Related papers: GMXPolymer: a generated polymerization algorithm b…
We report a novel multi-scale simulation methodology to quantitatively predict the thermodynamic behaviour of polymer mixtures, that exhibit phases with broken orientational symmetry. Our system consists of a binary mixture of oligomers and…
Given that the physical properties of polymeric liquids extend on a wide range of lengthscales, it is computationally convenient to represent them by coarse-grained (CG) descriptions at various granularities to investigate local and global…
In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…
The classic paradigm of structural biology is that the sequence of a biomolecule (protein, nucleic acid, lipid, etc) determines its conformation (shape) which determines its biological function. Protein folding programs like AlphaFold…
We review the recent literature on the simulation of the structure and deformation of amorphous glasses, including oxide and metallic glasses. We consider simulations at different length and time scales. At the nanometer scale, we review…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…
In this paper, we present a new approach to the discrete version of the Wormlike Chain Model (WCM) of semiflexible polymers. Our solution to the model is based on a new computational technique called the Generalized Borel Transform (GBT)…
Neural network potentials (NNPs) are rapidly changing the landscape of state-of-the-art molecular dynamics (MD) simulations. To make full use of this development, the community needs flexible, easy-to-use interfaces firmly integrated with…
A molecular level analysis of segmental trajectories obtained from molecular dynamics simulations is used to obtain the full relaxation time spectrum in aging polymer glasses subject to three different deformation protocols. As in…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…
Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…
We have connected the dynamic fragility, namely the rapidity of the relaxation time increase upon temperature reduction, to the excess entropy and heat capacity of a large number of glass-forming polymers. The connection was obtained in a…
In this study, a new alternative model algorithm has been proposed for assembling amorphous structures, unifying the bosonic paradigm applicable at low temperatures with crystalline models relevant at room and higher temperatures. Physical…
An innovative method is proposed to generate configurations of coarse grained models for polymer melts. This method, largely inspired by chemical ``radical polymerization'', is divided in three stages: (i) nucleation of radicals (reacting…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
We have generalized the Edwards' method of collective description of dense polymer systems in terms of effective potentials to polymer blends in the presence of a surface. With this method we have studied conformationally asymmetric…
High-Entropy Materials are composed of multiple elements on comparatively simpler lattices. Due to the multicomponent nature of such materials, the atomic scale sampling is computationally expensive due to the combinatorial complexity. We…
Polymer materials have the characteristic feature that they are multiscale systems by definition. Already the description of a single molecules involves a multitude of different scales, and cooperative processes in polymer assemblies are…
Transformer-based models trained on large and general purpose datasets consisting of molecular strings have recently emerged as a powerful tool for successfully modeling various structure-property relations. Inspired by this success, we…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…