• Figure 4: Coarse-grained molecular dynamics simulations showing asymmetry in ligand distribution for single nanoparticles and their self-assembled array residing at the air/water interface. (nature.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)
  • Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult because of the convergence issues involved in free energy methods and finite size effects. (aip.org)
  • Despite their massive importance, computing the chemical potential of solutions from atomistic simulations is notoriously difficult and has not become a routine task. (aip.org)
  • Approximately, 60 students each summer will complete research in their area of interest: Biology, Chemistry, Earth and Environmental Science or Molecular Biology and Biochemistry that finishes with a poster session . (wesleyan.edu)
  • In this work, two Polynomial Chaos (PC) surrogates were generated to reproduce Monte Carlo (MC) molecular simulation results of the canonical (single-phase) and the NVT-Gibbs (two-phase) ensembles for a system of normalized structureless Lennard-Jones (LJ) particles. (aip.org)
  • basics of Monte Carlo, basics of Molecular Dynamics. (lu.se)
  • Describe various techniques for Monte Carlo simulations of naturally stochastic processes, such as scattering processes. (lu.se)
  • Describe various techniques for Monte Carlo and molecular dynamics calculations of equilibrium properties of complex systems with many degrees of freedom. (lu.se)
  • Conduct Monte Carlo simulations of naturally stochastic processes. (lu.se)
  • Conduct Monte Carlo and molecular dynamics simulations of equilibrium properties of complex systems. (lu.se)
  • Recognise problems that can be approached with Monte Carlo or molecular dynamics methods. (lu.se)
  • The course begins with a brief introduction to methods for Monte Carlo and molecular dynamics simulations. (lu.se)
  • Dr. Gaurav Chopra and Professor Michael Levitt in the Department of Structural Biology used molecular dynamics simulations involving a state-of-the-art Quantum Mechanical Polarizable Force Field (QMPFF3) to study the hydration of buckminsterfullerene, the smallest hydrophobic nanosphere widely referred to as a buckyball or C 60 . (phys.org)
  • Protein Expression and Purification, Computational Modeling, Molecular Dynamic Simulations, X-ray Crystallography, Enzyme Activity and Enzyme Inhibition Assays, Structure Aided Drug Design. (umassmed.edu)
  • 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)
  • Earlier papers on computer simulation of the origin of life by Christoph and Hans Kuhn, which provide more background to the ideas presented in this paper, can be downloaded here (from the web site for Hans Kuhn's textbook Principles of Physical Chemistry ). (foresight.org)
  • Chemistry provides a fundamental understanding that is then used by an industrial researcher to create an innovation which makes a real difference in a specific context. (lu.se)
  • 120 credits) in Chemistry and compulsory for a degree of Master of Science (120 credits) in Organizing Molecular Matter. (lu.se)
  • All fundamentals required to understand the testbed's physics are discussed. (kobv.de)
  • From the solid ground beneath our feet to the flowing rivers and even the air we breathe, understanding the physical properties and behavior of these substances, such as Einstein condensate, is at the heart of condensed matter physics . (freescience.info)
  • In short, condensed matter physics unlocks a whole new dimension in our understanding of how materials, including graphene, behave and interact with each other. (freescience.info)
  • First principles calculations are an essential tool for understanding and predicting material properties from basic physical laws, such as body physics. (freescience.info)
  • Research in my group aims to apply a multi-disciplinary approach using biophysical and structural experimental methods, structural bioinformatic analysis and physics-based molecular simulation to develop an integrated understanding of the formation of biomolecular complexes. (bbk.ac.uk)
  • Our new model system offers the opportunity to better understand the physics of collectives with elastic properties and perhaps render them usable for technical applications in the future,' states the physicist Ulrich Schwarz. (news-medical.net)
  • Interesting applications in atomic or molecular physics require strong XUV radiation in the 40-50 eV range. (lu.se)
  • 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)
  • in silico via computer simulations seem to be both promising and economically efficient. (frontiersin.org)
  • Specifi city of these 2 PCRs was veri- rabbits may be infected by these fl eas lected from wild rabbits ( Oryctolagus fi ed in silico (computer simulation) and consequently become a potential cuniculus) from 3 regions in southern and by using a panel of 14 Bartonella source for B. alsatica transmission to France: Canohes (42°38N, 2°51E), species available in our laboratory humans. (cdc.gov)
  • This Communication presents the so-called S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal-isobaric ensemble. (aip.org)
  • In practice, only the static structure factors computed from equilibrium isothermal-isobaric (NPT) molecular dynamics (MD) simulations at different solute concentrations are needed. (aip.org)
  • Understanding Molecular Simulation" by D. Frenkel and B. Smith. (lu.se)
  • The simulation results indicated van der Waals forces promoted the attraction between water molecules and metal surfaces. (inderscience.com)
  • There were many challenges to overcome in designing and implementing QMPFF3-based molecular dynamics simulations especially to study the behavior of water molecules next to hydrophobic surfaces at atomic detail and subpicosecond time resolution. (phys.org)
  • To better understand the interactions of materials such as cotton fiber with their surroundings, chemists and materials scientists often resort to models of the molecules. (usda.gov)
  • These new time concepts will be applied in drug transport kinetics, such as drug (un)binding to protein binding sites and permeation of molecules through cell membranes, but the concepts will also be applicable to understand time in an endless range of other molecular processes. (ugent.be)
  • The chemical potential of a solute as a function of its concentration is pivotal for understanding many important physical and biological processes, such as osmosis, the solvation of organic molecules, the behavior of electrolytes, precipitation of crystals from solutions, and phase equilibria of mixtures. (aip.org)
  • Thermodynamic integration or overlapping distribution method from the real solution to a reference fluid 1,2 involves running multiple simulations with different coupling constants as well as along different thermodynamic paths, may have singularity problems at the end points of integration, 7,8 and is difficult to use for molecules with complex topology. (aip.org)
  • The relationship between the local solvation structures and global thermodynamics, specifically in the case of amphiphilic molecules, is a complex phenomenon and is not yet fully understood. (bvsalud.org)
  • With the prior knowledge that local solvation structures can impose a significant impact on the overall solvation process, we here combine THz spectroscopic analysis with MD simulations to investigate the impact of the altered hydrophobicity and polarity of amphiphilic solute molecules on the local solvation configurations. (bvsalud.org)
  • The multiscale coarse-graining methodology has also been employed to increase the simulation speed by a factor of 100 or more, thereby making it possible to study the mesoscopic behavior of ILs by computer simulations. (uchicago.edu)
  • Concentration-dependent mechanism of the binding behavior of ibuprofen to the cell membrane: A molecular dynamic simulation study. (iasp-pain.org)
  • One of the fundamental aspects of molecular science is understanding how individual particles come together to exhibit collective behavior. (freescience.info)
  • This research contributes to the advancement of science and our understanding of the behavior of metals. (freescience.info)
  • By understanding the behavior of the order parameter near critical points, physicists can explain phenomena like ferromagnetism, superfluidity, and the superconducting hall effect, as well as the science behind density changes. (freescience.info)
  • The mechanistic analysis of the kinetic behavior, including polaron-based activation and electronic tunneling, is supported by calculations of electronic structure and molecular and medium energetics. (aps.org)
  • A multiscale treatment can provide a basis for an understanding of material behavior on different scales. (lu.se)
  • We use mainly combined quantum mechanical and molecular mechanical (QM/MM) calculations with the density functional theory (DFT) method. (lu.se)
  • In this work, molecular simulations combined with wettability experimentation were performed. (inderscience.com)
  • From atomistic molecular dynamics simulations, the many-body electronic polarization effect was found to be important for modeling ILs, especially their dynamics. (uchicago.edu)
  • Several steps were completed from the modeling of the carbon structures and pollutants to simulations of molecular dynamics. (academicjournals.org)
  • In parallel we will develop a new multi-scale modeling framework which can integrate this quantitative data, to simulate both the molecular patterning and the mechanical growth of the developing limb bud. (europa.eu)
  • Utilizing computational methodologies, including molecular modeling and conventional molecular dynamics simulations to understand the relationship between the three-dimensional structures, dynamics and the biological functions of DNA-binding enzymes and proteins central to Type I Diabetes. (umassmed.edu)
  • For this reason, a recent Open Access publication in the Journal of Molecular Modeling is of substantial interest to those wishing to understand how molecular machines could evolve to execute complex functions. (foresight.org)
  • Computer simulations and theoretical modeling point to a possible mechanism of this biological molecular machine in which electron transport is coupled to proton translocation. (aps.org)
  • Using a series of diverse virology and computational methods, as well as molecular dynamics simulations for conformational mobility, the researchers showed that hypervariable region 1 (HVR1) acts as a "safety catch" that regulates entry. (who.int)
  • Understanding the physical properties of ionic liquids (ILs) via computer simulation is important for their potential technological applications. (uchicago.edu)
  • Based on our results, we are now able to design peptides better by computer simulation," said Muraoka. (eurekalert.org)
  • In this work, the adsorption of benzene, toluene and p -xylene on activated carbon was verified through a computer simulation. (academicjournals.org)
  • Quantum mechanics helps comprehend phenomena such as superconductivity or quantum tunneling, vital for advanced technologies like computer chips and quantum computers. (freescience.info)
  • So far, computer modelling has helped to understand some of the pieces of this puzzle, eg. (europa.eu)
  • presents a computer simulation of how, by a long sequence of chemical steps, a simple self-replicating oligomer in a specific environment could evolve into a machine to translate a genetic code into amino acid sequences. (foresight.org)
  • In the computer simulation, aggregates are assigned fitness scores according to the number of hairpins in the aggregate. (foresight.org)
  • Special computer simulations helped identify the mechanisms underlying these rotating movements. (news-medical.net)
  • Using so-called agent-based computer simulations, it was possible to precisely identify those laws that can explain all aspects of the experimental observations. (news-medical.net)
  • In this thesis we study three different metalloenzymes, nitrogenase, lytic polysaccharide monooxygenase (LPMO) and particulate methane monooxygenase (pMMO) with computer simulations. (lu.se)
  • In this talk, I will discuss how we use molecular dynamics simulations at the coarse-grained and atomistic resolutions to study the dynamics and interactions of membrane transport proteins and of signalling receptors in model membranes. (leeds.ac.uk)
  • As a molecular machine found in all living cells that is of central importance for the synthesis of the proteins upon which all life depends, the ribosome is perhaps the primordial example of a molecular machine. (foresight.org)
  • The proteins that make up the molecular machinery of life tends to fragment the research field into method-oriented have been perfected by several billion years of evolution subspecialties that rarely confront each other. (lu.se)
  • We are part of MOSBRI - the new European infrastructure for molecular-scale biophysics funded by Horizon2020 and dedicated to improving access to, and standards of, measurements of biomolecular function. (bbk.ac.uk)
  • MOlecular-Scale Biophysics Research Infrastructure. (bbk.ac.uk)
  • The aim of the MOlecular-Scale Biophysics Research Infrastructure (MOSBRI) is to enable integrative multi-technological studies of biological systems at the crucial intermediate level between atomic-resolution structural descriptions and cellular-scale observations. (bbk.ac.uk)
  • We also carried out molecular dynamics simulations to provide additional insight into ε conformational dynamics. (nist.gov)
  • For this reason, QMPFF3 is expected to have a profound effect in understanding key biological processes like protein folding. (phys.org)
  • Time matters: the interplay between fast and slow molecular processes determines the fate of living matter (protein folding, drug delivery, etc. (ugent.be)
  • The aim of the PASTIME project is to properly understand the role of time in biomedical processes. (ugent.be)
  • Quantum molecular modelling of complex molecular systems is an indispensable and integrated component in advanced material design, as such simulations provide microscopic insights into the underlying physical processes. (lu.se)
  • As the level of our understanding of the mechanistic basis of toxicokinetic processes improves, QSARs to provide a priori predictions of key chemical-specific PBPK parameters can be developed to expedite the internal dose-based health risk assessments in data-poor situations. (cdc.gov)
  • 3. Conduct research to better understand the toxicology (biological mechanisms) of mixed exposures. (cdc.gov)
  • In this dissertation, based on the Molecular Communication (MC) system, a macroscale aqueous-based testbed is used to imitate the propagation of biocompatible drug-loaded Superparamagnetic Iron Oxide Nanoparticles (SPIONs) through a human vessel for drug delivery applications. (kobv.de)
  • The molecular mechanism of entry remains largely undefined and presents a challenge both in the understanding of fundamental molecular aspects of HCV and in the potential design of new therapeutics beyond the current direct-acting antivirals. (who.int)
  • Breeding designs were optimised by comparing obtained rate of inbreeding and genetic gain using a stochastic simulation model of the breeding program. (europa.eu)
  • The advent of new methods to obtain large-scale surveys of various mathematical structures, such as systems of differen- gene expression in which transcript levels can be determined tial equations, graphical networks, stochastic functional re- for thousands of genes simultaneously has facilitated the ex- lations, and simulation models. (lu.se)
  • The main advantage of such surrogates, once generated, is the capability of accurately computing the needed thermodynamic quantities in a few seconds, thus efficiently replacing the computationally expensive MC molecular simulations. (aip.org)
  • Analyzing molecular dynamics (MD) simulations is a key aspect to understand protein dynamics and function. (eg.org)
  • To understand these phenomena more precisely, the experimental data were analyzed quantitatively. (news-medical.net)
  • Article: Influence of temperature on the metallic surface cleanliness in ICF facility: a combined experimental and molecular simulation study Journal: International Journal of Surface Science and Engineering (IJSURFSE) 2023 Vol.17 No.1 pp.30 - 43 Abstract: Wettability of metal surfaces is used to characterise the surface cleanliness of components in the inertial confinement fusion (ICF) facility. (inderscience.com)
  • On the other hand, the stability of numerical scheme, e.g. verlet algorithm used in MD, depends on local error propgation and is related to type of problem, system frequency and simulation dt. (imechanica.org)
  • Explain the different sources of errors in numerical simulations and how the choice of algorithm may influence the convergence of simulations. (lu.se)
  • At the same time developments in biomolecular simulations allows us to simulate increasing large and complex membrane systems. (leeds.ac.uk)
  • A fusion of cutting-edge methodologies, intertwining molecular dynamics simulations and the power of machine learning. (umassmed.edu)
  • To obtain a molecular understanding of IDPs, a combined approach of experiments and simulations is useful. (lu.se)
  • This project is mostly about simulations but could include participating to experiments as well. (lu.se)
  • This project consists in generating high order harmonics in atomic and molecular gases and to optimize the radiation strength in the 40-50 eV range. (lu.se)
  • The simulation reveals a plausible mechanism by which an environment that selects compact molecular aggregates isolated from their environments can lead to novel functions. (foresight.org)
  • However, the molecular interactions between ibuprofen and the cell membrane are not well understood. (iasp-pain.org)
  • Understanding this Janus-like membrane asymmetry opens up new avenues for designing nanoparticle superstructures. (nature.com)
  • The aim of this module is to give students the strongest grounding in our current understanding of excitable cell pharmacology and physiology through study of the key elements of membrane excitability. (manchester.ac.uk)
  • Simulation of excitable membrane behaviour to expand understanding of the Nernst equation and the ionic basis for excitability. (manchester.ac.uk)
  • This study corroborates the present understanding on this type of phenomenon. (academicjournals.org)
  • Using simulations from generalised linear mixed models to obtain power estimates for EHTs, we show how factors such as the number of mosquitoes entering the huts each night and the magnitude of included random effects can influence study power. (imperial.ac.uk)
  • However, in this study, our reaction diffusion simulations (RDSs) of Ca 2+ combined with a release calculation using vesicular sensor models indicate that a high concentration of EGTA decreases Ca 2+ and vesicular release in the nanodomain of single channels. (frontiersin.org)
  • Our study is aimed to determine the relative abundance of different hydrogen bonded conformers and to establish a correlation between the spectral signatures (as obtained from THz spectroscopic measurements) and microscopic solute-solvent interactions associated with the local solvation structures (as obtained from MD simulations). (bvsalud.org)
  • In this study, we report TaqMan probes (Applied Biosystems, from S. cuniculi fl eas from a European the molecular detection of B . alsatica Courtaboeuf, France) specifi c for a wildcat ( Felis silvestris silvestris) in in fl eas ( Spilopsyllus cuniculi ) collect- portion of the heat shock protein 60 Andalusia, Spain ( 7 ). (cdc.gov)
  • Therefore An will lay the theoretical foundations of memory reduction and memory tuning in molecular simulations. (ugent.be)
  • We understand that these findings are not limited to the specific system studied here but can be broadly extrapolated to other amphiphilic aqueous solutions. (bvsalud.org)
  • Having a precise description of water s structure is critical to constructing accurate simulations of molecular events, including protein folding, substrate binding, macromolecular recognition, and complex formation. (phys.org)
  • Atomically flat thin films of topological insulator Bi{sub 2}Se{sub 3} have been grown on double-layer graphene formed on 6H-SiC(0001) substrate by molecular beam epitaxy. (teen-hot.com)
  • S. Nosé, A unified formulation of the constant temperature molecular-dynamics methods. (esaim-m2an.org)
  • In addition to working on specific biological systems, e.g. in bacterial cell division, we are developing methods for measurement, data analysis and simulation of interactions. (bbk.ac.uk)
  • 4. Develop methods to understand and integrate experimental data from the molecular level to the whole organism. (cdc.gov)
  • Although considerable progress has been made in using experimental and computational techniques to determine start and final structural states, we have a limited understanding of what happens in between. (lu.se)
  • By enabling both time resolution and structural detail Time-Resolved Small Angle X-ray/Neutron Scattering (TR-SAXS/TR-SANS) is uniquely suited to interrogate complex self-assembly reactions and to provide a molecular understanding of self-assembly pathways. (lu.se)
  • I tried to use larger dt even at very low temperature (~1 K), still found that MD simulation is crashing immediately. (imechanica.org)
  • A collaboration mainly led by scientists from Tokyo University of Agriculture and Technology (TUAT) in Japan has developed a new method of molecular design to control both temperature reversibility and stiffness of nanofibers that are gel-forming peptides. (eurekalert.org)
  • S.D. Bond, B.J. Leimkuhler and B.B. Laird, The Nosé-Poincaré method for constant temperature molecular dynamics. (esaim-m2an.org)
  • P. Klein, Pressure and temperature control in molecular dynamics simulations: a unitary approach in discrete time. (esaim-m2an.org)
  • Molecular structure-based prediction of the temporal change in the concentration of environmental chemicals or their metabolites in blood and organs of exposed organisms is a challenge. (cdc.gov)
  • These lipoplexes are taken up by cells in a structure called an endosome,' explains Bart Bruininks, a PhD student in the group of Siewert-Jan Marrink, Professor of Molecular Dynamics at the University of Groningen. (sciencedaily.com)
  • My research interests are in the areas of computational ​​continuum mechanics, nanomechanics and material modelling at nano- and macro scale, molecular dynamic simulation and peridynamics. (lu.se)
  • These were very complex state-of-the-art simulations,' says Bruininks. (sciencedaily.com)
  • With increasing computational power, it is now possible to generate very long and complex simulations, which are cumbersome to explore using traditional 3D animations of protein movements. (eg.org)
  • Finally, we derived design guidelines for interactive visual analysis of complex MD simulation data. (eg.org)
  • Because the issue of mixed exposures affects all of these areas, it was selected as one of the priority areas of the National Occupational Research Agenda (NORA) to leverage collaborative research efforts for better understanding the complex interactions of mixed exposures. (cdc.gov)
  • To cap- lular phenotypes (e.g. disease) on a mechanistic level, and ture the complex network of nonlinear information process- to use genomic signals to classify disease on a molecular ing based upon multivariate inputs from inside and outside level. (lu.se)
  • They are important both for the understanding of biological life and for reactions of industrial interest, e.g. in the production of artificial fertilizers, the production of biomass or biofuels. (lu.se)
  • For a better understanding of this biological system, a dynamic model suits better than relatively rigid structures came across in the previous analyses. (biosolveit.de)
  • Even though this approach is conceptually applicable to non-volatile and high molecular weight organics as well, it is more challenging to predict the other PBPK model parameters required for modelling the kinetics of these chemicals (particularly tissue diffusion coefficients, association constants for binding and oral absorption rates). (cdc.gov)
  • Therefore it is not surpris- pansion of biological understanding from the analysis of in- ing that the advent of high-throughput genomic and pro- dividual genes to the analysis of systems of genes (and pro- teomic technologies is drawing a growing interest from the teins). (lu.se)
  • More- ing with the global understanding of functional genomics, over, signal processing is based on a holistic view of regu- with special emphasis on genomic regulation. (lu.se)
  • Leptospira species molecular epidemiology in the genomic era. (cdc.gov)
  • Understanding the complexity behind inhibitor design to mitigate formation of resistance in hyper-mutating viruses. (umassmed.edu)