Related papers: Fluctuation relations to calculate protein redox p…
The experimental search for the QCD critical point by means of relativistic heavy-ion collisions necessitates the development of dynamical models of fluctuations. In this work we study the fluctuations of the net-baryon density near the…
Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct…
The Metropolis Monte Carlo (MC) method is used to extract reaction kinetics from a given equilibrium distribution of states of a complex system. The approach is illustrated by the folding/unfolding reaction for two proteins - a model…
Constructing a self-consistent first-principles framework that accurately predicts the properties of electron transfer reactions through finite-temperature molecular dynamics simulations is a dream of theoretical electrochemists and…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
Although the importance of protein dynamics in protein function is generally recognized, the role of protein fluctuations in allosteric effects scarcely has been considered. To address this gap, the Kullback-Leibler divergence (Dx) between…
Anomalous dynamics characterized by non-Gaussian probability distributions (PDFs) and/or temporal long-range correlations can cause subtle modifications of conventional fluctuation relations. As prototypes we study three variants of a…
Machine learning potentials (MLPs) represent atomic interactions with quantum mechanical accuracy offering an efficient tool for atomistic simulations in many fields of science. However, most MLPs rely on local atomic energies without…
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields,…
Molecular dynamics is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to molecular dynamics, by replacing the…
The prediction of protein stability changes following single-point mutations plays a pivotal role in computational biology, particularly in areas like drug discovery, enzyme reengineering, and genetic disease analysis. Although…
The study of phenomena such as protein folding and conformational changes in molecules is a central theme in chemical physics. Molecular dynamics (MD) simulation is the primary tool for the study of transition processes in biomolecules, but…
We present a hybrid method for the simulation of colloidal systems, that combines molecular dynamics (MD) with the Lattice-Boltzmann (LB) scheme. The LB method is used as a model for the solvent in order to take into account the…
A classical approach to formal policy synthesis in stochastic dynamical systems is to construct a finite-state abstraction, often represented as a Markov decision process (MDP). The correctness of these approaches hinges on a behavioural…
Robust radiative transfer techniques are requisite for efficiently extracting the physical and chemical information from molecular rotational lines.We study several hypotheses that enable robust estimations of the column densities and…
We study fluctuation effects in a two species reaction-diffusion system, with three competing reactions $A+A\rightarrow\emptyset$, $B+B\rightarrow\emptyset$, and $A+B\rightarrow\emptyset$. Asymptotic density decay rates are calculated for…
Redox biology underpins signalling, metabolism, immunity, and adaptation, yet lacks a unifying theoretical framework capable of formalising structure, function, and dynamics. Current interpretations rely on descriptive catalogues of…
An algorithm is presented here to get more detailed information, of mixed culture type, based exclusively on the biomass concentration data for fermentation processes. The analysis is performed with only the on-line measurements of the…
Approximate expressions for correlation functions in binary inhomogeneous mixtures are derived in a framework of the mesoscopic theory [Ciach A., Mol. Phys., 2011, {\textbf{109}}, 1101]. Fluctuation contribution is taken into account in a…
Current all-atom potential based molecular dynamics (MD) allow the identification of a protein's functional motions on a wide-range of time-scales, up to few tens of ns. However, functional large scale motions of proteins may occur on a…