Related papers: Disordered peptide chains in an {\alpha}-C-based c…
Incorporating atomistic and molecular information into models of cellular behaviour is challenging because of a vast separation of spatial and temporal scales between processes happening at the atomic and cellular levels. Multiscale or…
We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet…
We show by numerical simulations that discretized versions of commonly studied continuum nonlinear growth equations (such as the Kardar-Parisi-Zhang equation and the Lai-Das Sarma equation) and related atomistic models of epitaxial growth…
Coarse-grained (CG) models are often parametrized to reproduce one-dimensional structural correlation functions of an atomically-detailed model along the degrees of freedom governing each interaction potential. While cross correlations…
Discrete Element Methods (DEM) are a useful tool to model the fracture of cohesive granular materials. For this kind of application, simple particle shapes (discs in 2D, spheres in 3D) are usually employed. However, dealing with more…
Using a weak-disorder scheme and real-space renormalization-group techniques, we obtain analytical results for the critical behavior of various q-state Potts models with correlated disordered exchange interactions along d1 of d spatial…
Using a coarse-grained model, self-organized assembly of proteins (e.g. CorA and its inner segment iCorA) is studied by examining quantities such as contact profile, radius of gyration, and structure factor as a function of protein…
Cells contain multiple condensates which spontaneously form due to the heterotypic interactions between their components. Although the proteins and disordered region sequences that are responsible for condensate formation have been…
Liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is a major undergirding factor in the regulated formation of membraneless organelles in the cell. The phase behavior of an IDP is sensitive to its amino acid…
We consider a class of singularly perturbed 2-component reaction-diffusion equations which admit bistable traveling front solutions, manifesting as sharp, slow-fast-slow, interfaces between stable homogeneous rest states. In many example…
We consider the propagation of a single particle in a random chain, assisted by the coupling to dispersive bosons. Time evolution treated with rate equations for hopping between localized states reveals a qualitative difference between…
We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…
In this paper, we present a coarse-grained model of DNA based on the soft ellipsoid contact potential (ECP) to evaluate the base pairing interaction properly. We extend the ellipsoid contact like potential model (ECP), suitably modified and…
A protein residue network (PRN) is a network of interacting amino acids within a protein. We describe characteristics of a sparser, highly central and more volatile sub-network of a PRN called the short-cut network (SCN), as a protein folds…
This study reports a general scenario for the out-of-equilibrium features of collapsing polymeric architectures. We use molecular dynamics simulations to characterize the coarsening kinetics, in bad solvent, for several macromolecular…
The presence of one or more species at some spatial locations but not others is a central matter in ecology. This phenomenon is related to ecological pattern formation. Nonlocal interactions can be considered as one of the mechanisms…
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…
The idea that structural disorder might be a novel mechanism of protein interaction is widespread in the Literature, although the number of statistically significant structural studies supporting this is surprisingly low. At variance with…
Large-scale coarse-grained molecular dynamics simulations of inhomogeneous gel networks were performed to investigate abnormal butterfly patterns in two-dimensional scattering. The networks were diamond lattice-based with distributions in…
A computational tool for coarse-graining nonlinear systems of ordinary differential equations in time is discussed. Three illustrative model examples are worked out that demonstrate the range of capability of the method. This includes the…