• 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)
  • In this work we have studied the folding pathways for four pairs of homologous proteins from thermophilic and mesophilic organisms from two different structural classes (class a, all-alpha proteins and class d, alpha + beta proteins) using Monte Carlo simulations. (nih.gov)
  • 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)
  • 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)
  • apply numerical methods, such as Molecular Dynamics Metropolis Monte Carlo simulations ยท use Statistical Mechanical tools with, as well as without, the aid of computer programs to calculate various properties of macroscopic systems. (lu.se)
  • Application areas range from molecular biology to astrophysics. (h-its.org)
  • 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)
  • The successful candidate will have strong experience in molecular modelling and simulations and statistical mechanics and will hold a PhD/DPhil in physics, chemistry, quantitative biology, applied mathematics, or a closely related field, with a strong interest in biological systems. (lu.se)
  • Genetics and molecular biology 2023 0 0. (cdc.gov)
  • 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)
  • Repast - agent-based modeling and simulation platform with versions for individual workstations and high performance computer clusters. (wikipedia.org)
  • 2010 3rd International Conference on Computer Modeling and Simulation (ICCMS 2011) is the premier forum for the presentation of technological advances and research results in the fields of Computer Modeling and Simulation. (wikicfp.com)
  • ICCMS 2011 will bring together leading engineers and scientists in Computer Modeling and Simulation from around the world. (wikicfp.com)
  • Several steps were completed from the modeling of the carbon structures and pollutants to simulations of molecular dynamics. (academicjournals.org)
  • Adversarial reverse mapping of condensed-phase molecular structures: Chemical transferability. (mpg.de)
  • 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)
  • find that reducing protein-water interactions by 10% in the Martini 3 coarse-grained force field enables self-assembly of transmembrane helix dimers in phospholipid micelles and bilayers in molecular dynamics simulations. (h-its.org)
  • Researchers in the Molecular and Cellular Modeling group (MCM) at HITS have recently released the first parameters of a micelle-forming lipid for the widely used coarse grained force field Martini 3. (h-its.org)
  • Much of this research is based on detailed thermodynamic simulations of protein chains in purpose-built software, but we also work with more coarse-grained models. (lu.se)
  • Lastly, we discuss some interpretations of the disjunction, mentioned in the abstract, that forms the conclusion of the simulation argument. (bibliotecapleyades.net)
  • Here, we use a simulation box size as an independent variable, to demonstrate how crucial it is to gather sufficient amounts of data before drawing any conclusions about the potential thermodynamic and kinetic effects. (elifesciences.org)
  • Molecular simulations sample well defined thermodynamic ensembles, thus providing a representation of the physical world in silico. (elifesciences.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)
  • 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)
  • In this work, the adsorption of benzene, toluene and p -xylene on activated carbon was verified through a computer simulation. (academicjournals.org)
  • Firstly, molecular simulations are conducted to investigate the adsorption isotherms, self-diffusivity, activation energy, permeability and selectivity of IRMOF-1 for CO 2 /CH 4 separation under different operating conditions. (nottingham.edu.cn)
  • Physical properties are reported for a benchmark system of 104 water molecules - to our knowledge, the largest system yet simulated using molecular dynamics with electronically-derived forces. (ibm.com)
  • Akselos - reduced-basis finite element-based simulation software for structural and thermal analyses. (wikipedia.org)
  • Actran - finite element-based simulation software to analyze the acoustic behavior of mechanical systems and parts. (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)
  • is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. (lu.se)
  • Computer simulations of lipid regulation by molecular semigrand canonical ensembles. (mpg.de)
  • 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 researchers recommend using this method for simulations of transmembrane proteins in micelles or for self-assembling bilayers with proteins using Martini 3. (h-its.org)
  • 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)
  • Computer simulation of molecular docking between methylene blue and some proteins of Porphyromonas gingivalis ]. (bvsalud.org)
  • As a first demonstration, we have calculated the structure of proteins in a simple lattice-based model on a quantum computer. (lu.se)
  • Computer Modeling in Engineering & Sciences 2021 , 128 (1), 339-357. (techscience.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)
  • 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)
  • Analyzing molecular dynamics (MD) simulations is a key aspect to understand protein dynamics and function. (eg.org)
  • 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)
  • Guided by requirements derived from multiple focus groups with protein engineering experts, we designed and developed a novel interactive visual analysis approach for long and crowded MD simulations. (eg.org)
  • However, these simulations showed something unexpected as well: transmembrane protein dimers were not encapsulated in lipid micelles, but rather interacted with the water in the solvent phase. (h-its.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)
  • We mostly used molecular mechanics (MM) in order to model the protein-ligand interactions, which is more approximate than quantum-mechanical (QM) methods, but necessary to reduce the computational cost when doing calculations on protein-ligand systems, which often contain tens of thousand of atoms. (lu.se)
  • In one study of a large set of protein-ligand complexes, we tried to improve the free energies of binding by using MD simulations with QM-derived charges, which sometimes led to improved results, but not always. (lu.se)
  • We are particularly interested in membrane-less organelles, protein aggregation and how molecular crowding affects protein properties. (lu.se)
  • The high-fidelity gates allow us to compute the dissociation energy of molecular hydrogen with a variational quantum eigensolver (VQE) algorithm, reaching an accuracy for the dissociation energy of around 20 mHa, limited by readout errors. (nature.com)
  • Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders. (mpg.de)
  • Rarefied Gas Dynamics: Theory and Simulations, Vol. 159 of Prog. (crossref.org)
  • We use mainly combined quantum mechanical and molecular mechanical (QM/MM) calculations with the density functional theory (DFT) method. (lu.se)
  • The course aims to both that theoretical and practical parts as treat basic molecular theory and molecular spectroscopy. (lu.se)
  • 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)
  • APMonitor - a tool for dynamic simulation, validation, and optimization of multi-domain systems with interfaces to Python and MATLAB. (wikipedia.org)
  • The project within these areas will feature multi-scale experiements, molecular modelling and simulation, pore-scale modelling, computaional fluid and solid dynamics, machine-learning and big data analytics, and process systems modelling and optimization. (imperial.ac.uk)
  • In the case of complex chemical mixtures and their interactions, the computer-assisted approach of Biochemical Reaction Network Modelling offers a ray of hope. (cdc.gov)
  • The possible linkage between this novel computational methodology and physiologically-based pharmacokinetic (PBPK) modelling could result in a multi-scale computer simulation platform capable of predicting complex pathway interactions and metabolite concentrations at the molecular level up to tissue and organ concentrations at the whole organism level. (cdc.gov)
  • Numerical simulations of particulate suspensions via a discretized Boltzmann equation. (crossref.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)
  • Advanced Simulation Library - open-source hardware accelerated multiphysics simulation software. (wikipedia.org)
  • AGX Dynamics - realtime oriented multibody and multiphysics simulation engine. (wikipedia.org)
  • Condensed-Phase Molecular Representation to Link Structure and Thermodynamics in Molecular Dynamics. (mpg.de)
  • Using ideas from computer vision, we adapt a specific type of neural network called a PointNet to identify local structural environments in molecular simulations. (osti.gov)
  • She has a long-standing interest in incorporating structural and dynamical information derived from all-atom molecular dynamics simulations in drug discovery programs, and has worked in a variety of disease areas, including infectious diseases and cancer. (nih.gov)
  • be able to analyse molecular spectra for diatomic and polyatomic molecules. (lu.se)
  • The written assignment can be of investigating nature on how molecular spectroscopy can be applied within science, industry or society. (lu.se)
  • 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)
  • 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)
  • Are there ideas here that could be useful in the design or laboratory evolution of artificial molecular machines? (foresight.org)
  • Jeffrey Biesiadecki has been a software engineer at NASAs Jet Propusion Laboratory since 1993, after completing his Masters degree in Computer Science at the University of Illinois, Urbana-Champaign. (nasa.gov)
  • Specificity of these 2 PCRs was verified in silico (computer simulation) and by using a panel of 14 Bartonella species available in our laboratory (data not shown). (cdc.gov)
  • AnyLogic - a multi-method simulation modeling tool for business and science. (wikipedia.org)
  • Eli holds a Bachelor of Science degree in Computer Science from the Oregon State University College of Engineering . (es.net)
  • Major research directions include complex simulations across scales, making sense of data, and enabling science via computational research. (h-its.org)
  • In contrast, our approach is a generic framework that requires no system-specific feature engineering and operates on the raw output of the simulations, i.e., atomic positions. (osti.gov)
  • 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)
  • Collaborative investigations of photophysics, photochemistry and ultrafast dynamics in molecular and heterogeneous systems carried out together with experimental colleagues. (lu.se)
  • This study shows the molecular mechanism of a selective vitamin D receptor modulator versus agonists and how they drive different interactions with co-regulators when associated with sequence-specific DNAs. (sciencedaily.com)
  • Molecular Dynamics with Long-Range Lennard-Jones Interactions ", Energy and Fuels, Volume 33, pp 848-858. (usna.edu)
  • We will create computer models of Spike - ACE2 interactions with different variants of ACE2. (boku.ac.at)
  • HITS conducts basic research in the natural, mathematical, and computer sciences. (h-its.org)
  • In this thesis we study three different metalloenzymes, nitrogenase, lytic polysaccharide monooxygenase (LPMO) and particulate methane monooxygenase (pMMO) with computer simulations. (lu.se)
  • Dr. Amaro's scientific interests lie at the intersection of computer-aided drug discovery and biophysical simulation methods. (nih.gov)
  • CIT): NIH Director's Wednesday Afternoon Lecture Series Annual DeWitt Stetten Jr. Lecture Dr. Amaro"s scientific interests lie at the intersection of computer-aided drug discovery and biophysical simulation methods. (nih.gov)
  • computer-assisted methods. (researchgate.net)
  • The groups of Ulrich Schwarz and Karl Rohr, head of the Biomedical Computer Vision Group at BioQuant Centre of Heidelberg University, used cutting-edge methods of image processing for this purpose. (news-medical.net)
  • Special computer simulations helped identify the mechanisms underlying these rotating movements. (news-medical.net)
  • COVID -19: From the Molecular Mechanisms to Treatment. (cdc.gov)
  • Simulations of DPC with these parameters showed micelle properties very similar to those obtained in experiments. (h-its.org)
  • Using advanced mass spectrometry technology, scientists from the Florida campus of The Scripps Research Institute (TSRI) have developed a molecular model that may provide a new framework for improving the design of osteoporosis treatments. (sciencedaily.com)
  • In case studies with different MD simulation data sets and research questions, we found that the proposed visual analysis approach facilitates exploratory analysis to generate, confirm, or reject hypotheses about causalities. (eg.org)
  • Since 1996 the Programme has undertaken research aimed at improving commercial computer programs' performance and supplying validation data. (imperial.ac.uk)
  • Her research explores the rational synthesis of new materials by combining the tools of molecular, solid-state and nanochemistry. (rsc.org)
  • 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)
  • Computational simulations, akin to wetlab experimentation, are subject to statistical fluctuations. (elifesciences.org)
  • be able to describe how temperature and molecular symmetry can affect this interaction. (lu.se)
  • 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)
  • Benchmark studies of a three-dimensional Lennard-Jones system have been carried out using a parallel MD simulation program implemented via a MPI-based message-passing interface on several parallel computers. (elsevierpure.com)
  • 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)
  • Many-body electronic responses such as dispersion and polarization (at and beyond dipole order) present fundamental challenges in the simulation of materials at the molecular scale. (ibm.com)