Search results

Items from 1 to 20 out of 42 results

article

Development of a bottom‐up coarse‐grained model for interactions of lipids with TiO $_{2}$ nanoparticles

Mikhail Ivanov, Alexander P. Lyubartsev

Journal of Computational Chemistry > 45 > 16 > 1364 - 1379

Understanding interactions of inorganic nanoparticles with biomolecules is important in many biotechnology, nanomedicine, and toxicological research, however, the size of typical nanoparticles makes their direct modeling by atomistic simulations unfeasible. Here, we present a bottom‐up coarse‐graining approach for modeling titanium dioxide (TiO

_{2}

) nanomaterials in contact with phospholipids that uses...

article

Long‐time scale simulations of virus‐like particles from three human‐norovirus strains

Agnieszka G. Lipska, Adam K. Sieradzan, Cezary Czaplewski, Andrea D. Lipińska, more

Journal of Computational Chemistry > 44 > 16 > 1470 - 1483

The dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long‐time (about 30 μs in the laboratory timescale) molecular dynamics simulations with the coarse‐grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction...

article

Efficient lattice Green's function method for bounded domain problems

Ankit Gupta, Max Hodapp, William A. Curtin

International Journal for Numerical Methods in Engineering > 123 > 23 > 5854 - 5883

The lattice Green's function method (LGFM) is the discrete counterpart of the continuum boundary element method and is a natural approach for solving intrinsically discrete solid mechanics problems that arise in atomistic‐continuum coupling methods. Here, the LGFM is extended to problems in a bounded domain with applied boundary conditions. An efficient controlled coarse‐graining method is introduced...

article

Process‐oriented stochastic perturbations applied to the parametrization of turbulence and shallow convection for ensemble prediction

Axelle Fleury, François Bouttier, Fleur Couvreux

Quarterly Journal of the Royal Meteorological Society > 148 > 743 > 981 - 1000

Weather forecasting nowadays often requires some estimation of uncertainties associated with the output of meteorological models, in order to better inform decision making, especially in the context of intense weather events. Ensemble prediction systems provide such information through sets of possible scenarios which are designed to represent various uncertainty sources, including model uncertainties...

article

Coarse‐Grained Molecular Simulation of Polymers Supported by the Use of the SAFT‐ $γ$ Mie Equation of State

Maziar Fayaz‐Torshizi, Erich A. Müller

Macromolecular Theory and Simulations > 31 > 1 > n/a - n/a

A framework to self‐consistently combine a classical equation of state (EoS) and a molecular force field to model polymers and polymer mixtures is presented. The statistical associating fluid theory (SAFT‐

γ

Mie) model is used to correlate the thermophysical properties of oligomers and generate robust and transferrable coarse‐grained (CG) molecular parameters which can be used both in particle...

article

The Martini Model in Materials Science

Riccardo Alessandri, Fabian Grünewald, Siewert J. Marrink

Advanced Materials > 33 > 24 > n/a - n/a

The Martini model, a coarse‐grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted,...

article

Dissipative Particle Dynamics Simulation: A Review on Investigating Mesoscale Properties of Polymer Systems

Jihao Wang, Yufen Han, Zhiyang Xu, Xiaozhen Yang, more

Macromolecular Materials and Engineering > 306 > 4 > n/a - n/a

Polymer systems have typical multiscale characteristics, both in space and time. The mesoscopic properties of polymers are difficult to describe through traditional experimental approaches. Dissipative particle dynamics (DPD) is a simulation method used for solving mesoscale problems of complex fluids and soft matter. The mesoscopic properties of polymer systems, such as conformation, dynamics, and...

article

Resolving Donor–Acceptor Interfaces and Charge Carrier Energy Levels of Organic Semiconductors with Polar Side Chains

Riccardo Alessandri, Selim Sami, Jonathan Barnoud, Alex H. Vries, more

Advanced Functional Materials > 30 > 46 > n/a - n/a

Organic semiconductors consisting of molecules bearing polar side chains have been proposed as potential candidates to overcome the limitations of organic photovoltaics owing to their enhanced dielectric constant. However, introducing such polar molecules in photovoltaic devices has not yet resulted in higher efficiencies. A microscopic understanding of the impact of polar side chains on electronic...

article

Ligand‐protein interactions in lysozyme investigated through a dual‐resolution model

Raffaele Fiorentini, Kurt Kremer, Raffaello Potestio

Proteins: Structure, Function, and Bioinformatics > 88 > 10 > 1351 - 1360

A fully atomistic (AT) modeling of biological macromolecules at relevant length‐ and time‐scales is often cumbersome or not even desirable, both in terms of computational effort required and a posteriori analysis. This difficulty can be overcome with the use of multiresolution models, in which different regions of the same system are concurrently described at different levels of detail. In enzymes,...

article

Energy Renormalization for Coarse‐Graining Polymers with Different Fragilities: Predictions from the Generalized Entropy Theory

Wen‐Sheng Xu, Wenjie Xia

Macromolecular Theory and Simulations > 29 > 2 > n/a - n/a

Bottom‐up prediction of physical performance of glass‐forming (GF) polymers via coarse‐grained (CG) modeling is challenging because these CG models normally experience significantly altered dynamics that strongly vary with temperature. Building upon the recently developed energy‐renormalization (ER) coarse‐graining method based on molecular dynamics simulations, generalized entropy theory (GET) is...

article

Constraining stochastic parametrisation schemes using high‐resolution simulations

Hannah M. Christensen

Quarterly Journal of the Royal Meteorological Society > 146 > 727 > 938 - 962

Stochastic parametrisations can be used in weather and climate models to improve the representation of unpredictable unresolved processes. When compared with a deterministic model, a stochastic model represents “model uncertainty”, that is, sources of error in the forecast due to the limitations of the forecast model. A technique is presented for systematically deriving new stochastic parametrisations...

article

Determining Optimal Coarse‐Grained Representation for Biomolecules Using Internal Cluster Validation Indexes

Zhenliang Wu, Yuwei Zhang, John Zenghui Zhang, Kelin Xia, more

Journal of Computational Chemistry > 41 > 1 > 14 - 20

The development of ultracoarse‐grained models for large biomolecules needs to derive the optimal number of coarse‐grained (CG) sites to represent the targets. In this work, we propose to use the statistical internal cluster validation indexes to determine the optimal number of CG sites that are optimized based on the essential dynamics coarse‐graining method. The calculated curves of Calinski‐Harabasz...

article

Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites

Sambit K. Mishra, Gaurav Kandoi, Robert L. Jernigan

Proteins: Structure, Function, and Bioinformatics > 87 > 10 > 850 - 868

Binding sites in proteins can be either specifically functional binding sites (active sites) that bind specific substrates with high affinity or regulatory binding sites (allosteric sites), that modulate the activity of functional binding sites through effector molecules. Owing to their significance in determining protein function, the identification of protein functional and regulatory binding sites...

article

Introduction of a bounded penalty function in contact‐assisted simulations of protein structures to omit false restraints

Emilia A. Lubecka, Adam Liwo

Journal of Computational Chemistry > 40 > 25 > 2164 - 2178

Contact‐assisted simulations, the contacts being predicted or determined experimentally, have become very important in the determination of the structures of proteins and other biological macromolecules. In this work, the effect of contact‐distance restraints on the simulated structures was investigated with the use of multiplexed replica exchange simulations with the coarse‐grained UNRES force field...

article

OPUS‐SSF: A side‐chain‐inclusive scoring function for ranking protein structural models

Gang Xu, Tianqi Ma, Qinghua Wang, Jianpeng Ma

Protein Science > 28 > 6 > 1157 - 1162

We introduce a side‐chain‐inclusive scoring function, named OPUS‐SSF, for ranking protein structural models. The method builds a scoring function based on the native distributions of the coordinate components of certain anchoring points in a local molecular system for peptide segments of 5, 7, 9, and 11 residues in length. Differing from our previous OPUS‐CSF [Xu et al., Protein Sci. 2018; 27: 286–292],...

article

Quantifying brain microstructure with diffusion MRI: Theory and parameter estimation

Dmitry S. Novikov, Els Fieremans, Sune N. Jespersen, Valerij G. Kiselev

NMR in Biomedicine > 32 > 4 > n/a - n/a

We review, systematize and discuss models of diffusion in neuronal tissue, by putting them into an overarching physical context of coarse‐graining over an increasing diffusion length scale. From this perspective, we view research on quantifying brain microstructure as occurring along three major avenues. The first avenue focusses on transient, or time‐dependent, effects in diffusion. These effects...

article

MARTINI bead form factors for the analysis of time‐resolved X‐ray scattering of proteins. Erratum

Stephan Niebling, Alexander Björling, Sebastian Westenhoff

Journal of Applied Crystallography > 51 > 3 > 968 - 968

A typographical error in the article by Niebling, Björling & Westenhoff [J. Appl. Cryst. (2014), 47, 1190–1198] is corrected.

article

Multiscale Modeling Scheme for Simulating Polymeric Melts: Application to Poly(Ethylene Oxide)

C. Wu

Macromolecular Theory and Simulations > 27 > 1 > n/a - n/a

The poly(ethylene oxide) (PEO) is employed as one typical example to demonstrate a new multiscale modeling scheme for simulating high‐molecular‐weight polymeric melts. In this scheme, the structural distributions and the densities at five elevated temperatures at 1 atm, which are obtained from molecular dynamics (MD) simulations of all‐atomistic oligomeric melt, are employed as the target functions...

article

OPUS‐CSF: A C‐atom‐based scoring function for ranking protein structural models

Gang Xu, Tianqi Ma, Tianwu Zang, Qinghua Wang, more

Protein Science > 27 > 1 > 286 - 292

We report a C‐atom‐based scoring function, named OPUS‐CSF, for ranking protein structural models. Rather than using traditional Boltzmann formula, we built a scoring function (CSF score) based on the native distributions (derived from the entire PDB) of coordinate components of mainchain C (carbonyl) atoms on selected residues of peptide segments of 5, 7, 9, and 11 residues in length. In testing OPUS‐CSF...

article

A multi‐resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand‐binding site

Aoife C. Fogarty, Raffaello Potestio, Kurt Kremer

Proteins: Structure, Function, and Bioinformatics > 84 > 12 > 1902 - 1913

In multi‐resolution simulations, different system components are simultaneously modeled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is needed in the active site to capture the chemistry of ligand binding. Global properties of the rest of the protein also play an essential role, determining the structure...

Publication date

Last year (1)
Last 3 years (5)

Close

Date range setting

Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.

From:

To:
Set your own date range

Keywords

COARSE‐GRAINING (42)
MOLECULAR DYNAMICS (15)
MULTISCALE MODELING (3)
ORGANIC SEMICONDUCTORS (3)
PROTEINS (3)
CHARGE TRANSPORT (2)
DECOY RECOGNITION (2)
DEVICE SIMULATION (2)
ELASTIC NETWORK MODELS (2)
ELECTROSPINNING (2)
ENSEMBLE WEATHER PREDICTION (2)
GLASS TRANSITION (2)
GROMOS (2)
MARTINI (2)
MODEL UNCERTAINTY (2)
MOLECULAR SIMULATION (2)
POLYMERS (2)
PROTEIN FOLDING (2)
PROTEIN STRUCTURE MODELING (2)
SCORING FUNCTION (2)
SIMULATIONS (2)
STOCHASTIC MODEL (2)
UNRES (2)
ACTIVE SITES (1)
ADAPTIVE RESOLUTION (1)
ALLOSTERY (1)
ALL‐ATOM RECONSTRUCTION (1)
ALUMINOSILICATES (1)
ATOMISTIC/CONTINUUM COUPLING (1)
BLOCK COPOLYMERS (1)
BOUNDARY ELEMENT METHOD (1)
BOUNDED RESTRAINED FUNCTION (1)
BRAIN (1)
CG (1)
CH INDEX (1)
CHAIN GROWTH (1)
CHARGE‐ON‐SPRING MODEL (1)
CHEMICAL KINETICS (1)
CLIMATE MODELLING (1)
COARSE‐GRAINED MODELS (1)
COMPUTATIONAL ALGORITHMS (1)
COMPUTER MODELLING (1)
COMPUTER SIMULATIONS (1)
CRYSTALLIZATION (1)
CYCLOHEXANE (1)
DENDRIMERS (1)
DENSITY FUNCTIONAL THEORY (1)
DIELECTRIC PERMITTIVITY (1)
DIFFUSION (1)
DONOR–ACCEPTOR INTERFACES (1)
DUAL‐RESOLUTION MODELING (1)
EFFECTIVE HESSIAN (1)
ELASTIC NETWORK MODEL (1)
ENTROPY (1)
EQUATION OF STATE (1)
FORCE FIELD (1)
FREE ENERGY (1)
FREE ENERGY CALCULATION (1)
FRICTION MATRIX (1)
FUEL CELL (1)
FUEL CELLS (1)
GENERALIZED ENTROPY THEORY (1)
GEOPOLYMERIZATION (1)
GOLD NANOPARTICLES (1)
GPU‐ACCELERATION (1)
GRAPHENE (1)
GRAPHICS PROCESSING UNITS (1)
HEAT CAPACITY (1)
HUMAN NOROVIRUS (1)
HYDROPHOBIC CHARGED INDUCTION CHROMATOGRAPHY (1)
INTERNAL CLUSTER VALIDATION INDEX (1)
INVERSE MONTE CARLO (1)
IONIC LIQUID (1)
ITERATIVE BOLTZMANN (1)
KINETIC TENSOR (1)
LARGE‐EDDY SIMULATIONS (1)
LATTICE GREEN'S FUNCTION (1)
LIPID MEMBRANE (1)
MACHINE LEARNING (1)
MESOSCOPIC SIMULATION (1)
MESOSCOPIC TRANSPORT (1)
MICROSTRUCTURE (1)
MOLECULAR DYNAMICS (MD) (1)
MOLECULAR MODELLING (1)
MOLECULAR SIMULATIONS (1)
MONTE CARLO (1)
MRI (1)
MULTIPLEXED REPLICA‐EXCHANGE MOLECULAR DYNAMICS (1)
MULTISCALE MODELLING (1)
MULTISCALE SIMULATION (1)
MULTISCALE SIMULATIONS (1)
MULTI‐GRAINING (1)
MULTI‐SCALE MODELING (1)
NAFION (1)
NANOTOXICITY (1)
NMA (1)
NMR SPECTROSCOPY (1)
NONEQUILIBRIUM DYNAMICS (1)
NORMAL MODE ANALYSIS (1)
NUCLEIC ACIDS (1)
more

INFONA - science communication portal

Search results

Development of a bottom‐up coarse‐grained model for interactions of lipids with TiO $_{2}$ nanoparticles

Long‐time scale simulations of virus‐like particles from three human‐norovirus strains

Efficient lattice Green's function method for bounded domain problems

Process‐oriented stochastic perturbations applied to the parametrization of turbulence and shallow convection for ensemble prediction

Coarse‐Grained Molecular Simulation of Polymers Supported by the Use of the SAFT‐ $γ$ Mie Equation of State

The Martini Model in Materials Science

Dissipative Particle Dynamics Simulation: A Review on Investigating Mesoscale Properties of Polymer Systems

Resolving Donor–Acceptor Interfaces and Charge Carrier Energy Levels of Organic Semiconductors with Polar Side Chains

Ligand‐protein interactions in lysozyme investigated through a dual‐resolution model

Energy Renormalization for Coarse‐Graining Polymers with Different Fragilities: Predictions from the Generalized Entropy Theory

Constraining stochastic parametrisation schemes using high‐resolution simulations

Determining Optimal Coarse‐Grained Representation for Biomolecules Using Internal Cluster Validation Indexes

Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites

Introduction of a bounded penalty function in contact‐assisted simulations of protein structures to omit false restraints

OPUS‐SSF: A side‐chain‐inclusive scoring function for ranking protein structural models

Quantifying brain microstructure with diffusion MRI: Theory and parameter estimation

MARTINI bead form factors for the analysis of time‐resolved X‐ray scattering of proteins. Erratum

Multiscale Modeling Scheme for Simulating Polymeric Melts: Application to Poly(Ethylene Oxide)

OPUS‐CSF: A C‐atom‐based scoring function for ranking protein structural models

A multi‐resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand‐binding site

Filter options

Publication date

Keywords

INFONA - science communication portal

Search results

Add recipient

Sending message cancelled

Are you sure you want to cancel sending this message?

Send message

Filter options

Publication date

Date range setting

Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.

Keywords

Reporting an error / abuse

Sending the report failed

Accessibility options