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• Integrated and multi-functional energy storage devices with excellent mechanical properties are fabricated. • The integrated paper-based supercapacitor displays ultrahigh areal specific capacitance. • The integrated paper-based supercapacitor shows excellent sensing and humidity power generation characteristics. • Zn2+ conductivity and transport mechanism are investigated by molecular dynamics simulation. The demand for flexible electric heating devices has increased due to technology advancement and improved living standards. These devices have various applications including personal thermal management, hyperthermia, defrosting, agricultural heating film, and oil-water separation. Joule heat, generated by electric currents, is commonly used in electrical appliances. To incorporate Joule heating into flexible electronics, new materials with excellent mechanical properties are necessary. Traditional polymers, used as reinforcements, limit the continuity of conductive networks in composites. Therefore, there is a need to develop flexible Joule thermal composite materials with enhanced mechanical strength and conductivity. Cellulose, a widely available renewable resource, is attracting attention for its excellent mechanical properties. It can be used as a dispersant and reinforcing agent for conductive fillers in cellulose-based composites, creating highly conductive networks. Various forms of cellulose, such as wood, nanocellulose, pulp fiber, bacterial cellulose, cellulose paper, textile clothing, and aramid fiber, have been utilized to achieve high-performance Joule thermal composites. Researchers have achieved excellent mechanical properties and developed efficient electric heating devices by designing cellulose-based composites with different structures. The scalable production methods enable large-scale application of cellulose-based devices, each with unique advantages in 1D, 2D, and 3D structures. This review summarizes recent advancements in cellulose-based Joule thermal composites, providing insights into different structural devices, and discussing prospects and challenges in the field. [Display omitted] [ABSTRACT FROM AUTHOR]

Researchers from the College of Engineering and Technology in Tamil Nadu, India, conducted a study on potential inhibitors of the multidrug efflux pump mepA in Helicobacter pylori, a Gram-negative bacterium that infects the human gastrointestinal mucosa. Through in-silico approaches like molecular docking and molecular dynamics simulations, they identified three natural compounds with high binding affinities towards mepA, suggesting their potential to inhibit the efflux pump and enhance antibiotic action against multidrug-resistant pathogens. The study highlights the promise of these compounds in developing novel therapeutic strategies. For more information, readers can refer to the Chemical Papers journal. [Extracted from the article]

In this paper, we introduce the concept of principal paths in data space; we show that this is a well-characterized problem from the point of view of cognition, and that it can lead to salient insights in the analyzed data enabling topological/holistic descriptions. These paths, interestingly, can be interpreted as local principal curves, and in this paper, we suggest that they are analogous to what, in the statistical mechanics realm, are called minimum free-energy paths. Here, we move that concept from physics to data space and compute them in both the original and the kernel space. The algorithm is a regularized version of the well-known $k$ -means clustering algorithm. The regularization parameter is derived via an in-sample model selection process based on the Bayesian evidence maximization. Interestingly, we show that this choice for the regularization parameter consistently leads to the same manifold even when changing the number of clusters. We apply the method to common data sets, dynamical systems, and, in particular, to molecular dynamics trajectories showing the generality, the usefulness of the approach and its superiority with respect to other related approaches. [ABSTRACT FROM AUTHOR]

A recent study by researchers at the University of Arizona College of Medicine - Phoenix and the University of California Davis Health has identified a new therapeutic target for treating atrial fibrillation (AFib), a common heart rhythm disorder. The study focused on the regulation of small-conductance calcium-activated potassium channels (SK channels) by phosphatidylinositol 4,5-bisphosphate (PIP2), a lipid found in cell membranes. The research provides insights into potential mechanisms for treating AFib and other cardiovascular diseases by modulating SK channels, offering new possibilities for therapy development. [Extracted from the article]

Researchers at the University of Biskra in Algeria have made new findings in the field of type 2 diabetes. They have developed five novel hybridized inhibitors of the dipeptidyl peptidase IV (DPP-4) enzyme, which is important for glucose homeostasis. These inhibitors show potential for improved selectivity and stability compared to currently authorized DPP-4 inhibitors. The research may contribute to the development of new and potent DPP-4 inhibitors for the treatment of type 2 diabetes. [Extracted from the article]

Researchers at Sharda University in Greater Noida, India have identified three potential dual inhibitors for thymic stromal lymphopoietin (TSLP) and interleukin-33 (IL-33) proteins, which play important roles in allergic diseases. The study used structure-based virtual screening and molecular dynamics simulations to evaluate the binding affinity, stability, and safety of these compounds. The identified compounds, ZINC01105767, ZINC08764679, and ZINC33833100, show promising potential as anti-allergy agents and could lead to the development of more effective therapies for allergic diseases. Further investigations and experimental validations are needed to confirm these findings. [Extracted from the article]

Purpose This paper aims to investigate the oxygen transport characteristics in the electrolyte membrane of proton exchange membrane fuel cell (PEMFC), in particular, the water content dependence and the microscopic view of the molecular transport.Design/methodology/approach Molecular dynamics simulation is used to examine the oxygen transport characteristics in the electrolyte membrane of PEMFC that we have experimentally observed in our previous study.Findings Molecular dynamics simulation well predicts the diffusion coefficient of oxygen in the membrane. It was found that the oxygen molecules have preference in their transport passage that governs the property.Originality/value First attempt is to theoretically examine the experimentally observed water uptake dependence of the oxygen diffusion coefficient in membrane and to explain the mechanism. [ABSTRACT FROM AUTHOR]

A recent study conducted at Manipal College of Pharmaceutical Sciences in Karnataka, India, focused on identifying potential DNA gyrase inhibitors as a means to combat antibiotic-resistant bacterial infections. The researchers used computational tools such as virtual screening, docking, and molecular dynamics simulation to screen a library of anti-bacterial compounds. Two compounds, AM1 and AM5, were identified as potential DNA gyrase inhibitors with good binding and stability. These findings suggest that AM1 and AM5 could be further developed as leads in the fight against antibiotic resistance. [Extracted from the article]

Recently, nano-refrigerant (NR) was proposed as a new heat transfer (HT) operation strategy. Until today, most research was done on the nanofluids (NFs) displacement HT. Studying the phenomena associated with phase change (PC), such as boiling, which can transfer heat on larger scales, seems very necessary. The boiling process is a very effective and common mechanism in HT which occurs in many engineering systems. Consequently, the research on using iron oxide magnetic nanoparticles (NPs) in ammonia base fluid (BF) pool boiling heat flux (PBHF) was done to increase the utilization and improve HF performance. The present paper studied the PBHF of ammonia/Fe 3 O 4 NR in a copper nanochannel using molecular dynamics (MD) simulation. Therefore, the effect of the number of NPs on the atomic and thermal behavior of simulated structure was studied. The results show that adding iron oxide NPs led to an increase in HF and a decrease in the duration of fluid PC. Moreover, by increased number of NPs, the structure's maximum velocity (V), and temperature (T) increased. Finally, it is expected that the results obtained from these MD simulations will be considered in the practical use of different NRs in various industrial and engineering uses. [ABSTRACT FROM AUTHOR]

Wound healing can be improved via various materials in clinical cases. Today, nanocomposites are regarded as promising structures for this purpose. In the current computational study, we introduced Polyethylene glycol (PEG) hydrogel-cellulose nanocomposite to improve wound healing. For this purpose, molecular dynamics (MD) simulations were used to analyze hydrogel-cellulose nanocomposite at standard conditions. Therefore, the present paper investigates the mechanical stability of PEG hydrogel reinforced with cellulose nanofibrils. MD simulations were done in two main phases: equilibrium and deformation process as initial and final phases, respectively. Our simulation results show the defined samples' physical stability at 300 K and 1 bar. This procedure predicted from temperature and total energy convergence after 10 ns. The results of the mechanical test outputs show that inserting cellulose into pure PEG hydrogel leads to improving their mechanical performance. Numerically, the ultimate strength and Young's modulus of the designed nanocomposite increased to 0.26 MPa and 0.39 MPa (respectively) in the presence of 3% cellulose nanofibrils. The increased mechanical strength shows hydrogel-cellulose nanocomposite can be used for wound healing in clinical applications. [ABSTRACT FROM AUTHOR]

Considering the increase in using the biodiesels in the fuel industry, and the need to study its effect on the combustion processes, and the formation of greenhouse gases, the thermal performance of methyl ester-biodiesel fuel was studied in the present paper. The present study was carried out by molecular dynamics method. Furthermore, the effect of hybridaluminiumoxide/copper oxide nanoparticles on this biodiesel fluid's thermal performance and combustion processes was studied. Soy methyl ester was utilized as the study's base fluid. The poiseuille flow in the simulation box was shown by the fluid atomic behavior. Heat flux and the thermal conductivity of methyl ester converged to 1107.56 W/m2 and 0.1412 W/m.K, according to the base fluid's thermal efficiency. The findings demonstrate that the base fluid's thermal efficiency is improved by the addition of NPs. The heat flux and thermal conductivity of the nanostructure thus reach 2860 W/m2 and 0.6020 W/m.K. by adding hybrid NPs to the base fluid. Finally, the combustion processes in nanofluid is studied with the penetrated oxygen atoms number in the nanoparticles, and the radial distribution function (RDF). The results show that 25 oxygen atoms penetrated hybrid nanoparticles after 10 ns. Moreover, the maximum value of RDF increased by changing the time step from initial to final. The increase in the RDF showed the probability of finding oxygen atoms inside the hybrid nanoparticles. [ABSTRACT FROM AUTHOR]

Purpose - The purpose of this paper is to focus on the condensation process of hot vapor on smooth/rough walls and find how the condensation film forms and grows. The influences of the roughness and the wettability on condensation are especially analyzed. Design/methodology/approach - The non-equilibrium molecular dynamics simulation method is used to simulate the condensation. In order to maintain the process, a simple and effective molecule insertion mechanics is proposed. Findings - The results show that the wall-neighboring liquid structure becomes more regular with stronger wettability. The temporal parametric profiles show that the condensation does not progress at a constant rate but exhibit obvious unsteady characteristics of gradual deceleration, especially for strong wettability cases. Analysis based on heat and mass transfer indicates that the influence of wettability is quite superior to that of the roughness. The enhancement should be explained by the more fluent and effective energy exchange between solid and liquid particles caused by strong solid-liquid coupling other than by the ordering structure itself. Practical implications - The paper's findings suggest that the wettability should be paid special attention when the heat transfer performance of the microscale condensation is predominantly focused on. Originality/value - The paper provides a vapor-liquid-solid model with molecule insertion. This model can be used to evaluate the contact thermal resistance and the thermal boundary conditions in condensation under different geometric conditions. [ABSTRACT FROM AUTHOR]

Purpose: This paper aims to investigate atoms type and channel roughness effects on fluid behavior in nanochannel. Design/methodology/approach: The results of mechanical properties of these structures are reported in this work by using molecular dynamics method. Findings: The results show that nanochannel roughness is a limiting factor in flowing fluid in nanochannel. Moreover, fluids with less atomic weight have more free movement in ideal and non-ideal nanochannels. Originality/value: For the study of mechanical properties of fluid/nanochannel system, the authors calculated parameters such as potential energy, density, temperature and velocity profiles of simulated fluids. [ABSTRACT FROM AUTHOR]

Researchers from Sultan Moulay Slimane University in Beni Mellal, Morocco, have used computational methodologies to identify potential inhibitors for the nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3), which plays a critical role in inflammation and various diseases. Through statistical techniques and regression analysis, the researchers developed a two-dimensional quantitative structure-activity relationship (2D-QSAR) model and proposed five potential compounds. One of these compounds showed promising binding affinity and drug-like properties. The study highlights the power of computational techniques in drug discovery and suggests a potential candidate for therapeutic intervention against NLRP3-mediated inflammatory conditions. [Extracted from the article]

The tobacco flavoring process is an important procedure in production stage. During the flavoring process, the cut tobacco is endowed with a unique flavor to stabilize the production quality. Most of the flavoring process in tobacco enterprises is finished in the drum, and the internal structure of the drum (including the number, angle and installation position of the baffle plate) will affect the flavoring effect and efficiency. Therefore, this paper studied the particle behavior of the cut tobacco in the drum based on molecular dynamics analysis to explore the influence of the drum structure on the flavoring effect and to find the optimal structure parameters. Based on the discrete element simulation, an original rotary drum is structurally modified twice, and the corresponding field test is carried out to evaluate the performance of the modified drum. The results suggest that the flavoring effect is significantly improved through the structural modification, the content of menthol and citronellol are increased by 24.70% and 23.74% in the first test after modification, and reached 83.2% and 85.4% of the theoretical value respectively, and the error of the running time in the drum between the simulation and the test result is only 6.3% [ABSTRACT FROM AUTHOR]

From batteries to biology, many important technologies and physical phenomena operate as out-of-equilibrium reactive systems. Accurately modeling the nanoscale dynamics of non-equilibrium reactive systems and how they respond to external stimuli is challenging, especially if both atomistic resolution and large scales (>105 atoms) are required. REACTER is a protocol for modeling chemical reactions during classical molecular dynamics (MD) simulations. Coupling traditional fixed-valence force fields with heuristic reactive MD is advantageous for large-scale simulations of dynamic systems that can include the complex reaction mechanisms common in organic chemistry. This paper details the current features of the LAMMPS implementation of REACTER, known as fix bond/react , and surveys recent applications of the protocol in a variety of fields, including photopolymers, high-performance composites, and membranes. Conceived as a tool for modeling polymerization processes, the scope of REACTER is expanding as it is applied to new materials and supporting features are implemented. Three new case studies are presented that highlight the capabilities of REACTER, including modeling hierarchical materials, the mechanics of molecular machines, and large-scale dynamics of heterogeneous catalysis. [ABSTRACT FROM AUTHOR]

The Mercedes-Benz (MB) water model is a simple two-dimensional toy model of water that can reproduce many of the anomalous properties of water. Within the model, the water particles are represented as Lennard-Jones disks with explicitly added orientation-dependent interactions that mimic the formation of hydrogen bonds. Due to the simple implementation of the MB model in Monte Carlo simulations, it was mainly studied with Monte Carlo simulations in different ensembles. The implementation of the model in molecular dynamics simulations is not trivial. In this paper we present the code for molecular dynamics simulations. The structural and thermodynamic properties of the model were calculated using molecular dynamics and compared with data from Monte Carlo simulations to confirm that the molecular dynamics code works correctly. We also used molecular dynamics to calculate the dynamic properties of the model. The Fortran source code of our molecular dynamics simulation of the MB water model is provided. [ABSTRACT FROM AUTHOR]

One of the key ways to improve energy storage performance is to use advanced materials and elements in building coatings. Dense exterior walls with high thermal insulation properties and absorbent and heat-retaining elements can be made by intelligently combining products to store latent heat based on PCMs. In the present study, the thermal behaviour of glass in the presence of PCM (Decane) has been investigated by molecular dynamics simulation. In this paper, the atomic behaviour of the structure is investigated by temperature and density profiles. And the thermal behaviour of the simulated structure is investigated by heat flux and thermal conductivity. The numerical results show that the maximum density and temperature in fluid particles are 0.09643 atom/Å3 and 1067.51 K. The structure's heat flux and thermal conductivity reach 650.27 W/m2 and 0.74 W/m.K, respectively. In general, the use of phase-change materials can prevent energy loss, reduce energy costs, and while changing the phase of materials, quickly has a positive effect on the appearance of the building (as a result of beauty and performance, which are an integral part) Will leave. [ABSTRACT FROM AUTHOR]

Abstract Understanding the mechanical behaviour of nanostructures is of great importance due to their applications in nanodevices such as in nanomechanical resonators, nanoscale mass sensors, electromechanical nanoactuators and nanogenerators. Due to the difficulties of performing accurate experimental measurements at nanoscales and the high computational costs associated with the molecular dynamics simulations, the continuum modelling of nanostructures has attracted a considerable amount of attention. Since size influences have a crucial role in the mechanics of structures at nanoscale levels, classical continuum-based theories have been modified to incorporate these effects. Among various modified continuum-based theories, the nonlocal elasticity and the nonlocal strain gradient elasticity have been employed to estimate the mechanical behaviour of nanostructures. In this review paper, first these two modified elasticity theories are briefly explained. Then, the nonlocal motion equations for different nanostructures including nanorods, nanorings, nanobeams, nanoplates and nanoshells are derived. Several papers which reported on the size-dependent mechanical behaviour of nanostructures using modified continuum models are reviewed. Furthermore, important results reported on the vibration, bending and buckling of nanostructures as well as the results of size-dependent wave propagation analyses are discussed. [ABSTRACT FROM AUTHOR]

Purpose -- Whether a fire can be initiated in an explosion accident depends on the explosion and deflagration process. In the methane-air explosion in a tunnel, the flame accelerates from the ignition point. However, where it begins to decelerate is not clear. The purpose of this paper is to examine the explosion overpressure, flow and flame propagation beyond the premixed area of methane-air in a tunnel. Design/methodology/approach -- The numerical simulation was used to study the explosion processes of methane-air mixtures in a tunnel. Based on the numerical simulation and its analysis, the explosion overpressure, flow and flame propagation rules beyond the premixed area were demonstrated for a methane-air explosion. Findings -- The peak overpressure of methane-air mixture explosion was observed to reach its maximum beyond the original premixed area of methane-air. The hazardous effects beyond the premixed area may be stronger than those within the premixed area for a methane-air explosion in a tunnel. Under the conditions of this study, the ratio between the length of combustion area (40 m) and that of original premixed area (28 m) reaches 1.43. Originality/value -- Little attention has been devoted to investigating the explosion overpressure, flow and flam propagations beyond the original premixed area of methane-air in a tunnel. Based on the numerical simulation and the analysis, the propagation rule of overpressure wave and flow inside and outside the space occupied by methane/air mixture at the volume fraction of 9.5 percent in a tunnel were obtained in this work. [ABSTRACT FROM AUTHOR]

Keywords: Antibacterials; Antibiotics; Antimicrobials; Artificial Intelligence; Drugs and Therapies; Emerging Technologies; Engineering; Health and Medicine; Machine Learning; Molecular Dynamics; Physics; Texas A&M University EN Antibacterials Antibiotics Antimicrobials Artificial Intelligence Drugs and Therapies Emerging Technologies Engineering Health and Medicine Machine Learning Molecular Dynamics Physics Texas A&M University 334 334 1 08/28/23 20230901 NES 230901 2023 SEP 1 (NewsRx) -- By a News Reporter-Staff News Editor at Drug Week -- What if artificial intelligence (AI) could be used to spur discovery in areas such as biotechnology, drug discovery and fluid dynamics? "Since AI for science is a relatively new area, there is not a lot of literature on the subject to reference", Ji said. [Extracted from the article]

Purpose – The purpose of this paper is to use comprehensive model to investigate the effects of particle physical properties on in-flight nano-particles behavior for the radio frequency suspension plasma spray. Design/methodology/approach – In this paper, both the effects thermal properties of solvent and solid particle on the evolution of particle size, velocity and temperature are discussed. Besides, the numerical analysis is also conducted to investigate the influences of particle physical properties on the characteristic distributions of particles for poly-disperse cases. Findings – Results show the thermal properties of solvent have critical effects on the discharged point of the solid particles, but little influence on the final particle velocity and size, as well as their distributions. The final state of particle temperature is mainly determined by the solid particle thermal properties, especially depending on the boiling point. Originality/value – Most of the former studies took the experimental approaches and mainly focussed on the operating conditions effects. While beyond the operating conditions, the variety of particle physical and thermal properties also has strong effect on particle heating performance. [ABSTRACT FROM AUTHOR]

The proper choice of collective variables (CVs) is central to biased-sampling free energy reconstruction methods in molecular dynamics simulations. The PLUMED 2 library, for instance, provides several sophisticated CV choices, implemented in a C++ framework; however, developing new CVs is still time consuming due to the need to provide code for the analytical derivatives of all functions with respect to atomic coordinates. We present two solutions to this problem, namely (a) symbolic differentiation and code generation, and (b) automatic code differentiation, in both cases leveraging open-source libraries (SymPy and Stan Math, respectively). The two approaches are demonstrated and discussed in detail implementing a realistic example CV, the local radius of curvature of a polymer. Users may use the code as a template to streamline the implementation of their own CVs using high-level constructs and automatic gradient computation. Program summary Program Title: Practical approaches to the differentiation of collective variables in free energy codes: computer-algebra code generation and automatic differentiation Program Files doi: http://dx.doi.org/10.17632/r4r67bvkdn.1 Licensing provisions: GNU Lesser General Public License Version 3 (LGPL-3) Programming languages: C++, Python Nature of problem: The C++ implementation of collective variables (CVs, functions of atomic coordinates to be used in biased sampling applications) in biasing libraries for atomistic simulations, such as PLUMED [1], requires computation of both the variable and its gradient with respect to the atomic coordinates; coding and testing the analytical derivatives complicate the implementation of new CVs. Solution method: The paper shows two approaches to automate the computation of CV gradients, namely, symbolic differentiation with code generation and automatic code differentiation, demonstrating their implementation entirely with open-source software (respectively, SymPy and the Stan Math Library). Additional comments: The paper’s accompanying code serves as an example and template for the methods described in the paper; it is distributed as the two modules curvature_codegen and curvature_autodiff integrated in PLUMED 2’s source tree; the latest version is available at https://github.com/tonigi/plumed2-automatic-gradients . [1] Tribello GA, Bonomi M, Branduardi D, Camilloni C, Bussi G. PLUMED 2: New feathers for an old bird. Computer Physics Communications. 2014 Feb;185(2):604-13. [ABSTRACT FROM AUTHOR]

A new report from the University of Campinas in Brazil explores the use of the homogeneous coordinate system as an alternative framework for simplifying calculations in chemical physics. The researchers found that computing interatomic distances using the Euclidean model of 3D space requires almost 60% more operations than the homogeneous model. This finding has implications for molecular dynamics simulations and could lead to more efficient computation of interatomic distances and their derivatives using internal coordinates. The research has been peer-reviewed and published in Advanced Theory and Simulations. [Extracted from the article]

• Ductile to brittle transition (DBT) phenomenon is elucidated using MD simulation. • DBT curve is correlated with the temperature sensitivity of fracture stress. • Ni lowers the DBT temperature of BCC Fe by reducing its fracture stress sensitivity. • Crack blunting effect of Ni improves the fracture toughness of Fe. Ductile to brittle transition (DBT) phenomenon is commonly observed in BCC Fe-based systems, which significantly deteriorates their low temperature fracture toughness. Ni is known to be an effective alloying element to improve the low temperature toughness by reducing the ductile to brittle transition temperature (DBTT). The present article investigates the role of Ni in tailoring the DBT curve of BCC Fe by employing molecular dynamics (MD) simulation. Here, we performed mode-I loading of different pre-cracked systems (pure Fe, Fe-2 wt% Ni and Fe-4 wt% Ni alloys) over a temperature range of 1–800 K to construct their DBT curves. The DBT curves are subsequently correlated with the temperature sensitivity of fracture stress, which is estimated using the concept of critical strain energy release rate (G IC). The role of Ni in reducing the fracture stress sensitivity is responsible for decreasing the DBTT as well as the slope of the DBT region. The underlying mechanism is discussed in terms of the crack blunting effect of Ni which effectively increases the G IC and hence the fracture stress, particularly at the low temperature regimes. Besides, the significantly large strain rate imposed in MD simulation is mainly responsible for the higher DBTT values when compared with the experimental results. The present paper tackles this strain rate issue by using an appropriate strain rate sensitivity factor to rescale the simulated DBTT values down to the experimental ones, resulting in a good match between the simulated and experimental DBTT. [Display omitted] [ABSTRACT FROM AUTHOR]

Life processes in single cells and at the molecular level are inherently stochastic. Quantifying the noise is, however, far from trivial, as a major contribution comes from intrinsic fluctuations, arising from the randomness in the times between discrete jumps. It is shown in this paper how a noise-filtering setup with an operator theoretic interpretation can be relevant for analyzing the intrinsic stochasticity in jump processes described by master equations. Such interpretation naturally exists in linear noise approximations, but it also provides an exact description of the jump process when the transition rates are linear. As an important example, it is shown in this paper how, by addressing the proximity of the underlying dynamics in an appropriate topology, a sequence of coupled birth-death processes, which can be relevant in gene expression, tends to a pure delay; this implies important limitations in noise suppression capabilities. Despite the exactness, in a linear regime, of the analysis of noise in conjunction with the network dynamics, we emphasize in this paper the importance of also analyzing dynamic behavior when transition rates are highly nonlinear; otherwise, steady-state solutions can be misinterpreted. The examples are taken from systems with macroscopic models leading to bistability. It is discussed that bistability in the deterministic mass action kinetics and bimodality in the steady-state solution of the master equation neither always imply one another nor do they necessarily lead to efficient switching behaviours: the underlying dynamics need to be taken into account. Finally, we explore some of these issues in relation to a model of the lac operation. [ABSTRACT FROM AUTHOR]

Keywords: Tehran; Iran; Gram-Negative Bacteria; Gram-Negative Bacterial Infections; Health and Medicine; Molecular Dynamics; Physics EN Tehran Iran Gram-Negative Bacteria Gram-Negative Bacterial Infections Health and Medicine Molecular Dynamics Physics 1815 1815 1 04/03/23 20230407 NES 230407 2023 APR 7 (NewsRx) -- By a News Reporter-Staff News Editor at Health & Medicine Week -- Data detailed on Gram-Negative Bacteria have been presented. The news reporters obtained a quote from the research from the Baqiyatallah University of Medical Sciences, "Our findings showed that the peptide was strongly bound to the GP membrane type in comparison with the GN membrane and was stabilized quickly. [Extracted from the article]

We describe a data-driven, multiscale technique to model reactive wetting of a silver–aluminum alloy on a Kovar™ (Fe-Ni-Co alloy) surface. We employ molecular dynamics simulations to elucidate the dependence of surface tension and wetting angle on the drop's composition and temperature. A design of computational experiments is used to efficiently generate training data of surface tension and wetting angle from a limited number of molecular dynamics simulations. The simulation results are used to parameterize models of the material's wetting properties and compute the uncertainty in the models due to limited data. The data-driven models are incorporated into an engineering-scale (continuum) model of a silver–aluminum sessile drop on a Kovar™ substrate. Model predictions of the wetting angle are compared with experiments of pure silver spreading on Kovar™ to quantify the model-form errors introduced by the limited training data versus the simplifications inherent in the molecular dynamics simulations. The paper presents innovations in the determination of "convergence" of noisy MD simulations before they are used to extract the wetting angle and surface tension, and the construction of their models which approximate physio-chemical processes that are left unresolved by the engineering-scale model. Together, these constitute a multiscale approach that integrates molecular-scale information into continuum scale models. • Constructed a data-driven wetting model from molecular dynamics simulations. • Studied wetting of molten silver-aluminum alloy on a Kovar™ substrate for brazing. • Performed molecular dynamics simulation to predict surface tension & wetting angle. • Calibrated probabilistic, data-driven surrogate model using limited training data. • Integrated wetting model into engineering-scale finite element brazing model. • Compared model to experiment, identifying missing physics in simulations. [ABSTRACT FROM AUTHOR]

This paper presents a detailed study of the uniform motion of a Holstein polaron as it moves along a chain in a constant electric field. The calculations showed that, depending on the parameters of the system, the duration of the uniform motion of the polaron along the chain can reach tens and hundreds of Bloch periods for a given value of the electric field intensity. It is shown that in the process of the uniform motion, the macro-part of the polaron moves at a constant velocity, retaining its shape. At the same time, the low-density components of the polaron, which arise immediately when a constant electric field is instantaneously switched on, have their own internal dynamics and demonstrate characteristic elements of the Bloch oscillations, such as the period of Bloch oscillations and the maximum Bloch amplitude. It is shown that not only the velocity and duration of the uniform motion of the polaron, but also the characteristics of the low-density components of the polaron depend on the value of the electric field intensity. • It was first showed that Bloch oscillations are observed in uniform polaron motion. • The duration of the uniform polaron motion in a constant electric field is finite. • With uniform polaron motion, the low-density components of the polaron are formed. • Low-density components of polaron shows the characteristics of Bloch oscillations. • Low-density components characteristics persists throughout the uniform motion. [ABSTRACT FROM AUTHOR]

Purpose -- The purpose of this paper is to investigate the effect of narrow gap on the fluid flow and heat transfer through an eccentric annular region is numerically. Flow through an eccentric annular geometry is a model problem of practical interest. Design/methodology/approach -- The approach involves standard finite volume-based SIMPLE scheme. The numerical simulations cover the practically relevant Reynolds number range of 104-106. Findings -- In the narrow gap region, temperature shoot up was observed due to flow maldistribution with an attendant reduction in the heat removal from the wall surfaces. CFD analysis is presented with the aid of, streamlines, isotherms, axial velocity contours, etc. The engineering parameters of interest such as, Nusselt number, wall shear stress, etc., is presented to study the effect of eccentricity and radius ratio. Research limitations/implications -- The present investigation is a simplified model for the rod bundle heat transfer studies. However, the detailed study of sectorial mass flux distribution is a useful precursor to the thermal hydraulics of rod bundles. Practical implications -- For nuclear reactor fuel rods, the effect of eccentricity is going to be detrimental and might lead to the condition of critical heat flux. A thorough sub-channel analysis is very useful. Social implications -- Nuclear safety standards require answers to a wide a range of what-if type hypothetical scenarios to enable preparedness. This study is a highly simplified model and a first step in that direction. Originality/value -- The narrow gap region has been systematically investigated for the first time. A detailed sectorial analysis reveals that, flow maldistribution and the attendant temperature shoot up in the narrow gap region is detrimental to the safe operation. [ABSTRACT FROM AUTHOR]

It has been found recently in experiments that diamond/lonsdaleite biphase could possess excellent thermal-mechanical properties, implying that the properties of carbon materials can be improved by reasonably designing their internal structures. The mechanism of the excellent performance arising from biphasic structure is still unknown and needs to be revealed. In this paper, we established a series of possible diamond/lonsdaleite biphasic structures and revealed the optimization mechanism of the biphasic structure using first principles calculations. It shows in our ab-initio molecular dynamics simulations that the lonsdaleite cannot exist stably at room temperature, which could explain why pure lonsdaleite can hardly be found or synthesized. Detailed analysis shows that partial slip would occur in the lonsdaleite region if the applied strain is sufficiently large, leading to the transition from biphasic phase to cubic phase. Then, further shear strain would be applied along the hard shear direction of the cubic structure, resulting in an ascent of stress. The results presented could offer an insight into the structural transformation at high temperature and large strain. [ABSTRACT FROM AUTHOR]

The article discusses a paper by researcher David Shaw concerning an Anton molecular dynamics (MD) engine. An Anton engine applies leading computer science concepts to the critical issue of modeling molecular interactions, the article states. Topics include measuring or simulating molecular underpinnings, simulations that run for milliseconds, and computers that can run a specific molecular dynamics workload well. Also discussed are electrostatic interactions between two atoms, infrequent bonded interactions, and experimentation with "force field" models.

Biological and crystalline membranes exhibit noticeable fluctuations at room temperature due to their low bending stiffness. These fluctuations have a significant impact on their overall mechanical behavior and interactions with external objects. When two membranes come into proximity, they mutually suppress each other's fluctuations, leading to a repulsive force that plays a pivotal role in the mechanical behavior of these membranes. From the mechanics point of view, crystalline membranes are modeled as solid membranes with inherent shear resistance, whereas biological membranes are commonly described as fluidic entities without shear resistance. Under this premise, the entropic force between two fluctuating biological membranes is proposed to scale as p ∝ 1 / d 3 , where d is the intermembrane distance. Yet, there are numerous instances where these membranes display shear resistance and behave akin to solid membranes. In this paper, we develop a statistical mechanics model within nonlinear elasticity to study the entropic force acting on a confined, fluctuating solid membrane. We demonstrate that, due to the nonlinear elasticity of solid membranes, the entropic force scales differently compared to that of fluid membranes. Our predictions align well with the results obtained from molecular dynamics simulations involving graphene, a representative of a solid membrane, confined between two rigid walls. [ABSTRACT FROM AUTHOR]

The chemical vapor deposition (CVD) of graphene on metal substrate serves as a robust method to synthesize large graphene flakes. Therefore, understanding the thermodynamics and kinetics of graphene–metal interface is an important step towards synthesizing defect-free graphene during CVD. The focus of this paper is on the phenomenon of surface reconstruction of a metal substrate during the deposition of a 2D material. Key features of surface reconstruction include the formation of straight and pyramidal facets of size ∼ 300 nm in width and ∼ 15–80 nm in height. In addition, discontinuities in facet directions under a single graphene flake distributed over two grains highlight the strong crystallographic influence on surface reconstruction. In this paper, we present an atomistically informed continuum model of a graphene–metal interface in three dimensions. Graphene is modeled as an elastic surface that is in contact with a rigid metal substrate. Due to the weak van der Waals interaction between graphene and metal, the kinematics of the model incorporates sliding of graphene. However, since we assume that graphene is always in contact with the substrate, its normal displacement is mediated by surface diffusion of metal atoms. Based on evidence from recent molecular dynamics simulations and experiments, we model the graphene-covered-metal surface energy to include in-plane elasticity and bending energy of graphene, and an interaction energy that depends on the orientation of graphene relative to the substrate. We compare the predictions of our model with surface reconstructions observed during the CVD of graphene on forged thin film palladium polycrystals. As we continue to unravel the atomic scale mechanisms responsible for surface reconstruction during CVD, we expect the current continuum framework and its generalizations will serve to bridge the atomic- and the meso-scales. [ABSTRACT FROM AUTHOR]

Purpose – The purpose of this paper is to investigate the gas flow characteristics in near wall region and the velocity slip phenomenon on the wall in nano-channels based on the molecular dynamics simulation. Design/methodology/approach – An external gravity force was employed to drive the flow. The density and velocity profiles across the channel, and the velocity slip on the wall were studied, considering different gas temperatures and gas-solid interaction strengths. Findings – The simulation results demonstrate that a single layer of gas molecules is adsorbed on wall surface. The density of adsorption layer increases with the decrease of gas temperature and with increase of interaction strength. The near wall region extents several molecular diameters away from the wall. The density profile is flatter at higher temperature and the velocity profile has the traditional parabolic shape. The velocity slip on the wall increases with the increase of temperature and with decrease of interaction strength linearly. The average velocity decreases with the increase of gas-solid interaction strength. Originality/value – This research presents gas flow characteristics in near wall region and the velocity slip phenomenon on the wall in nano-channels. Some interesting results in nano-scale channels are obtained. [ABSTRACT FROM AUTHOR]

Purpose – The purpose of this paper is to study nanoparticles diffusion and coagulation processes in a twin-jet. Design/methodology/approach – Large eddy simulation (LES) and Taylor-series expansion moment method (TEMOM) are employed to deal with a nanoparticle-laden twin-jet flow. Findings – The numerical results show that the interaction of the two jets and turbulence eddy structures rolling-up, paring and shedding in flow sharply affects particles number concentration. Particle diameter grows quickly at the interfaces of jets. Coagulation shows more obvious effect at initial stage than that in the subsequent period. Then diffusion makes the particle diameter distribution much more uniform. Originality/value – In recent years a great number of attentions have been focussed on the issue of particulate dynamics processes including diffusion, coagulation and deposition, etc. However, up to now few works have been focus on the nanoparticles coagulation and dispersion in turbulent flows. The investigation on the diffusion and coagulation process of nanoparticles using TEMOM in a twin-jet flow has not been found. [ABSTRACT FROM AUTHOR]

Purpose – The purpose of this paper is to investigate tensile properties of TiC particle-reinforced titanium matrix composites (PRTMC) using the elasto-plastic finite element (FE) programs and the homogenization method and the fixed point iteration method. Design/methodology/approach – Two quasi-static and dynamic transient programs of elasto-plastic FE were coded by using FORTRAN. Based on the FE programs, the FE model of the TiC PRTMC with typical microstructures was established by using the fixed point iteration method and the homogenization theory. The hot deformation behavior of TiC PRTMC under different temperatures were analyzed by using the above model and programs. Findings – Calculation results are presented to investigate the influence of different temperatures on the hot deformation behavior of TiC PRTMC. Based on the experimental data, a good agreement was obtained between the numerical predictions and the experimental results, and the feasibility of this method was verified. Originality/value – The work is original and findings are new, which demonstrates this FE frame combined with the homogenization method and the fixed point iteration method can be used to investigate the tensile behavior of particle-reinforced metal matrix composites. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to analyze simulated trajectories, either interactively or via scripts, to derive quantities of interest and provide insight for further experiments. This paper presents the Density Profile Tool, a package that enhances the Visual Molecular Dynamics environment with the ability to interactively compute and visualize 1-D projections of various density functions of molecular models. We describe how the plugin is used to perform computations both via a graphical interface and programmatically. Results are presented for realistic examples, all-atom bilayer models, showing how mass and electron densities readily provide measurements such as membrane thickness, location of structural elements, and how they compare to X-ray diffraction experiments. Program summary: Program title: Density Profile Tool Catalogue identifier: AEQM_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEQM_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: yes No. of lines in distributed program, including test data, etc.: 1742 No. of bytes in distributed program, including test data, etc.: 12764 Distribution format: tar.gz Programming language: TCL/TK. Computer: Any, with or without graphical display. Operating system: Linux/Unix, OSX, Windows. RAM: VMD should be able to hold the trajectory in memory. Classification: 3, 23. External routines: VMD (version 1.9 or higher) (http://www.ks.uiuc.edu/Research/vmd/). Nature of problem: Compute and visualize one-dimensional density profiles of molecular dynamics trajectories in the VMD environment, either interactively or programmatically. Solution method: Density profiles are computed by binning the simulation space into slabs of finite thickness. A graphical user interface allows the choice of the atomic property (number, mass, charge, electrons) and the details of the binning. Restrictions: The current version only supports orthorhombic cells. Unusual features: The Density Profile Tool is not a standalone program but a plug-in that enhances VMD’s analysis features. Running time: A contemporary PC completes the analysis of 500 frames of the example system discussed in the paper (35,000 atoms) in under 1 min. [ABSTRACT FROM AUTHOR]

This paper studies the dynamics of twisted vortex bundles, which were detected in experimental investigations of superfluid turbulence in superfluid 3He-B. The analysis shows that a linear torsion oscillation of a vortex bundle is a particular case of the slow vortex mode related with the inertia] wave, which was already investigated in the past in connection with observation of the Tkachenko waves in superfluid 4He and the experiments on the slow vortex relaxation in superfluid 3He-B. This paper addresses also a twisted vortex bundle terminating at a lateral wall of a container, starting from the elementary case when the bundle reduces to a single vortex. The theory considers the laminar regime of the vortex-bundle evolution and investigates the Glaberson-Johnson-Ostermeier instability of the laminar regime, which is a precursor for the transition to the turbulent regime at strong twist of the bundle. The propagation and the rotation velocities of the vortex front (the segment of the vortex bundle diverging to the wall) can be found from the equations of balance for the linear and the angular momenta and the energy. It is demonstrated that the vortex front can move with finite velocity even in the absence of mutual friction (the T = 0 limit). The theory is compared with experimental results on vortex-front propagation in superfluid 'He-B. [ABSTRACT FROM AUTHOR]

In traditional molecular dynamics (MD) simulations, atoms and coarse-grained particles are modeled as point masses interacting via isotropic potentials. For studies where particle shape plays a vital role, more complex models are required. In this paper we describe a spectrum of approaches for modeling aspherical particles, all of which are now available (some recently) as options within the LAMMPS MD package. Broadly these include two classes of models. In the first, individual particles are aspherical, either via a pairwise anisotropic potential which implicitly assigns a simple geometric shape to each particle, or in a more general way where particles store internal state which can explicitly define a complex geometric shape. In the second class of models, individual particles are simple points or spheres, but rigid body constraints are used to create composite aspherical particles in a variety of complex shapes. We discuss parallel algorithms and associated data structures for both kinds of models, which enable dynamics simulations of aspherical particle systems across a wide range of length and time scales. We also highlight parallel performance and scalability and give a few illustrative examples of aspherical models in different contexts. [ABSTRACT FROM AUTHOR]

Experimental tests show that nonlinear viscoelasticity characterizes the mechanical behavior of boehmite nanoparticle (BNP)/epoxy nanocomposites. This paper presents the development and numerical implementation of a physically based constitutive model for BNP/epoxy nanocomposites undergoing finite strain. The proposed constitutive model allows capturing the main features of the stress-strain relationship of BNP/epoxy nanocomposites, including the nonlinear hyperelastic, time-dependent and softening behavior. The characterizing feature of this study is to propose a methodological framework based on molecular dynamics simulations and experimental tests to identify the material parameters for the model. Molecular simulations in conjunction with the Eyring viscosity theory are used to characterize the viscoelastic deformation of epoxy resins under loading. The concept of strain amplification is also adopted to account for the effect of nanoparticles on the stress–strain response of the nanocomposites. The stress softening behavior is captured by a monotonically increasing function of deformation, so-called damage variable. The results show that the model predictions of stress-strain relationships are in good agreement with experimental data at different BNP weight fractions. Finally, the constitutive model is implemented in the finite element analysis and examined by means of a benchmark example. Experimental–numerical validation confirms the predictive capability of the present modeling framework, which provides a suitable tool for analyzing BNP/epoxy nanocomposites. [ABSTRACT FROM AUTHOR]

Abstract We present an algorithm and its implementation to calculate the propertiesof electronic excitations in molecules and clusters from first principles, using time-dependent density functional theory (TDDFT). The algorithm assumes the use of some localized functions as a basis set to represent the spatial degrees of freedom. It relies on an iterative computation of the induced density according to the Dyson-like equation for the linear response function. The current implementation is built upon so-called numerical atomic orbitals. It is suitable for a wide variety of density functional theory (DFT) software. In this work, we demonstrate TDDFT calculations starting from preceding DFT runs with SIESTA, GPAW and PySCF packages, while a coupling with the other DFT packages such as Fireball and OpenMX is planned. The mentioned packages are capable of performing ab initio molecular dynamics simulations, and the speed of our TDDFT implementation makes feasible to perform a configuration average of the optical absorption spectra. Our code is written mostly in Python language allowing for a quick and compact implementation of most numerical methods and data-managing tasks with the help of NumPy/SciPy libraries and Python intrinsic constructs. Part of the code is written in C and Fortran to achieve a competitive speed in particular sections of the algorithm. Many parts of the current algorithm and implementation are useful in other ab initio methods for electronic excited states, such as Hedin's G W , Bethe–Salpeter equation and DFT with hybrid functionals. Corresponding proof-of-principles implementations are already part of the code. Program summary Program Title: PySCF-NAO Program Files doi: http://dx.doi.org/10.17632/9wgp6255hn.1 Licensing provisions: Apache License, Version 2.0 Programming language: Python (2 or 3), Fortran90 and C Supplementary material: We provide the source code and input files to organize example and benchmark calculations discussed in the paper. Nature of the problem: The study of the interaction of photons and charged particles with matter depends upon understanding of electronic excitations in matter. A description of the electronic excitations within time-dependent density functional theory (TDDFT) is popular due to the combination of its reasonable accuracy and its relatively low computational cost. Despite the relative simplicity of TDDFT, its application becomes difficult for quantum systems containing several hundreds of atoms. Such microscopically small systems are relevant in organic electronics, plasmonics and surface science. Therefore, much work has been devoted to the development of adequate electronic structure methods. Moreover, thermal motion of atoms and the presence of solvents affects the properties of electronic excited states in a decisive manner. Modeling of the electronic excited states including the system's dynamics within the Born–Oppenheimer approximation leads to even stronger efficiency requirements from the corresponding electronic structure methods. Solution method: We discretize the Kohn–Sham Hamiltonian using a basis of numerical atomic orbitals. The induced electronic density is determined in response to a dipolar external perturbation, according to linear response TDDFT, using an iterative algorithm. The method takes advantage of the sparsity generated by the finite support of the numerical atomic orbitals. This allows computing the dynamical polarizability of molecules and clusters containing up to several thousands of atoms. Additional comments including Restrictions and Unusual features: The current algorithm is formulated within the formalism of density response functions. Therefore, one needs to know explicitly an exchange–correlation kernel (second-derivative of energy with respect to variation of the density). The exchange–correlation kernel is analytically known for (semi-)local density functionals, but not for the hybrid density functionals. To date, we implemented only the local density approximation (LDA) for the exchange–correlation kernel to be used with the iterative TDDFT in PySCF-NAO. Spin-restricted formalism for finite systems is covered in the current implementation. Moreover, although our code is prepared to compute the electronic response of all-electron systems, our current implementation of an auxiliary product basis (density-fitting basis) is working best in combination with the use of pseudopotentials. [ABSTRACT FROM AUTHOR]

• Modeling of phase separation of ternary mixture using SPH. • Calculation of diffusion coefficients from MD simulations using GROMACS. • Different molar weight and density of the components. In the preparation process of porous polymer membranes, multi-component mass transfer during phase separation leads to the formation of pores. In this paper, we study the Generalized Fickian approach for a phase separating ternary fluid mixture using the Smoothed Particle Hydrodynamics (SPH) method. The thermodynamics are based on the Flory–Huggins equation of state for polymer mixtures with different molar weight and density of the components. We present a validation of the discrete balance equation and study the effect of different molar weight and density on the accuracy of the method separately by considering phase separation in a periodic box in two dimensions. We analyze the mass fraction distribution and the time-evolving reduction of the amount of interface using a mapping scheme based on the rheological Doi–Ohta model. We find good agreement with the diffusion-dominant power law for coarsening. Finally, we apply the proposed SPH model on a realistic Polyvinylidenfluorid/Dimethylformamid/water system. The corresponding, composition-dependent diffusion coefficients are estimated using molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

Abstract Despite numerous theoretical investigations on the mechanical properties of graphene, an accurate identification of its material behavior is still unattained. One hypothesis for this uncertainty is that modeling graphene as a static membrane cannot describe the strong coupling between mechanics and thermodynamics of this structure. Therefore, characterization methods built upon static models could not capture these effects. In this paper, we propose a new method for building a reduced order model for the dynamics of thermalized graphene membranes. We apply the proper orthogonal decomposition algorithm on time responses obtained from molecular dynamics simulations. As a result, a set of orthogonal modes is obtained which are then employed to build a reduced order model. The proposed model can describe the motion of the suspended graphene membrane over the whole spatial domain accurately. Moreover, due to its computational efficiency, it is more versatile for exploring the nonlinear dynamics of the system. This model is then employed for studying the nonlinear dynamics of graphene membranes at large amplitudes to extract Young's modulus. The obtained Young's modulus incorporates the effects of nano-scaled thermally induced dynamic ripples and hence, is temperature and size dependent. Our proposed atomistic modal order reduction method provides a framework for studying the dynamics and extracting the mechanical properties of other nano-structures at the molecular level. [ABSTRACT FROM AUTHOR]

Abstract This paper reports on a molecular dynamics study of structural rearrangements in a copper nanocrystal during nucleation of plastic deformation under uniaxial tension. The study shows that the resulting nucleation of partial dislocations on the free surface and their glide occurs through local fcc→bcc→hcp transformations via consistent atomic displacements. We propose an atomic model for the generation of dislocations and twins based on local reversible fcc→bcc→fcc transformations, with the reverse one proceeding through an alternative system. The model gives an insight into possible causes and mechanisms of the generation of partial dislocations and mechanical twins in two and more adjacent planes of plastically deformed nanocrystals. The obtained data allow a better understanding of how plasticity is generated in nanostructured materials. [ABSTRACT FROM AUTHOR]

The mechanical properties of nano-scale Cu/FeS composite were simulated by molecular dynamics (MD) simulation in this paper. Through the analysis on the stress-strain curves, the results of MD simulation were in good agreement with mechanisms of macroscopic deformation. When the size of particles was smaller than a certain value, the relationship between yield strength and size, which was different from the large size crystals abided by the contrary Hall-Petch relationship. Based on the discussion of nano-scale Cu/FeS composite, some interesting conclusions were obtained. For example, the “S” type curves were discovered in stress-strain curves and the anisotropy of FeS was very evident when the exposures of reinforcing phase (FeS) were different and so on. The basic theories and calculations of the composite that contains nano-scale particles were discussed. At the same time, a new modeling building method of composites, which was close to actual experiences, were considered in this paper. [Copyright &y& Elsevier]

Abstract: Synchronization is an important phenomenon commonly observed in nature. It is also often artificially induced because it is desirable for a variety of applications in physics, applied sciences and engineering. In a recent paper [Mahmoud GM, Mohamed AA, Aly SA. Strange attractors and chaos control in periodically forced complex Duffing’s oscillators. Physica A 2001;292:193–206], a system of periodically forced complex Duffing’s oscillators was introduced and shown to display chaotic behavior and possess strange attractors. Such complex oscillators appear in many problems of physics and engineering, as, for example, nonlinear optics, deep-water wave theory, plasma physics and bimolecular dynamics. Their connection to solutions of the nonlinear Schrödinger equation has also been pointed out. In this paper, we study the remarkable phenomenon of chaotic synchronization on these oscillator systems, using active control and global synchronization techniques. We derive analytical expressions for control functions and show that the dynamics of error evolution is globally stable, by constructing appropriate Lyapunov functions. This means that, for a relatively large set initial conditions, the differences between the drive and response systems vanish exponentially and synchronization is achieved. Numerical results are obtained to test the validity of the analytical expressions and illustrate the efficiency of these techniques for inducing chaos synchronization in our nonlinear oscillators. [Copyright &y& Elsevier]

Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesoscale to continuum. Reasons for its popularity are that it provides a wide variety of particle interaction models for different materials, that it runs on any platform from a single CPU core to the largest supercomputers with accelerators, and that it gives users control over simulation details, either via the input script or by adding code for new interatomic potentials, constraints, diagnostics, or other features needed for their models. As a result, hundreds of people have contributed new capabilities to LAMMPS and it has grown from fifty thousand lines of code in 2004 to a million lines today. In this paper several of the fundamental algorithms used in LAMMPS are described along with the design strategies which have made it flexible for both users and developers. We also highlight some capabilities recently added to the code which were enabled by this flexibility, including dynamic load balancing, on-the-fly visualization, magnetic spin dynamics models, and quantum-accuracy machine learning interatomic potentials. Program Title: Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) CPC Library link to program files: https://doi.org/10.17632/cxbxs9btsv.1 Developer's repository link: https://github.com/lammps/lammps Licensing provisions: GPLv2 Programming language: C++, Python, C, Fortran Supplementary material: https://www.lammps.org Nature of problem: Many science applications in physics, chemistry, materials science, and related fields require parallel, scalable, and efficient generation of long, stable classical particle dynamics trajectories. Within this common problem definition, there lies a great diversity of use cases, distinguished by different particle interaction models, external constraints, as well as timescales and lengthscales ranging from atomic to mesoscale to macroscopic. Solution method: The LAMMPS code uses parallel spatial decomposition, distributed neighbor lists, and parallel FFTs for long-range Coulombic interactions [1]. The time integration algorithm is based on the Størmer-Verlet symplectic integrator [2], which provides better stability than higher-order non-symplectic methods. In addition, LAMMPS supports a wide range of interatomic potentials, constraints, diagnostics, software interfaces, and pre- and post-processing features. Additional comments including restrictions and unusual features: This paper serves as the definitive reference for the LAMMPS code. [1] S. Plimpton, Fast parallel algorithms for short-range molecular dynamics. J. Comp. Phys. 117 (1995) 1–19. [2] L. Verlet, Computer experiments on classical fluids: I. Thermodynamical properties of Lennard–Jones molecules, Phys. Rev. 159 (1967) 98–103. [ABSTRACT FROM AUTHOR]

In order to capture important subcellular dynamics, researchers in computational biology have begun to turn to mesoscopic models in which molecular interactions at the gene level behave as discrete stochastic events. While the trajectories of such models cannot be described with deterministic expressions, the probability distributions of these trajectories can be described by the set of linear ordinary differential equations known as the chemical master equation (CME). Until recently, it has been believed that the CME could only be solved analytically in the most trivial of problems, and the CME has been analyzed almost exclusively with kinetic Monte Carlo (KMC) algorithms. However, concepts from linear systems theory have enabled the finite state projection (FSP) approach and have significantly enhanced our ability to solve the CME without resorting to KMC simulations. In this paper, we review the FSP approach and introduce a variety of systems-theory-based modifications and enhancements to the FSP algorithm. Notions such as observability, controllability, and minimal realizations enable large reductions and increase efficiency with little to no loss in accuracy. Model reduction techniques based upon linear perturbation theory allow for the systematic projection of multiple time-scale dynamics onto a slowly varying manifold of much smaller dimension. We also present a powerful new reduction approach, in which we perform computations on a small subset of configuration grid points and then interpolate to find the distribution on the full set. The power of the FSP and its various reduction approaches is illustrated on few important models of genetic regulatory networks. [ABSTRACT FROM AUTHOR]

Oscillatory behavior is a key property of many biological systems. The small-gain theorem (SGT) for input/output monotone systems provides a sufficient condition for global asymptotic stability of an equilibrium, and hence its violation is a necessary condition for the existence of periodic solutions. One advantage of the use of the monotone SGT technique is its robustness with respect to all perturbations that preserve monotonicity and stability properties of a very low-dimensional (in many interesting examples, just one-dimensional) model reduction. This robustness makes the technique useful in the analysis of molecular biological models in which there is large uncertainty regarding the values of kinetic and other parameters. However, verifying the conditions needed in order to apply the SGT is not always easy. This paper provides an approach to the verification of the needed properties and illustrates the approach through an application to a classical model of circadian oscillations, as a nontrivial "case study," and provides a theorem in the converse direction of predicting oscillations when the SGT conditions fail. [ABSTRACT FROM AUTHOR]