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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…
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Keywords:
grained simulations;
parallel implementation;
optimization parallel;
implementation unres ... See more keywords
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Published in 2018 at "Physical Review E"
DOI: 10.1103/physreve.97.042608
Abstract: In this work, electrostatic forces between charged nanogels are explored through coarse-grained simulations. These simulations allow us to explicitly consider the complex topology of these nanoparticles and provide reliable force values to examine highly charged…
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Keywords:
forces charged;
charge;
direct determination;
coarse grained ... See more keywords
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Published in 2023 at "Biointerphases"
DOI: 10.1116/6.0002736
Abstract: Protein coronas, formed by proteins and nanomaterials, have various applications in the biomedical field. Here, large-scale simulations of protein coronas have been carried out by an efficient mesoscopic coarse-grained method with the BMW-MARTINI force field.…
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Keywords:
grained simulations;
protein coronas;
coarse;
simulations lysozyme ... See more keywords
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Published in 2022 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2022.826505
Abstract: Riboswitch RNAs regulate gene expression by conformational changes induced by environmental conditions and specific ligand binding. The guanidine-II riboswitch is proposed to bind the small molecule guanidinium and to subsequently form a kissing loop interaction…
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Keywords:
single molecule;
guanidine riboswitch;
grained simulations;
riboswitch ... See more keywords