• AMHERST, Mass. - Jianhan Chen , a University of Massachusetts Amherst chemistry and biochemistry and molecular biology professor, has received a five-year, $2 million National Institutes of Health (NIH) grant to support research in his computational biophysics lab aimed at better understanding the role of intrinsically disordered proteins (IDPs) in biology and human disease. (umass.edu)
  • In his lab, Chen and colleagues focus on using computer simulations to model the molecular structure and dynamics of proteins. (umass.edu)
  • Our goal is really trying to combine simulation and experiments in collaboration with other labs to tease out what are the hidden features of these disordered proteins that are crucial to their function," Chen says. (umass.edu)
  • Researchers at Rochester Institute of Technology developed computer simulations that show the coronaviruses use their spike proteins to attach themselves to the host cells in both bats and humans in much the same way. (rit.edu)
  • The scientists used a computer simulation method called molecular dynamics to put proteins in a solvated simulation and then watch them move. (rit.edu)
  • While many studies have been focused on the membrane structure, the dynamics of such systems are crucial for the function of the membrane including membrane bound proteins. (lu.se)
  • For both proteins, the oxygen-17 relaxation depended only very weakly on pD, showing that ionic residues do not perturb hydration water dynamics more than other surface residues. (lu.se)
  • The course covers both the principles that determine the properties of proteins and the experimental methods that are used to study these properties in modern molecular protein science. (lu.se)
  • Mobility Testbed - an open-source multi-agent simulation testbed for transport coordination algorithms. (wikipedia.org)
  • Considering the stochastic nature of common sampling algorithms such as molecular dynamics simulations, biomolecular trajectories represent a multidimensional random walk of which the analysis is especially prone to suffer from sampling deficiencies ( Hess, 2002 ). (elifesciences.org)
  • Quantum computers will efficiently run algorithms that their classical counterparts can't manage. (deloitte.com)
  • He has shown from first principles that the very first luminous objects are very massive stars and has developed novel numerical algorithms using adaptive-mesh-refinement simulations that capture over 14 orders of magnitude in length and time scales. (stanford.edu)
  • Molecular Workbench offers 2D and 3D interactive molecular dynamics simulations for teaching physics, chemistry, and biology. (concord.org)
  • His research is at the confluence of statistical mechanics, molecular biology, hybrid modeling and large-scale computer simulations. (foresight.org)
  • Genetics and molecular biology 2023 0 0. (cdc.gov)
  • A common problem that affects simulations of complex systems within the computational physics and chemistry communities is the so-called sampling problem or rare event problem where proper sampling of energy landscapes is impeded by the presences of high kinetic barriers that hinder transitions between metastable states on typical simulation time s. (researchgate.net)
  • Enhanced sampling methods are indispensable in computational chemistry and physics, where atomistic simulations cannot exhaustively sample the high-dimensional configuration space of dynamical systems due to the sampling problem. (researchgate.net)
  • To achieve our goals we applied an integrated strategy, which involves elements of synthetic organic chemistry, molecular enzymology (recombinant expression and targeted modification of eicosanoid synthesising enzymes by site-directed mutagenesis) and computer-assisted modelling (structural and kinetic modelling and simulation of molecular dynamics). (europa.eu)
  • 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)
  • Our research ideology is to work on theoretical models of complex fluids and use extensive computer simulations to inform and verify these models. (reading.ac.uk)
  • Our studies are performed using hybrid molecular dynamics/Monte Carlo simulations and theoretical modelling. (reading.ac.uk)
  • Our research interests include studies of equilibrium and dynamical behaviour of complex molecular liquids and ionic solutions in bulk, at interfaces and in confined environments and also of molecular clusters based on theoretical and computational methods. (iitk.ac.in)
  • Prof. Thomas Mazzuchi (EMSE) presented an invited lecture titled " Use of Expert Judgment in Risk Assessments Involving Complex State Spaces " at the Rutgers University's Center for Discrete Mathematics and Theoretical Computer Science Workshop on The Science of Expert Opinion, October 24-25. (gwu.edu)
  • Such practice is needed in atomistic simulations of complex systems where even thousands of degrees of freedom are sampled. (researchgate.net)
  • 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)
  • The simulation techniques include Molecular Dynamics, Monte-Carlo and Brownian Dynamics, as well as field-theoretic simulations. (reading.ac.uk)
  • apply numerical methods, such as Molecular Dynamics Metropolis Monte Carlo simulations · use Statistical Mechanical tools with, as well as without, the aid of computer programs to calculate various properties of macroscopic systems. (lu.se)
  • Several steps were completed from the modeling of the carbon structures and pollutants to simulations of molecular dynamics. (academicjournals.org)
  • The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. (nature.com)
  • Because of their chaotic state, IDPs must be described using ensembles of structures, and computer simulations play a crucial role in the quantitative description of these disordered ensembles. (umass.edu)
  • Unlike most molecular viewers that show static structures, molecular dynamics models show functions of molecules, primarily through visualizing the cause-effect relationships set up by properly-chosen initial conditions or directed by user operations in the middle of a simulation. (concord.org)
  • This will give them an advantage in solving problems that involve multiple, complex interdependencies and correlations (such as predicting molecular structures). (deloitte.com)
  • Arena - a flowchart-based discrete event simulation software developed by Rockwell Automation Automation Studio - a fluid power, electrical and control systems design and simulation software developed by Famic Technologies Inc. Chemical WorkBench - a chemical kinetics simulation software tool developed by Kintech Lab. (wikipedia.org)
  • This indicates that, if at all, the simulation box size only minimally affects both the thermodynamics and kinetics of the type of biomolecular systems presented in this work. (elifesciences.org)
  • Computer simulations, specifically, first-principles nonadiabatic quantum molecular dynamics simulations, reproduced the conversion of light energy to lattice vibrations. (nanowerk.com)
  • 1 Quantum computing could be a game-changer for any industry that needs to accurately calculate and finely tune molecular properties, predict material behaviour, and understand how this behaviour will vary with the slightest molecular change. (deloitte.com)
  • Although quantum computers exist primarily in labs, their capabilities continue to grow. (deloitte.com)
  • With quantum computers in their toolkits, scientists will be able to not only conduct more efficient and accurate simulations, but explore molecular and chemical reactions beyond classical computers' current capabilities. (deloitte.com)
  • At this writing, the world's highest-performing quantum computers don't yet have enough computing power to compete with classical machines. (deloitte.com)
  • nute 1:50) and includes visualizations of genetic molecular dynamics, electromechanical behavior of heart tissue, microscale climate modelling, astrophysics, and quantum mechanics. (visual.ly)
  • Structure and dynamics of molecular solutions in bulk and confined systems, Structure and dynamics of molecular clusters with charge defects, Chemical reaction dynamics in condensed phases and in clusters, Molecular properties of solid-liquid, liquid-liquid and liquid-vapour interfaces, Structure and dynamics of supercooled and supercritical fluids, Structure and Dynamics of macromolecular solutions, Computer simulations of clusters and condensed phases using classical and quantum methods. (iitk.ac.in)
  • Employing quantum simulation method based on density functional theory (DFT), Prof. Li and his collaborators have discovered new insights into the electronic origin of photoluminescence in Silicon nanocrystals embedded in amorphous silicon oxide matrix. (gwu.edu)
  • 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)
  • We have brilliant colleagues who are in the forefront of their respective research and focused on an understanding of protein structure and dynamics, and how we might understand how life actually works by probing these things at an intimate level of detail. (nih.gov)
  • We showed how the presence of ions affects the structure and dynamics of hydrogen bonds in aqueous systems. (iitk.ac.in)
  • Physics Abstraction Layer - an open-source physics simulation package. (wikipedia.org)
  • Project Chrono - an open-source multi-physics simulation framework. (wikipedia.org)
  • SOFA - an open-source framework for multi-physics simulation with an emphasis on medical simulation. (wikipedia.org)
  • Step - an open-source two-dimensional physics simulation engine (KDE). (wikipedia.org)
  • CircuitLogix - an electronics simulation software developed by Logic Design Inc. COMSOL Multiphysics - a predominantly finite element analysis, solver and simulation software package for various physics and engineering applications, especially coupled phenomena, or multi-physics. (wikipedia.org)
  • The aim is to achieve a molecular understanding of the underlying physics by utilizing the toolbox we have developed for more than a decade for Hst5, combining computer simulations and experiments. (lu.se)
  • A few of many examples are studies in, and research on, environment and climate change, accelerator physics, cell dynamics and super novae. (lu.se)
  • The course also includes computer and experiment laboratory exercises in order to introduce the students to methods used in modern nuclear physics. (lu.se)
  • 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)
  • abstract = "A domain is conventionally defined as a stationary sub-region of the simulated system in a domain-decomposition scheme for molecular dynamics (MD) simulations on parallel computers. (elsevierpure.com)
  • V. E. Taylor, Stevens, R. L., and Arnold, K., "Parallel Molecular Dynamics: Communication Requirements for Massively Parallel Machines", in Proceedings of the Fifth Symposium on the Frontiers of Massively Parallel Computation (Frontiers'95), 1995. (anl.gov)
  • In this paper, a simple MD simulation using a Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) was developed to calculate the hydrogen uptake in ZSM5, Graphite Nanofiber, Graphene Oxide Framework, and reduced Graphene Oxide. (ui.ac.id)
  • Even powerful supercomputers can't make exact calculations, and imprecise estimations aren't accurate enough to simulate molecular and atomic interactions, especially in complex molecules. (deloitte.com)
  • So we carried out molecular dynamics simulations in various quasi-two-dimensional densities of water molecules on the ice nucleation protein. (elsevierpure.com)
  • We have established the connections of observed spectral diffusion to underlying molecular dynamics of water molecules from first principles calculations. (iitk.ac.in)
  • Molecular dynamics simulations of aqueous NaCl and KCl solutions: Effects of ion concentration on thesingle particle, pair and collective dynamical properties of ions and water molecules,J. Chem. (iitk.ac.in)
  • Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. (jyu.fi)
  • Actran - finite element-based simulation software to analyze the acoustic behavior of mechanical systems and parts. (wikipedia.org)
  • A simulation for a self-driving car would need high resolution 3D models of the environment and predefined behavioral rules regarding traffic signs and probabilistic behavior of other vehicles and pedestrians. (google.com)
  • Here we use mole- cular dynamics computer simulations to study the behavior of such hydration water when it is subjected to time-dependent electric fields. (fu-berlin.de)
  • Dynamical behavior of anion-water and water-water hydrogen bonds in aqueous electrolyte solutions: Amolecular dynamics study,J. Phys. (iitk.ac.in)
  • Phys.1996, 105, 2414-2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to the poor scaling of that code with respect to the number of titratable sites. (jyu.fi)
  • To overcome this limitation, we implemented an alternative scheme for interpolating the Hamiltonians of the protonation states that makes the constant pH molecular dynamics simulations almost as fast as a normal MD simulation with GROMACS. (jyu.fi)
  • With the combination of a more efficient interpolation scheme and multisite representation of titratable groups, we anticipate a rapid uptake of constant pH molecular dynamics simulations within the GROMACS user community. (jyu.fi)
  • Available projects also include computational investigations of reaction mechanisms and reaction dynamics for solar energy conversion and catalysis/photocatalysis. (lu.se)
  • The team led by Empa researcher Peter Nirmalraj from the Transport at Nanoscale Interfaces lab is investigating this hypothesis using imaging techniques and chemical spectroscopy as well as, in collaboration with the team of Damien Thompson at the University of Limerick, computer simulations. (neurosciencenews.com)
  • With this Dynamics workshop, our goal is to bring together leading experts in the field of membrane dynamics, with a particular focus on neutrons and X-rays, but also complementary techniques including NMR, single molecule spectroscopy and computer modeling. (lu.se)
  • Molecular dynamics models can be used as a complementary tool to molecular visualization tools widely used in classrooms, such as Jmol. (concord.org)
  • Supercomputing is a documentary that uses data visualization to talk about the impact of computer simulations in science and our daily lives. (visual.ly)
  • Simulation data visualization starts after the intro (mi. (visual.ly)
  • While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. (jyu.fi)
  • It would be dangerous to do experiments where we reinfected bats with human viral strains, so our computer-based simulations offered a much safer alternative," said Babbitt. (rit.edu)
  • Despite the reliance on an army of high-powered technologies, computational molecular simulation is iterative, time-consuming, and based on meticulous trial-and-error experiments. (deloitte.com)
  • Based on our simulation, the calculations generally agreed with the results of experiments conducted for all the materials. (ui.ac.id)
  • To make predictions, analysis or to replace experiments, we make use of numerical simulations and machine learning on large computers. (lu.se)
  • By developing a general approach that combines theory, experiment and simulation, we reveal, in molecular detail, the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. (nih.gov)
  • COVID -19: From the Molecular Mechanisms to Treatment. (cdc.gov)
  • Very recently, we have gone beyond the use of pair potentials and has used the technique of Car-Parrinello molecular dynamics to study the relaxation of hydrogen bonds and associated vibrational spectral diffusion in aqueous and other associated liquids from first principles without using any pair potentials. (iitk.ac.in)
  • Pressure effects on the dynamics and hydrogen bond properties of aqueous electrolyte solutions: Therole of ion screening,J. Phys. (iitk.ac.in)
  • Effects of ion atmosphere on hydrogen-bond dynamics in aqueous electrolyte solutions, Phys. (iitk.ac.in)
  • Molecular Dynamics with Long-Range Lennard-Jones Interactions ", Energy and Fuels, Volume 33, pp 848-858. (usna.edu)
  • To develop new engineered materials and chemical compounds, researchers typically evaluate thousands of chemical reactions and molecular interactions. (deloitte.com)
  • In this article, we review new analysis of the macro physical behaviour and relate this to the latest evidence for the molecular interactions that govern HA behaviour at the local oligosaccharide level. (gr.jp)
  • Through molecular modelling, these liposomes were predicted to be capable of encapsulating cannabinoids within their membrane based on their structural and chemical similarity to cholesterol. (bvsalud.org)
  • Studies of hydrogen bond dynamics in associated liquids constitute a major area of our research in recent years. (iitk.ac.in)
  • i) Rheology of weakly attractive suspensions (computer simulations), ii) Best packing protocols for amorphous samples, tapping or oscillations (computer simulations), iii) Suspensions rheology of particles with tiny anisotropy (computer simulations), iv) Morphology of drying polymer blends (computer simulations together with Petter Persson). (lu.se)
  • Numerical simulations of particulate suspensions via a discretized Boltzmann equation. (crossref.org)
  • Advanced Simulation Library - open-source hardware accelerated multiphysics simulation software. (wikipedia.org)
  • AGX Dynamics - realtime oriented multibody and multiphysics simulation engine. (wikipedia.org)
  • This scientific discussion makes the simulation box size variable an interesting candidate for further investigation in the light of statistical significance of the calculated thermodynamic and kinetic measures. (elifesciences.org)
  • Investigation using molecular dynamics simulation has been conducted in order to clarify the stability and to obtain the fundamental understanding of CO2 clathrate-hydrate. (elsevierpure.com)
  • Henrik Vinther Sørensen has together with Marie Skepö and Michael Bakker has already submitted a paper with the title Exploring the Role of Globular Domain Locations on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation. (lu.se)
  • rubber, and cement and is also commonly used as an interme- investigation) used computational fluid dynamics (CFD) to esti- diate in the synthesis of other industrial chemicals. (cdc.gov)
  • The simulations were performed on resources provided by the CSC-IT Center for Science, Finland, and the Swedish National Infrastructure for Computing (SNIC 2021/1- 38). (jyu.fi)
  • Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X. (jyu.fi)
  • Toward that end, Chen's lab will study the molecular basis of how the anti-cancer drug EGCG, an antioxidant found in green tea extract, and their derivatives interact with the p53 gene, a tumor suppressor and the most important protein involved in cancer. (umass.edu)
  • We performed Molecular Dynamics simulation study to generate both biaxial smectic and nematic phases using this new potential. (arxiv.org)
  • Simulation study offers an easy method to overcome this challenge, but primarily requires powerful computing resources. (ui.ac.id)
  • BECC researchers study how direct and indirect human impacts on the climate and ecosystems influence biodiversity and ecosystem functioning from local to global scales, and how knowledge about these dynamics may inform mitigation and adaptation decisions in the face of such changes. (lu.se)
  • W.G. Hoover, Canonical dynamics: Equilibrium phase-space distributions. (esaim-m2an.org)
  • Collaborative investigations of photophysics, photochemistry and ultrafast dynamics in molecular and heterogeneous systems carried out together with experimental colleagues. (lu.se)
  • The teaching consists of lectures, computer exercises and laboratory sessions. (lu.se)
  • Compulsory participation is required in computer exercises, laboratory sessions and associated elements. (lu.se)
  • FlightGear - a free, open-source atmospheric and orbital flight simulator with a flight dynamics engine (JSBSim) that is used in a 2015 NASA benchmark to judge new simulation code to space industry standards. (wikipedia.org)
  • The above screenshot shows an editing mode of the 3D Molecular Simulator. (concord.org)
  • The reaction occurring during friction between zinc phosphate glasses and steel native iron oxide layer is investigated by both an experimental approach and by Molecular Dynamics simulations (MD). The importance of this "tribochemical" reaction in the general ZDDP antiwear process is discussed. (elsevierpure.com)
  • The comparisons between simulation and experimental results were also presented. (ui.ac.id)
  • Projects are often closely connected with experimental investigations of ultrafast reaction dynamics. (lu.se)
  • In various systems, ranging from solvation free energies to protein conformational transition rates, we showcase how the proposed simulation box size effect disappears with increased sampling. (elifesciences.org)
  • Special attention has been paid to conformational changes of protein matrix (inter domain movement of 12/15-lipoxygenase) in solution and molecular dynamics of oxygen as second lipoxygenase substrate. (europa.eu)
  • Gekko - simulation software in Python with machine learning and optimization GNU Octave - an open-source mathematical modeling and simulation software very similar to using the same language as MATLAB and Freemat. (wikipedia.org)
  • APMonitor - a tool for dynamic simulation, validation, and optimization of multi-domain systems with interfaces to Python and MATLAB. (wikipedia.org)
  • Simulations can use just numerical data, or they can include graphical or 3D geometry data - the type and amount of data needed is dependent on the intended outcome of the simulation. (google.com)
  • Molecular simulations sample well defined thermodynamic ensembles, thus providing a representation of the physical world in silico. (elifesciences.org)
  • Most of the problems of polymer dynamics arise from the lack of clear definition of polymer entanglement. (reading.ac.uk)
  • 1 Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA. (nih.gov)
  • In fact, the conversion is nearly 100 percent efficient and occurs in a trillionth of a second ( Nature Communications , 'Ultrafast non-radiative dynamics of atomically thin MoSe 2 ' ). (nanowerk.com)
  • We're using radiation to break down the molecular structure of substances and form nanoparticles - a synthetic approach that is flexible and versatile for making large quantities of superalloy nanoparticle compositions that can't be easily created otherwise. (science20.com)
  • The researchers are targeting a protein that is involved in several molecular processes in the development of Parkinson's: alpha-synuclein. (neurosciencenews.com)
  • The researchers also analyzed the binding of copper ions to alpha-synuclein using molecular dynamics computer simulations in tiny steps of 10 to 100 nanoseconds. (neurosciencenews.com)
  • Simantics System Dynamics - used for modelling and simulating large hierarchical models with multidimensional variables created in a traditional way with stock and flow diagrams and causal loop diagrams. (wikipedia.org)
  • In this article, we argue that simulations, or digital models that imitate the operations or processes within a system, can be used in healthcare to develop new innovations and scale them. (google.com)