This study developed a system dynamics model to understand the spread of coronavirus disease (COVID-19) in Japan. The model is built on the generic SEIR (Susceptible, Exposed, Infected, and Recovered) framework adopted by Ghaffarzadegan and Rahmandad (2020) to build a system dynamics model for the spread of COVID-19 in Iran. Japan seems to be successful in containing the spread compared with other countries, and its first peak has passed. However, because this also leaves a large population still susceptible to the virus, it could cause a second and potentially higher peak of infection after the state of emergency aimed at reducing contact rate is lifted. As the government has proposed the “New Lifestyle,” it is critical to behave cautiously so as not to be infected. While the model focuses on the SEIR structure, the reflection of other sub-structures such as economy and hospital capacity that have tradeoffs with reducing contact rate should be beneficial. However, before extending the model, it is also critical to conduct estimates using confidence intervals rather than point estimates to better reflect uncertainties.

We performed for the first time to our knowledge fully ab initio molecular dynamics simulations of additive tribochemistry in boundary lubrication conditions. We consider an organophosphourus additive that has been experimentally shown to reduce friction in steel-on-steel sliding contacts thanks to the tribologically-induced formation of an iron phosphide tribofilm. The simulations allow us to observe in real time the molecular dissociation at the sliding iron interface under pressure and to understand the mechanism of iron phosphide formation. We discuss the role played by the mechanical stress by comparing the activation times for molecular dissociation observed in the tribological simulations at different applied loads with that expected on the basis of the dissociation barrier.

With the diversified development of media forms, livestreaming e-commerce has become a new sales model. Unlike the traditional sales model, this paper constructs a three-party game model composed of manufacturers, social media influencers and consumers based on the livestreaming model. It explores the equilibrium strategy selections of each participant in the supply chain system. In analyzing the evolutionary game stability of each participant, this paper obtains the equilibrium strategy and stability factors by analysis of the income and expenditure matrix. It uses the simulation model to analyze reasons for strategy selections of different game participants in the livestreaming e-commerce model. The results show that the strategies of manufacturers, social media influencers and consumers' selections have different impacts on their decision-making mechanism, and man-ufacturers are more sensitive to consumers' active participation in livestreaming e-commerce.

Heavy metal contamination of drinking water is a public health concern that requires the development of more efficient bioremediation techniques. Absorption technologies, including biosorption, provide opportunities for improvements to increase the diversity of metal ions removed and overall binding capacity. Microorganisms are a key component in wastewater treatment plants and they naturally bind metal ions through surface macromolecules but with limited capacity. The long-term goal of this work is to engineer capsule polymerases to synthesize molecules with novel functionalities. In previously published work, we showed that the Neisseria meningitidis serogroup W (NmW) galactose-sialic acid (Gal—NeuNAc) heteropolysaccharide binds lead effectively, thereby demonstrating the potential for using this capsular polysaccharide in environmental decontamination applications. In this study, computational analysis of the NmW capsule polymerase galactosyltransferase (GT) domain was used to gain insight into how the enzyme could be modified to enable the synthesis N-acetylgalactosamine-sialic acid (GalNAc—NeuNAc) heteropolysaccharide. Various computational approaches, including molecular modeling with I-TASSER and molecular dynamics simulations (MD) with NAMD, were utilized to identify key amino acid residues in the substrate binding pocket of the GT domain that may be key to conferring UDP-GalNAc specificity. Through these combined strategies and using BshA, a UDP-GlcNAc transferase, as a structural template, several NmW active site residues were identified as mutational targets to accommodate the proposed N-acetyl group in UDP-GalNAc. Thus, a rational approach for potentially conferring new properties to bacterial capsular polysaccharides is demonstrated.

The aim of this paper is to expose the main involved physical phenomena underlying the alteration of convective heat transfer in a heat exchanger subjected to imposed vibrations. This technique seems to have interesting features and industrial applications, such as efficiency increase, heat transfer rate control and cleanliness action. However, a clear description and comprehension of how vibrations may alter the convective heat transfer coefficient in a heat exchanger is no still reached due to the complexity of the involved physical mechanisms. For this reason, after a presentation and a schematisation of the analyzed thermodynamic system, the fundamental alterations of the thermo-fluid dynamics fields are described. Then, the main involved physical phenomena are exposed for the three cases of gaseous, monophasic liquid and boiling liquid mediums. Finally, on the basis of the characteristics of these described phenomena, some considerations and indications of general validity are presented.

The novel coronavirus pneumonia epidemic is still raging around the world. Therefore, during the period of a global pandemic, maintaining the normal circulation of medicine and health fields is the key to fight against the epidemic. This paper based on relevant data such as the export volume of cross-border e-commerce in Hangzhou, China from 2015 to 2019, the article uses system dynamics modeling to explore the impact of overseas warehouse services on cross-border e-commerce export transactions. Studies have shown that the introduction of overseas warehouses has significantly improved customer satisfaction and improved the quality of cross-border logistics services, which has a positive impact on cross-border e-commerce export transactions. Through sensitivity analysis, it can be seen that under the same conditions, the efficiency of customs clearance has the greatest impact on overseas warehouse services. Therefore, when allocating various investments in overseas warehouses, you can favor the customs clearance process to enhance the competitiveness of the cross-border e-commerce market and provide a feasible experience for healthcare supplies export from cross-border e-commerce.

We consider a random dynamical system arising in a model of associative memory. This system can be seen as a small (stochastic and deterministic) perturbation of a determinstic system having two weak attractors which are destroyed after the perturbation. We show, with a computer aided proof, that the system has a kind of chaotic itineracy. Typical orbits are globally chaotic, while they spend relatively long time visiting attractor's ruins.

Identifying or authenticating a computer user are necessary steps to keep systems secure on the network and to prevent fraudulent users from accessing accounts. Keystroke dynamics authentication can be used as an additional authentication method. Keystroke dynamics involves in-depth analysis of how you type on the keyboard, analysis of how long a key is pressed or the time between two consecutive keys. This field has seen a continuous growth in scientific research. In the last five years alone, about 10,000 scientific researches in this field have been published. One of the main problems facing researchers is the small number of public data sets that include how users type on the keyboard. This paper aims to provide researchers with a data set that includes how to type free text on the keyboard by 80 users. The data were collected in a single session via a web platform. The dataset contains 410,633 key-events collected in a total time interval of almost 24 hours. In similar research, most datasets are with texts written by users in English. The language in which the users wrote for this research is Romanian. This paper also provides an extensive analysis of the data set collected and presents relevant information for the analysis of the data set in future research.

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.

Bimetallic nanoparticles are of interest since they lead to many interesting electrical, chemical, catalytic, and optical properties. They are particularly important in the field of catalysis since they show superior catalytic properties than their monometallic counterparts. The structures of bimetallic nanoparticles depend mainly on the synthesis conditions and the miscibility of the two components. In this work, PdPt alloyed-bimetallic nanoparticles (NPs) were synthesized through the polyol method, and characterized using spherical aberration (Cs) corrected scanning transmission electron microscopy (STEM). High-angle annular dark-field (HAADF)-STEM images of bimetallic nanoparticles were obtained. The contrast of images shows that nanoparticles have an alloy structure with an average size of 8.2 nm. Together with the characterization of nanoparticles, a systematic molecular dynamics simulations study, focused on the structural stability and atomic surface segregation trends in 923-atom PdPt alloyed-bimetallic NPs was carried out.

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.

To build a representation of what we see, the human brain recruits regions throughout the visual cortex in cascading sequence. Recently, an approach was proposed to evaluate the dynamics of visual perception in high spatiotemporal resolution at the scale of the whole brain. This method combined functional magnetic resonance imaging (fMRI) data with magnetoencephalography (MEG) data using representational similarity analysis and revealed a hierarchical progression from primary visual cortex through the dorsal and ventral streams. To assess the replicability of this method, here we present results of a visual recognition neuro-imaging fusion experiment, and compare them within and across experimental settings. We evaluated the reliability of this method by assessing the consistency of the results under similar test conditions, showing high agreement within participants. We then generalized these results to a separate group of individuals and visual input by comparing them to the fMRI-MEG fusion data of Cichy et al. (2016), revealing a highly similar temporal progression recruiting both the dorsal and ventral streams. Together these results are a testament to the reproducibility of the fMRI-MEG fusion approach and allows for the interpretation of these spatiotemporal dynamic in a broader context.

The outbreak of COVID-19, the disease caused by SARS-CoV-2, continues to affect millions of people around the world. The absence of a globally distributed effective treatment makes the exploration of new mechanisms of action a key step to address this situation. Stabilization of non-native Protein-Protein Interactions (PPIs) of the nucleocapsid protein of MERS-CoV has been reported as a valid strategy to inhibit viral replication. In this study, the applicability of this unexplored mechanism of action against SARS-CoV-2 is analyzed. During our research, we were able to find three inducible interfaces of SARS-CoV-2 N protein NTD, compare them to the previously reported MERS-CoV stabilized dimers, and identify those residues that are responsible for their formation. A drug discovery protocol implemented consisting of docking, molecular dynamics and MM-GBSA enabled us to find several compounds that might be able to exploit this mechanism of action. In addition, a common catechin skeleton was found among many of these molecules, which might be useful for further drug design. We consider that our findings could motivate future research in the fields of drug discovery and design towards the exploitation of this previously unexplored mechanism of action against COVID-19.

Quantum loops are processes that constitute quantum objects. In the causal model of quantum loops and quantum objects presented here, the nonlinear processes involve the elementary units of spacetime and the associated elementary units of quantum fields. As such, quantum loop processes are the sources of gravitational fields (i.e., spacetime curvature) and of the quantum objects wave function. The model may be viewed as a derivative of loop quantum gravity, spin networks and causal dynamical triangulation, although significant deviations to these theories exist. The causal model of quantum loops is based on a causal model of spacetime dynamics where space(-time) consists of interconnected space points, each of which is connected to a small number of neighboring space points. The curvature of spacetime is expressed by the density of these space points and by the arrangement of the connections between them. The quantum loop emerges in a nonlinear collective behavioral process from a collection of space points that carry energy and quantum field attributes.

Background: Colorectal cancer is considered the third most fetal among all type of cancer. Spleen tyrosine kinase (SYK) is a non-receptor type tyrosine-protein that plays crucial role in signaling mediated via immune receptor. We adopted an onco-informatics analysis to evaluate the SYK expression and prognostic value of SYK in colorectal cancer, and identification of potential phytochemicals which may inhibit overexpression of SYK protein as well as minimized colorectal cancer. Materials & Methods: Differential expression of SYK gene was analyzed using the several transcriptomic databases including Oncomine, UALCAN, GENT2 and GEPIA2. The server, cBioPortal was used to analyze mutation and copy number alterations whereas GENT2, GEPIA, OncoLnc and PrognoScan were employed to examine the survival rate. A protein-protein interaction network of SYK and co-expressed genes of SYK was conducted via GeneMANIA. Considering SYK gene encoding protein as drug target, selected phytochemicals were assessed by molecular docking using PyRx 0.8 packages. YASARA molecular dynamics simulators were applied for the post validation of the molecular docking data. Results: We have observed significant overexpression of mRNA expression levels of SYK gene colorectal adenocarcinoma (COAD) samples compared with normal tissues. Significant methylation level and various genetic alterations are assembled in SYK gene which can lead to the development of colorectal cancer. As a result, lower level of SYK expression was related to the more chances of patients’ survival by which all the outcomes from the multiple bioinformatics platforms and web resources have demonstrated the significant evidences that the SYK kinsase can possess as a potential biomarker for the treatment of colorectal cancer. Here, aromatic phytochemicals namely, Kaempferol and Glabridin targeting SYK showed more stability compared to controls and may be useful for the treatment of colorectal cancer. Conclusion: Our study showed dysregulated expression of SYK in colorectal cancer and potentiality to act as a biomarker for the prognosis of CRC. Moreover, we have shown phytochemicals (Kaempferol and Glabridin) target SYK as potential treatment strategies and drug repositioning potentiality in colorectal cancer.

In this work it is acknowledged that important attempts to devise an emergent quantum (gravity) theory require space-time to be discretized at the Planck scale. It is therefore conjectured that reality is identical to a sub-quantum dynamics of ontological micro-constituents that are connected by a single interaction law. To arrive at a complex system-based toy-model identification of these micro-constituents, two strategies are combined. First, by seeing gravity as an entropic phenomenon and generalizing the dimensional reduction of the associated holographic principle, the universal constants of free space are related to assumed attributes of the micro-constituents. Second, as the effective field dynamics of the micro-constituents must eventually obey Einstein’s field equations, a sub-quantum interaction law is derived from a solution of these equations. A Planck-scale origin for thermodynamic black hole characteristics and novel views on entropic gravity theory result from this approach, which eventually provides a different view on quantum gravity and its unification with the fundamental forces.

The coordination planning between land use and transportation system is an important premise of solving urban transportation problems and realizing land use integration. This study investigates the interactive and feedback relationship between land use and transportation system from the perspective of access management. By integrating the land use and traffic data from Las Vegas Metropolitan area with the system dynamics model, the causal relationship and causal loop diagrams (CLDs) are introduced to analyze the cause-and-effect relationship and quantitative relationship between the factors of the combined system of land use and transportation, and then sub-models partition and system simulation are performed. The systems dynamics model is established by analyzing the relationship between a series of access management techniques, traffic characteristics, and land use features. The results show that system dynamics model can be used as an effective alternative to model the symbiosis relationship of land use and transportation system for urban planning and construction.

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.

In a thin-volume photobioreactor where a concentrated suspension of microalgae is circulated throughout the established spatial irradiance gradient, microalgal cells experience a time-variable irradiance. Deploying this feature is the most convenient way of obtaining the so-called “flashing light” effect, improving biomass production in high irradiance. This work investigates the light flashing features of sloping wavy photobioreactors, a recently proposed type, by introducing and validating a Computational Fluid Dynamics model. Two characteristic flow zones (straight top-bottom stream and local recirculation stream), both effective toward light flashing, have been found and characterised: a recirculation-induced frequency of 3.7 Hz and straight flow-induced frequency of 5.6 Hz were estimated. If the channel slope is increased, the recirculation area becomes less stable while the recirculation frequency is nearly constant with flow rate. The validated CFD model is a mighty tool that could be reliably used to further increase the flashing frequency by optimising the design, the dimensions, the installation and the operational parameters of the sloping wavy photobioreactor.

Time recordings of impulse-type oscillation responses are short and highly transient. These characteristics may complicate the usage of classical spectral signal processing techniques for a) describing the dynamics and b) deriving discriminative features from the data. However, common model identification and validation techniques mostly rely on steady-state recordings, characteristic spectral properties and non-transient behavior. In this work, a recent method, which allows reconstructing differential equations from time series data, is extended for higher degrees of automation. With special focus on short and strongly damped oscillations, an optimization procedure is proposed that fine-tunes the reconstructed dynamical models with respect to model simplicity and error reduction. This framework is analyzed with particular focus on the amount of information available to the reconstruction, noise contamination and non-linearities contained in the time series input. Using the example of a mechanical oscillator, we illustrate how the optimized reconstruction method can be used to identify a suitable model and to extract features from uni-variate and multivariate time series recordings in an engineering-compliant environment. Moreover, the determined minimal models allow for identifying the qualitative nature of the underlying dynamical systems as well as testing for the degree and strength of non-linearity. The reconstructed differential equations would then be potentially available for classical numerical studies, such as bifurcation analysis. These results represent a physically interpretable enhancement of data-driven modeling approaches in structural dynamics.

A new approach was presented in this study to simulate a stable atom along with subatomic particles in it. Subatomic particles in an atom are treated as conventional particles, exhibiting attraction and repulsion between them, giving a stable atom simulation. This new approach leads to developing new potentials for subatomic particles to simulate a stable atom. Subatomic particle dynamics (SPD) simulations were developed for within-atom simulations that give a stable atom structure for infinite time and provide many insights into electron trajectories and atom properties like energies and radius of the atom. The effect of protons and neutrons movement in the nucleus on electron trajectories was captured in SPD. Hydrogen and Carbon atom SPD were reported in this study. The Pilot-wave theory was implemented in this study to simulate the wave nature of subatomic particles in an atom. Electrons motion was guided by the interference pattern produced by the electron’s aether medium waves in SPD. SPD was implemented on molecules, resulting in a stable molecular structure giving insights into electron trajectories shared by multiple atoms.

Studies performed at single-cell resolution have demonstrated the physiological significance of cell-to-cell variability. Various types of mathematical models and systems analyses of biological networks have further been used to gain a better understanding of the sources and regulatory mechanisms of such variability. In this work, we present a novel sensitivity analysis method, called molecular density function perturbation (MDFP), for the dynamical analysis of cellular heterogeneity. The proposed analysis is based on introducing perturbations to the density or distribution function of the cellular state variables at specific time points, and quantifying how such perturbations affect the state distribution at later time points. We applied the MDFP analysis to a model of signal transduction pathway involved in TRAIL (tumor necrosis factor-related apoptosis-inducing ligand)-induced apoptosis in HeLa cells. The MDFP analysis showed that caspase-8 activation regulates the timing of the switch-like increase of cPARP (cleaved poly(ADP-ribose) polymerase), an indicator of apoptosis. Meanwhile, the cell-to-cell variability in the commitment to apoptosis depended on mitochondrial outer membrane permeabilization (MOMP) and events following MOMP, including the release of Smac (second mitochondria-derived activator of caspases) and cytochrome-C from mitochondria, the inhibition of XIAP (X-linked inhibitor of apoptosis) by Smac and the formation of apoptosome.

In the current work, in continuation of our recent research [1] we synthesized and studied new chimeric compounds comprising the ribosome-targeting antibiotic chloramphenicol (CHL) and the membrane-penetrating cation triphenylphosphonium (TPP) connected by alkyl linkers of different lengths. Using various biochemical assays, we showed that these CAM-Cn-TPP compounds bind to the bacterial ribosome, inhibit protein synthesis in vitro and in vivo in a way similar to that of the parent CHL, and significantly decrease membrane potential. Similar to CAM-C4-TPP, the mode of action of CAM-C10-TPP and CAM-C14-TPP on bacterial ribosomes differ from that of CHL. By simulating the dynamics of complexes of CAM-Cn-TPP with bacterial ribosomes, we have proposed a possible explanation for the specificity of the action of these analogs on the translation process. CAM-C10-TPP and CAM-C14-TPP stronger inhibit the growth of the Gram-positive bacteria in comparison to the CHL and suppress some strains of CHL-resistant bacteria. Thus, we have shown that TPP derivatives of CHL are dual-acting compounds that target the ribosomes and the cellular membranes of bacteria. The TPP fragment of CAM-Cn-TPP compounds contributes to the inhibitory effect on bacteria. Moreover, since the mitochondria of eukaryotic cells have qualities similar to those of their prokaryotic ancestors, we demonstrate the possibility of targeting chemoresistant cancer cells with these compounds.

Structural and biochemical studies have recently revealed a range of rationally engineered nanobodies with efficient neutralizing capacity against SARS-CoV-2 virus and resilience against mutational escape. In this work, we combined atomistic simulations and conformational dynamics analysis with the ensemble-based mutational profiling of binding interactions for a diverse panel of SARS-CoV-2 spike complexes with nanobodies. Using this computational toolkit, we identified dynamic signatures and binding affinity fingerprints for the SARS-CoV-2 spike protein complexes with nanobodies Nb6 and Nb20, VHH E, a pair combination VHH E+U, a biparatopic nanobody VHH VE, and a combination of CC12.3 antibody and VHH V/W nanobodies. Through ensemble-based deep mutational profiling of stability and binding affinities, we identify critical hotspots and characterize molecular mechanisms of SARS-CoV-2 spike protein binding with single ultra-potent nanobodies, nanobody cocktails and biparatopic nanobodies. By quantifying dynamic and energetic determinants of the SARS-CoV-2 S binding with nanobodies, we also examine the effects of circulating variants and escaping mutations. We found that mutational escape mechanisms may be controlled through structurally and energetically adaptable binding hotspots located in the host receptor-accessible binding epitope that are dynamically coupled to the stability centers in the distant epitope targeted by VHH U/V/W nanobodies. The results of this study suggested a mechanism in which through cooperative dynamic changes, nanobody combinations and biparatopic nanobody can modulate the global protein response and induce the increased resilience to common escape mutants.

In this contribution, we aim to show that opinion dynamics and population balance modeling can benefit from an exchange of problems and methods. To support this claim, the Deffuant-Weisbuch model, a classical approach in opinion dynamics, is formulated as a population balance model. This new formulation is subsequently analyzed in terms of moment equations, and conservation of the first and second order moment is shown. Exemplary results obtained by our formulation are presented and agreement with the original model is found. Also the influence of the initial distribution is studied. Additionally, the Deffuant-Weisbuch model is transferred to engineering and interpreted as mass transfer between liquid droplets which results in a more flexible formulation compared to alternatives from the literature. On the one hand, it is concluded that the transfer of opinion-dynamics problems to the domain of population balance modeling offers some interesting insights as well as stimulating challenges for the population-balance community. On the other hand, it is inferred that population-balance methods can contribute to the solution of problems in opinion dynamics. In a broad outlook, some further possibilities of how the two fields can possibly benefit from a close interaction are outlined.

Quadruplex-interactive small molecules have a wide potential application, not only as drugs but also as sensors of quadruplexes structures. The purpose of this work is the synthesis of analogues of the bis-methylquinolinium-pyridine-2,6-dicarboxamide G4 ligand 360A, to identify relevant structure-activity relationships to apply to the design of other G4-interactive small molecules bearing bis-quinoline or bis-isoquinoline moieties. Thermal denaturation experiments revealed that non-methylated derivatives with a relative 1,4 position between the amide linker and the nitrogen of the quinoline ring are moderate G4 stabilizers, with a preference for the hybrid h-Telo G4. Insertion of a positive charge upon methylation of quinoline/isoquinoline nitrogen increases compounds capacity to selectively stabilize G4s compared to duplex DNA, with a preference for parallel structures. Among these, compounds having a relative 1,3-position between the charged methylquinolinium/isoquinolinium nitrogen and the amide linker are the best G4 stabilizers. More interestingly, these ligands showed different capacities to selectively block DNA polymer-ization in a PCR-stop assay and to induce G4 conformation switches of hybrid h-Telo G4. Mo-lecular dynamic simulations with the parallel k-RAS G4 structure showed that the relative spatial orientation of the two methylated quinoline/isoquinoline rings determines the ligands mode and strength of binding to G4s.

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.

In this research, the computational fluid dynamic (CFD) approach that has been used in wind power generation field was applied for the solution of the problems of local strong wind areas in railway fields, and the mechanism of wind generation was discussed. At the same time, the affectivity of the application of computational fluid dynamic approach to railway field was discussed. The problem of local wind that occurs on the railway line in winter was taken up in this research. A computational simulation for the prediction of wind conditions by LES was implemented and it was clarified that the local strong wind area is mainly caused by separated flows originating from the small‐scale terrain positioned at its upstream (at approximately 180.0 m above sea level). Meanwhile, the effects of the size of calculation area and spatial grid resolution on the result of calculation and the effect of atmospheric stability were also discussed. It was clarified that when the air flow characteristic of the separated flow originating from the small‐scale terrain (at altitude of approximately 180.0 m) targeted in this research is reproduced at high accuracy by computational simulation of wind conditions, approximately 10.0 m of spatial resolution of computational grid in horizontal direction is required. As a result of the computational simulation of wind conditions of stably stratified flow (Fr = 1.0), lee waves were excited at the downstream of the terrain over time. As a result, the reverse‐flow region lying behind the terrain that had been observed at a neutral time was inhibited. Consequently, local strong wind area was generated at the downstream of the terrain and the strong wind area passing through the observation mast was observed. By investigating the speed increasing rate of local strong wind area induced at the time of stable stratification, it was found that the wind was approximately 1.2 times stronger than what was generated at a neutral time.

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.

In this paper, the current technologies of the regenerative shock absorber systems have been categorized and evaluated. Three drive modes of the regenerative shock absorber systems, namely the direct drive mode, the indirect drive mode and hybrid drive mode are reviewed for their readiness to be implemented. The damping performances of the three different modes are listed and compared. Electrical circuit and control algorithms have also been evaluated to maximize the power output and to deliver the premium ride comfort and handling performance. Different types of parameterized road excitations have been applied to vehicle suspension systems to investigate the performance of the regenerative shock absorbers including that of the nonlinear regenerative shock absorber. The research gaps for comparison of the different drive modes and the nonlinearity analysis of the regenerative shock absorbers are identified and, the corresponding research questions have been proposed for future work.

Current progress in the prediction of mechanical behavior of solids requires understanding of spatiotemporal complexity of plastic flow caused by self-organization of crystal defects. It may be particularly important in hexagonal materials because of their strong anisotropy and combination of different mechanisms of plasticity, such as dislocation glide and twinning. These materials often display complex behavior even on the macroscopic scale of deformation curves, e.g., a peculiar three-stage elastoplastic transition, the origin of which is a matter of debates. The present work is devoted to a multiscale study of plastic flow in α-Ti, based on simultaneous recording of deformation curves, 1D local strain field, and acoustic emission (AE). It is found that the average AE activity also reveals three-stage behavior, but in a qualitatively different way depending on the crystallographic orientation of the sample axis. On the finer scale, the statistical analysis of AE events and local strain rates testifies to an avalanche-like character of dislocation processes, reflected in power-law probability distribution functions. The results are discussed from the viewpoint of collective dislocation dynamics and are confronted to predictions of a recent micromechanical model of Ti strain hardening.

The establishment and spread of exotic species is a contemporary major concern. Alien species may become invasive in their new habitat, leading to both/either environmental and/or economic impacts. I briefly reviewed the literature in the last decade about the relationship of exotic species and native communities. I identified that professionals usually approach the subject in two main points of view: (1) researchers tend to point out the impacts of alien species on entire communities, evaluating if the relationship is positive, negative or neutral; (2) they focus on the eco-evolutionary processes involved in the introductions, the dynamics of invasion, and individual study cases. When evaluating the response of introductions to entire communities, evidence seems to be ambiguous and may support positive, negative or neutral relationship, especially depending on the scale approached. The unique eco-evolutionary pathways of each introduction may be a great shortcoming in the searching for generalities. On the other hand, advances have been made in understanding the dynamics of invasion on different lineages through a more selective/individualized approach. I suggest that the dynamics of invasion might be studied through a perspective in which different eco-evolutionary processes, levels of organization (from gene to entire communities), the history of the organism(s) and time are taken into account. Individual cases might be compared in attempt to understand how the relationship exotic and native works and in the search for generalities.

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.

To understand functions of biomolecules such as proteins, not only structures but their conformational change and kinetics are important to be characterized but its atomistic details are hard to obtain both experimentally and computationally. We review our recent computational studies using novel enhanced sampling techniques for conformational sampling of biomolecules and calculations of their kinetics. For efficiently characterizing the free energy landscape of a biomolecule, we introduce the multiscale enhanced sampling method, which uses a combined system of atomistic and coarse-grained models. Based on the idea of Hamiltonian replica exchange, we can recover the statistical properties of the atomistic model without any biases. We next introduce the string method as a path search method to calculate the minimum free energy pathways along a multidimensional curve in high dimensional space. Finally we introduce novel methods to calculate kinetics of biomolecules based on the ideas of path sampling: One is the Onsager-Machlup action method, and the other is the weighted ensemble method. Some applications of above methods to biomolecular systems are also discussed and illustrated.

Molecular dynamics(MD) simulations are carried out to characterize the mechanicalproperties and failure behavior of van der Waals heterostructures composed ofgraphene and hexagonal boron nitride(hBN) single layer sheets. The graphene–hBNand hBN–graphene–hBN heterostructures simulations are carried out under tensileand shear deformation. Accordingly, stress versus strain curves of each systemare plotted and various properties of heterostructures, namely elastic modulusand shear modulus as well as failure stress and failure strain, are evaluatedand compared with one another as well as with the pristine graphene and hBNsheets. Subsequently, the failure mechanism/characterization of each sheet in theheterostructures is described. Alternatively, the elastic and shear modulus of eachheterostructure are computed by means of rule of mixture(ROM) which are in goodagreement with results that are obtained from MD simulations.

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.

COVID-19 appeared as an infectious disease of global health emergency and the highest public health concern of 21st century for this world due to its high-speed of spread across the globe. The disease started as one single case to a cluster of cases in Wuhan, China (Dec 2019) and within few months with its continuous upsurge of cases spreading globally which has created enormous threat and tension across the global Public health care field. Most significantly to share the fact that, this disease caused high level of Risk Group mortality, high morbidity, health care services burden, panic anxiety, mental trauma and tension, social and economic insecurity, which also collectively surfaced by diverse range of social reaction and political pressure across the world. Also with the appearance of new and unknown pathogenesis of the disease has created the most and significant attention and concern for the scientific community and political leaders as well. The disease also varies much with its pattern of virus, sign, symptoms, characteristics including its epidemiological and public health response (like prevention strategy, diagnoses, case management, treatment pattern) across the countries. However, this variance is comparatively less rather even more in commonality while it comes to basic public health prevention interventions like frequent hand washing, wearing face mask, maintaining social/physical distancing (2 - 6 meter in between), individual isolation and community quarantine for suspected exposure and lockdown in community areas where cases are identified. These are with the most commonly practiced public health interventions to deal with this disease in majority of the epicenters across countries. Also with the progress of the disease with its diverse categorical appearance of sign symptoms which are uniquely portraying this disease is more of a kind of COVID-19 syndrome than as COVID-19. Moreover, various factors including socio economic status, health status, population dynamics, health system and infrastructure, health behavioral pattern, nutrition and food habit and access to information and knowledge made this viral disease one of the historically counted on expensive disease of the modern world to fight for. Specially to mention here, the case fatality rate distinctively vary with the population dynamics and the health system infrastructure and ability factors which have already created clear evidence as explained in this paper how these factors are uniquely distinguished and different from country to country. Apart from the contextual differences, the various kind of ongoing preventive measures (like prevention, diagnosis and treatment) learnt every day from the emerging characteristics and pattern of this viral disease which are most commonly practiced across countries with a variance. According to the Public health prevention practice and interventions, the total world is connected and learning from each other’s public health experiences to fight for the virus. However, the world communities are eagerly waiting to see the result and outcome of the ongoing therapeutics and vaccine trial initiated in several countries, the people of the world are quite optimistic and hopeful that, global scientific community will be able to invent some miraculous and magic solution in upcoming months which ultimately will free the world from this most terrifying COVID-19 pandemic of 21st century.

Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains connected by amino acid linkers, the sequence TGQKP connects ZF1 and ZF2, and TGEKP connects ZF2 with ZF3. Linkers act to tune the zinc finger protein in the right position to bind its DNA target, the type of amino acid residues and length of linkers reflect on ZF1-ZF2-ZF3 interactions and contribute to the search and recognition process of ZF protein to its DNA target. Linker mutations and the affinity of the resulting mutants to specific and nonspecific DNA targets were studied by MD simulations and MM_GB(PB)SA. The affinity of mutants to DNA varied with type and position of amino acid residue. Mutation of K in TGQKP resulted in loss in affinity due to the loss of positive K interaction with phosphates, mutation of G showed loss in affinity to DNA, WT protein and all linker mutants showed loss in affinity to a nonspecific DNA target, this finding confirms previous reports which interpreted this loss in affinity as due to ZF1 having an anchoring role, and ZF3 playing an explorer role in the binding mechanism. The change in ZFP-DNA affinity with linker mutations is discussed in view of protein structure and role of linker residues in binding.

Salmonella, especially invasive non-typhoidal Salmonella (iNTS) are responsible for developing various invasive diseases, and possess higher mortality rate, due to their higher antibiotic resistance profile than the other bacteria. Therefore, the present study was concerned to develop epitope based peptide vaccine against iNTS species as a successive and substitute protective measures. The study considered comprehensive Immunoinformatic approaches, followed by molecular docking and molecular dynamics simulation to predict the efficient vaccine candidate T cell and B cell epitopes, based on the outer membrane proteins. The study identified two best epitopes YGIFAITAL and KVLYGIFAI from total iNTS outer membrane proteins, which showed higher immunity, non-allergenicity, non-toxicity and also showed higher conservancy and population coverage values. Both epitopes showed higher binding affinity and stability towards HLA-C* 03:03. The MM-PBSA binding free energy showed the YGIFAITAL epitope binds more tightly with both MHC-I and MHC-II molecules. The total contact, H-bond analysis and RMSF results also validate the efficiency of these epitopes as vaccine candidate. The projected B cell epitopes AAPVQVGEAAGS, TGGGDGSNT and TGGGDGSNTGTTTT showed higher antigenicity. Overall, the study concluded that these epitopes can be considered as the potential vaccine candidate to make a successive vaccine against iNTS species. However, this result further needs to be validate by wet lab research to make successive vaccine with these projected epitopes.

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.

In quantum many-body systems, a Hamiltonian is called an ``extensive entropy generator'' if starting from a random product state the entanglement entropy obeys a volume law at long times with overwhelming probability. We prove that (i) any Hamiltonian whose spectrum has non-degenerate gaps is an extensive entropy generator; (ii) in the space of (geometrically) local Hamiltonians, the non-degenerate gap condition is satisfied almost everywhere. Specializing to many-body localized systems, these results imply the observation stated in the title of Bardarson et al. [PRL 109, 017202 (2012)].

Complex colloidal fluids, depending on particulates’ shapes and packing fractions, may have a wide range of shear thinning and thickening behaviors. A particular interesting way to transition between different types of such behavior is by infusing functional complex particles that can be manufactured using modern techicques such as 3D printing. In this paper, we display 2D molecular dynamics simulations of such fluids with infused star-shaped functional particles, with variable leg length and number of legs, as they are infused in a non-interacting, coarse-grained fluid. We vary the packing fraction (ϕ) of the system, and for each different system we apply shear with various strain rate that turns the fluid into a jammed state and rise the apparent viscosity of fluid. We demonstrate the dependence of viscosity with the particles’ packing fraction. We show the role of shape and design dependence of the functional particles towards the transition to a shear thickening fluid .

The main regulatory factors during the adaptation of cancer cells to hypoxic stress are the hypoxia-inducible factors (HIFs), which are being increasingly recognized as an interesting and challenging target for the design of new chemotherapeutic molecules. HIF2A was found to have an large internal hydrophilic cavity within its PAS-B domain, unique to this sub-unit and is suggested to be a possible ligand-binding site. Regulation of HIF2A by cellular molecules is still greatly unknown. In This paper we have employed in-silico techniques, such as molecular docking and dynamic simulation, to design new direct inhibitors against HIF-2A subunit via targeting one of its critical domains and the final top screened molecules have been tested on hypoxic cancer cells for further validation of their inhibitory potential. we targeted the hydrophilic cavity inside the PAS-B domain of the HIF2A to identify novel molecules with a high binding capacity. Virtual Screening methodology was used for molecular docking of NSC library against the target domain inside the HIF2A PAS-B domain with the top 5% compounds with significant MolDock and Re-rank scores were selected for further analysis. The NSC 106416, NSC 217021, NSC 217026, and NSC 215639 compounds were selected based on their docking scores. NSC 215639 had the minimum polar solvation energy and also had a relative strong binding energy. NSC 217026 had the strongest binding energy among other compounds.

Due to failure of the continuum hypothesis for higher Knudsen numbers, rarefied gases and microflows of gases are particularly difficult to model. Macroscopic transport equations compete with particle methods, such as DSMC to find accurate solutions in the rarefied gas regime. Due to growing interest in micro flow applications, such as micro fuel cells, it is important to model and understand evaporation in this flow regime. Here, evaporation boundary conditions for the R13 equations, which are macroscopic transport equations with applicability in the rarefied gas regime, are derived. The new equations utilize Onsager relations, linear relations between thermodynamic fluxes and forces, with constant coefficients, that need to be determined. For this, the boundary conditions are fitted to DSMC data and compared to other R13 boundary conditions from kinetic theory and Navier-Stokes-Fourier (NSF) solutions for two one-dimensional steady-state problems. Overall, the suggested fittings of the new phenomenological boundary conditions show better agreement to DSMC than the alternative kinetic theory evaporation boundary conditions for R13. Furthermore, the new evaporation boundary conditions for R13 are implemented in a code for the numerical solution of complex, two-dimensional geometries and compared to NSF solutions. Different flow patterns between R13 and NSF for higher Knudsen numbers are observed.

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.

One of the principal hallmarks of Alzheimer’s disease (AD) is related to the aggregation of amyloid-β fibrils in an insoluble form in the brain, also known as amyloidosis. Therefore, a prominent therapeutic strategy against AD consists either in blocking the amyloid aggregation and/or destroying the already formed aggregates. Natural products have shown significant therapeutic potential as amyloid inhibitors from in vitro studies as well as in vivo animal tests. In this study, the interaction of five natural biophenols (curcumin, dopamine, (-)-Epigallocatechin-3-gallate, Quercetin, and Rosmarinic acid) with the amyloid-β(1-40) fibrils has been studied through computational simulations. The results allowed the identification and characterization of the different binding modalities of each compounds and their consequences on fibril dynamics and aggregation. It emerges that the lateral aggregation of the fibrils is strongly influenced by the intercalation of the ligands, which modulate the double-layered structure stability.

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.

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.

Tissue engineering has the potential for repairing large bone defects, which impose a heavy financial burden on the public health. However, difficulties with O₂ delivery to the cells residing in the interior of tissue engineering scaffolds make it challenging to grow artificial tissues of clinically-relevant sizes. This study uses image-based simulation in order to provide insight into how to better optimize the scaffold manufacturing parameters, and the culturing conditions, in order to resolve the O₂ bottleneck. To do this, high resolution 3D X-ray images of two common scaffold types (salt leached foam and non-woven fiber mesh) are fed into a Lattice Boltzmann Method fluid dynamics and reactive Lagrangian Scalar Tracking mass transfer solvers. The obtained findings indicate that the scaffolds should have maximal surface area-to-solid volume ratios, for higher chances of the molecular collisions with the cells. Furthermore, the cell culture media should be flown through the scaffold pores as fast as practically possible (without detaching or killing the cells). Finally, we have provided a parametric sweep that maps how the molecular transport within the scaffolds is affected by variations in rates of O₂ consumption by the cells. Ultimately, the results of this study are expected to benefit the computer-assisted design of tissue engineering scaffolds and culturing experiments.

Plants produce above- and below-ground biomass. However, our understanding of both production and decomposition of below-ground biomass is poor, largely because of the difficulties of accessing study materials. Below-ground organic matter decomposition studies are scanty and especially rare in the tropics. Here, we used a litter bag experiment to quantify the mass loss and nutrients dynamics of decomposing twigs and fine roots from an arbuscular mycorrhizal fungal associated tree, Parashorea chinensis, in a tropical rain forest in Southwest China. Overall, twig litter decomposed 1.9 times faster than fine roots (decay rate (k) twig=0.255, root=0.134). The difference in decomposition rates can be explained by a difference in phosphorus (P) concentration, availability and use by decomposers or C quality. Both materials showed an increase in N concentration, with final measurements still higher than initial levels. This suggests N may not be available due to microbial immobilization. Both carbon and nitrogen dynamics were significantly predicted by mass loss and showed a negative and positive relationship, respectively. Our study results imply that fine roots carbon and nitrogen contribute more to soils organic matter and enlarge the resident time. Therefore, better understanding of carbon cycle requires better understanding of mechanisms governing below ground biomass decomposition.

The last few decades have witnessed a surge of interest in adventure sports, and an emerging research focus on these activities. However, recent conceptual analyses and scientific reviews have highlighted a major, fundamental question that remains unresolved: what constitutes an adventure sport (and are they ‘sports’ at all)? Despite several proposals for definitions, the field still seems to lack a shared conceptualization. This deficit may be a serious limitation for research and practice, restricting the development of a more nuanced theoretical explanation of participation and prac-tical implications within and across adventure sports. In this article we address another crucial question, how can adventure sports be better understood for research and practice? We briefly summarize previous definitions to address evident confusion and lack of conceptual clarity in the discourse. Alternatively, we propose how an ecological perspective on human behaviors, as in-teractions with the environment, may provide an appropriate conceptualization to guide and enhance future research and practice, using examples from activities such as freeride skiing / snowboarding, white-water kayaking, climbing, mountaineering and the fields of sport science, psychology and avalanche research and education. We draw on ecological dynamics as a trans-disciplinary approach to discuss how this holistic framework presents a more detailed, nuanced, and precise understanding of adventure sports.

We develop an action principle to construct the field equations for dissipative/resistive general relativistic two-temperature plasmas, including a neutrally charged component. The total action is a combination of four pieces: an action for a multi-fluid/plasma system with dissipation/resistivity and entrainment; the Maxwell action for the electromagnetic field; the Coulomb action with a minimal coupling of the four-potential to the charged fluxes; and the Einstein-Hilbert action for gravity (with the metric being minimally coupled to the other action pieces). We use a pull-back formalism from spacetime to abstract matter spaces to build unconstrained variations for the neutral, positively, and negatively charged fluid species and for three associated entropy flows. The full suite of field equations is recast in the so-called ``$3 + 1$'' form (suitable for numerical simulations), where spacetime is broken up into a foliation of spacelike hypersurfaces and a prescribed ``flow-of-time''. A previously constructed phenomenological model for the resistivity is updated to include the modified heat flow and the presence of a neutrally charged species. We impose baryon number and charge conservation as well as the Second Law of Thermodynamics in order to constrain the number of free parameters in the resistivity. Finally, we take the Newtonian limit of the ``$3 + 1$'' form of the field equations which can be compared to existing non-relativistic formulations. Applications include main sequence stars, neutron star interiors, accretion disks, and the early universe.

Systems Chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the Graded Autocatalysis Replication Domain (GARD) formalism embodied in a Lipid World scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in Molecular Dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions and micellar formation, growth and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with Molecular Dynamics analyses. We present a roadmap for simulating GARD’s kinetic and thermodynamic behavior using various Molecular Dynamics methodologies. We review different approaches for testing the validity of the GARD model, by following micellar accretion and fission events and examining compositional changes over time. Near future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding.

In this study, an optimization of the first blade in new test rig presented. Blade tuning is conducted using 3D geometrical parameters. Sweep and dihedral play an essential role in this study. Compressor characteristics and blades vibrational behavior are the main objective of the evaluation. Here, the attachments are designed to isolate blade dynamics from Disk. So, the Vibrational behaviors of the one's blade are tuned based on the self-excited and forced vibration phenomenon. Using a semi analytical MATLAB code instability conditions are satisfied. The code takes advantages of whitehead and force response theory to predict classically and stall flutter speeds. Beside, Forced vibrations instability is controlled using a theory presented by Campbell. Aerodynamics of new blade geometry determined using multistage simulations Computational fluid dynamics (CFD) software. Numerical results show increasing performance near the surge line and working interval along with increasing mass flow.

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.

The past two decades have witnessed the introduction of and then a steady increase in the use of computational techniques in the study and development of molecularly imprinted polymers (MIPs). Molecular dynamics (MD) based studies have had a significant role in this development as they can provide insights concerning the mechanisms governing the molecular level events underlying MIP synthesis and MIP-ligand interactions and can be used for the identification of preferred monomer compositions and for the prediction of MIP properties. We here review the role that MD has played in the development of molecular imprinting and examine the different types of MD strategies that have been used, including their advantages and challenges. Recent trends in the application of MD to the study of MIPs are presented, along with a perspective on the future importance of MD-based studies for the development of molecular imprinting science and technology.

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.

The combination of artificial intelligence algorithms and numerical methods has recently become popular in the prediction of macroscopic and microscopic hydrodynamics parameters of bubble column reactors. The multi inputs and outputs machine learning can cover small phase interactions or large fluid behavior in industrial domains. This numerical combination can develop the smart multiphase bubble column reactor with the ability of low-cost computational time. It can also decrease case studies for the optimization process when big data is appropriately used during learning. There are still many model parameters that need to be optimized for a very accurate artificial algorithm, including data processing and initialization, the combination of inputs and outputs, number of inputs and model tuning parameters. For this study, we aim to train four inputs big data during learning process by an adaptive neuro-fuzzy inference system or adaptive-network-based fuzzy inference system (ANFIS) method, and we consider the superficial gas velocity as one of the input variables, while for the first time, one of the computational fluid dynamics (CFD) outputs named gas velocity is used as an output of the artificial algorithm. The results show that the increasing number of input variables improves the intelligence of the ANFIS method up to , and the number of rules during learning process has a significant effect on the accuracy of this type of modeling. The results also show that propper selection of model parameters results in more accuracy in prediction of the flow characteristics in the column structure.

A computational simulation of a PT6A gas turbine engine operating at off-design conditions is described in the present article. The model consists of a 0-dimensional thermo-fluidic description of the engine by applying the mass, linear momentum, angular momentum, and energy balances in each engine's component. The transient behavior of the engine is simulated for different blends of the original JET-A1 fuel with bio-diesel. Simulated thermodynamic variables of the air at each engine's component, as well as some performance parameters correspond to the reported experimental measurements. The numerical results also demonstrate the ability of the computational simulation to predict acceptable fuel blends, such that the efficiency of the engine is maximized and its structural integrity is maintained.

In this work we discuss the insights from activity landscape, docking and molecular dynamics towards the understanding of the structure-activity relationships of dual inhibitors of major epigenetic targets: lysine metiltransferase (G9a) and DNA metiltranferase 1 (DNMT1). The study was based on a novel data set of 50 published compounds with reported experimental activity for both targets. The activity landscape analysis revealed the presence of activity cliffs, e.g., pairs of compounds with high structure similarity but large activity difference. Activity cliffs were further rationalized at the molecular level by means of molecular docking and dynamics simulations that led to the identification of interactions with key residues involved in the dual activity or selectivity with the epigenetic targets.

Nanoparticles -- regularly patterned or randomly dispersed -- are a key ingredient for emerging technologies in photonics. Of particular interest are scattering and field enhancement effects of metal nanoparticles for energy harvesting and converting systems. An often neglected aspect in the modeling of nanoparticles are light interaction effects beyond classical electrodynamics stemming from electron dynamics in confined and accelerated systems. We give a detailed account on free electron phenomena in metal nanoparticles and discuss analytic expressions, stemming from microscopic and semi-classical theories. These can improve standard computational schemes to produce more reliable results on the optical properties of metal nanoparticles. We combine these solutions into a single framework and study their joint impact on isolated Au, Ag, and Al nanoparticles as well as dimer structures.

This paper presents an overview of the principal structural and dynamics characteristics of reverse micelles (RMs) in order to highlight their structural flexibility and versatility, along with the possibility to modulate their parameters in a controlled-manner. The multifunctionality in a large range of different scientific fields is exemplified in two distinct directions: a theoretical model for mimicry of biological microenvironment and practical application in the field of nanotechnology and nano-based sensors. RMs represents a convenient experimental approach that limits the drawbacks of the conventionally biological studies in vitro, while the particular structure confers them the status of simplified mimics of cells by reproducing a complex supramolecular organization in an artificial system. The biological relevance of RMs is discussed in some particular cases referring to the confinement and crowding environment, molecular dynamics of water and cell membrane structure. The use of RMs in different range of applications seems to be more promising due to their structural and compositional flexibility, a high efficiency and selectivity being achieved. The advance in nanotechnology is based on developing new methods of nanomaterials synthesis and deposition. This review highlighting the advantages of using RMs in synthesis of nanoparticles with specific properties and in nano (bio)sensors design.

InGaN/GaN samples grown on c-plane sapphire substrate with different In concentrations by metal organic chemical vapor deposition are demonstrated. The subsequent capping GaN layer growth opens a possibility for dislocation reduction due to the lateral strain relaxation in growth geometry. We present the further growth optimization and innovative characterization of InGaN layers overgrown on different structures with varying In concentrations. The photoelectrical and optical properties of the InGaN layers with or without capping GaN layer were investigated by time-resolved picosecond transient grating and temperature dependence photoluminescence. We note a 10-fold increase in carrier lifetime in the InGaN layers when the sample structure changes from PIN to single InGaN layer.

The Finite size Lyapunov exponent (FSLE) has been used extensively since the late 1990’s to diagnose turbulent regimes from Lagrangian experiments and to detect Lagrangian coherent structures in geophysical flows and two-dimensional turbulence. Historically, the FSLE was defined in terms of its computational method rather than via a mathematical formulation, and the behavior of the FSLE in the turbulent inertial ranges is based primarily on scaling arguments. Here we propose an exact definition of the FSLE based on conditional averaging of the finite amplitude growth rate (FAGR) of the particle pair separation. With this new definition, we show that the FSLE is a close proxy for the inverse structural time, a concept introduced a decade before the FSLE. The (in)dependence of the FSLE on initial conditions is also discussed, as well as the links between the FAGR and other relevant Lagrangian metrics, such as the finite time Lyapunov exponent and the second order velocity structure function.

Wave energy converter (WEC) arrays deployed in coastal regions may create physical disturbances potentially resulting in environmental stresses. Presently, limited information is available on the nature of these physical disturbance or the resultant effects. A quantitative Spatial Environmental Assessment Tool (SEAT) for evaluating potential effects of wave energy converter (WEC) arrays on nearshore hydrodynamics and sediment transport is presented for the central Oregon coast (USA) through coupled numerical model simulations of an array of WECs. Derived climatological wave conditions were used as inputs to the model to allow for the calculation of risk metrics associated with various hydrodynamic and sediment transport variables such as maximum shear stress, bottom velocity, and change in bed elevation. The risk maps provided simple, quantitative, and spatially-resolved means of evaluating physical changes in the vicinity of a hypothetical WEC array in response to varying wave conditions. Near-field risk of sediment mobility was determined to be moderate in the lee of the densely spaced array, where the potential for increased sediment deposition could result in benthic habitat alteration. Modifications to the nearshore sediment deposition and erosion patterns were observed near headlands and topographic features, which could have implications for littoral sediment transport. The results illustrate the benefits of a risk evaluation tool for facilitating coastal resource management at early market marine renewable energy sites.

In this effort we propose a data-driven learning framework for reduced order modeling of fluid dynamics. Designing accurate and efficient reduced order models for nonlinear fluid dynamic problems is challenging for many practical engineering applications. Classical projection-based model reduction methods generate reduced systems by projecting full-order differential operators into low-dimensional subspaces. However, these techniques usually lead to severe instabilities in the presence of highly nonlinear dynamics, which dramatically deteriorates the accuracy of the reduced-order models. In contrast, our new framework exploits linear multistep networks, based on implicit Adams-Moulton schemes, to construct the reduced system. The advantage is that the method optimally approximates the full order model in the low-dimensional space with a given supervised learning task. Moreover, our approach is non-intrusive, such that it can be applied to other complex nonlinear dynamical systems with sophisticated legacy codes. We demonstrate the performance of our method through the numerical simulation of a two-dimensional flow past a circular cylinder with Reynolds number Re = 100. The results reveal that the new data-driven model is significantly more accurate than standard projection-based approaches

I present an experimental paradigm to explore the interpersonal dynamics generating a collective mind. I hypothesized that collective organization is based on dual interpersonal modes: (1) symmetrical and (2) anti‑symmetrical. I specified the geometric topology of these modes by detecting the spatiotemporal patterns that embed cooperative agents in a three‑dimensional matrix. I found that the symmetrical mode is executed automatically and without guidance. Conversely, the anti‑symmetrical mode required explicit direction and recruited attention for execution. I demonstrate that self‑other mirror‑symmetry stabilized group dynamics, enabled fast and efficient symmetrical imitation that optimized information transmission, whereas anti‑symmetrical imitation was comparatively slow, inefficient, and unstable. I determined that the anti‑symmetrical mode spontaneously transitioned to the symmetrical mode under perturbations. Crucially, this renormalization mechanism never transitioned from symmetrical to anti‑symmetrical. These self-organizing dynamics speak to interpersonal symmetry‑breaking. In the present work, spontaneous group choice mandated that agents synchronize cooperative cycles in symmetrical space under internal or external perturbations. I provide examples to illustrate that this self-regulating pullback attractor manifests in invertebrates and vertebrates alike. I conclude by suggesting that inter‑agent symmetry provides the social stability manifold through which attention-driven interactions enable intrapersonal and interpersonal change.

Full-order state-space models represent the starting point for the development of advanced control methods for wind turbine systems (WTSs). Regarding existing control-oriented WTS models, two research gaps must be noted: (i) There exists no full-order WTS model in form of one overall ordinary differential equation that considers all dynamical effects which significantly influence the electrical power output; (ii) all existing reduced-order WTS models are subject to rather arbitrary simplifications and are not validated against a full-order model. Therefore, in this paper, two full-order nonlinear state-space models (of 11th and 9th-order in the (a, b, c)- and (d, q)-reference frame, resp.) for variable-speed variable-pitch permanent magnet synchronous generator WTSs are derived. The full-order models cover all relevant dynamical effects with significant impact on the system’s power output, including the switching behavior of the power electronic devices. Based on the full-order models, by a step-by-step model reduction procedure, two reduced-order WTS models are deduced: A non-switching (averaging) 7th-order WTS model and a non-switching 3rd-order WTS model. Comparative simulation results reveal that all models capture the dominant system dynamics properly. The full-order models allow for a detailed analysis covering the high frequency oscillations in the instantaneous power output due to the switching in the power converters. The reduced-order models provide a time-averaged instantaneous power output (which still correctly reflects the energy produced by the WTS) and come with a drastically reduced complexity making those models appropriate for large-scale power grid controller design.

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(2^2d) for 2d-partite two-level systems into 2^2d-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 2^2d-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.

Most mature companies have started some kind of “transformation”, either digital, or agile transformations, to cope with changes in the environment, yet most fail, ending up delivering nothing or just one more reorganization. We postulate that considering the Organization as a self-aware Complex Adaptative System (CAS) is paramount, as the common conception (Industrial: mechanistic and predictive) results in bringing the systems in a frozen or defensive mode. Stimulating the system enables us to use its adaptative power to develop new capabilities, and all layers should be tackled simultaneously, to prevent the system from collapsing back into its original state. To ensure this, it is necessary to create a seed per level, and a mechanism to propagate the transformation, with a focus on development instead of growth, that is qualitative change rather than quantitative. A common vocabulary should also be provided, so conversations can occur at every level. Finally, changing mindsets is key, and both concepts and techniques should be provided as enablers to the adequate mindset level. We detail one such transformation that resulted in distributed leadership and more intrinsic motivation, providing both an account of the transformation itself and a model to read it.

Sustainable consumption became the community’s attention as the respond of worrying consumption growth direction that tends to excessively exploit nature without considering the continuity of the next generation. Take into account the growing coffee consumption in Indonesia, this article tries to prove whether the connoisseur consumers (CCs) are capable to mediate dynamics capabilities (DCs) of single origin coffee shops (SOCSs) and to encourage the consumption sustainability. In-depth interview to 30 SOCS managers, 60 baristas and 450 consumers, it is found that CCs are capable of supporting the business continuity of SOCSs because they are loyal consumers with the contribution of more than 20% from the total consumers. Correlation testing between connoisseurs’ attributes and the number of visits also shows positive value. It means there is a significant relationship. In addition, related to the sustainability attribute, the existence of CCs has encouraged the practice of consumption sustainability. At the same time, CCs are capable to moderate SOCSs to improve sensing, seizing, and transforming shop management to put up with the competition. Based on the above findings, CCs are moderating SOCSs in improving their DCs to be more potential in improving the sustainable consumption of coffee commodity in the future.

In this paper, an attempt has been made to analyze the effect of spool port/ groove geometry on the pressure drop and chamber pressures which effect the performance parameters of the flow distributor valve. The work mainly involves formulation of detailed mathematical model of the valve and compare them on the same platform. For mathematical modelling, Matlab has been used. The size of the orifices is considered same throughout the model for better comparison. Initially the construction and functioning of flow distributor valve along with working principles of hydrostatic motor (Rotary Piston) is shown. Next shown the analytical analysis of area change and pressure drops due to different geometry of the spool valve ports. After that the computational fluid dynamics (CFD) analysis has been shown. A complete mathematical model to describe such flow distributor valve is developed after having a comprehensive knowledge of orifice characteristics, flow interactions based on valve geometry. Equations of flow through different orifices (fixed and variable area) of the valve have been developed based on the relationships obtained earlier.

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.

This study aims to explore the possibility of estimating a multitude of kinematic and dynamic quantities using subject-specific musculoskeletal models in real-time. The framework was designed to operate with marker-based and inertial measurement units enabling extensions far beyond dedicated motion capture laboratories. We present the technical details for calculating the kinematics, generalized forces, muscle forces, joint reaction loads, and predicting ground reaction wrenches during walking. Emphasis was given to reduce computational latency while maintaining accuracy as compared to the offline counterpart. Notably, we highlight the influence of adequate filtering and differentiation under noisy conditions and its importance for consequent dynamic calculations. Real-time estimates of the joint moments, muscle forces, and reaction loads closely resemble OpenSim's offline analyses. Model-based estimation of ground reaction wrenches demonstrates that even a small error can negatively affect other estimated quantities. An application of the developed system is demonstrated in the context of rehabilitation and gait retraining. We expect that such a system will find numerous applications in laboratory settings and outdoor conditions with the advent of predicting or sensing environment interactions. Therefore, we hope that this open-source framework will be a significant milestone for solving this grand challenge.

Molecular Dynamics (MD) simulations model motion of molecules in atomistic detail and aid in drug design. While simulations on large systems may require several days to complete, analysis of terabytes of data generated in the process could also be time consuming. Recent studies captured exciting and dramatic drug-receptor interactions under cell-like complex conditions. Such advances make simulations of biomolecular interactions more realistic, insightful, and informative and have potential to make drug design more realistic. However, currently available resources and techniques do not provide, in reasonable time, a comprehensive understanding of events seen in simulations. We demonstrate that big data approach results in significant speedups, and provides rapid insights into simulations performed. Advancing this improvement, we propose a scalable, self-tuning, and responsive framework based on Cloud-infrastructure to accomplish the best possible MD studies with given priorities and within available resources.

Culture exploits the acquisition of meaningful content by crafting regimes of shared attention, determining what is relevant, valuable, and salient. Culture changes the field of relevant social affordances worthy of being acted upon in a context-sensitive manner. When relevant affordances are highly weighted, their attentional capture and their salience increase the probability of them being enacted due to the associated expectation for minimizing prediction error. This process is known as active inference. In the digital era, individuals need to infer the action-related attributes of digital cues, here characterized as digital affordances. The digital affordances of digital social platforms are of particular interest here. Digital social affordances are defined as online possibilities of social interactions. By their own nature, these are salient because they are related to social interactions and relevant social cues. However, the problem of digital social platforms is that they are not equivalent to situated social interactions because their structure is built, mediated, and defined by third-parties with diverse interests. The third-parties behind the digital social platforms are using the same mechanism exploited by culture to manipulate the shared patterns of attention. Moreover, digital social platforms are deliberately designed to be hyper-stimulating, making digital social affordances highly rewarding and increasingly salient. This appropriation, for economic purposes, is an issue of great importance, especially as the COVID-19 pandemic brought deep global changes, pushing societies to an online digital way of life. Here, we examined different types of digital social affordances under an active inference view, placing them into two categories, those for self-identity formation, and those for belief-updating. This paper aims to analyze digital social affordances in light of the prediction error dynamics they might elicit to their users. Although each of the analyzed digital social affordances allows different epistemic and instrumental digital actions, they all share the characteristic of having an "easy" and a fast expected rate of error reduction. Here, we aim to provide a new hypothesis about how the design behind digital social affordances is built on our natural attractiveness to minimize prediction error and the resulting positive embodied feelings when doing so. Finally, it is suggested that because digital social affordances are becoming highly weighted in the field of affordances, this might be putting at risk our context-sensitive grip on a rich, dynamic and varied field of relevant affordances.

A new formulation for a proposed solution to the 3D Navier-Stokes Equations in cylindrical co-ordinates coupled to the continuity and level set convection equation is presented in terms of an additive solution of the three principle directions in the radial, azimuthal and z directions of flow and a connection between the level set function and composite velocity vector for the additive solution is shown. For the case of a vertical tube configuration with small inclination angle, results are obtained for the level set function defining the interface in both the radial and azimuthal directions. It is found that the curvature dependent part of the problem alone induces sinusoidal azimuthal interfacial waves wheras when the curvature together with the equation for the composite velocity is considered oscillating radial interfacial waves occur. The implications of two extremes indicate the importance of looking at the full equations including curvature.

The COVID-19 pandemic of 2020 changed the way we interact and engage in commerce at a fundamental level. Social distancing and stay-at-home orders leave businesses and cities wondering what economic activity will look like in the future. Given a likely reduction in face-to-face interactions, it is important to better understand how social interactivity influences economic outcomes. Here we measure the effect of social interactions in the workforce on patent production and economic efficiency. We decompose U.S. occupations into individual work activities, determine which of those activities are associated with face-to-face interactions, and reaggregate the labor force of each U.S. metropolitan statistical area (MSA) into a metric of social interactiveness. We then calculate each MSA’s density of social work activities and find that this measure is more highly correlated with an MSA’s per capita patent production than simple population density. This suggests that density of face-to-face interactions is the important driver of a city’s rate of invention. We close by exploring analogies between the development of cities and the development of stars, suggesting ways these analogies may help frame future research on cities.

Amorphous solid dispersions are considered a promising formulation strategy for the oral delivery of poorly soluble drugs. The limiting factor for the applicability of this approach is the physical (in)stability of the amorphous phase in solid samples. Minimizing the risk of reduced shelf life for a new drug by establishing a suitable excipient/polymer-type from first principles would be desirable to accelerate formulation development. Here we perform Molecular Dynamics simulations to determine properties of blends of eight different polymer-small molecule drug combinations for which stability data is available from a consistent set of literature data. We calculate thermodynamic factors (mixing energies) as well as mobilities (diffusion rates and roto-vibrational fluctuations). We find that either of the two factors, mobility and energetics, can determine the relative stability of the amorphous form for a given drug. Which factor is rate limiting depends on physico-chemical properties of the drug and the excipients/polymers. The methods outlined here can be readily employed for an in-silico pre-screening of different excipients for a given drug to establish a qualitative ranking of the expected relative stabilities, thereby accelerating and streamlining formulation development.

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.

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.

In the present study, we compare energy transition scenarios from a new set of Integrated Assessment Models, the suite of MEDEAS models, based on a systems dynamic modelling approach, with scenarios from two already well know structurally and conceptually different Integrated Assessment Models, the Integrated MARKAL-EFOM System (TIMES) and the Long-range Energy Alternatives Planning system (LEAP). The investigation was carried out to cross-compare and benchmark the response of MEDEAS models with TIMES and LEAP in depicting the energy transition in two different countries, Austria and Bulgaria. The preliminary results show a good agreement across all the models in representing scenarios projecting historical trends, while a major discrepancy is detectable when the rate of implementation of renewable energy is forced to increase to achieve energy system decarbonization. The discrepancy is mainly traceable to the differences in the models’ conception and structures rather than in a real mismatch in representing the same scenarios. The present study is put forward as a guideline for validating new modelling approaches that link energy policy decision tools to the global biophysical and socioeconomic constraints.

Purification of biologically-derived therapeutics is a major cost contributor to the production of this rapidly growing class of pharmaceuticals. Monoclonal antibodies comprise a large percentage of these products therefore new antibody purification tools are needed. Small peptides, as opposed to traditional antibody affinity ligands such as Protein A, may have advantages in stability and production costs. Multiple heptapeptides that demonstrate Fc binding behavior that have been identified from a combinatorial peptide library using M13 Phage Display are presented herein. Seven unique peptide sequences of diverse hydrophobicity and charge were identified. All seven peptides showed strong binding to the four major human IgG isotypes, human IgM, as well as binding to canine, rat, and mouse IgG. These seven peptides were also shown to bind human IgG4 from DMEM cell culture media with 5% FCS and 5 g/L ovalbumin present. These peptides may be useful as surface ligands for antibody detection and purification purposes. Molecular docking and classical molecular dynamics (MD) simulations were conducted to elucidate the mechanisms and energetics for the binding of these peptides to the Fc region. The binding site was found to be located between the two glycan chains inside the Fc fragment. Both hydrogen bonding and hydrophobic interactions were found to be crucial for the binding interactions. Excellent agreement for the binding strength was obtained between experimental results and simulations.

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.

Remote sensing (RS) has been widely adopted as a tool to investigate several biotic and abiotic factors, directly and indirectly, related to biodiversity conservation. European grasslands are one of the most biodiverse habitats in Europe. Most of these habitats are subject to priority conservation measure, and they are threatened by several human induced process. The broad expansions of few dominant species are widely reported as drivers of biodiversity loss. In this context, using Sentinel-2 (S2) images, we investigate the distribution of one of the most spreading species: <i>Brachypodium genuense</i>. We performed a binary Random Forest (RF) classification of <i>B. genuense</i> using a RS image and field sampled presence/absence points. Then, we integrate the occurrences obtained from RS classification into niche models to identify the topographic drivers of <i>B. genuense</i> distribution. Lastly, the impact of <i>B. genuense</i> distribution in the N2k habitats was assessed by overlay analysis. The RF classification process detected <i>B. genuense</i>'s cover with an overall accuracy of 91.18%. The integration of RS and topographic niche models shows that the most relevant topographic variables that influence the distribution of <i>B. genuense</i> are slope, elevation, solar radiation and Topographic Wet Index (TWI) in order of importance. The overlay analysis shows that 74.04% of the <i>B. genuense</i> identified in the study area falls on the semi-natural dry grasslands. The study highlights the importance of the RS classification and the topographic niche models as an integrated approach for mapping a broad-expansion species such as <i>B. genuense</i>. The coupled techniques presented in this work should be applicable to other plant communities with remotely recognizable characteristics for more effective management of N2k habitats.

This review summarises the main numerical models of fuel droplet heating and evaporation (DHE) in combustion engines across the different scales by accessing the nano/micro, meso and macroscopic fluid elements. The phenomena of multi-physics, multi-scale and multi-phase fluid flow and heat transfer are fully investigated when the fuel droplet (dodecane) is heating and evaporated into a background gas (nitrogen) crossing the liquid-vapour (LV) interface, kinetic region (i.e., Knudsen layer) and the bulk regions of liquid and gas in terms of molecular dynamics (MD) simulations, kinetic theory modelling (i.e., direct numerical solutions of Boltzmann equations) and convectional fluid dynamics approach, respectively. The evaporation coefficient of fuel evaporating molecules and their velocity distributions at the LV interface derived from MD simulations formulate a new kinetic boundary condition (KBC). Moreover, a novel kinetic model considering the inelastic collision between fuel molecules alongside the new KBC enables us to describe the non-equilibrium gas dynamics of fuel vapour and gas mixture in Knudsen layer (KL). Heat and mass flux analysis of the fuel droplet under combustion engine conditions can be accurately assessed by implementing the inelastic collision between fuel molecules in KL and a temperature-dependent evaporation coefficient at the LV interface into DHE. The surface temperature of fuel droplet and its evaporation time, which play a significant role in resolving the ignition delay and hence the combustion phasing in engines, can also be well estimated. The multi-scale modelling of fuel DHE will make significantly potential input into the cleaner engine targeting the low-carbon emissions and enhance the capability of the existing computational fluid dynamics (CFD) solvers.

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.

Utility perceived by individuals is believed to be different from the utility experienced by that individual. System dynamicists implicitly categorize this phenomenon as a form of bounded rationality and traditionally employ a simple smoothing function to capture it. We challenge this generalization by testing it against an alternative formulation of utility perception that is suggested by modern theories of behavioral economics. In particular, the traditional smoothing formulation is compared with the peak-end rule in a simple theoretical model as well as in a medium-size model of electronic health record implementation. Experimentation with the models reveals that the way utility perception is formulated is important and might affect behavior and policy implications of system dynamics models.

Chlorotoxin (CTX) is a 36–amino acid peptide with 8 Cys residues that forms four Cys-Cys bonds. It has high affinity for the glioma-specific chloride channel and matrix metalloprotease-2. Structural and binding properties of CTX analogs with various Cys residue substitutions with L-a-aminobutyric acid (Abu) have been previously reported. Using 4.2 ìs molecular dynamics, we compared the conformational and essential space sampling of CTX and analogs [Abu/Ser^2,19]CTX, [Abu/Ser^5,28]CTX, [Abu/Ser^16,33]CTX, [Abu/Ser^20,35]CTX, and [Abu/Ser^{2,5,16,19,20,28,33,35}]CTX. The native and substituted peptides maintained a high degree of a-helix propensity from residues 8 through 21, with the exception of [Ser^5,28]CTX and [Abu^16,33]CTX. In agreement with previous circular dichroism spectropolarimetry results, the C-terminal b-sheet content varied less from residues 25 through 29 and 32 through 36 and was well conserved in all analogs, except: [Abu^16,33]CTX, [Ser^20,35]CTX, [Abu^{2,5,16,19,20,28,33,35}]CTX, and [Ser^{2,5,16,19,20,28,33,35}]CTX. The Cys¹⁶-Cys³³ and Cys²⁰-Cys³⁵ Cys-Cys bonds appear to be required to maintain the ab-motif of CTX. Their selective substitution with Ser^16,33 however, may mitigate the destabilizing effect of Cys¹⁶-Cys³³ substitution by the formation of an inter residue H-bond from OgH of Ser¹⁶ to OgH of Ser³³ bridged by a water molecule. All peptides shared considerable sampled conformational space, which explains the retained receptor binding of the nonnative analogs.

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.

To investigate the optimum layouts of small vertical axis wind turbines, a two-dimensional analysis of dynamic fluid body interaction is performed via computational fluid dynamics for a rotor pair in various configurations. The rotational speed of each turbine rotor (diameter: D = 50 mm) varies based on the equation of motion. First, the dependence of rotor performance on the gap distance (gap) between two rotors is investigated. For parallel layouts, counter-down (CD) layouts with blades moving downwind in the gap region yield a higher mean power than counter-up (CU) layouts with blades moving upwind in the gap region. CD layouts with gap/D = 0.5–1.0 yield a maximum average power that is 23% higher than that of an isolated single rotor. Assuming isotropic bidirectional wind speed, co-rotating (CO) layouts with the same rotational direction are superior to the combination of CD and CU layouts regardless of the gap distance. For tandem layouts, the inverse-rotating configuration (IR) shows an earlier wake recovery than the CO configuration. For 16-wind-direction layouts, both the IR and CO configurations indicate similar power distribution at gap/D = 2.0. For the first time, this study demonstrates the phase synchronization of two rotors via numerical simulation.

Micro-plasma is generated in ultra-high-pure hydrogen gas filled inside a cell at a pressure of (1.08 ± 0.033) × 10⁵ Pa (810 ± 25 Torr) by using a Q-switched Nd:YAG laser device operated at 1064 nm wavelength and 14 ns pulse duration. Micro-plasma emission spectra of the hydrogen Balmer alpha line, H_α, are recorded with a Czerny-Turner type spectrometer and an intensified charge-coupled device. The spectra are calibrated for wavelength and corrected for detector sensitivity. During the first few tens of nanoseconds after initiating optical breakdown, significantly Stark-broadened and Stark-shifted H_α lines mark the well-above hypersonic outward expansion. The vertical diameters of the spectrally resolved plasma images are measured for time delays of 10 ns to 35 ns to determine expansion speeds of the order of 100 km/s to 10 km/s. For time delays of the order of 0.5 µs to 1 µs, the expansion decreases to the speed of sound of 1.3 km/s in the near ambient temperature and pressure hydrogen gas.

Land degradation a serious and nationwide environmental concern in Ethiopia. The problem is its iterative relationship between land degradation, climate change, and agriculture, exacerbating one another via negative and positive feedback loops. Due to the need for an efficient response to land degradation in the country, different sustainable land management practices have been implemented since the late 1980s. The objective of this study was to analyze land degradation neutrality status using remote sensing data in the study area. We have studied the land degradation neutrality conditions of the North Wello Zone by using indicators data, namely land cover change, land productivity dynamics, and soil organic carbon stock. The result shows that the settlement areas consistently expanded at the fifth speed (2010-2018) from 1995 to 2010. Between 1995 and 2010, forestland declined by 18 percent, while an increasing trend of 26.8 percent from 2010 to 2018. The assessment results also indicate that 52.8 percent of the total area is stable and characterized by less stressed land productivity. The soil organic carbon is comparatively abundant in the high and midland vegetation areas but very thin in lowland areas. Most of the highland and midland parts of the study areas are in the conditions of stable and increasing land productivity with high biomass and soil organic content. However, most lowland areas showed a decline in land productivity conditions.

We used atomistic molecular dynamics (MD) simulations to study polyelectrolyte brushes based on anionic α-L-glutamic acid and α-L-aspartic acid grafted on cellulose in the presence of divalent CaCl2 salt at different concentrations. The motivation is the search of the ways to control properties such as sorption capacity and the structural response of the brush to multivalent salts. For this detailed understanding of the role of side chain length, chemical structure and their interplay is required. It was found that in the case of glutamic acid oligomers, the longer side chains facilitate attractive interactions with the cellulose surface, which forces the grafted chains to lie down on the surface. The additional methylene group in the side chain enables side chain rotation enhancing this effect. On the other hand, the shorter and more restricted side chains of aspartic acid oligomers prevent attractive interactions to a large degree and push the grafted chains away from the surface. The difference in side chain length also leads to differences in other properties of the brush in divalent salt solutions. At a low grafting density, the longer side chains of glutamic acid allow the adsorbed cations to be spatially distributed inside the brush resulting in a charge inversion. With an increase in grafting density, the difference in the total charge of the aspartic and glutamine brushes disappears, but new structural features appear. The longer sides allow for ion bridging between the grafted chains and the cellulose surface without a significant change in main chain conformation. This leads to the brush structure being less sensitive to changes in salt concentration.

Keyhole laser beam welding (LBW) of stainless steel sheets with a gap in between is numerically simulated with a three-dimensional, transient multi-physical model for laser material processing. At first, the model’s ability to reproduce experimental results on a relatively coarse computational mesh within reasonable computing time, so as to serve as process optimization tool, is presented. An example of process optimization, where a given set of weld seam quality criteria is fulfilled by iteratively optimizing a secondary laser beam, is shown. The relatively coarse mesh, in combination with a good model calibration to the experimental conditions, allows for sufficiently fast simulations to use this approach for optimization tasks. Finally, using a finer spatial and temporal discretization, the dynamic processes in the vicinity of the keyhole leading to the formation of pores are investigated. The physical phenomena predicted by the simulation are coherent with experimental observations found in literature.

This review presents an updated overview of research concerning Leishmania protein structures, primarily sourced from the Protein Data Bank (PDB), that play a role in the metabolic pathways of the Leishmania parasite. Furthermore, we assess the current progress in the identification and development of bioactive chemical agents aimed at addressing this substantially overlooked tropical disease. We have analyzed experimental data obtained from in vitro, in vivo and in silico sources. This data has been categorized into four main areas: a) vector taxonomy and geographic distribution; b) parasite taxonomy and geographic distribution; c) enzymatic functions of proteins engaged in parasite/host interactions throughout various developmental stages (such as oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases, and cytokines); and d) established and experimental treatments employing bioactive chemical compounds. Our objective is to establish a foundational point of reference for research efforts concentrating on the elucidation of interaction mechanisms and the processes of ligand-protein activation/inactivation, specifically linked to Leishmania infections. Consequently, we emphasize enzymes recognized for their involvement in the biochemical pathways incited during Leishmania infection episodes. This review encapsulates the current understanding, offering insights to inform and direct future explorations aimed at targeting proteins and pathways to enhance the management of Leishmania-related diseases.

Matrix Metaloproteinase-2 (MMP-2) is an extracellular Zn²⁺ protease specific to type I and IV collagens. Its expression is associated with several inflammatory, degenerative, and malignant diseases. Conformational properties, domain movements, and interactions between MMP-2 and its associated metal ions were characterized using a 1.0 µs molecular dynamics simulation. Dihedral principle component analysis revealed 10 families of conformations with the greatest degree of variability occurring in the link region connecting the catalytic and hemopexin domains. Dynamics cross correlation analysis indicated domain movements corresponding to opening and closing of the hemopexin domain in relation to the fibronectin and catalytic domains facilitated by the link region. Interaction energies were calculated using the MMPBSA-interaction entropy analysis method and revealed strong binding energies for the catalytic Zn²⁺ ion 1, Ca²⁺ ion 1, and Ca²⁺ ion 3 with significant conformational stability at the binding sites of Zn²⁺ ion 1 and Ca²⁺ ion 1. Ca²⁺ ion 2 diffuses freely away from its crystallographically defined binding site. Zn²⁺ ion 2 plays a minor role in conformational stability of the catalytic domain while Ca²⁺ ion 3 is strongly attracted to the highly electronegative sidechains of the Asp residues around the central β-sheet core of the hemopexin domain.

ND1 subunit possesses the majority of the inhibitor binding domain of the human MRC-I. This is an attractive target for the search for new inhibitors that seek mitochondrial dysfunction. It is known, from in vitro experiments, some metabolites from Annona muricata called acetogenins have important biological activities such as anticancer, antiparasitic, and insecticide. Previous studies propose an inhibitory activity of bovine MRC-I by bis-THF acetogenins such as annocatacin B, however, there are few studies on its inhibitory effect on human MRC-I. In this work, we evaluate the molecular and energetic affinity of the annocatacin B molecule with the human ND1 subunit in order to elucidate its potential capacity to be a good inhibitor of this subunit. For this purpose, QM optimizations, MD simulations and MM/PBSA analysis were performed. As a control to compare our outcomes, the molecule rotenone, which is a known MRC-I inhibitor, was chosen. Our results show that annocatacin B has a greater affinity for the ND1 structure, its size and folding were probably the main characteristics that contributed to stabilize the molecular complex. Furthermore, the MM/PBSA calculations showed a 35% stronger BFE compared to the rotenone complex. Detailed analysis of the BFE shows that the aliphatic chains of annocatacin B play a key role in molecular coupling by distributing favorable interactions throughout the major part of the ND1 structure. These results are consistent with experimental studies that mention that acetogenins may be good inhibitors of MRC-I.

Mitochondria are essential to cell homeostasis, and alterations in mitochondrial distribution, segregation or turnover have been linked to complex pathologies such as neurodegenerative diseases or cancer. Understanding how these functions are coordinated in specific cell types is a major challenge to discover how mitochondria globally shape cell functionality. In this review, we will first describe how mitochondrial transport and dynamics are regulated throughout the cell cycle in yeast and in mammals. Second, we will explore the functional consequences of mitochondrial transport and partitioning on cell proliferation, fate acquisition, stemness, and on the way cells adapt their metabolism. Last, we will focus on how mitochondrial clearance programs represent a further layer of complexity for cell differentiation, or in the maintenance of stemness. Defining how mitochondrial transport, dynamics and clearance are mutually orchestrated in specific cell types may help our understanding of how cells can transition from a physiological to a pathological state.

For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because of temporal and spatial discontinuity problems. To overcome these problems, in a previous study, we proposed a corrective QM/MM method, size-consistent multipartitioning (SCMP) QM/MM, and successfully demonstrated that, using SCMP, it is possible to perform stable molecular dynamics simulations by effectively taking into account solvent quantum chemical effects. The SCMP method is characterized by two original features: size-consistency of a QM region among all QM/MM partitioning and partitioning update. However, in our previous study, the performance was not fully elicited compared to the theoretical upper bound, and the optimal partitioning update protocol and parameters were not fully verified. To elicit the potential performance, in the present study, we simplified the theoretical framework and modified the partitioning protocol.