Related papers: Sequence Engineering of Copolymers using Evolution…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
The ability to tune the microstructures formed by block copolymers using accessible physical approaches provides control for practical material applications. A common strategy involves the addition of homopolymers, which can induce…
Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…
Epoxy polymers are used in wide range of applications. The properties and performance of epoxy polymers depend upon various factors like the type of constituents and their proportions used and other process parameters. The conventional way…
Over the past two decades polymer nanocomposites have received tremendous interest from industry and academia due to their advanced properties comparative to polymer blends. Many computational studies have revealed that the macroscopic…
The detailed analysis of molecular structures and properties holds great potential for drug development discovery through machine learning. Developing an emergent property in the model to understand molecules would broaden the horizons for…
Evolutionary algorithms have been frequently applied to constrained continuous optimisation problems. We carry out feature based comparisons of different types of evolutionary algorithms such as evolution strategies, differential evolution…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints on each residue site. Selective constraints on residue sites are…
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…
Polymer properties are inherently multi-scale in nature, where delicate local interaction details play a key role in describing their global conformational behavior. In this context, deriving coarse-grained (CG) multi-scale models for…
We develop Monte Carlo simulations for uniformly charged polymers and machine learning algorithm to interpret the intra-polymer structure factor of the charged polymer system, which can be obtained from small-angle scattering experiments.…
Spider silks are remarkable materials characterized by superb mechanical properties such as strength, extensibility and lightweightedness. Yet, to date, limited models are available to fully explore sequence-property relationships for…
Rapid advancements in machine learning (ML) are transforming materials science by significantly speeding up material property calculations. However, the proliferation of ML approaches has made it challenging for scientists to keep up with…
Peptides are recognized for their varied self-assembly behaviors, forming a wide array of structures and geometries, such as spheres, fibers, and hydrogels, each presenting a unique set of material properties. The functionalities of these…
Mechanical product engineering often must comply with manufacturing or geometric constraints related to the shaping process. Mechanical design hence should rely on robust and fast tools to explore complex shapes, typically for design for…
We present simulations on a binary blend of bead-spring polymer chains. The introduction of monomer size disparity yields very different relaxation times for each component of the blend. Competition between two different arrest mechanisms,…
This document presents a combinatorial framework for analyzing assembly systems using generating functions. We explore the theory through concrete examples, such as linear polymers, and develop recursive equations to characterize valid…