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Intrinsically disordered proteins participate in many biological processes by folding upon binding with other proteins. However, coupled folding and binding processes are not well understood from an atomistic point of view. One of the main…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
Eukaryotic cells can move spontaneously without being guided by external cues. For such spontaneous movements, a variety of different modes have been observed, including the amoeboid-like locomotion with protrusion of multiple pseudopods,…
A kinetic model for the nucleation mechanism of protein folding is proposed. A protein is modeled as a heteropolymer consisting of hydrophobic and hydrophilic beads with equal constant bond lengths and bond angles. The total energy of the…
We present a computational study of the dynamic behavior of a Ziff-Gulari-Barshad model of CO oxidation with CO desorption on a catalytic surface. Our results provide further evidence that below a critical desorption rate the model exhibits…
Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a…
In conventional glassformers at sufficiently short times and low enough temperatures, molecules are mutually caged by the intermolecular potential. The fluctuation and dissipation from motion of caged molecules when observed by elastic…
Molecular docking, a key technique in structure-based drug design, plays pivotal roles in protein-ligand interaction modeling, hit identification and optimization, in which accurate prediction of protein-ligand binding mode is essential.…
Heterogeneous catalysts consisting of supported metallic nanoparticles typically derive exceptional catalytic activity from their large proportion of under-coordinated surface sites which promote adsorption of reactant molecules.…
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…
Bacterial chemotaxis for E.coli is controlled by methylation of chemoreceptors, which in a biochemical pathway regulates the concentration of the CheY-P protein that finally controls the tumbling rate. As a consequence, the tumbling rate…
With the growing adoption of deep learning models in different real-world domains, including computational biology, it is often necessary to understand which data features are essential for the model's decision. Despite extensive recent…
The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the…
The bacterium E. coli maneuvers itself to regions with high chemoattractant concentrations by performing two stereotypical moves: `runs', in which it moves in near straight lines, and `tumbles', in which it does not advance but changes…
Fitness effects of mutations fall on a continuum ranging from lethal to deleterious to beneficial. The distribution of fitness effects (DFE) among random mutations is an essential component of every evolutionary model and a mathematical…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
Bacterial colonies are a well-known example of living active matter, exhibiting collective behaviors such as nematic alignment and collective motion that play an important role in the spread of microbial infections. While the underlying…
The secretion of vesicles for intracellular transport often rely on the aggregation of specialized membrane-bound proteins into a coat able to curve cell membranes. The nucleation and growth of a protein coat is a kinetic process that…