A review of advancements in coarse-grained molecular dynamics simulations

SY Joshi, SA Deshmukh - Molecular Simulation, 2021 - Taylor & Francis
Over the last few years, coarse-grained molecular dynamics has emerged as a way to model
large and complex systems in an efficient and inexpensive manner due to its lowered …

Coarse-graining methods for computational biology

MG Saunders, GA Voth - Annual review of biophysics, 2013 - annualreviews.org
Connecting the molecular world to biology requires understanding how molecular-scale
dynamics propagate upward in scale to define the function of biological structures. To …

Evolutionary multi-objective optimization and Pareto-frontal uncertainty quantification of interatomic forcefields for thermal conductivity simulations

A Krishnamoorthy, A Mishra, N Grabar… - Computer Physics …, 2020 - Elsevier
Abstract Predictive Molecular Dynamics simulations of thermal transport require forcefields
that can simultaneously reproduce several structural, thermodynamic and vibrational …

A minimalist model of protein diffusion and interactions: the green fluorescent protein within the cytoplasm

F Trovato, R Nifosì, A Di Fenza, V Tozzini - Macromolecules, 2013 - ACS Publications
In this work, we present a minimalist model (one-bead-per-amino acid resolution) of a tracer
protein (the green fluorescent protein) embedded in a meso scale cytoplasm (one-bead-per …

Methods for accurate and efficient simulation of the conformational landscape of ligands

JP Dos Santos Morado - 2022 - eprints.soton.ac.uk
Ligand modelling is an essential element of drug discovery. To accurately simulate chemical
and physical phenomena, it is necessary to employ molecular models that provide reliable …

Modeling Nucleic Acids

F Leonarski, J Trylska - … Methods to Study the Structure and …, 2018 - books.google.com
Coarse-grained models and force fields have become useful in the studies of the dynamics
and physicochemical properties of nucleic acids. Reduced representations of DNA or RNA …

Modeling Nucleic Acids at the Residue–Level Resolution

F Leonarski, J Trylska - Computational Methods to Study the Structure and …, 2019 - Springer
Coarse–grained models and force fields have become useful in the studies of the dynamics
and physicochemical properties of nucleic acids. Reduced representations of DNA or RNA …