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Showing 1 to 20 of 100 for “"md simulation"”.
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Motion in the solid state studied by NMR and extended time scale MD simulation
… magnetic resonance (NMR) and molecular dynamics (MD) simulations are two, highly complementary techniques that can be used in this pursuit, with NMR providing robust measurements of kinetic parameters across a large range of time-scales while MD can give insight into the form that the motion …
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Simulate Time-integrated Coarse-grained Molecular Dynamics with Geometric Machine Learning
Molecular dynamics (MD) simulation is the workhorse of various scientific domains but is limited by high computational cost. Learning-based force fields have made major progress in accelerating ab-initio MD simulation but are still not fast enough for many real-world applications that require …
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Computational analysis of thermodynamic and mechanical properties of nano-materials
… conditions by employing the molecular dynamics (MD) simulation technique. In addition, we also employ the MD simulation to investigate the thermal expansion coefficient variation of silicon nano-slabs with different thicknesses and propose a theoretical expression for thermal expansion …
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Atomistic simulation of strength and deformation of ceramic materials
… ceramic materials, utilizing molecular dynamics (MD) simulation that incorporates newly developed theoretical models and computational algorithms to probe the microstructural effects in crystalline, amorphous, and nanocrystalline media. Specific issues of a materials property or mechanics of …
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Efficient sampling of protein conformational dynamics and prediction of mutation effects.
Molecular dynamics (MD) simulation is a powerful tool enabling researchers to gain insight into biological processes at the atomic level. There have been many advancements in both hardware and software in the last decade to both accelerate MD simulations and increase their predictive accuracy; …
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Molecular Dynamics Study of Nano-confinement Effect on Hydrocarbons Fluid Phase Behavior and Composition in Organic Shale
… and challenge conventional macroscale reservoir simulation predictions. Moreover, the unusual high temperatures and pressures have increased the cost as well as the hazardous level for reservoir analyzes by lab experiments. Molecular Dynamics (MD) simulation of reservoirs can be a safe and …
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Hydration Mechanisms in Sulfonated Polysulfones for Desalination Membrane Applications
… on these ionic polysulfones molecular dynamics (MD) simulation is used to investigate ion aggregation and hydration at the atomic scale. MD simulations show that the sulfonate and sodium ions are not simply paired. Instead, they form an ionic network. The molecular nature of melting water within …
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A study of Asphalt Aging Behavior Using Molecular Dynamics Simulations
… in asphalt. Therefore, Molecular Dynamics (MD) simulation method is used in this study to understand how the chemical composition and property changes of asphalt after oxidative aging affect the physical, thermodynamic, rheological and mechanical performance of the asphalt, and how the …
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Computational modeling of intrinsic dissipation in nano-structure
… (NEMS). We, first, use molecular dynamics (MD) simulation and gain an understanding of the underlying loss mechanisms. Using insights from the MD simulation, a multi-scale method to model intrinsic damping is developed. The high frequency vibration in NEMS have important applications. A few …
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Exploration of the Application of Machine Learning to the Improvement of Interatomic Potentials
Current methods for atomistic simulations of material systems suffer from limitations which restrict the ability of the simulations to correctly characterize certain material behavior and physical phenomena. Small scale ab initio molecular dynamics (AIMD) modeling is highly accurate but is …
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Energetics Calculation of {10-12} Twin Nucleation and Growth in Magnesium and Alloys using Density Functional Theory and Atomistic Simulation
… nucleation and growth using molecular dynamics (MD) simulations and Density Functional Theory (DFT) calculation for Mg and its alloys. For MD simulations, the embedded atom method (EAM) potential and modified embedded atom method (MEAM) potentials are used. All simulations are conducted with …
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Molecular Dynamic Simulation of Bio-molecular Dynamics, Folding, and Assembly
… organism. Computational molecular dynamics (MD) simulations can characterize biomolecules at a microscopic level. These indispensable tools use classical mechanical approaches to describe biomolecular dynamics, folding, and binding mechanisms. Although there are many different types of MD …
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MARKOV STATE MODELS AND THEIR APPLICATIONS IN PROTEIN FOLDING SIMULATION, SMALL MOLECULE DESIGN, AND MEMBRANE PROTEIN MODELING
… glutamic acid to valine. Molecular dynamics (MD) simulations could be utilized to study protein folding and effects of perturbations on protein energy landscape; however, due to its inherent atomic resolution, MD simulations usually provide enormous amount of data even for small proteins. A …
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Thermal Transport Across Nano Engineered Solid-Liquid Interfaces
… for the nanoscale phenomena, molecular dynamics (MD) simulation is used to explore the mechanism of thermal transport at the nanometer scale interfaces. With the aid of MD simulation, several interfacial geometric parameters are investigated. It was found that solid-liquid interaction strength …
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Structure, function, and dynamics of cell motility proteins
"Molecular dynamics (MD) simulation techniques have been employed to investigate structure and function relationships in cell motility proteins at atomic resolution. (1) To analyze motions in cell motility proteins an algorithm is described to identify and visualize the movements of rigid domains …
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Selective molecular transport in nanopore systems
… dielectrophoresis. Third, I introduce the first simulation of molecular artificial water channel pillar[5]arene (PAP) and uncover the mechanics of its water transport and self-aggregation properties. Fourth, I characterize the water permeability and ion rejection of truncated human membrane …
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Dynamics Of Biopolymers On Nanomaterials Studied By Quasielastic Neutron Scattering And Mdsimulations
… neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, β-Casein and Inorganic …
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Markov state modeling of binding and conformational changes of proteins
… is investigated with molecular dynamics (MD) simulations of the protein-peptide system Mdm2-PMI and by analysis of data from relaxation experiments. The central task it to uncover the binding mechanism, which is described by the sequence of (partial) binding events and conformational …
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Molecular Dynamics Study of Characterization in Metal-Free Friction Materials
… with the assistance of molecular dynamics (MD) tools at the nano scale.</p> <p>First, the concept of the contacted surfaces in friction at the atomic scale was introduced in order to get accurate understanding of the friction process compared to the macro scale. A MD model of 3C-SiC …
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Nanoscale control in biological and synthetic systems
… microscope” of the molecular dynamics (MD) simulation method provides insight into the behavior of systems at the atomic level, enabling the visualization of systems far beyond the limits of any experimental method. Moreover, MD facilitates experimentation with a virtually unlimited …
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