stability and oscillation. The proposed model offers potential insights into the malfunctioning mechanisms of biological neural networks implicated in neurological disorders like Parkinson's disease tremors and epilepsy seizures, which are characterized by abnormal oscillations.
ARTICLE | doi:10.20944/preprints202305.0678.v1
Subject: Engineering, Metallurgy And Metallurgical Engineering Keywords: Steel slag; CO2 sequestration; CCUS; Molecular dynamics simulation
Online: 10 May 2023 (03:51:50 CEST)
A large amount of steel slag (SS) and CO2 are generated in the steelmaking process. The indirect CO2 capture using SS is a promising way for co-treatment of the wastes. Ammonium salt solution is widely used to extract Ca2+ from the SS since it is recyclable. Several works have focus on improving the carbonation rate by adjusting various parameters (e.g., temperature and pH). However, there is little detail information about the associating behaviors and interaction strength between the various ions in the ammonia solution during the carbonation process. In this work, the Ca2+–CO32-–NH4+–Cl-–H2O system was established by using Material studio software. The effects of temperature and concentration of CO32- on CaCO3 growth were explored at the atomic scale by calculating the binding energy, mean square displacement, and diffusion coefficient between particles. Furthermore, the microstructure, bonding characteristics, and occurrence behavior of each particle were studied though molecular dynamics simulation methods. The results showed that with the increase of temperature (20–80 ℃), the binding ability and diffusion coefficients of Ca2+ and CO32- increase in the system, which is beneficial to the formation of CaCO3 clusters. With the increase of the concentration of CO32- (15–25 vol.%), the binding ability and diffusion coefficient of Ca2+ and CO32- in the system are enhanced, which is beneficial to the formation of CaCO3 clusters.
ARTICLE | doi:10.20944/preprints202305.0066.v1
Subject: Physical Sciences, Mathematical Physics Keywords: Entropy; Complex Fluid Dynamics; Boltzmann principle; Planck law
Online: 2 May 2023 (07:26:37 CEST)
We consider that the relationship between the entropy in statistical mechanics, which is the Boltzmann principle, and the complex velocity potential in complex fluid dynamics. We define the generalized complex entropy which extends the entropy from real space to complex space. We show that the change of entropy can be expressed by the composition of the source and the sink of the complex velocity potential. Therefore, the complex entropy is considered a special case of the complex fluid dynamics, that is, the complex velocity potential. Moreover, we show that a complex number is expressed by the complex entropy. Thus, we show that the complex velocity potential is expressed by the complex entropy.
ARTICLE | doi:10.20944/preprints202212.0311.v1
Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: meteor radar; quasi 16-day wave; mesospheric dynamics
Online: 19 December 2022 (02:51:19 CET)
In this study, we present more than 8 years of observations of the quasi-16-day wave (Q16DW) in the mesosphere and lower thermosphere (MLT) wind at middle latitudes observed by the Mengcheng (33.4°N, 116.5°E) meteor radar. The long-term variation in amplitudes calculated from the data between April 2014 and December 2022 shows enhanced wave activity during winter and early spring (near equinox) and suppressed wave activity during the summer. The Q16DWs are relatively weak in the meridional wind. During the winter months, the Q16DWs in the zonal component exhibit a burst below 85 km, and their amplitudes reach up to 10 m/s. In the early spring, the Q16DWs strengthen above 90 km with amplitudes in excess of 12 m/s. The phase differences between the zonal and meridional components of the Q16DW are, on average, slightly smaller than 90°, suggesting the existence of orthogonal relationships between them. During strong bursts, the periods of the Q16DW in winter range between 15 and 18 d, whereas in winter, the periods tend to be more diffuse. The wintertime Q16DW is amplified, on average, when the zonal wind shear peaks, suggesting that barotropic instability may be one source of Q16DW. Q16DW amplitudes exhibit considerable interannual variability; however, a relationship between the 11-year solar cycle and the Q16DW is not found.
ARTICLE | doi:10.20944/preprints202211.0283.v1
Subject: Chemistry And Materials Science, Theoretical Chemistry Keywords: dioxins; lipid membranes; molecular dynamics; QM/MM; EDA
Online: 15 November 2022 (09:50:18 CET)
The permeation of dioxin-like pollutants, namely, chlorinated dibenzodioxins and dibenzofurans, through lipid membranes has been simulated using classic molecular dynamics (CMD) combined with the umbrella sampling approach. The most toxic forms of chlorinated dibenzodioxin and dibenzofuran, 2,3,7,8-tetrachloro-p-dibenzodioxin (TCDD) and 2,3,7,8-tetrachlorodibenzofuran (TCDF), and a dioleyl-phosphatidylcholine (DOPC) lipid membrane of 50 Å wide have been chosen for our study. The free energy profile shows the penetration process is largely favoured thermodynamically (DG≈-12 kcal/mol), with a progressively decrease of the free energy until reaching the energy minima at distances of 8Å and 9.5Å from the centre of the membrane for, respectively, TCDD and TCDF. At the centre of the membrane, both molecules display subtle local maxima with free energy differences of 0.5 and 1 kcal/mol with respect to the energy minima for TCDD and TCDF, respectively. Furthermore, the intermolecular interactions between the molecules and the lipid membrane have been characterized at the minima and the local maxima using hybrid quantum mechanics/molecular mechanics energy decomposition analysis (QM/MM-EDA). Total interaction energies of -17.5 and -16.5 kcal/mol have been found at the energy minima for TCDD and TCDF, respectively. In both cases, the dispersion forces govern the molecule-membrane interactions, no significant changes have been found at the local maxima, in agreement with the classical free energy profile. The small differences found in the results obtained for TCDD and TCDF point out the adsorption and diffusion processes through the cell membrane are not related to the different toxicity shown by these pollutants.
ARTICLE | doi:10.20944/preprints202209.0403.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Cell Disease; Stroke; Neuroimaging; Hematology; Computational fluid dynamics
Online: 27 September 2022 (02:38:29 CEST)
The main objective of this study is to demonstrate proof of principle that computational fluid dynamics (CFD) modeling is a tool for studying the contribution of covert and overt vascular architecture to the risk of cerebrovascular disease in in sickle cell disease (SCD) as well as uncover one or more mechanism of response to therapy such as chronic red blood cell (cRBC) transfusion. We analyzed baseline (screening), pre-randomization and study exit magnetic resonance angiogram (MRA) images from 10 (5 each from the transfusion and observation arms) pediatric sickle SCD participants in the silent cerebral infarct transfusion (SIT) trial, using CFD modeling. We reconstructed the intracranial portion of the internal carotid artery and branches and extracted the geometry using 3D Slicer. We cut specific potions of the large intracranial artery to include segments of the internal carotid, middle, anterior, and posterior cerebral artery such that the vessel segment analyzed extended from the intracranial beginning of the internal carotid artery up to immediately after (~0.25 inches) the middle cerebral artery branching point. Cut models were imported into Ansys 2021R2/2022R1 and laminar and time-dependent flow simulation was performed. Change in time averaged mean velocity, wall shear stress, and vessel tortuosity were compared between the observation and cRBC arm. We did not observe a correlation between time averaged mean velocity (TAMV) and mean transcranial doppler (TCD) velocity at study entry. There was also no difference in change in time average mean velocity, wall shear stress (WSS), and vessel tortuosity between the observation and cRBC transfusion arms. WSS and TAMV were abnormal for 2 (developed TIA) out of the 3 participants (one participant had SCI) that developed neurovascular outcomes. CFD approaches allows for the evaluation of vascular topology and hemodynamics in SCD using MRA images. In this proof of principle study, we show that CFD could be a useful tool and we intend to carry out future studies with a larger sample to enable more robust conclusions.
REVIEW | doi:10.20944/preprints202207.0108.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: membrane curvature; molecular dynamics; simulations; BAR domain; trafficking
Online: 7 July 2022 (04:19:42 CEST)
Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma membrane to the highly curved membranes of organelles, vesicles, and membrane protrusions. These curvatures are generated and sustained by curvature-inducing proteins, peptides, and lipids, and describing these mechanisms is an important scientific challenge. In addition to that, some molecules can sense membrane curvature and a thereby be trafficked to specific locations. The description of curvature-sensing is another fundamental challenge. Curved lipid membranes and their interplay with membrane-associated proteins can be investigated with molecular dynamics (MD) simulations, given the right tools. Various methods for simulating curved membranes with MD are discussed here, including tools for setting up simulation of vesicles, and methods for sustaining membrane curvature. The latter are divided into methods that exploit scaffolding virtual beads, methods that use curvature-inducing molecules, and methods applying virtual forces. The variety of simulation tools allow the researcher to closely match the conditions of experimental studies of membrane curvatures.
ARTICLE | doi:10.20944/preprints202204.0018.v1
Subject: Physical Sciences, Applied Physics Keywords: Droplet; Laser shock; High temperatures; Dynamics; Focusing enhancement
Online: 4 April 2022 (12:02:37 CEST)
The temperature-assisted laser shock process has shown promising prospects in the fields of forming manufacturing and surface strengthening. However, large-scale application of this process is limited by the instability and failure of confinement medium at high temperatures (≥300 ℃). Aiming at this problem, we propose a novel laser shock strategy based on Leidenfrost effect, where the suspended droplets are utilized as the confinement medium. According to the sequence of images acquired by time delay system and high-speed camera, the droplet dynamics behavior is studied. The focusing enhancement effect of the droplet is comprehensively explored. And the correlations between droplet size, ambient temperature, vapor layer thickness and focusing effect are investigated. Combining the dynamics and focusing enhancement effect of droplets, a theoretical model of laser shock pressure under droplet confinement is established. Finally, the effectiveness and feasibility of the droplet-based laser shock strategy in high temperature processing environments are verified by typical applications in laser shock forming and laser shock peening fields. The results show that the droplet-based laser shock process presents better forming effect. And the mechanical property tests demonstrate that this process can obtain the simultaneous improvement of the strength (~51%) and ductility (~6.4%) of annealed Cu. The multiscale plasticity mechanisms of the strengthened material are comprehensively investigated. We believe that this low-energy, low-cost and high-quality process can provide a new solution for the industrial application of laser shock at high temperatures.
HYPOTHESIS | doi:10.20944/preprints202201.0124.v1
Subject: Social Sciences, Media Studies Keywords: epistemic community; social media; active inference; opinion dynamics
Online: 10 January 2022 (15:14:16 CET)
The spread of ideas is a fundamental concern of today’s news ecology. Understanding the dynamics of the spread of information and its co-option by interested parties is of critical importance. Research on this topic has shown that individuals tend to cluster in echo-chambers and are driven by confirmation bias. In this paper, we leverage the active inference framework to provide an in silico model of confirmation bias and its effect on echo-chamber formation. We build a model based on active inference, where agents tend to sample information in order to justify their own view of reality, which eventually leads to them to have a high degree of certainty about their own beliefs. We show that, once agents have reached a certain level of certainty about their beliefs, it becomes very difficult to get them to change their views. This system of self-confirming beliefs is upheld and reinforced by the evolving relationship between agent's beliefs and its observations, which over time will continue to provide evidence for their ingrained ideas about the world. The epistemic communities that are consolidated by these shared beliefs, in turn, tend to produce perceptions of reality that reinforce those shared beliefs. We provide an active inference account of this community formation mechanism. We postulate that agents are driven by the epistemic value that they obtain from sampling or observing the behaviors of other agents. Inspired by digital social networks like Twitter, we build a generative model in which agents generate observable social claims or posts (e.g. `tweets') while reading the socially-observable claims of other agents, that lend support towards one of two mutually-exclusive abstract topics. Agents can choose which other agent they pay attention to at each timestep, and crucially who they attend to and what they choose to read influences their beliefs about the world. Agents also assess their local network’s perspective, influencing which kinds of posts they expect to see other agents making. The model was built and simulated simulated using the freely-available Python package pymdp. The proposed active inference model can reproduce the formation of echo-chambers over social networks, and gives us insight into the cognitive processes that lead to this phenomenon.
ARTICLE | doi:10.20944/preprints202109.0275.v1
Subject: Medicine And Pharmacology, Pharmacy Keywords: Cloud infrastructure; Spark; Molecular Dynamics simulations; Drug design.
Online: 16 September 2021 (11:02:38 CEST)
Molecular Dynamics (MD) simulations model motion of molecules in atomistic detail and aid in drug design. While simulations on large systems may require several days to complete, analysis of terabytes of data generated in the process could also be time consuming. Recent studies captured exciting and dramatic drug-receptor interactions under cell-like complex conditions. Such advances make simulations of biomolecular interactions more realistic, insightful, and informative and have potential to make drug design more realistic. However, currently available resources and techniques do not provide, in reasonable time, a comprehensive understanding of events seen in simulations. We demonstrate that big data approach results in significant speedups, and provides rapid insights into simulations performed. Advancing this improvement, we propose a scalable, self-tuning, and responsive framework based on Cloud-infrastructure to accomplish the best possible MD studies with given priorities and within available resources.
ARTICLE | doi:10.20944/preprints202108.0280.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Pozol; lactic acid bacteria; fermentation; starch; microbial dynamics
Online: 12 August 2021 (15:50:05 CEST)
Pozol is a Mexican beverage prepared from fermented nixtamalized maize dough. To contribute to understanding its complex microbial ecology, the effect of inoculating on MRS-starch pure and mixed cultures of amylolytic Sii-25124 and non-amylolytic W. confusa 17, isolated from pozol, were studied on their interactions and fermentation parameters. These were compared with L. plantarum A6, an amylolytic strain isolated from cassava. Microbial growth, kinetic parameters, amylolytic activity, lactic acid production, and hydrolysis products from starch fermentation were measured. The population dynamics were followed by qPCR. L. plantarum A6 showed higher enzymatic activity, lactic acid, biomass production, and kinetic parameters than pozol LAB in pure cultures. Mixed culture of each pozol LAB with L. plantarum A6 showed a significant decrease in amylolytic activity, lactic acid yield, specific growth rate, and specific rate of amylase production. The interaction between Sii-25124 and W. confusa 17 increased the global maximum specific growth rate (µ), the lactic acid yield from starch (Ylac/s), lactic acid yield from biomass (Ylac/x), and specific rate of lactic acid production (qlac) by 15, 30, 30, and 40%, respectively compared with the pure culture of Sii-25124. Interactions between the two strains are essential for this fermentation.
ARTICLE | doi:10.20944/preprints202108.0113.v1
Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: computational fluid dynamics; OpenFOAM; docked vessel; gas pollutants
Online: 4 August 2021 (13:12:08 CEST)
Docked ships are a source of contamination for the city while they keep their engine working. Plumes emissions from large boats can carry a number of pollutants to the nearby cities causing a detrimental effect on the life quality and health of local citizens and ecosystems. A computational fluid dynamics model of the harbour area of Tromsø has been built in order to model the deposition of CO2 gas emitted by docked vessels within the city. The ground level distribution of the emitted gas has been obtained and the influence of the wind speed and direction, vessel chimney height, ambient temperature and exhaust gas temperature has been studied. The deposition range is found to be the largest when the wind speed is low. At high wind speeds, the deposition of pollutants along the wind direction is enhanced and spots of high pollutant concentration can be created. The simulation model is intended for the detailed study of the contamination in cities near the coast or an industrial pollutant source of any type of gas pollutants and can easily be extended for the study of particulate matter.
CONCEPT PAPER | doi:10.20944/preprints202105.0664.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Pathogen; Herd Immunity Threshold; R-naught; Infection dynamics
Online: 27 May 2021 (10:33:34 CEST)
In this article we have presented a new perception of herd immunity threshold (HIT) which considers that only a “band of population” are susceptible to any pathogenic infection. This is termed as the “effective herd immunity threshold” (EHIT) and the progression of the disease (caused by this pathogenic infection) is mainly determined by this EHIT value. We have argued here that this EHIT value (considering the immunity band picture in the population) will be substantially lower than the estimated canonical HIT values obtained from various existing models. We propose that the actual prediction of the disease progression should now be calculated using the EHIT values.
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Complexity; population dynamics; Red Queen; scales; coevolution; extinction
Online: 16 April 2021 (11:02:26 CEST)
Leigh Van Valen was an American evolutionary biologist who made major contributions to evolutionary theory and is particularly remembered by his groundbreaking paper "A New Evolutionary Law" (1973) where he provided evidence from fossil record data that this law maintains that the probability of extinction within any group remains essentially constant through time. In order to explain such unexpected result, Van Valen formulated a very influential idea that he dubbed the "Red Queen hypothesis". It states that the constant decay must be a consequence of evolutionary interactions among connected species within ecological networks. In Van Valen's picture, species do not merely evolve: they also coevolve with other species. As a consequence, when thinking in adaptation to an external environment, the other species must be considered as part (may be a major part) of such external world. Van Valen's law provided the first complex systems theory of coevolutionary dynamics and inspired a whole range of theoretical and experimental developments and scholars from very diverse fields, from economics to physics. In that respect, Leigh Van Valen's contribution percolated far beyond its original formulation. Red Queen arms races are nowadays considered a widespread feature of complex adaptive systems.
REVIEW | doi:10.20944/preprints202103.0043.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: zinc, mitochondria, neurodegeneration, calcium, energy metabolism, mitochondrial dynamics
Online: 2 March 2021 (09:03:05 CET)
Zinc is a highly abundant cation in the brain, where it is essential for cellular function, including transcription, enzymatic activity, and cell signaling. However, zinc can also trigger injurious cascades in neurons, contributing to the pathology of neurodegenerative diseases. Mitochondria, critical for meeting the high energy demands of the central nervous system (CNS), are a principal target of the deleterious actions of zinc. An increasing body of work suggests that intracellular zinc, can, under certain circumstances, contribute to neuronal damage by inhibiting mitochondrial energy processes, including dissipation of the mitochondrial membrane potential, leading to ATP depletion. Additional consequences of zinc-mediated mitochondrial damage include reactive oxygen species (ROS) generation, mitochondrial permeability transition, and calcium deregulation. Zinc can also induce mitochondrial fission, resulting in mitochondrial fragmentation, as well as inhibition of mitochondrial motility. Here, we review the known mechanisms responsible for the deleterious actions of zinc on the organelle, within the context of neuronal injury associated with neurodegenerative processes. Elucidating the critical contributions of zinc-induced mitochondrial defects to neurotoxicity and neurodegeneration may provide insight into novel therapeutic targets in the clinical setting.
ARTICLE | doi:10.20944/preprints202101.0258.v1
Subject: Business, Economics And Management, Economics Keywords: Innovation; Sociality; Economic Impact; Labor Dynamics; Urban Density
Online: 13 January 2021 (16:21:31 CET)
The COVID-19 pandemic of 2020 changed the way we interact and engage in commerce at a fundamental level. Social distancing and stay-at-home orders leave businesses and cities wondering what economic activity will look like in the future. Given a likely reduction in face-to-face interactions, it is important to better understand how social interactivity influences economic outcomes. Here we measure the effect of social interactions in the workforce on patent production and economic efficiency. We decompose U.S. occupations into individual work activities, determine which of those activities are associated with face-to-face interactions, and reaggregate the labor force of each U.S. metropolitan statistical area (MSA) into a metric of social interactiveness. We then calculate each MSA’s density of social work activities and find that this measure is more highly correlated with an MSA’s per capita patent production than simple population density. This suggests that density of face-to-face interactions is the important driver of a city’s rate of invention. We close by exploring analogies between the development of cities and the development of stars, suggesting ways these analogies may help frame future research on cities.
ARTICLE | doi:10.20944/preprints202101.0148.v1
Subject: Physical Sciences, Atomic And Molecular Physics Keywords: Contact angle; Molecular Dynamics; C sharp; hydrophobic; hydrophilic
Online: 8 January 2021 (11:41:35 CET)
In this work, a tool for estimating the contact angle from the molecular dynamics simulations is developed and presented. The tool (Achilles) can detect water droplet on hydrophobic and hydrophilic surfaces. The tool can reconstruct the droplets broken across the periodic boundaries. Further a neighbor density based accurate filter is used to find the droplet liquid vapor interface and a circle is fitted using it after removing the dense layers of water next to solid surface. This fitted circle is solved for contact angle and results are outputted in the form of graphical images and text. The entire content of the internal computations of the tool is broken down into 4 phases and users can monitor the outcomes at every phase through output images. The tool is tested using sample molecular dynamics results of water droplet on hydrophobic and hydrophilic surfaces. We believe this tool can be a good addition to the molecular dynamics simulation community who work on the interfacial physics, droplet evaporation, super hydrophobic surfaces, and wettability etc.
TECHNICAL NOTE | doi:10.20944/preprints202012.0179.v1
Subject: Engineering, Automotive Engineering Keywords: Python; Molecular Dynamics; Scientific Computing; Periodic Boundary Condition
Online: 8 December 2020 (06:47:59 CET)
In this paper, we introduce a simple yet powerful and working version of the molecular dynamics code using the Python 3.9 language. The code contents are published in the link given in the appendix 1. The structure and components of the program is given in detail using flowcharts and code snippets. The program consists of major features like velocity verlet integrator, thermostats, COM removal, input and output modules, virial, pressure, and other thermodynamic quantities estimation etc. The author believes that this program will be helpful to graduate students who perform research in molecular dynamics simulations who intend to write their own code instead of the sophisticated open source packages.
ARTICLE | doi:10.20944/preprints202012.0016.v1
Subject: Physical Sciences, Acoustics Keywords: Open quantum systems, Tensor networks, non-equilibrium dynamics
Online: 1 December 2020 (12:20:25 CET)
Simulating the non-perturbative and non-Markovian dynamics of open quantum systems is a very challenging many body problem, due to the need to evolve both the system and its environments on an equal footing. Tensor network and matrix product states (MPS) have emerged as powerful tools for open system models, but the numerical resources required to treat finite temperature environments grow extremely rapidly and limit their applications. In this study we use time-dependent variational evolution of MPS to expore the striking theory of Tamescelli et al. that shows how finite temperture open dyanmics can be obtained from zero temperature, i.e. pure wave function, simulations. Using this approach, we produce a benchmark data set for the dynamics of the Ohmic spin-boson model across a wide range of coupling and temperatures, and also present detailed analysis of the numerical costs of simulating non-equilibrium steady states, such as those emerging from the non-perturbative coupling of a qubit to baths at different temperatures. Despite ever growing resource requirements, we find that converged non-perturbative results can be obtained, and we discuss a number of recent ideas and numerical techniques that should allow wide application of MPS to complex open quantum systems.
ARTICLE | doi:10.20944/preprints202011.0353.v1
Subject: Physical Sciences, Acoustics Keywords: Bose-Einstein condensates; quantum decoherence; full quantum dynamics
Online: 12 November 2020 (14:40:51 CET)
Decoherence with recurrences appear in the dynamics of the one-body density matrix of an $F = 1$ spinor Bose-Einstein condensate, initially prepared in coherent states, in the presence of an external uniform magnetic field and within the single mode approximation. The phenomenon emerges as a many-body effect of the interplay of the quadratic Zeeman effect, that breaks the rotational symmetry, and the spin-spin interactions. By performing full quantum diagonalizations very accurate time evolution of large condensates are analyzed, leading to heuristic analytic expressions for the time dependence of the density matrix, in the weak and strong interacting regimes. We are able to find accurate analytical expressions for both the decoherence and the recurrence times, in terms of the number of atoms and strength parameters, that show remarkable differences depending on the strength of the spin-spin interactions. We discuss the nature of these limits in the light of the thermodynamic limit.
ARTICLE | doi:10.20944/preprints202010.0062.v1
Subject: Business, Economics And Management, Accounting And Taxation Keywords: Participation; community; systems dynamics; sustainable development; decision making.
Online: 5 October 2020 (10:48:12 CEST)
This research article presents the integration of participatory modeling and system dynamics as a novel methodology for the consolidation of social dynamic models for the subsequent evaluation and prioritization of green projects in Colombian post-conflict communities. In the first instance, through participatory work carried out along with the community, it was possible to identify, evaluate and systematize citizen factors in relation to the problems and needs of the region. Second, based on the results obtained, to calibrate a simulation model based on system dynamics that facilitates decision making with regard to the evaluation of green projects. The proposed methodology leads to the conclusion that, with the participation of the community and with a model based on the dynamics of variables such as supply and demand for natural resources of water and land, it is possible to warn decision makers about the variables that can lead to the maximization of investments and thus prioritize and select the most appropriate environmental, social or economic initiatives, that certainly meet the needs or expectations of the involved community. In the future, the model could be used to facilitate the management, administration and control of water and land resources by creating alerts called reserve margins.
ARTICLE | doi:10.20944/preprints202009.0326.v1
Subject: Medicine And Pharmacology, Pharmacology And Toxicology Keywords: HepG2 cells; cytotoxicity; apoptosis; Hoechst staining; molecular dynamics
Online: 15 September 2020 (04:18:12 CEST)
The natural products and conventional chemotherapeutic drugs are believed to increase the cure rates of anti-cancer treatment while reducing their toxicity. The current study investigates the cytotoxic and apoptogenic effects of bioactive compounds from Monotheca buxifolia on Hep G2 cell lines. The effect on the viability of Hep G2 cells was evaluated by MTT assay; Morphological changes were studied, the apoptotic activity was demonstrated through Annexin-V-FITC/ PI, a molecular dynamics simulation study was conducted to explore the binding pattern of the compounds in the active site of the PPRAδ protein. The isolated compounds lauric acid, oleanolic acid, and bis(2-ethylhexyl) phthalate inhibited the growth of hepatocellular cancer cells, as determined by MTT assay and annexin V-FITC/PI. The IC50 value for lauric acid was 56.4584 ± 1.20 µg/ml, that for oleanolic acid was 31.9421 ± 1.03 µg/ml, and that for bis(2-ethylhexyl) phthalate was 83.8019 ± 2.18 µg/ml. After 24 h of treatment, 29.5% of Hep G2 cells treated with lauric acid, 52.1% of those treated with oleanolic acid, and 22.4% of those treated with bis(2-ethylhexyl) phthalate were apoptotic. Morphological assay and Hoechst staining microscopy revealed the morphological alterations of cell membrane accompanied by nuclear condensation after treatment. The high fluctuation indicates the high potency and adopting various interactions, and vice versa, the oleanolic acid showed highly residues fluctuation, which remains stable in the active site of PPARδ protein and involved in various interactions while remaining locally fluctuated in the binding site the other two compounds. In conclusion, a significant apoptogenic effect was exhibited by lauric acid, oleanolic acid, and bis(2-ethylhexyl) phthalate against HepG2 cells in inducing apoptosis. Our findings indicate that these bioactive compounds hold promise as potential therapeutic for hepatocellular carcinoma.
ARTICLE | doi:10.20944/preprints202007.0267.v1
Online: 12 July 2020 (16:46:04 CEST)
We extend our high-resolution MRI-based Finite Element (FE) head model, previously presented and validated in [1–3], by considering the heterogeneities of the white matter structures captured through the use of Magnetic Resonance Elastography (MRE). This approach imparts more sophistication to our numerical model and yields results that more closely match experimental results. It is found that the peak pressure more closely matches the experiments as compared to the heterogeneous case. Qualitatively, we find differences in stress wave propagation near the corpus callosum and the corona radiata, which are stiffer on average than the global white matter. We are able to study the effects of these stiff structures on transient stress wave propagation within the cerebrum, something that cannot be done with a homogenized material model.