Related papers: A statistical-mechanical study of evolution of rob…
By means of Monte Carlo simulations on the three-dimensional Ising spin-glass model, we have studied aging phenomena with various temperature($T$)-change protocols. Particularly, a $T$-shift protocol, in which a system is first quenched to…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
A unified model of molecular and atomistic spin dynamics is presented enabling simulations both in microcanonical and canonical ensembles without the necessity of additional phenomenological spin damping. Transfer of energy and angular…
The jamming transition characterizes athermal systems of particles interacting via finite range repulsive potentials, and occurs on increasing the density when particles cannot avoid making contacts with those of their first coordination…
Evolution is simultaneously driven by a number of processes such as mutation, competition and random sampling. Understanding which of these processes is dominating the collective evolutionary dynamics in dependence on system properties is a…
In this work, we study the dynamics of complex systems with time-dependent transition rates, focusing on $p$-adic analysis in modeling such systems. Starting from the master equation that governs the stochastic dynamics of a system with a…
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…
Evolutionary dynamics can be studied in well-mixed or structured populations. Population structure typically arises from the heterogeneous distribution of individuals in physical space or on social networks. Here we introduce a new type of…
Environment plays a fundamental role in the competition for resources, and hence in the evolution of populations. Here, we study a well-mixed, finite population consisting of two strains competing for the limited resources provided by an…
Spatial distribution of the human population is distinctly heterogeneous, e.g. showing significant difference in the population density between urban and rural areas. In the historical perspective, i.e. on the timescale of centuries, the…
We study the dynamics of macroscopically-coherent matter waves of an ultra-cold atomic spin-one or spinor condensate on a ring lattice of six sites and demonstrate a novel type of spatio-temporal internal Josephson effect. Using a discrete…
We investigate a simple quantitative genetics model subjet to a gradual environmental change from the viewpoint of the phylogenies of the living individuals. We aim to understand better how the past traits of their ancestors are shaped by…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
Phenotypic evolution implies sequential fixations of new genomic sequences. The speed at which these mutations fixate depends, in part, on the relative fitness (selection coefficient) of the mutant vs. the ancestor. Using a simple…
We propose a model describing $N$ spin-1/2 systems coupled through $N$-order homogeneous interaction terms, in presence of local time-dependent magnetic fields. This model can be experimentally implemented with current technologies in…
Biological systems encode function not primarily in steady states, but in the structure of transient responses elicited by time-varying stimuli. Overshoots, biphasic dynamics, adaptation kinetics, fold-change detection, entrainment, and…
In order to understand the dynamics of active matter, we examine a minimalistic model where interacting spins on a one-dimensional lattice are driven by a self-propelled spin at the centre with a fixed rotational velocity $({\omega}_{0})$.…
We consider a trait-structured population subject to mutation, birth and competition of logistic type, where the number of coexisting types may fluctuate. Applying a limit of rare mutations to this population while keeping the population…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…