ARTICLE | doi:10.20944/preprints201607.0050.v1
Subject: Engineering, Mechanical Engineering Keywords: Nanochannel; Molecular Dynamics Method; Nanoparticle, Argon; Boiling Process
Online: 18 July 2016 (10:37:40 CEST)
In this paper, the boiling flow inside a nanochannel with 700000 argon particle has been simulated by molecular dynamics (MD) simulation. This approach has been employed to analysis the superheated flow and its heat transfer pattern as well. For all simulations an external thrust force varying from 1 PN to 12 PN is exerted on inlet nanoparticles along the channel to have the forced annular boiling flow. Computations reveal that saturation condition and superheat degree have significant impacts on the liquid-vapor interface. Furthermore, because of the major influence of surface tension throughout a nanochannel, the x-velocity of liquid film and vapor core has not considerable fluctuations and stay smooth. All provided results show the behaviors completely similar to the available outcomes in the literature.
ARTICLE | doi:10.20944/preprints201611.0131.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: adaptation; mental model refinement; food systems; knowledge management participatory modeling; system dynamics; systems thinking
Online: 27 November 2016 (04:12:49 CET)
Food systems will need to undergo considerable transformation. To be better prepared for and resilient to uncertainty and disturbances in the future, resource users and managers need to further develop knowledge about the food and farming system, with its dominating feedback structures and complexities, and to test robust and integrated system-based solutions. This paper investigates how participatory system dynamics modeling can be adapted to groups at the community level with low or no formal educational background. The paper also analyzes the refinement of workshop participants’ mental models as a consequence of a participatory system dynamics intervention. For this purpose, we ran two workshops with small-scale farmers in Zambia. Analysis of workshop data and post-workshop interviews shows that participatory system dynamics is well adaptable to support an audience-specific learning-by-doing approach. The use of pictures, objects and water glasses in combination with the basic aspects of causal loop diagramming makes for a well-balanced toolbox. Participants acquire understanding that is also relevant beyond systems thinking in that is offers a range of practical insights such as a critical evaluation of common food security strategies.
ARTICLE | doi:10.20944/preprints201611.0059.v1
Subject: Engineering, Automotive Engineering Keywords: automotive, fuel consumption; Fuel Reduction Value (FRV); Life Cycle Assessment (LCA); light-weighting; vehicle system dynamics
Online: 10 November 2016 (16:45:36 CET)
A tailored model for the assessment of environmental benefits achievable by “light-weighting” in the automotive field is presented. The model is based on the Fuel Reduction Value (FRV) coefficient, which expresses the Fuel Consumption (FC) saving involved by a 100 kg mass reduction. The work is composed of two main sections: simulation and environmental modelling. Simulation modelling performs an in-depth calculation of weight-induced FC whose outcome is the FRV evaluated for a wide range of Diesel Turbocharged (DT) vehicle case studies. Environmental modelling converts fuel saving to impact reduction basing on the FRVs obtained by simulations. Results show that for the considered case studies, FRV is within the range 0.115–0.143 and 0.142–0.388 L/100 km × 100 kg, respectively, for mass reduction only and powertrain adaptation (secondary effects). The implementation of FRVs within the environmental modelling represents the added value of the research and makes the model a valuable tool for application to real case studies of automotive lightweight LCA.
ARTICLE | doi:10.20944/preprints201611.0111.v1
Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: Y-shaped microfluidic device; wall shear stress; adenosine triphosphate (ATP) signal; combined effect; vascular endothelial cells; calcium dynamics
Online: 22 November 2016 (09:51:31 CET)
The intracellular calcium dynamics in vascular endothelial cells (VECs) in response to wall shear stress (WSS) and/or adenosine triphosphate (ATP) have been commonly regarded as an important factor in regulating VEC function and behavior including proliferation, migration and apoptosis. However, the effects of time-varying ATP signals have been usually neglected in the past investigations in the field of VEC mechanobiology. In order to investigate the combined effects of WSS and dynamic ATP signals on the intracellular calcium dynamic in VECs, a Y-shaped microfluidic device, which can provide the cultured cells on the bottom of its mixing micro-channel with stimuli of WSS signal alone and different combinations of WSS and ATP signals in one single micro-channel, is proposed. Both numerical simulation and experimental studies verify the feasibility of its application. Cellular experimental results also suggest that a combination of WSS and ATP signals rather than a WSS signal alone might play a more significant role in VEC Ca2+ signal transduction induced by blood flow.
ARTICLE | doi:10.20944/preprints201611.0077.v1
Subject: Chemistry And Materials Science, Physical Chemistry Keywords: computational theoretical chemistry; photochemistry; nonadiabatic dynamics; ultrafast processes; surface hopping; nucleobases; thymine
Online: 15 November 2016 (11:06:06 CET)
After UV excitation, gas phase thymine returns to ground state in 5 to 7 ps, showing multiple time constants. There is no consensus on the assignment of these processes, with a dispute between models claiming that thymine is trapped either in the first (S1) or in the second (S2) excited states. In the present study, nonadiabatic dynamics simulation of thymine is performed on the basis of ADC(2) surfaces, to understand the role of dynamic electron correlation on the deactivation pathways. The results show that trapping in S2 is strongly reduced in comparison to previous simulations considering only non-dynamic electron correlation on CASSCF surfaces. The reason for the difference is traced back to the energetic cost for formation of a CO p bond in S2.
ARTICLE | doi:10.20944/preprints201611.0083.v2
Subject: Engineering, Civil Engineering Keywords: air shock wave; rock-fall; two-phase model; computational fluid dynamics (CFD)
Online: 23 January 2017 (09:15:34 CET)
In this paper, a two-phase model of air shock wave induced by rock-fall was described. The model was made up of the uniform motion phase (velocity was close to 0 m·s-1) and the acceleration movement phase. The uniform motion phase was determined by experience, meanwhile the acceleration movement phase was derived by the theoretical analysis. A series of experiments were performed to verify the two-phase model and obtained the law of the uniform motion phase. The acceleration movement phase was taking a larger portion when height of rock-fall was higher with the observations. Experimental results of different falling heights showed good agreements with theoretical analysis values. Computational fluid dynamics (CFD) numerical simulation had been carried out to study the variation velocity with different falling height. As a result of this, the two-phase model could accurately and convenient estimating the velocity of air shock wave induced by rock-fall. The two-phase model could provide a reference and basis for estimating the air shock waves' velocity and designing the protective measures.
ARTICLE | doi:10.20944/preprints201608.0015.v1
Subject: Engineering, Control And Systems Engineering Keywords: Finite-time control; nonlinear system; non-Lipschitzian dynamics; lyapunov function
Online: 2 August 2016 (10:40:38 CEST)
This paper focuses on the problem of finite-time stabilization of homogeneous, non-Lipschitz systems with dilations. A key contribution of this paper is the design of a virtual recursive Hölder, non-Lipschitz state feedback which renders the non-Lipschitz systems in the special case dominated by a lower-triangular nonlinear system, finite-time stable. The proof is based on a recursive design algorithm developed recently, to construct the virtual Hölder continuous, finite-time stabilizer as well as a C1 positive definite and proper Lyapunov function that guarantees finite-time stability of the non-Lipschitz non-linear systems.
ARTICLE | doi:10.20944/preprints201610.0016.v1
Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: molecular dynamics simulation; virtual screening; molecular docking; prostate cancer; caveolin-1
Online: 7 October 2016 (12:09:06 CEST)
Caveolin-1 (Cav-1) is 22 kDa caveolae protein, acts as a scaffold within caveolar membranes. It interacts with alpha subunits of G-protein and thereby regulates their activity. Earlier studies reported elevated or up-regulated levels of caveolin-1 in the serum of prostate cancer patients. Secreted Cav-1 promotes angiogenesis, cell proliferation and anti-apoptotic activities in prostate cancer patients. Cav-1 upregulation is mainly related to prostate cancer metastasis. Keeping above facts in view, the present study was designed to explore Cav-1 as a target for prostate cancer therapy using computational approach. Molecular docking, structural base molecular modelling and molecular dynamics simulations were performed to investigate Cav-1 inhibitors. A predictive model was generated and validated to establish a stable structure. ZINC database of biogenic compounds was used for induced fit docking (IFD) and high throughput virtual screening. The H-bond interactions of the compounds with active site residues of Cav-1 were estimated by IFD and 100 ns long molecular dynamic simulations. The reported compounds showed significant binding and thus can be considered as potent therapeutic inhibitors of Cav-1. This study provides a valuable insight into biochemical interactions of Cav-1 for therapeutic applications and warrants for experimental validation of the predicted ‘active(s)’.
ARTICLE | doi:10.20944/preprints201703.0115.v1
Subject: Physical Sciences, Astronomy And Astrophysics Keywords: foundations of science; cosmology: observations; cosmology: theory; galaxies: kinematics and dynamics; inertia; MoND
Online: 16 March 2017 (09:31:27 CET)
First, this paper broaches the epistemological status of scientific tenets and approaches: phenomenological (descriptive only), well-founded (solid first principles, conducive to deep understanding), provisional (can be falsified if universal and verified if existential), and imaginary (fictitious entities or processes, conducive to empirically unsupported beliefs). The ΛCDM “concordance model” involves such beliefs: the emanation of the universe out of a non-physical stage, cosmic inflation (invented ad hoc), Λ (fictitious energy), and exotic dark matter. Big Bang cosmology further faces conceptual and pragmatic problems in delimiting what expands from what does not. The problems dissolve after untying inertia from space. The cosmology that emerges appears immediately compatible with the considered observations and the ‘perfect cosmological principle’. Waves and field perturbations that propagate at c expand exponentially with distance (a gravitational effect). The cosmic web of galaxies does not. Potential -Φ varies as H/(cz) instead of 1/r. Inertial forces arise from the gravitational action of the rest of the universe. Due to dilatation, they are reduced disproportionately at low accelerations. A cut-off value a0 = 0.168 cH is deduced. This explains the successful description of galaxy rotation curves by MoND. A fully elaborated physical theory is still pending. Wider implications are briefly discussed.
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
Subject: Physical Sciences, Thermodynamics Keywords: gravitation; dynamics; aether
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.
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/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.
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/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/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.
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/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/preprints202305.0603.v1
Subject: Physical Sciences, Optics And Photonics Keywords: Laser; network; ring; dynamics; coupling
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/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/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.
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.
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/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.
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/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.
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.
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/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/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/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.
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.
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/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/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
Subject: Engineering, Marine Engineering Keywords: low-dimensional models; vortex dynamics; wakes
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.
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/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/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/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/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/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/preprints201712.0114.v1
Subject: Engineering, Control And Systems Engineering Keywords: flight simulation; flight control; optimization; CFD; flight dynamics
Online: 18 December 2017 (07:03:18 CET)
The optimization methods are increasingly used to solve challenging problems of aeronautical engineering. Typically, the optimization methods are utilized in design of aircraft airframe or its structure. The presented study is focused on an improvement of aircraft-flight-control procedures through the numerical optimization approach. The optimization problems concern selected phases of flight of light gyroplane - a rotorcraft using an unpowered rotor in autorotation to develop lift and an engine-powered propeller to provide thrust. An original methodology of computational simulation of rotorcraft flight was developed and implemented. In this approach the aircraft-motion equations are solved step-by-step, simultaneously with the solution of the Unsteady Reynolds-Averaged Navier-Stokes equations, which is conducted to assess aerodynamic forces acting on the aircraft. As a numerical optimization method, the BFGS algorithm was adapted. The developed methodology was applied to optimize the flight-control procedures in selected stages of gyroplane flight in direct proximity of the ground, where properly conducted control of the aircraft is critical to ensure flight safety and performance. The results of conducted computational optimizations proved qualitative correctness of the developed methodology. The research results can be helpful in design of easy-to-control gyroplanes and also in the training of pilots of this type of rotorcraft.
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/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/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/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.
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.
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.
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/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.
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.
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/preprints202111.0406.v1
Subject: Biology And Life Sciences, Biophysics Keywords: CBNs; amino acids; Molecular dynamics
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/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/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.
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/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.
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.
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.
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/preprints201711.0139.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: statistical mechanics; resource partitioning; stochastic processes; population dynamics
Online: 22 November 2017 (06:31:17 CET)
Many species of plants are found in regions to which they are alien. Their global distributions are characterised by a family of exponential functions of the kind that arise in elementary statistical mechanics (an example in ecology is MacArthur's broken stick). We show here that all these functions are quantitatively reproduced by a model containing a single parameter – some global resource partitioned at random on the two axes of species number and site number. A dynamical model generating this equilibrium is a two fold stochastic process and suggests a curious and interesting biological interpretation in terms of niche structures fluctuating with time and productivity; with sites and species highly idiosyncratic. Idiosyncrasy implies that attempts to identify a priori those species likely to become naturalized are unlikely to be successful. Although this paper is primarily concerned with a particular problem in population biology, the two fold stochastic process may be of more general interest.
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.
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/preprints202007.0267.v1
Subject: Medicine And Pharmacology, Other Keywords: mTBI, MRI; MRE; FE model; brain wave dynamics
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.
ARTICLE | doi:10.20944/preprints201802.0074.v2
Subject: Chemistry And Materials Science, Physical Chemistry Keywords: statistical mechanics; irreversibility; arrow of time; chemical dynamics
Online: 5 March 2018 (05:54:00 CET)
The second law of thermodynamics states the increase of entropy, ΔS > 0, for real processes from state A to state B at constant energy from chemistry over biological life and engines to cosmic events. The connection of entropy to information, phase-space and heat is helpful, but does not immediately convince observers of the validity and basis of the second law. This gave grounds for finding a rigorous, but more easily acceptable reformulation. Here we show using statistical mechanics that this principle is equivalent to a force law 〈〈f〉〉> 0 in systems where mass centres and forces can be identified. The sign of this net force - the average mean force along a path from A to B - determines the direction of the process. The force law applies to a wide range of processes from machines to chemical reactions. The explanation of irreversibility by a driving force appears more plausible than the traditional formulation as it emphasizes the cause instead of the effect of motions.
ARTICLE | doi:10.20944/preprints202102.0427.v1
Subject: Chemistry And Materials Science, Biomaterials Keywords: molecular dynamics; diffusion; mass transport of water; polymer matrix
Online: 19 February 2021 (09:50:39 CET)
The diffusion process of water molecules within a polyetherimide (PEI) glassy matrix has been analyzed by combining the experimental analysis of water sorption kinetics performed by FTIR spectroscopy with theoretical information gathered from Molecular Dynamics simulations and with the expression of water chemical potential provided by a non-equilibrium lattice fluid model able to describe the thermodynamics of glassy polymers. This approach allowed to construct a convincing description of the diffusion mechanism of water in PEI providing molecular details of the process related to the effects of the cross- and self-hydrogen bondings established in the system on the dynamics of water mass transport.
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/preprints201811.0010.v1
Subject: Physical Sciences, Optics And Photonics Keywords: forecasting; complex dynamics; fiber laser; chaos; ordinal patterns
Online: 2 November 2018 (04:21:25 CET)
Being able to forecast events is of great importance in many fields, from brain behavior to earthquakes or stock markets. Because each dynamical system has intrinsic features, different statistical tools have to be used for each system. Here we study the time series of the output intensity of a fiber laser with an ordinal patterns analysis, and we look for temporal correlations in order to statistically forecast the most intense events. We set two thresholds, a low one and a high one, to distinguish between low intensity versus high intensity events. We find that when the time series is performing events below the low threshold it shows some preferred temporal patterns before performing events above a high threshold.
ARTICLE | doi:10.20944/preprints201811.0074.v1
Subject: Medicine And Pharmacology, Psychiatry And Mental Health Keywords: system dynamics modeling; big data; mental distress; diet
Online: 5 November 2018 (02:34:30 CET)
Dietary factors are one of the risk factors that can impact the brain chemistry, which leads to mental distress. Based on our data mining approach, we found that mental distress in men is associated with eating unhealthy food. Our aim in this paper is to apply results from our big data analytics approach to inform system dynamics (SD) modeling to investigate the causal relationships between brain structures, nutrients from food and dietary supplements, and mental health. We perform descriptive analysis based on a large data set to estimate the SD modeling parameters. Finally, we calibrate the model towards a time series data collected for individuals on their dietary and distress patterns. The results reveal that bridging these different methodologies leads to further insights from the SD model and decreases the error of calibrated parameter values. Future research is needed to validate our initial results for investigating the relationship between mental distress and dietary intake.
ARTICLE | doi:10.20944/preprints202003.0470.v1
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: EthA; ethionamide resistance; BVMO; molecular dynamics; thermodynamic integration
Online: 31 March 2020 (23:21:53 CEST)
Mutation in the ethionamide (ETH) activating enzyme, EthA, is the main factor determining resistance to this drug, used to treat TB patients infected with MDR and XDR Mycobacterium tuberculosis isolates. Many mutations in EthA of ETH resistant (ETH-R) isolates have been described but their roles in resistance remain uncharacterized, partly because structural studies on the enzyme are lacking. Thus, we took a two-tier approach to evaluate two mutations (Y50C and T453I) found in ETH-R clinical isolates. First, we used a combination of comparative modeling, molecular docking, and molecular dynamics to build an EthA model in complex with ETH that has hallmark features of structurally characterized homologs. Second, we used free energy computational calculations for the reliable prediction of relative free energies between the wild type and mutant enzymes. The ΔΔG values for Y50C and T453I mutant enzymes in complex with FADH2-NADP-ETH were 3.34 (+/−0.55) and 8.11 (+/−0.51) kcal/mol, respectively, compared to the wild type complex. The positive ΔΔG values indicate that the wild type complex is more stable than the mutants, with the T453I complex being the least stable. These are the first results shedding light on the molecular basis of ETH resistance, namely reduced complex stability of mutant EthA.
ARTICLE | doi:10.20944/preprints202010.0586.v2
Subject: Physical Sciences, Astronomy And Astrophysics Keywords: reference systems; galaxies: kinematics and dynamics; cosmology: dark matter
Online: 24 May 2021 (10:15:05 CEST)
When dealing with galactic dynamics, or more specifically, with galactic rotation curves, one basic assumption is always taken: the frame of reference relative to which the rotational velocities are given is assumed to be inertial. In other words, fictitious forces are assumed to vanish relative to the observational frame of a given galaxy. It might be interesting, however, to explore the outcomes of dropping that assumption; that is, to search for signatures of non-inertial behavior in the observed data. In this work, we show that the very discrepancy in galaxy rotation curves could be attributed to non-inertial effects. We derive a model for spiral galaxies that takes into account the possible influence of fictitious forces and find that the additional terms in the new model, due to fictitious forces, closely resemble dark halo profiles. Following this result, we apply the new model to a wide sample of galaxies, spanning a large range of luminosities and radii. It turns out that the new model accurately reproduces the structures of the rotation curves and provides very good fittings to the data.
ARTICLE | doi:10.20944/preprints202006.0212.v1
Subject: Physical Sciences, Condensed Matter Physics Keywords: neural synchronization; consciousness; quantum biology; brain dynamics; brain connectivity
Online: 17 June 2020 (09:29:28 CEST)
One of the biggest queries in cognitive sciences is the emergence of consciousness from matter. Modern neurobiological theories of consciousness propose that conscious experience is the result of interactions between large-scale neuronal networks in the brain, traditionally described within the realm of classical physics. Here, we propose a generalized connectionist framework in which the emergence of “conscious networks” is not exclusive of large brain areas, but can be identified in sub-cellular networks exhibiting non-trivial quantum phenomena. The essential feature of such networks is the existence of strong correlations in the system (classical or quantum coherence) and the presence of an optimal point at which the system’s complexity is maximized, expressed either by maximization of the information content in large scale functional networks or by achieving optimal efficiency through the quantum Goldilock effect.
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/preprints201809.0389.v1
Subject: Engineering, Mechanical Engineering Keywords: Extrapolative Predictions, Model Validation, Bayesian Inference, Structural Dynamics
Online: 19 September 2018 (16:05:50 CEST)
The creation of computer models is often driven by the need to make predictions in regions where there is no data (i.e. extrapolations). This makes validation challenging as it is difficult to ensure that a model will be suitable when it is applied in a region where there are no observations of the system of interest. The current paper proposes a method that can reveal flaws in a model which may be difficult to identify using traditional approaches for model calibration and validation. The method specifically targets the situation where one is attempting to model a dynamical system that is believed to possess time-invariant calibration parameters. The proposed approach allows these parameters to vary with time, even though it is believed that they are time-invariant. The of such an analysis is to identify key discrepancies - indications that a model has inherent flaws and, as a result, should not be used to influence decisions in regions where there is no data. The proposed method isn't necessarily a predictor of extrapolation performance, rather, it is a stringent test that, the authors believe, should be applied before extrapolation is attempted. The approach could therefore form a useful part of wider validation frameworks in the future.
ARTICLE | doi:10.20944/preprints201808.0332.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: Inner Asia; Altai; glaciers; shrinkage; LIA; present dynamics
Online: 18 August 2018 (08:38:09 CEST)
The study is based on the results of long-term field studies, satellite and aerial data analysis. In the maximum of the Little Ice Age (LIA) 243 glaciers with a total area of 353.4 km2 were reconstructed. By the results of interpretation of Corona images by 1968 the number of glaciers increased (236), the total area reduced to 242 km2. In 2010 glaciation was represented by 237 glaciers with a total area of 201 km2. Thus, from the maximum of the LIA, the glaciation of the Tavan-Bogd mountains decreased by 43%, which is somewhat less than the neighboring glacial centers (Ikh-Turgen, Tsambagarav, Tsengel-Khayrkhan and Mongun-Taiga mountains). The probable cause is the predominance of larger glaciers relatively resistant to warming and higher altitudes. The effect of glacier size on their stability is supported by differences in the relative shrinkage of glaciers in different parts of the Tavan-Bogdo-Ola massif: the smallest decline occurred in the basins of the Tsagan-Gol (31.7%) and Sangadir (36.4%) rivers where the largest glaciers are located. On the contrary, on the lower periphery of the massif, where small glaciers predominate, the relative reduction was large (74-79%). On the background of the general retreat trend large valleys glaciers retreated faster in 1968-1977 and after 2010. In 1990-s the retreat was slow. After 2010 the glacial retreat was extremely fast. The retreat of glaciers in the last 50-60 years was caused by a trend towards a decrease in the amount of precipitation until the mid-1970s and a sharp warming in the 1990s and early 2000s.
ARTICLE | doi:10.20944/preprints201804.0284.v1
Subject: Biology And Life Sciences, Biophysics Keywords: peptide; self-assembly; molecular dynamics; peptergency; beta structure
Online: 23 April 2018 (11:27:51 CEST)
By manipulating the various physico-chemical properties of amino acids, design of peptides with specific self-assembling properties has been emerging since more than a decade. In this context, short peptides possessing detergent properties (so-called “peptergents”) have been developed to self-assemble into well-ordered nanostructures that can stabilize membrane proteins for crystallization. In this study, the peptide with “peptergency” properties, called ADA8 extensively described by Zhang et al., is studied by molecular dynamics for its self-assembling properties in different conditions. In water, it spontaneously forms beta sheets with a β barrel-like structure. We next simulated the interaction of this peptide with a membrane protein, the bacteriorhodopsin, in the presence or absence of a micelle of dodecylphosphocholine. According to the literature, the peptergent ADA8 is thought to generate a belt of β structures around the hydrophobic helical domain that could help stabilize purified membrane proteins. Molecular dynamics is here used to challenge this view and to provide further molecular details for the replacement of detergent molecules around the protein. To our best knowledge, this is the first molecular mechanism proposed for ''peptergency''. In addition, our calculation approach should serve as a predicting tool for the design of beta peptergent with diverse amphipathic properties.
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/preprints201906.0279.v1
Subject: Chemistry And Materials Science, Nanotechnology Keywords: molecular dynamics; phase-field; polycrystalline materials; phase transformation
Online: 27 June 2019 (05:56:10 CEST)
In this research, atomistic molecular dynamics simulations are combined with mesoscopic phase-field computational methods in order to investigate phase-transformation in polycrystalline Aluminum microstructure. In fact, microstructural computational modeling of engineering materials could help to optimize their mechanical properties for industrial applications (e.g. directional solidification for turbine blades). As a result, a multiscale modeling approach is developed to find a relation between manufacturing variables (e.g. temperature) and microstructural properties of crystalline materials (e.g. grain size), which could be used to develop an advanced manufacturing process for sensitive applications. The results show that atomistic modeling of grain growth could be used as a first-principle approach in order to study phase transformation's kinetics, which could capture morphology of polycrystalline materials more accurately. On the other hand, phase-field mesoscopic approach needs less computational efforts, but still it relies on semi-empirical data to capture accurate phase transformation regimes, which makes this approach suitable for rapid examining of new manufacturing conditions as well as its effects on microstructural properties of polycrystalline materials.
ARTICLE | doi:10.20944/preprints202001.0069.v1
Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: DEHP; biochemical pathways; immobilization; MBR; bacterial community dynamics
Online: 9 January 2020 (05:00:48 CET)
A bacterial strain that could effectively degrade DEHP was isolated from the activated sludge and identified as Bacillus sp. by DNA sequencing. The biochemical degradation pathway of DEHP was further analyzed by GC-MS, and the results showed that DEHP was first decomposed into phthalates (DBP). Diuretic sylycol (DEP) was then generated, and phthalates (PA) were generated by a continuous de-ehelateization reaction. Phthalic acid (PA) was oxidized, dehydrogenated, and decarboxylated into protocatechins. Protocatechins enter the TCA cycle through orthotopic ring opening. To enhance DEHP degradation, sodium alginate and calcium chloride were used as embedding and cross-linking materials, and the strain was immobilized. The immobilization conditions were optimized via an orthogonal experiment, and the results showed that the optimal immobilization conditions were SA mass fraction of 4%, CaCl2 mass fraction of 5%, ratio of bacteria to SA of 1:1, and the crosslinking time of 6 hours. The immobilized bacteria agent was further applied to MBR systems. The results showed that the removal rate of DEHP (5mg/L) in the system by immobilized bacteria was 91.9%, which is significantly higher than that of free bacteria. The 3, 4-dioxygenase gene and microbial community dynamics were analyzed by q-PCR and Illumina Miseq sequencing. The q-PCR results showed that the number of copies of 3, 4-dioxygenase gene in the immobilized system was significantly higher than that of free bacteria. Illumina Miseq sequencing results showed that Micromonospora, Rhodococcus, Bacteroides and Pseudomonas were the dominant generas in the MBR system. The analysis of bacterial community structure indicated that immobilization technology had a positive impact on the system stability. The results implied that this immobilized technique had potential applications in DEHP wastewater treatment.
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/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/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/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/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/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.
ARTICLE | doi:10.20944/preprints202009.0151.v1
Subject: Physical Sciences, Applied Physics Keywords: Hertz impact dynamics; exact solution; numerical solution; inversion; Maple
Online: 7 September 2020 (03:20:09 CEST)
This paper revisits a classic problem in physics - Hertz elastic dynamics of two colliding elastic spheres. This study obtains impact period in terms of hypergeometric function and successfully combines Deresiewicz's three segmental solutions into one single solution. Our numerical investigation confirms that Deresiewicz's inversion is a good approximation. As an essential part of this study, a general Maple code is provided.
ARTICLE | doi:10.20944/preprints201810.0409.v1
Subject: Physical Sciences, Condensed Matter Physics Keywords: molecular dynamics; crystal growth; Avrami coefficients; Pt-Pd alloy
Online: 18 October 2018 (10:02:21 CEST)
This work aims to investigate the effect of Pt concentration on crystal growth mechanism of Platinum-Palladium (Pt-Pd) binary alloy system during the annealing process starting from amorphous phase until some definite temperatures. The calculations have been performed by using molecular dynamic (MD) simulations. Interatomic interactions are described by on Sutton-Chen type Embedded Atom Potential Energy function. In order to understand the main structural properties at the stable and unstable phases, changes in RDF curves versus time have been analysed for different annealing temperatures. Crystalline type bonded pairs have been determined using MD calculations which is required for the computation of Avrami coefficients and for understanding crystal growth mechanism. The results demonstrate that the increase in concentration of Pt during annealing leads to migration of atoms in the crystal lattice points, elimination of dislocations and formation of perfect crystal structure.
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/preprints202007.0366.v1
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: mTBI; MRI; MRE; brain wave dynamics; FE brain model
Online: 17 July 2020 (06:21:09 CEST)
Tissues of the brain, especially white matter, are extremely heterogeneous - with constitutive response varying spatially. In this paper, we implement a high-resolution Finite Element (FE) head model where heterogeneities of white matter structures are introduced through Magnetic Resonance Elastography (MRE) experiments. Displacement of white matter under shear wave excitation is captured and the material properties determined though an inversion algorithm are directly used in the FE model. This approach is found to improve model predictions when compared to experimental results. In the first place, responses in the cerebrum near stiff structures such as the corpus callosum and corona radiata are markedly different compared with a homogenized material model. Additionally, the heterogeneities introduce additional attenuation of the shear wave due to wave scattering within the cerebrum.
Subject: Physical Sciences, Acoustics Keywords: Kullback–Leibler divergence; granular gases; kinetic theory; molecular dynamics
Online: 8 October 2020 (10:43:55 CEST)
Finding the proper entropy functional associated with the inelastic Boltzmann equation for a granular gas is a yet unsolved challenge. The original H-theorem hypotheses do not fit here and the H-functional presents some additional measure problems that are solved by the Kullback–Leibler divergence (KLD) of a reference velocity distribution function from the actual distribution. The right choice of the reference distribution in the KLD is crucial for the latter to qualify or not as a Lyapunov functional, the “homogeneous cooling state” (HCS) distribution of the freely cooling system being a potential candidate. Due to the lack of a formal proof, the aim of this work is to support this conjecture aided by molecular dynamics simulations of inelastic hard disks and spheres in a wide range of values for the coefficient of restitution (α). Our results reject the Maxwellian distribution as a possible reference, whereas reinforce the HCS one. Moreover, the KLD is used to measure the amount of information lost on using the former rather than the latter, and reveals a nonmonotonic dependence with α. Additionally, a Maxwell-demon-like velocity-inversion experiment highlights the microscopic irreversibility of the granular gas dynamics.
CASE REPORT | doi:10.20944/preprints202110.0047.v1
Subject: Environmental And Earth Sciences, Geophysics And Geology Keywords: shock waves; mechanism and dynamics of destruction; quartz; granites; calcite
Online: 4 October 2021 (11:03:20 CEST)
The spectra of the plasma emitted from the studied samples consist of several dozens of narrow bands superimposed on each other. Tables of spectral lines were used to interpret the spectra. It turned out that the largest number of bands corresponds to the radiation of positively charged ions and atoms of elements that make up the crystal lattices of minerals that make up the studied rocks. Thus, the spectra of the plasma emitted from quartz corresponded to the radiation of atoms and positively charged silicon ions, the charge of which varied from 1 to 4, as well as atoms and positively charged oxygen ions, the charge of which varied from 1 to 3. Positively charged ions and atoms of Si, O, K, Ca, Al and Na, which are part of the crystal lattices of quartz and feldspar, flew out of granites. Positively charged ions and Ca, C and O atoms flew out of the calcite.
ARTICLE | doi:10.20944/preprints202112.0467.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: landsat; pasture degradation; brazilian pasturelands dynamics; low carbon agriculture
Online: 29 December 2021 (12:54:56 CET)
The Brazilian livestock is predominantly extensive, with approximately 90% of the production being sustained on pasture, which occupies around 20% of the territory. In the current climate change scenario and where cropland is becoming a limited resource, there is a growing need for a more efficient land use and occupation. It is estimated that more than half of the Brazilian pastures have some level of degradation; however there is still no mapping of the quality of pastures on a national scale. In this study, we mapped and evaluated the spatio-temporal dynamics of pasture quality in Brazil, between 2010 and 2018, considering three classes of degradation: Absent (D0), Intermediate (D1), and Severe (D2). There was no variation in the total area occupied by pastures in the evaluated period, in spite of the accentuated spatial dynamics, with a retraction in the center-south and expansion to the north, over areas of native vegetation. The percentage of non-degraded pastures increased ~12%, due to the recovery of degraded areas and the emergence of new pasture areas as a result of the prevailing spatial dynamics. However, about 44 Mha of the pasture area is currently severely degraded. The dynamics in pasture quality were not homogeneous in property size classes. We observed that in the approximately 2.68 million properties with livestock activity, the proportion with quality gains was twice as low in small properties compared to large ones, and the proportion with losses was three times greater, showing an increase in inequality between properties with more and less resources (large and small, respectively). The areas occupied by pastures in Brazil present an unique opportunity to increase livestock production and make available areas for agriculture, without the need for new deforestation in the coming decades.
ARTICLE | doi:10.20944/preprints202305.0281.v1
Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Antibody; PG16; HIV-1; peptides; antibody mimetic peptides; molecular dynamics
Online: 5 May 2023 (03:08:46 CEST)
PG16 is a broadly neutralizing antibody that binds to the gp120 subunit of the HIV-1 Env protein. The major interaction site is formed by the unusually long complementarity determining region (CDR) H3. The CDRH3 residue Tyr100H is known to represent a tyrosine sulfation site; however, this modification is not present in the experimental complex structure of PG16 with full-length HIV-1 Env. To investigate the role of sulfation for this complex, we modeled the sulfation of Tyr100H and compared the dynamics and energetics of the modified and unmodified complex by atomistic molecular dynamics simulations. Our results show that sulfation does not affect the overall conformation of CDRH3, but still enhances gp120 interactions both at the site of mutation and for the neighboring residues. This stabilization affects not only protein-protein contacts, but also the interactions between PG16 and the gp120 glycan shield. Further, we also investigated whether PG16-CDRH3 is a suitable template for the development of peptide mimetics. For a peptide spanning residues 93-105 of PG16 we obtained an experimental EC50 value of 3nM for the binding of gp120 to the peptide. This affinity can be enhanced by almost one order of magnitude by artificial disulfide bonding between residues 99 and 100F. In contrast, any truncation results in significantly lower affinity, suggesting that the entire peptide segment is involved in gp120 recognition. Their high affinity makes PG16-derived peptides useful building blocks for further optimization to obtain a potent inhibitor that efficiently blocks HIV-1 infection.