Related papers: Conformational selection and induced changes along…
The article seeks to formulate a synergetic law that is posited to be of common physicochemical and biological nature: an evolving system, possessing free energy and elements with chiral asymmetry may change the type of symmetry inside one…
The genetic code underlying protein synthesis is a canonical example of a degenerate biological system. Degeneracies in physical and biological systems can be lifted by external perturbations thus allowing degenerate systems to exhibit a…
A continuum dynamical model is developed to determine the morphological and compositional instabilities on the free surface of heteroepitaxial alloy films in the absence of growth. We use linear stability analysis to study the early…
In this study, we explore nucleation and the transition state ensemble of the ribosomal protein S6 using a Monte Carlo Go model in conjunction with restraints from experiment. The results are analyzed in the context of extensive…
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…
Collagen is a key structural protein in the human body, which undergoes mineralization during the formation of hard tissues. Earlier studies have described the mechanical behavior of bone at different scales highlighting material features…
The objective of this paper is to study the dynamical behaviour systematically of an ecological system with Beddington-DeAngelis functional response which avoids the criticism occurred in the case of ratio-dependent functional response at…
Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for…
The simultaneous effect of both disorder and crystal-lattice pinning on the equilibrium behavior of oriented elastic objects is studied using scaling arguments and a functional renormalization group technique. Our analysis applies to…
We explored the Protein DataBank (PDB) to collect protein-ssDNA structures and create a multiconformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
Collective motion is a phenomenon observed across length scales in nature, from bacterial swarming and tissue migration to the flocking of animals. The mechanisms underlying this behavior vary significantly depending on the biological…
We examine time-resolved X-ray diffraction from molecules in the gas phase which undergo nonadiabatic avoided-crossing dynamics involving strongly coupled electrons and nuclei. Several contributions to the signal are identified,…
The symport of lactose and H+ is an important physiological process in E. coli, for it is closely related to cellular energy supply. In this paper, the symport of H+ and lactose by E. coli LacY protein is computationally simulated using a…
In systems biology and pharmacology, large-scale kinetic models are used to study the dynamic response of a system to a specific input or stimulus. While in many applications, a deeper understanding of the input-response behaviour is highly…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most organisms due to the high cost and complexity of experimental…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the last few years fold-change detecting mechanisms, based on transcriptional networks, have been…
Despite numerous experimental and theoretical studies devoted to the oxygen evolution reaction, the mechanism of the OER on transition metal oxides remains controversial. This is in part owed to the ambiguity of electrochemical parameters…