Atomistic molecular dynamics. Medical search. Frequent questions

Atomistic simulations can illuminate detailed mechanisms of brittle and ductile fracture and plasticity. (cornell.edu)
Computational studies can elucidate unfolding mechanisms on an atomistic scale. (fu-berlin.de)
In this project, atomistic simulations will be used to complement in-situ experiments to gain insights in the fundamental deformation mechanisms at the nanoscale. (imechanica.org)
Atomistic Mechanisms of ZnO Aggregation from Ethanolic Solution: Ion Association, Proton Transfer, and Self Organization. (mpg.de)
Inspired by the transient testing experiments we carried out molecular dynamics simulations of stress drops in the regimes similar to those experimentally performed, with the aim to explore the mechanisms responsible for GB accommodation and to verify whether dislocations are still emitted when strain rates after the stress drops are up to 2 or 3 orders of magnitude lower than those usually applied in atomistic deformation simulations. (psi.ch)
To study deformation mechanisms using molecular dynamics, very high strain rates have to be applied. (psi.ch)
As a consequence, atomistic models of microporous carbons are invaluable to get insight into experimental results and molecular mechanisms. (cecam.org)
In this project, a number of proposed and hypothesised microscopic mechanisms leading to the onset of ASB will be explored at the atomistic and mesoscopic scales. (findaphd.com)
Available projects also include computational investigations of reaction mechanisms and reaction dynamics for solar energy conversion and catalysis/photocatalysis. (lu.se)

In this study, the effects of ultrathin films on surface dynamics of these polymers were investigated. (ncsu.edu)
Industrially sourced polymers are typically polydisperse (comprising a broad distribution of molecular weights), making their rheology more suitable for processing. (lu.se)

From atomistic molecular dynamics simulations, the many-body electronic polarization effect was found to be important for modeling ILs, especially their dynamics. (uchicago.edu)
We introduce atomistic modeling techniques and its importance for solving problems in modern engineering sciences, with an emphasis on mechanical properties. (mit.edu)
We demonstrate how atomistic modeling can be used to understand how materials fail under extreme loading, involving unfolding of proteins and propagation of cracks. (mit.edu)
Students will learn the basics of atomistic modeling, including choosing interatomic potentials, visualization and data analysis. (mit.edu)
Atomistic modeling of fracture of a nanocrystal of copper. (mit.edu)
With the increasing availability of computational power and advances in modeling, atomistic simulations are rapidly growing in scale and complexity. (uic.edu)
3. Atomistic and Experimental Modeling for Adsorption of Metal Ions With Carbon Nanotubes in Aqueous Environment. (routledge.com)
Since 2013 he leads the laboratory for Computational Science and Modeling, in the institute of Materials at EPFL, that focuses on method development for atomistic materials modeling based on statistical mechanics and machine learning. (epfl.ch)
He is one of the core developers of several open-source software packages, including http://ipi-code.org and http://chemiscope.org , and proudly serves the atomistic modeling community as an associate editor of the Journal of Chemical Physics, as a moderator of the physics.chem-ph section of the arXiv, and as an editorial board member of Physical Review Materials. (epfl.ch)
Here we explore the translation of biological composites to engineering applications, using a variety of tools including molecular modeling, AI and machine learning, and experimental synthesis and characterization. (mrs.org)
Atomistic modeling of apatite-collagen composites from molecular dynamics simulations extended to hyperspace. (mpg.de)
MOLSIM is a software for atomistic and coarse-grain modeling of molecular, colloidal, and polymer systems, with extensive static and dynamic analyses, employing molecular dynamics, stochastic dynamics, and Monte Carlo simulation techniques. (lu.se)

Dissipative particle dynamics (DPD) is an off-lattice mesoscopic simulation technique which involves a set of particles moving in continuous space and discrete time. (wikipedia.org)
1. Theory, Molecular/Mesoscopic Simulations, and Experimental Techniques of Aqueous Phase Adsorption. (routledge.com)

Tungsten surface binding energy is calculated by molecular dynamic and many-body potentials. (purdue.edu)
Advances in interaction potentials [17], including machine learning based force fields [18], are crucial in making a range of atomistic structures available, corresponding to carbons synthesised using various conditions, and opening new avenues of research. (cecam.org)

This paper presents the QuantumATK ForceField module and its algorithms, such as molecular dynamics (MD), adaptive kinetic Monte Carlo (AKMC) and nudged elastic band (NEB). (synopsys.com)
This research uses molecular dynamics, kinetic Monte Carlo and binary collision approximation methods to model fusion relevant material bombarded by energetic particles to investigate retention, deposition, sputtering, erosion, blistering effects, diffusion, and so on. (purdue.edu)
Several approaches ranging from atomistic Molecular Dynamics, kinetic Monte Carlo, and Density Functional Theory to continuum mass transport were reported. (sbir.gov)

This book covers theoretical aspects of adsorption, followed by an introduction to molecular simulations and other numerical techniques that have become extremely useful as an engineering tool in recent times to understand the interplay of different mechanistic steps of adsorption. (routledge.com)
Once suitable atomistic models have been generated, additional challenges come with the simulation of adsorption processes. (cecam.org)

5. Coating of Nanoparticles in Aqueous Solutions : Insights from Molecular Dynamics Simulations. (routledge.com)
At the Max Planck Institute for Polymer Research we have taken a closer look at the processes taking place on molecular length scales and thus gained fundamental insights into the chemical reactions at electrodes. (mpg.de)

Particles represent whole molecules or fluid regions, rather than single atoms, and atomistic details are not considered relevant to the processes addressed. (wikipedia.org)
We also describe a scalable, distributed GPU ray-casting implementation capable of rendering complex atomistic simulations with millions of atoms in real-time. (uic.edu)
Our recent studies of the moving contact-line problem via molecular dynamics simulations have shown that the dynamic contact angle effect (Lukyanov, Likhtman 2013) is essentially conditioned by the microscopic processes in a small region, several atoms wide, around the contact line, basically at nanoscale. (reading.ac.uk)

DPD was initially devised by Hoogerbrugge and Koelman to avoid the lattice artifacts of the so-called lattice gas automata and to tackle hydrodynamic time and space scales beyond those available with molecular dynamics (MD). It was subsequently reformulated and slightly modified by P. Español to ensure the proper thermal equilibrium state. (wikipedia.org)

The analysis of the sputtered tungsten angular distributions show that molecular dynamic accurately reproduced the [111] most prominent preferential ejection directions in bcc tungsten, while the distinct shapes by typical Monte Carlo codes is caused by the treatment of amorphous target. (purdue.edu)
The simulation techniques include Molecular Dynamics, Monte-Carlo and Brownian Dynamics, as well as field-theoretic simulations. (reading.ac.uk)
Our studies are performed using hybrid molecular dynamics/Monte Carlo simulations and theoretical modelling. (reading.ac.uk)
Early attempts to generate atomistic models commonly involved Reverse Monte Carlo (RMC) approaches. (cecam.org)
In the former projects atomistic and coarse-grained molecular dynamics and Monte Carlo simulations will be used together with experimental techniques such as scattering and circular dichroism, whereas the third project is focused on atomistic simulations solely. (lu.se)

We used all-atom molecular dynamics (MD) simulations to investigate the interactions between dendrimers and hydrocarbons. (confex.com)
In this project we will use molecular dynamics (MD) simulations to investigate local fluctuations in proteins. (lu.se)

The mesoscale picture provided by pore size distributions remains insufficient to model a number of phenomena as adsorbate-adsorbent interactions at the atomistic scale can affect macroscopic properties significantly. (cecam.org)
Instead, no regular assembly is obtained from solutions with high peptide concentrations, as their dynamics is dominated by strong repulsive peptide-peptide electrostatic interactions, and from solutions at pH 10, in which the total peptide charge is zero. (ibecbarcelona.eu)
The quality of molecular dynamics simulations strongly depends on the accuracy of the underlying force fields (FFs) that determine all intra- and intermolecular interactions of the system. (q-chem.com)
However, in contrast to mononuclear systems, the multidimensional dynamics of the PSS in solvated molecular arrays have not yet been elucidated due to the expected complications associated with the connectivity between the metal centers and the strong interactions with the surroundings. (lu.se)

We review a series of studies focused on the mechanical behavior of materials, especially deformation and fracture, and how these phenomena can be modeled using a combination of molecular dynamics and machine learning, to generate a novel simulated evolutionary process that offers directed adaptation of biomaterial properties. (mrs.org)

After the class, students should have a basic understanding about the fundamentals, application areas and potential of classical molecular dynamics for problems in mechanics of materials. (mit.edu)

Using molecular dynamics (MD) and multiscale methods, adaptations can be made to allow MD to answer problems relevant to engineers. (cornell.edu)

Using molecular dynamics and previous results from the literature, we demonstrate the correlation between the self-diffusion coefficient of water in silica nanopores and the concentration of proteins or nanoparticles contained therein. (springer.com)

We also present case studies of protein material optimization using genetic algorithms, applied to 3D printed composites, molecular design, and a translation of protein folding to music and back. (mrs.org)

Additionally, support of classical atomistic, coarse-grained molecular dynamics methods, phase-field simulations, self-consistent field theoretic approaches as well as Deep Learning methods are also available. (ornl.gov)
These effects are likely to be due to creation of persistent localised defects, which are impossible to study using non-atomistic methods. (wias-berlin.de)
to develop data-driven and high-throughput atomistic simulation methods for model validation and the discovery of novel materials. (icams.de)

The effect of repeat unit structure on the shape and internal organization of various dendrimers was probed using atomistic molecular dynamics simulations. (ncsu.edu)
Molecular structure-property relationships for electron-transfer rate attenuation in redox-active core dendrimers. (ncsu.edu)
Further consideration of these data indicated that, while the dendrimers containing rigid ligands had better encapsulated redox cores for a given molecular weight, these molecules had higher electron-transfer rates for a given molecular radius. (ncsu.edu)

Molecular dynamic simulations of Si surfaces and growth. (icams.de)

Third, the effect of aging on fatigue crack growth is studied by varying the resistance to dislocation motion in the dislocation dynamics region of CADD. (cornell.edu)
All these reactions will be mapped into a purpose-built thermo-elastodynamic code of dislocation dynamics, which will enable the study of the formation of ASBs at larger lengthscales and over extended timescales than those molecular dynamics allow. (findaphd.com)

This information is relevant in bio-electron transfer schemes and in emerging molecular electronics schemes such as storage of information using individual molecules. (ncsu.edu)

In this work, we shed light on this matter through atomic-scale molecular dynamics simulations of eight different one-component lipid bilayers comprised of PCs with 18 carbons in their acyl chains. (sharcnet.ca)

The objective herein is to discuss an algorithm for generating nanocrystalline structures for use in molecular dynamics simulations. (dtic.mil)

Using lattice dynamics and molecular dynamics (MD), the role of the kinematic generation of dislocations (a dislocation core instability that leads to the multiplication of dislocations moving at moderate "resonance" speeds) will be explored in Ti and W alloys. (findaphd.com)

Despite the plethora of molecular visualization techniques, visualizing and exploring large-scale atomistic simulations remain difficult. (uic.edu)
In this paper, we present an application for the interactive visualization and exploration of large-scale atomistic simulations in ultra-resolution immersive environments. (uic.edu)

This will concern both lattice dynamics theoretical studies and observational MD studies of the kinematic reactions, and result in a mapping of resonance speeds vs multiplication rates with which to determine whether on its own, kinematic generation suffices to account for the fundamental instability that causes ASB. (findaphd.com)

This distribution, however, did not preclude a molecular surface composed of a substantial portion of the topologically terminal groups. (ncsu.edu)

The development of accurate and efficient molecular dynamics force fields are a crucial step in an overall materials discovery workflow that complements experiments with theoretical simulations. (mrs.org)

The Complex Fluids and Theoretical Polymer Physics research group focuses on the structure and dynamics of complex fluids, with polymeric fluids being the overarching theme. (reading.ac.uk)

In this technique, care was taken to ensure complete structural equilibration by implementing a high temperature dynamics/simulated annealing protocol prior to evaluation of the molecular structure and dynamics. (ncsu.edu)

Spectroscopic studies and atomistic molecular dynamics simulations reveal significant differences between the secondary structures of CREKA and CRENKA. (ibecbarcelona.eu)

Molecular Dynamics is becoming a principle methodology in the study of nanoscale systems, paving the way for innovations in battery design and alternative fuel applications. (uic.edu)

Here we present a molecular dynamics simulation study of this behaviour. (wias-berlin.de)

Particular emphasis is on developing a sensitivity for the significance of mechanics in different areas, and how atomistic and continuum viewpoints can be coupled. (mit.edu)

This file is an annotated version of class notes "Molecular Dynamics I" and explains N coupled equations, conservation of the total energy, phase space evolution, thermodynamical averages, and the computational experiment. (mit.edu)
Overall, the accuracy, user-friendliness, and minimal computational overhead of the Q-Force protocol, make it widely applicable for atomistic molecular dynamics simulations. (q-chem.com)

The goal of our IL research is to obtain a unified understanding of the properties of ILs with respect to their underlying molecular structure. (uchicago.edu)
We investigate the properties of the water/alumina interface using molecular dynamics simulations to determine rates for aluminum ion diffusion in the corrosion process. (aps.org)
In this paper, thermal transport properties of armchair/zigzag graphene superlattice nanoribbons (A/Z graphene SLNRs) are investigated by performing nonequilibrium molecular dynamics simulations. (springer.com)
During his Ph.D., he worked on the prediction of dielectric properties of organic materials for photovoltaic applications and was also the main developer of Q-Force, which derives molecular dynamics force fields from quantum mechanical calculations. (q-chem.com)
Applications of quantum chemical calculations to investigations of molecular and materials properties, as well as development and applications of classical reaction dynamics simulations. (lu.se)

In recent years, atomistic carbon models generated without any input from experimental data have become more common. (cecam.org)
Collaborative investigations of photophysics, photochemistry and ultrafast dynamics in molecular and heterogeneous systems carried out together with experimental colleagues. (lu.se)
Projects are often closely connected with experimental investigations of ultrafast reaction dynamics. (lu.se)

Because they are dense, highly crosslinked, and chemically stable, diamond-like carbon (DLC) films and silicon oxide films (SiOx) were deposited on poly(ethylene terephthalate) by plasma-enhanced chemical vapor deposition to restrict polymer surface dynamics. (ncsu.edu)
We perform large scale molecular dynamics simulations of dense polymeric systems of various topology (linear, stars, rings) and propose microscopic definition of polymer entanglements. (reading.ac.uk)

The CNE currently supports large-scale electronic structure codes that allow direct ab-initio simulations of nanoscale systems as well as specialized codes for strongly correlated materials and to support atomistic simulations of magnetic nanosystems. (ornl.gov)

2. Graphene Nanopores-Based Separation of Impurities from Aqueous Medium: An insight from molecular simulation. (routledge.com)

Existing molecular representations are not perceptually scalable and often adopt a rigid definition of surfaces, making them inappropriate for nanostructured materials where boundaries are inherently ill-defined. (uic.edu)

This conclusion is consistent with the computed radial density distributions of the different generations calculated from molecular dynamics simulations. (ncsu.edu)

We employ a hybrid representation which combines solid ball-and-stick glyphs with volumetric surfaces to visually convey the uncertainty in molecular boundaries at the nanoscale. (uic.edu)

This distinguishes DPD from Brownian dynamics in which each particle experiences a random force independently of all other particles. (wikipedia.org)

In the last decades, the advent of nanotechnologies enabled the design of tailored molecular sensors to detect different pollutants in water, such as pathogens, organic, and inorganic chemicals [ 6 ]. (springer.com)

Chemicals and Drugs17

Analytical, Diagnostic and Therapeutic Techniques and Equipment14

Phenomena and Processes41

Disciplines and Occupations4

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture1

Information Science7

Health Care2

Mechanisms9

Polymers2

Modeling12

Mesoscopic2

Potentials2

Kinetic3

Adsorption2

Insights2

Atoms3

Scales1

Monte-Carlo5

Simulations to investigate2

Interactions4

Fracture1

Classical Molecular Dynamics1

Multiscale1

Nanoparticles1

Composites1

Methods3

Dendrimers3

Dynamic simulations1

Dislocation dynamics2

Molecules1

Lipid1

Nanocrystalline1

Dislocations1

Visualization2

Lattice dynamics1

Topologically1

Experiments1

Polymeric fluids1

Structure and dyna1

Structures1

Methodology1

Study1

Continuum1

Computational2

Properties5

Experimental3

Dense2

Strongly1

Graphene1

Representations1

Distributions1

Surfaces1

Force1

Pollutants1