Related papers: High-resolution coarse-grained modeling using orie…
Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used.…
For optimal processing and design of entangled polymeric materials it is important to establish a rigorous link between the detailed molecular composition of the polymer and the viscoelastic properties of the macroscopic melt. We review…
In this study, the distributions of protein structure classes (or folding types) of experimentally determined structures from a legacy dataset and a comprehensive database (SCOP) are modeled precisely with geometric constructs such as…
We formulate thermodynamically consistent coarse-graining procedures for molecular systems undergoing thermally and photo-induced transitions: starting from elementary vibronic transitions, we derive effective photo-isomerization reactions…
A strategy is developed for generating equilibrated high molecular-weight polymer melts described with microscopic detail by sequentially backmapping coarse-grained (CG) configurations. The microscopic test model is generic but retains…
Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…
We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and…
Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of…
We formulate an effective-description framework for the dynamics of open quantum systems by extending the time-coarse-graining formalism to open systems. Our coarse-graining procedure efficiently removes high-frequency processes which are…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
Planar/flat configurations of fixed-angle chains and trees are well studied in the context of polymer science, molecular biology, and puzzles. In this paper, we focus on a simple type of fixed-angle linkage: every edge has unit length…
The inapplicability of amino acid covariation methods to small protein families has limited their use for structural annotation of whole genomes. Recently, deep learning has shown promise in allowing accurate residue-residue contact…
We propose a systematic coarse-grained representation of block copolymers, whereby each block is reduced to a single ``soft blob'' and effective intra- as well as intermolecular interactions act between centres of mass of the blocks. The…
After the recent ground-breaking advances in protein structure prediction, one of the remaining challenges in protein machine learning is to reliably predict distributions of structural states. Parametric models of fluctuations are…
A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4'-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain…
We propose a novel fine-grained cross-view localization method that estimates the 3 Degrees of Freedom pose of a ground-level image in an aerial image of the surroundings by matching fine-grained features between the two images. The pose is…
Data-based discovery of effective, coarse-grained (CG) models of high-dimensional dynamical systems presents a unique challenge in computational physics and particularly in the context of multiscale problems. The present paper offers a…
Figuring out small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many virtual and real drug-discovery scenarios. Since it is not always easy to find such binding sites based on…
The calibration of discrete element method (DEM) models is commonly performed by tuning model parameters to match an experimental measurements, most commonly the angle of repose (AOR). Although widely used, AOR-based calibration metrics do…