• Here, we use fully atomistic simulations with an effective potential for the silver substrate derived from first-principles calculations to investigate possible ways of peeling silicene solely by mechanical force. (asme.org)
  • Sondre KvalvÃ¥g Schnell is an Associate Professor at the Department of Materials Science and Engineering, where he is working with atomistic simulations of nano-systems and materials for energy storage. (ntnu.no)
  • 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)
  • Along this process, we will refer to different computational tools and databases that will help us to search, analyze and model the different molecular systems studied in this course. (uc3m.es)
  • Computational simulations, akin to wetlab experimentation, are subject to statistical fluctuations. (elifesciences.org)
  • In order to better understand the shape and function of the inner ear, and aiming at the creation of computational models for surgical planning and simulation, we have worked on the analysis of cadaveric high resolution microCT datasets. (upf.edu)
  • Computational modelling of functional molecules and materials. (lu.se)
  • Applied computational science can be divided into several components: mathematics, modelling, statistics, and programming. (lu.se)
  • Using tools from statistical and computational physics, we construct models and investigate biomolecular processes and properties. (lu.se)
  • Atomistic models of the Spike proteins and the ACE2 receptor are available, with the glycan structures reduced to the first 1-2 sugar residues. (boku.ac.at)
  • Here we use microsecond molecular dynamics simulations to explore the effect of stalk deletion on enzymatic activity, contrasting NA proteins from the A/swine/Shandong/N1/2009 strain both with and without a stalk deletion. (nih.gov)
  • The model shows that some proteins have a much less rigid structure in cells than they do in isolation, whilst others are able to work together more closely to carry out certain tasks. (elifesciences.org)
  • Native membrane derived polymer-supported lipid bilayers (nSLBs) are poised to bridge the gap between live cell experiments and traditional model membrane architectures that by offering a combination of accessibility by surface sensitive analytical instrumentation and a composition which more closely resembles cellular membranes by displaying a diversity of endogenous membrane proteins, lipids, and carbohydrates. (lu.se)
  • As a first demonstration, we have calculated the structure of proteins in a simple lattice-based model on a quantum computer. (lu.se)
  • These calculations were the first step in the combined modeling-experimental study aiming to engineer palladium surfaces with enhanced electrochemical storage of hydrogen. (synopsys.com)
  • We will create computer models of Spike - ACE2 interactions with different variants of ACE2. (boku.ac.at)
  • this has been under-represented by the limitations due to approximate modeling of atomic interactions in the empirical force fields widely used for the past decades. (phys.org)
  • However, the molecular interactions between ibuprofen and the cell membrane are not well understood. (iasp-pain.org)
  • In this paper, we propose a structural causal molecular dynamics model (SCMD), the first causality-based framework to model interatomic and dynamical interactions in molecular systems by inferring causal relationships among atoms from observational data. (openreview.net)
  • Our core research areas include scientific computing, the development of computer models and simulations of chemical and biochemical processes and entities and create visual representations of reaction pathways, molecular interactions, and related phenomena. (nesvard.org)
  • The Lorentz-Berthelot combining rule is used for modeling the unlike LJ interactions between the ions and the solvent molecules. (confex.com)
  • Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. (elifesciences.org)
  • This model suggested new possible interactions between molecules inside cells that cannot currently be studied in real cells. (elifesciences.org)
  • Using light scattering (LS), small-angle X-ray scattering (SAXS), and coarse-grained Monte Carlo (MC) simulations, we studied the self-interactions of two monoclonal antibodies (mAbs), PPI03 and PPI13. (lu.se)
  • Such models mostly concern kinetics and include gene and protein interactions as well as cell population dynamics. (lu.se)
  • Gene and protein interactions governing these processes can be modeled by binary Boolean rules or by continuous-valued models with interactions set by binding strengths. (lu.se)
  • The materials we make are niche polymers with tailor-made sites that facilitate selective molecular interactions. (lu.se)
  • The MIPs are produced by various polymerization methods but in all cases specifi c interactions, molecular partitioning and polymer structure are key properties that we focus on. (lu.se)
  • For aqueous sodium chloride (NaCl) solution, both models correlate the experimental mean ionic activity coefficient (γ ± ) data satisfactorily up to salt saturation concentration, that is, ionic strength around 6 m. (ttu.edu)
  • 1. Theory, Molecular/Mesoscopic Simulations, and Experimental Techniques of Aqueous Phase Adsorption. (routledge.com)
  • 2. Graphene Nanopores-Based Separation of Impurities from Aqueous Medium: An insight from molecular simulation. (routledge.com)
  • 3. Atomistic and Experimental Modeling for Adsorption of Metal Ions With Carbon Nanotubes in Aqueous Environment. (routledge.com)
  • 4. Water and Aqueous Phase Adsorption in Metal-Organic Frameworks: From Experiments to Simulations. (routledge.com)
  • 5. Coating of Nanoparticles in Aqueous Solutions : Insights from Molecular Dynamics Simulations. (routledge.com)
  • 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)
  • This paper presents the QuantumATK ForceField module and its algorithms, such as molecular dynamics (MD), adaptive kinetic Monte Carlo (AKMC) and nudged elastic band (NEB). (synopsys.com)
  • Using Monte Carlo methods as well as ground state variational and diffusion Monte Carlo (DMC) simulations, the author explains how to obtain temperature and quantum effects. (routledge.com)
  • In this paper, we present MD-TRACKS, an advanced statistical analysis toolkit for Molecular Dynamics and Monte Carlo simulations. (ugent.be)
  • Received May 14, 1997 variability and to use this measure of variability to Using the Monte Carlo method and physiologically derive a safe exposure limit or guidance value for inha- based pharmacokinetic modeling, an occupational in- lation of trichloroethylene (TRI) in an occupational set- halation exposure to trichloroethylene consisting of ting. (cdc.gov)
  • and the use of Monte Carlo simulations to represent the combined effects of multiple sources of uncertainty and variability. (cdc.gov)
  • 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)
  • 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)
  • Molecular modelling and simulations are integral part of biomolecular research. (lu.se)
  • Notably, molecular modeling and molecular dynamics simulations have become powerful tools that bridge the gap between structure and function while providing dynamic insights and illustrating essential mechanistic characteristics. (tau.ac.il)
  • Simulations based on channel models may yield insights into possible ion conduction and selectivity mechanisms. (ox.ac.uk)
  • By comparing simulation and experimental results, we validated our models and obtained insights. (lu.se)
  • By comparing simulation and experimental results, we validated our models and obtained insights into the mAbs' self-interaction properties, highlighting the role of both ion binding and charged patches on the mAb surfaces. (lu.se)
  • Conceptual insights along with tested predictions have emerged from such kinetic models. (lu.se)
  • His studies in the area of toxicogenomics include the development and application of standards for DNA microarray experiments, and phenotypic anchoring of response of human cells, model organisms (yeast) and target organs (rodents) to toxicants, providing insights into dose and temporal responses, as well as mechanisms of action. (cdc.gov)
  • Nowadays, there are huge quantities of data surrounding the different fields of biology derived from experiments and theoretical simulations, where results are often stored in biological databases that are growing at a vertiginous rate every year. (uc3m.es)
  • 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)
  • This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. (elifesciences.org)
  • As cell and molecular biology is becoming increasingly quantitative, there is an upsurge of interest in mechanistic modeling at different levels of resolution. (lu.se)
  • 7.2 Data from molecular biology. (who.int)
  • 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)
  • Pitzer and electrolyte nonrandom two-liquid (eNRTL) models are the two most widely used electrolyte thermodynamic models. (ttu.edu)
  • 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)
  • In the present work, we apply molecular simulation based on classical force fields with explicit solvent models to determine thermodynamic and structural properties of organic electrolyte solutions. (confex.com)
  • In the present work, basic thermodynamic properties of organic electrolyte solutions with the solvents methanol and ethanol are predicted by molecular simulation. (confex.com)
  • 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)
  • We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. (uea.ac.uk)
  • Including corresponding data into 3D pharmacophore modeling is essential for efficient high throughput virtual screening. (acs.org)
  • Mobility Testbed - an open-source multi-agent simulation testbed for transport coordination algorithms. (wikipedia.org)
  • The book develops finite temperature statistical simulation tools and real-time algorithms for the exact solution of the Schrödinger equation. (routledge.com)
  • Recent work has focused on the construction of these statistical models, notably on the algorithms for correspondence establishment, needed to align all datasets prior to the computation of the SSM. (upf.edu)
  • The results from this macroscopic model are in good agreement with nonequilibrium molecular dynamics simulations, which validates its use for interpreting electrochemical impedance experiments. (univ-toulouse.fr)
  • However, even without matured predictions, kinetic models serve the purpose of compressing a plurality of experimental results into something that can empower the data interpretation, and importantly, suggesting new experiments by turning "knobs" in silico. (lu.se)
  • To make predictions, analysis or to replace experiments, we make use of numerical simulations and machine learning on large computers. (lu.se)
  • Scaled-charge models have been recently introduced for molecular simulations of electrolyte solutions and molten salts to attempt to implicitly represent polarizability. (princeton.edu)
  • The implemented routines analyze the protein environment of water molecules in molecular dynamics (MD) simulations and can differentiate between hydrogen bonded waters as well as waters in a protein environment of hydrophobic, charged, or aromatic atom groups. (acs.org)
  • PyRod adds a new perspective to structure-based screening campaigns by providing easy-to-interpret dMIFs and purely protein-based pharmacophores that are solely based on tracing water molecules in MD simulations. (acs.org)
  • 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)
  • At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules. (uea.ac.uk)
  • Finally, the model predicted that small molecules such as food, water and drugs would move more slowly through cells as they become stuck or trapped by larger molecules. (elifesciences.org)
  • Quantitative predictions of reactive flow dynamics from large-scale simulations of Liquid Rocket Engines (LRE) appear to be model dependent. (sbir.gov)
  • TY - BOOK AU - Edler,Lutz AU - Kitsos,Christos P. TI - Recent advances in quantitative methods in cancer and human health risk assessment SN - 0470857560 U1 - 616.994071015118 22 PY - 2005/// CY - New York PB - Wiley KW - Neoplasms KW - Risk factors KW - Models, Theoretical N1 - Preface. (who.int)
  • Theoretical methods for the simulation of nucleic acids. (irbbarcelona.org)
  • We then examine theoretical approaches to the description of nucleic acids based on: i) a rigid or quasi-rigid description of the molecule, ii) molecular mechanics optimization, and iii) molecular dynamics. (irbbarcelona.org)
  • This book covers theoretical aspects of adsorption, followed by an introduction to molecular simulations and other numerical techniques that have become extremely useful as an engineering tool in recent times to understand the interplay of different mechanistic steps of adsorption. (routledge.com)
  • Concentration-dependent mechanism of the binding behavior of ibuprofen to the cell membrane: A molecular dynamic simulation study. (iasp-pain.org)
  • Actran - finite element-based simulation software to analyze the acoustic behavior of mechanical systems and parts. (wikipedia.org)
  • The asymptotic behavior of the activity coefficient predicted by the eNRTL model is consistent with the molecular simulation results and supersaturation experimental data. (ttu.edu)
  • It draws on potential energy models to gain insight into the behavior of minima and transition states. (routledge.com)
  • Akselos - reduced-basis finite element-based simulation software for structural and thermal analyses. (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)
  • Our automatic framework is able to generate patient-specific models for subsequent finite element simulations. (upf.edu)
  • Developmental processes, in particular those of stem and progenitor cell commitments, are not only topical but also particularly suitable for kinetic modeling due to the finite number of key genes involved in cellular decisions. (lu.se)
  • Our models provide useful information about mAbs' self-interaction properties and can assist the screening of conditions driving to colloidal stability. (lu.se)
  • Once formulated, kinetic models can be executed in terms of molecular rate equations for concentrations or by stochastic simulations when only a limited number of copies are involved. (lu.se)
  • 8. Stochastic Carcinogenesis Models (Annette Kopp-Schneider, Iris Burkholder and Jutta Groos). (who.int)
  • 8.2 Stochastic models for hepatocarcinogenesis. (who.int)
  • Computer Modeling in Engineering & Sciences 2021 , 128 (1), 339-357. (techscience.com)
  • In this study, we present an overview of molecular modeling and simulations of ubiquitin and the ubiquitin system, evaluate the status of the field, and offer our perspective on future progress in this area of research. (tau.ac.il)
  • : Quantum Methods in Flat and Curved Spaces presents advanced quantum simulation techniques for condensed matter. (routledge.com)
  • Specifically, a non-bonded quantum mechanical-based model is used to capture the mean polarization and charge transfer contributions to the interatomic forces within the metal site. (researchwithrutgers.com)
  • Applications of quantum chemical calculations to investigations of molecular and materials properties, as well as development and applications of classical reaction dynamics simulations. (lu.se)
  • Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. (uea.ac.uk)
  • Reanalyzing the trajectories generated from the scaled-charge model with full charges improves the estimation of the liquid-phase chemical potential but not the vapor pressure. (princeton.edu)
  • The gathered information is further processed to generate dynamic molecular interaction fields (dMIFs) for visualization and pharmacophoric features for virtual screening. (acs.org)
  • We have created a complete model of the Spike-ACE2 interaction, with full glycosylation. (boku.ac.at)
  • The model confirms that the glycans can play a significant role in the interaction. (boku.ac.at)
  • Specifically, we leverage the structural causal model (SCM) to model the interaction system of MD. To infer the SCM, we construct the graph in SCM as the dynamic Bayesian network (DBN), which is learned by a sequential generative model named SC-VAE. (openreview.net)
  • Scilab - free open-source software for numerical computation and simulation similar to MATLAB/Simulink. (wikipedia.org)
  • DFT simulations were performed to study how electronic structure changes due to adsorption. (synopsys.com)
  • 6. Lattice-Boltzmann Modeling of Adsorption Breakthrough in Packed Beds. (routledge.com)
  • Dr. Singh 's current research interest is in material modeling, self assembly, energy storage, wetting transition, nanotribology and selective adsorption. (routledge.com)
  • He has also developed lattice Boltzmann method-based mathematical models for adsorption and flow systems. (routledge.com)
  • We are particularly interested in membrane-less organelles, protein aggregation and how molecular crowding affects protein properties. (lu.se)
  • 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)
  • We demonstrate the efficacy of SCMD through empirical validations on the complex molecular system (i.e., single-chain coarse-grained polymers in implicit solvent) for long-duration simulation and dynamical property prediction. (openreview.net)
  • Skin permeation of solutes from metalworking fluid s to build prediction models and test a partition theory. (cdc.gov)
  • are usually modeled with several residues in alternative conforma- basis of elementary statistical mechanics and generic features of tions, each with its own set of AMSDs. (lu.se)
  • 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)
  • Molecular dynamics (MD) simulations describe the mechanical behaviors of molecular systems through empirical approximations of interatomic potentials. (openreview.net)
  • Meanwhile, we will learn some methods that help us to generate models of these structures. (uc3m.es)
  • Special emphasis is made ion current state of the art molecular dynamics simulations of nucleic acids structures. (irbbarcelona.org)
  • First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. (uea.ac.uk)
  • Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. (uea.ac.uk)
  • APMonitor - a tool for dynamic simulation, validation, and optimization of multi-domain systems with interfaces to Python and MATLAB. (wikipedia.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)
  • We performed molecular dynamics (MD) simulations of a model liquid-crystal system to assess the accuracy of some variations of the PRF method in low-charge-density systems. (elsevierpure.com)
  • Collaborative investigations of photophysics, photochemistry and ultrafast dynamics in molecular and heterogeneous systems carried out together with experimental colleagues. (lu.se)
  • Here we review kinetic modeling efforts applied to stem cell developmental systems with focus on hematopoiesis. (lu.se)
  • 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)
  • 4. Biological Carcinogenesis: Theories and Models (Sylvia Solakidi, Constantinos E. Vorgias and Constantine E. Sekeris). (who.int)
  • 4.2 Models of human carcinogenesis. (who.int)
  • 4.3 The multistage mouse skin carcinogenesis model. (who.int)
  • 9.2 Conventional approach to modeling carcinogenesis. (who.int)
  • We examine this divergence by calculating the mean ionic activity coefficient over a wide range of concentration based on molecular simulations and Kirkwood-Buff theory. (ttu.edu)
  • The program is compatible with different molecular simulation codes, and the analysis results can be loaded into spreadsheet software and plotting tools. (ugent.be)
  • With a specialisation in Chemistry, you will first study the mandatory course Molecular Driving Forces and Chemical Bonding, KEMM30. (lu.se)
  • Second, the effect of crystallinity and crystal form (/) on mechanical properties of semi-crystalline PA6 was investigated via a multiscale simulation approach. (dtic.mil)
  • The sensitivity of their novel method for detecting surface roughness shows that the hydrophobic effect is much stronger at short- and long-range for QMPFF3 compared to empirical force fields simulations. (phys.org)
  • Journal of Molecular Graphics and Modelling , 46 , 29-40. (tau.ac.il)
  • There is a great need to find molecular biomarkers predicting increased progression risk in GERD-Barrett's metaplasia-dysplasia-adenocarcinoma sequence to improve risk assessment and stratification of patients to surveillance program. (who.int)
  • 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)
  • Therefore, there is an increasing research interest in the application of mathematical and physical models able to produce reliable predictions and explanations to understand and rationalize that information. (uc3m.es)
  • 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)
  • Relationships and coupling among the dominant mechanisms most responsible for destabilization are obscured by the complexities of the model and subtle consequences of inherent ad hoc approximations not supported by mathematical rationale. (sbir.gov)
  • The predictions of the reduced liquid solution density from molecular simulation are in excellent agreement with experimental data, which are measured in the present work. (confex.com)
  • The final goal of these models is to provide experimental predictions, which is now taking on. (lu.se)
  • 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 complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention. (nature.com)
  • Cryo-EM structural data have been deposited in the EMDataBank under accession codesEMD-5582 andEMD-5639, and the MDFF atomic model of the CA HOH and models of HIV-1 capsid have been deposited in the Protein Data Bank under accession numbers 3J34 , 3J3Q , 3J3Y . (nature.com)
  • 2. Molecular Epidemiology in Cancer Research (Gerassimos Voutsinas, Anastasia Apostolidou and Natalia Spyrou). (who.int)
  • 2.6 New tools in molecular epidemiology. (who.int)
  • 7. Modeling Exposure and Target Organ Concentrations (Karen H. Watanabe). (who.int)