• 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)
  • Practical applications of molecular dynamics include studying large molecules such as proteins for drug development. (acm.org)
  • Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. (plos.org)
  • 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)
  • 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)
  • However, partitioned simulations require stable and accurate coupling 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)
  • 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)
  • Quantum computers will efficiently run algorithms that their classical counterparts can't manage. (deloitte.com)
  • 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)
  • Such practice is needed in atomistic simulations of complex systems where even thousands of degrees of freedom are sampled. (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)
  • 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)
  • 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)
  • 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)
  • Computational physics, computer science, applied mathematics, statistics and the integration of large data streams are central to scientific discovery and innovation. (lanl.gov)
  • The Computer, Computational, and Statistical Sciences (CCS) Division strengthens the visibility and impact of computer science and computational physics research for the strategic directions at the Laboratory. (lanl.gov)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. (plos.org)
  • Available projects also include computational investigations of reaction mechanisms and reaction dynamics for solar energy conversion and catalysis/photocatalysis. (lu.se)
  • 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)
  • The extended discrete element method (XDEM) is a numerical technique that extends the dynamics of granular material or particles as described through the classical discrete element method (DEM) (Cundall and Allen) by additional properties such as the thermodynamic state, stress/strain or electro-magnetic field for each particle. (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)
  • 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)
  • 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)
  • 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)
  • He works on methods to improve protein engineering of metalloproteins using deep learning and molecular modeling. (foresight.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)
  • The researchers are targeting a protein that is involved in several molecular processes in the development of Parkinson's: alpha-synuclein. (neurosciencenews.com)
  • 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)
  • ACM awards recognize achievements by young computing professionals, educators, theoretical computer scientists, software systems innovators, and pioneers who have made humanitarian and cross-discipline contributions. (acm.org)
  • 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)
  • Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. (jyu.fi)
  • 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)
  • Herein, classical molecular dynamics simulations are performed to investigate the effect of edge mode on mass sensing for a doubly clamped strained graphene resonator. (mdpi.com)
  • Molecular dynamics models can be used as a complementary tool to molecular visualization tools widely used in classrooms, such as Jmol. (concord.org)
  • Building on research in human perception, our visualization researchers are exploring how to best emphasize features within extremely large simulations such as MPAS, so that important information is quickly and succinctly communicated to scientists. (lanl.gov)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • ACM, the Association for Computing Machinery, named a nine-member team, drawn from Chinese and American institutions, recipients of the 2020 ACM Gordon Bell Prize for their project, "Pushing the limit of molecular dynamics with ab initio accuracy to 100 million atoms with machine learning. (acm.org)
  • 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)
  • 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)
  • Molecular dynamics (MD) is a computer simulation method that analyzes how atoms and molecules move and interact during a fixed period of time. (acm.org)
  • A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. (plos.org)
  • Oligomeric species populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer's disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. (nih.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)
  • Scientists at Osaka University have simulated heat transport at the smallest scales using a molecular dynamics computer simulation. (phys.org)
  • A single time step from an MPAS (Model for Prediction Across Scales) simulation, showing the temperature of the ocean. (lanl.gov)
  • 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)
  • Collaborative investigations of photophysics, photochemistry and ultrafast dynamics in molecular and heterogeneous systems carried out together with experimental colleagues. (lu.se)
  • 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)
  • Our ML model enables us to accelerate first-principles data generation by interpolating existing high fidelity data, and extend the simulation scale by extrapolating high fidelity data (10 2 atoms) to the mesoscale (10 4 atoms). (sandia.gov)
  • 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)
  • Other research interests include algorithmic information theory, in which the concepts of information and randomness are developed in terms of the input/output relation of universal computers, and the analogous use of universal computers to define the intrinsic complexity or 'logical depth' of a physical state as the time required by a universal computer to simulate the evolution of the state from a random initial state. (unipd.it)
  • 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)
  • 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)
  • Projects are often closely connected with experimental investigations of ultrafast reaction dynamics. (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)
  • 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)
  • 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)
  • W.G. Hoover, Canonical dynamics: Equilibrium phase-space distributions. (esaim-m2an.org)
  • 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)
  • ACM recognizes excellence through its eminent awards for technical and professional achievements and contributions in computer science and information technology. (acm.org)
  • In 1983-5 as visiting professor of computer science at Boston University, he taught courses on cryptography and thephysics of computation. (unipd.it)
  • We are working on new computational methods such as forward flux sampling and others to speed up MD and slip-springs simulations. (reading.ac.uk)
  • S. Nosé, A unified formulation of the constant temperature molecular-dynamics methods. (esaim-m2an.org)
  • computer-assisted methods. (researchgate.net)
  • Standard analysis and linear algebra, Numerical analysis of ordinary differential equations (including the corresponding programming skills), Basic probability theory, fundamentals of the concepts of SDEs and how to develop and analyse numerical methods for their simulation. (lu.se)
  • Simulation methods. (lu.se)
  • Due to foundational advances in machine learning, simulation is now possible even when the underlying mechanics of the process to be simulated are not known a priori. (google.com)
  • Molecular dynamics is a computer simulation technique widely used in academic research to assist scientists to discover new materials, new chemicals, and increasingly important, new drugs. (concord.org)
  • MD simulations allow scientists to gain a better sense of how a system (which could include anything from a single cell to a cloud of gas) progresses over time. (acm.org)
  • The level of precision that can be gained through AIMD has made it the preferred simulation method of scientists for more than 35 years. (acm.org)
  • Rarefied Gas Dynamics: Theory and Simulations, Vol. 159 of Prog. (crossref.org)
  • A single chain stochastic model (Likhtman, 2005) represents a crucial step in hierarchical modelling, bridging the gap between multi-chain molecular dynamics simulation and the tube theory. (reading.ac.uk)