Local and long range potentials for heparin-protein systems for coarse-grained simulations.
Sign Up to like & getrecommendations! Published in 2019 at "Biopolymers"
DOI: 10.1002/bip.23269
Abstract: Heparin belongs to glycosaminoglycans (GAGs), a class of periodic linear anionic polysaccharides, which are functionally important components of the extracellular matrix owing to their interactions with various protein targets. Heparin is known to be involved… read more here.
Keywords: potentials heparin; coarse; long range; coarse grained ... See more keywords
Rheology of debris flows: Insights from experiments with coarse‐grained matrix
Sign Up to like & getrecommendations! Published in 2025 at "Earth Surface Processes and Landforms"
DOI: 10.1002/esp.6069
Abstract: Debris flow is characterized by a heterogeneous mixture of water and sediment with varying rheology. The granular effects on rheology are usually attributed to the bulk concentration of solids without considering the variability of granular… read more here.
Keywords: rheology; debris; coarse grained; debris flow ... See more keywords
A rapid solvent accessible surface area estimator for coarse grained molecular simulations
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.24709
Abstract: The rapid and accurate calculation of solvent accessible surface area (SASA) is extremely useful in the energetic analysis of biomolecules. For example, SASA models can be used to estimate the transfer free energy associated with… read more here.
Keywords: solvent accessible; surface area; accessible surface; solvent ... See more keywords
Extension of CAVS coarse‐grained model to phospholipid membranes: The importance of electrostatics
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.24770
Abstract: It is evident from experiment that electrostatic potential (or dipole potential) is positive inside PC or PE lipid bilayers in the absence of ions. MARTINI coarse‐grained (CG) model, which has been widely used in simulating… read more here.
Keywords: electrostatics; model; coarse grained; dipole potential ... See more keywords
ESCASA: Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance‐assisted protein structure modeling. I. Backbone and Hβ protons
Sign Up to like & getrecommendations! Published in 2021 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26695
Abstract: A method for the estimation of coordinates of atoms in proteins from coarse‐grained geometry by simple analytical formulas (ESCASA), for use in nuclear‐magnetic‐resonance (NMR) data‐assisted coarse‐grained simulations of proteins is proposed. In this paper, the… read more here.
Keywords: estimation; nuclear magnetic; magnetic resonance; geometry ... See more keywords
Optimization of parallel implementation of UNRES package for coarse‐grained simulations to treat large proteins
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.27026
Abstract: We report major algorithmic improvements of the UNRES package for physics‐based coarse‐grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to… read more here.
Keywords: grained simulations; parallel implementation; optimization parallel; implementation unres ... See more keywords
Development of a bottom‐up coarse‐grained model for interactions of lipids with TiO 2 nanoparticles
Sign Up to like & getrecommendations! Published in 2024 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.27310
Abstract: 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… read more here.
Keywords: coarse; development bottom; coarse grained; bottom coarse ... See more keywords
Analysis of static and dynamic mechanical properties of carbon black/carbon nanotubes hybrid filled natural rubber nanocomposites using coarse‐grained molecular dynamics
Sign Up to like & getrecommendations! Published in 2024 at "Polymer Composites"
DOI: 10.1002/pc.28117
Abstract: Nanoparticle (NP)‐filled natural rubber (NR) has attracted much attention owing to their prominent mechanical strength, stiffness, and wear resistance. In this study, the static and dynamic mechanical properties of carbon black (CB)/carbon nanotubes (CNTs) hybrid… read more here.
Keywords: coarse; coarse grained; rubber; filled natural ... See more keywords
Dissecting the general mechanisms of protein cage self‐assembly by coarse‐grained simulations
Sign Up to like & getrecommendations! Published in 2022 at "Protein Science"
DOI: 10.1002/pro.4552
Abstract: The development of artificial protein cages has recently gained massive attention due to their promising application prospect as novel delivery vehicles for therapeutics. These nanoparticles are formed through a process called self‐assembly, in which individual… read more here.
Keywords: self assembly; protein cage; general mechanisms; self ... See more keywords
Relationship between the Microstructure and Impact Toughness of the Coarse‐Grained Heat‐Affected Zone for Offshore Engineering Steels with Different Mg Contents
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DOI: 10.1002/srin.202100099
Abstract: The relationship between the microstructure and impact toughness of coarse‐grained heat affected zone for offshore engineering steels with 0.0002 and 0.0042 wt% Mg, termed as 2 and 42Mg, respectively, is clarified. With increasing the Mg content… read more here.
Keywords: microstructure impact; impact toughness; coarse grained; grained heat ... See more keywords
Effects of Cooling Rate on the Microstructure and Properties of Coarse‐Grained Zone in Complex‐Phase Steel 780HE
Sign Up to like & getrecommendations! Published in 2025 at "steel research international"
DOI: 10.1002/srin.202500911
Abstract: A thermomechanical simulator Gleeble‐3800 is used to simulate the thermal cycles experienced by coarse‐grained heat‐affected zonecoarse‐grained heat‐affected zone (CGHAZ) of 780HE steel under different cooling rates during welding. The effects of cooling rate on the… read more here.
Keywords: effects cooling; rate; coarse grained; rate microstructure ... See more keywords