Molecular Dynamics Simulations of the Antithrombin upon Ligand Recognition: A MM/GBSA Approach
Abstract not provided
59 BASIC BIOLOGICAL SCIENCES↗
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A coupled ordinates method for solution acceleration of rarefied gas dynamics simulations
Non-equilibrium rarefied flows are frequently encountered in a wide range of applications, including atmospheric re-entry vehicles, vacuum technology, and microscale devices. Rarefied flows at the microscale can be effectively modeled using the ellipsoidal statistical Bhatnagar–Gross–Krook (ESBGK) form of the Boltzmann kinetic equation. Numerical solutions of these equations are often based on the finite volume method (FVM) in physical space and the discrete ordinates method in velocity space. However, existing solvers use a sequential solution procedure wherein the velocity distribution functions are implicitly coupled in physical space, but are solved sequentially in velocity space. This leads to explicit coupling of the distribution function values in velocity space and slows down convergence in systems with low Knudsen numbers. Furthermore, this also makes it difficult to solve multiscale problems or problems in which there is a large range of Knudsen numbers. In this paper, we extend the coupled ordinates method (COMET), previously developed to study participating radiative heat transfer, to solve the ESBGK equations. In this method, at each cell in the physical domain, distribution function values for all velocity ordinates are solved simultaneously. This coupled solution is used as a relaxation sweep in a geometric multigrid method in the spatial domain. Enhancements to COMET to account for the non-linearity of the ESBGK equations, as well as the coupled implementation of boundary conditions, are presented. The methodology works well with arbitrary convex polyhedral meshes, and is shown to give significantly faster solutions than the conventional sequential solution procedure. Acceleration factors of 5–9 are obtained for low to moderate Knudsen numbers on single processor platforms.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Molecular Dynamics Simulations of Water Structure and Diffusion in a 1 nm Diameter Silica Nanopore as a Function of Surface Charge and Alkali Metal Counterion Identity
Water confined in nanopores-particularly in pores narrower than 2 nm-displays distinct physicochemical properties that remain incompletely examined despite their importance in nanofluidics, molecular biology, geology, and materials sciences. In this study, we use molecular dynamics simulations to investigate the coordination structure and mobility of water and alkali metals (Li, Na, K, Cs) inside a 1 nm diameter cylindrical silica nanopore as a function of surface charge density, a model system particularly relevant to the alteration kinetics of silicate glasses and minerals in geologic formations. We find that the presence of a negative surface charge and adsorbed counterions within the pore strongly impacts water structure and dynamics. In particular, it significantly orients water O-H bonds toward the surface and slows water diffusion by almost 1 order of magnitude. Ion crowding in the charged nanopore enhances the tendency of counterions to coordinate closely with the silica surface, which moderates the impact of ions on water dynamics. Co-ions are strongly excluded from the nanopore at all surface charges, suggesting that the 1 nm diameter cylindrical silica nanopores likely exhibit nearly ideal semipermeable membrane transport properties.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Erratum: “How accurate are stochastic rotation dynamics simulations of polymer dynamics?” [J. Rheol. 57, 1177–1194 (2013)]
No abstract prepared.
36 MATERIALS SCIENCE↗
Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations
The dynamic properties of liquid B{sub 2}O{sub 3} under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B{sub 2}O{sub 3} shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Visual Analytics for Deep Embeddings of Large Scale Molecular Dynamics Simulations
Molecular Dynamics (MD) simulation have been emerging as an excellent candidate for understanding complex atomic and molecular scale mechanism of bio-molecules that control essential bio-physical phenomenon in a living organism. But this MD technique produces large-size and long-timescale data that are inherently high-dimensional and occupies many terabytes of data. Processing this immense amount of data in a meaningful way is becoming increasingly difficult. Therefore, specific dimensionality reduction algorithm using deep learning technique has been employed here to embed the high-dimensional data in a lower-dimension latent space that still preserves the inherent molecular characteristics i.e. retains biologically meaningful information. Subsequently, the results of the embedding models are visualized for model evaluation and analysis of the extracted underlying features. However, most of the existing visualizations for embeddings have limitations in evaluating the embedding models and understanding the complex simulation data. We propose an interactive visual analytics system for embeddings of MD simulations to not only evaluate and explain an embedding model but also analyze various characteristics of the simulations. Our system enables exploration and discovery of meaningful and semantic embedding results and supports the understanding and evaluation of results by the quantitatively described features of the MD simulations (even without specific labels).
Chae, Junghoon↗
Look-ahead Dynamic Simulation
Look-ahead dynamic simulation software system incorporates the high performance parallel computing technologies, significantly reduces the solution time for each transient simulation case, and brings the dynamic simulation analysis into on-line applications to enable more transparency for better reliability and asset utilization. It takes the snapshot of the current power grid status, functions in parallel computing the system dynamic simulation, and outputs the transient response of the power system in real time.
Jin, Shuangshuang↗
Grouping techniques for large-scale cluster dynamics simulations of reaction diffusion processes
Not provided.
Materials Science↗
Interfacial Reactivity and Speciation Emerging from Na-Montmorillonite Interactions with Water and Formic Acid at 200 °C: Insights from Reactive Molecular Dynamics Simulations, Infrared Spectroscopy, and X-ray Scattering Measurements
Reactive organic fluid - mineral interactions at elevated temperatures contribute to the evolution of planetary matter. One of the less studied but important transformations in this regard involves the reactions of formic acid with naturally occurring clays such as sodium montmorillonite. To advance a mechanistic understanding of these interactions, we use ReaxFF reactive molecular dynamics simulations in conjunction with infrared (IR) spectroscopy and X-ray scattering experiments to investigate the speciation behavior of water-formic acid mixtures on sodium montmorillonite interfaces at 473 K and 1 atm. Using a newly developed reactive forcefield, we show that the experimental IR spectra of unreacted and reacted mixture can be accurately reproduced by ReaxFF/MD. We further benchmark the simulation predictions of sodium carbonate and bicarbonate formation in the clay interlayers using Small and Wide-Angle X-ray Scattering measurements. Subsequently, leveraging the benchmarked forcefield, we interrogate the pathway of speciation reactions with emphasis on carbonate, formate, and hydroxide groups elucidating the energetics, transition states, intermediates, and preferred products. Further, we also delineate the differences in reactivities and catalytic effects of clay edges, facets, and interlayers owing to their local chemical environments, which have far reaching consequences in their speciation behavior. The experimental and simulation approaches described in this study and the transferable forcefields can be applied translationally to advance the science of clay-fluid interactions for several applications including subsurface fluid storage and recovery and clay-pollutant dynamics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
High-Performance Molecular Dynamics Simulation for Biological and Materials Sciences: Challenges of Performance Portability, Dallas, TX, November 2018.
Highly-optimized parallel molecular dynamics programs have allowed researchers to achieve ground-breaking results in biological and materials sciences. This type of performance has come at the expense of portability: a significant effort is required for performance optimization on each new architecture. Using a metric that emphasizes speedup, we assess key accelerating programming components of four different best-performing molecular dynamics programs - GROMACS, NAMD, LAMMPS and CP2K-- each having a particular scope of application, for contribution to performance and for portability. We use builds with and without these components, tested on HPC systems. We also analyze the code-bases to determine compliance with portability recommendations. We find that for all four programs, the contributions of the non-portable components to speed are essential to the programs' performances; without them we see a reduction in time-to-solution of a magnitude that is insufferable to domain scientists. This characterizes the performance efficiency that must be approached for good performance portability on a programmatic level, suggesting solutions to this difficult problem, which should come from developers, industry and funding institutions, and possibly new research in programming languages.
Computer Science↗
Water-In-Salt LiTFSI Aqueous Electrolytes (2): Transport Properties and Li+ Dynamics Based on Molecular Dynamics Simulations
Explore the source record for details and available documents.
Zhang, Yong↗
Atomic and micro-structure features of nanoporous aluminosilicate glasses from reactive molecular dynamics simulations
Not provided.
Materials Science↗
Molecular dynamics simulation studies of structural and dynamical properties of rapidly quenched Al
The structural and dynamical properties of rapidly quenched Al are studied by molecular dynamics simulations. The pair-correlation function of high temperature liquid Al agrees well with the experimental results. Different cooling rates are applied with high cooling rates leading to glass formation, while low cooling rates leading to crystallization. The local structures are characterized by Honeycutt–Andersen indices and Voronoi tessellation analysis. The results show that for high cooling rates, the local structures of the liquid and glassy Al are predominated by icosahedral clusters, together with considerable amount of face-centered cubic and hexagonal close packed short-range orders. These short-range order results are further confirmed using the recently developed atomic cluster alignment method. Moreover, the atomic cluster alignment clearly shows the crystal nucleation process in supercooled liquid of Al. Finally, the mean square displacement for the liquid is also analyzed, and the corresponding diffusion coefficient as a function of temperature is calculated.
36 MATERIALS SCIENCE↗
Surface hopping molecular dynamics simulation of ultrafast methyl iodide photodissociation mapped by Coulomb explosion imaging
Our simulation demonstrates the robustness of the Coulomb explosion imaging technique in studying methyl iodide photodissociation, and shows that it can be effectively used for imaging non-adiabatic transitions in coordinate space.
Ding, Yijue↗
Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes
The architecture of a biological membrane hinges upon the fundamental fact that its properties are determined by more than the sum of its individual components. Studies on model membranes have shown the need to characterize in molecular detail how properties such as thickness, fluidity, and macroscopic bending rigidity are regulated by the interactions between individual molecules in a non-trivial fashion. Simulation-based approaches are invaluable to this purpose but are typically limited to short sampling times and model systems that are often smaller than the required properties. To alleviate both limitations, the use of coarse-grained (CG) models is nowadays an established computational strategy. We here present a new CG force field for cholesterol, which was developed by using measured properties of small molecules, and can be used in combination with our previously developed force field for phospholipids. The new model performs with precision comparable to atomistic force fields in predicting the properties of cholesterol-rich phospholipid bilayers, including area per lipid, bilayer thickness, tail order parameter, increase in bending rigidity, and propensity to form liquid-ordered domains in ternary mixtures. We suggest the use of this model to quantify the impact of cholesterol on macroscopic properties and on microscopic phenomena involving localization and trafficking of lipids and proteins on cellular membranes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
ReaxFF molecular dynamics simulations on the structure and dynamics of electrolyte water systems at ambient temperature
Here, ReaxFF molecular dynamics simulations have been performed to study the effect of cations Li + , Na+ and K + and anion Cl - on the structural and dynamical properties of water, using the force field recently developed by Fedkin and co-workers. The structural relationship of ion and water has been analyzed from the radial distribution function and angular distribution. Comparisons of ReaxFF angle variation of ions and water within the first solvation shell were made and found to be in good agreement with literature. The disruption of hydrogen bond network of water by ions is elucidated by ion-water residence times, water-water hydrogen bond dynamics and reorientational dynamics. ReaxFF diffusion coefficient and residence times of electrolyte water system were compared with ab initio and non-reactive potentials to analyze the difference in dynamics. We gained insight into the ion interaction with water and how it can accelerate or decelerate water dynamics. ReaxFF outlines the formation and dissolution of metal hydroxides and metal chlorides over the course of simulation to explain the diffusion dynamics of water in salt solutions, allowing us to elucidate the impact of concentration on the self-diffusivity of water and ions in solutions, and to reveal that this effect always decreases the mobility and is not at all ion-specific. The obtained findings have opened new opportunities to extend the ReaxFF methodology towards systems involving electrolytes.
42 ENGINEERING↗