Related papers: Critical fluctuations in proteins native states
The eukaryotic cell nucleus harbors the DNA genome that is organized in a dynamic chromatin network and embedded in a viscous crowded fluid. This environment directly affects enzymatic reactions and target search processes that access the…
We use a three dimensional cubic lattice model of proteins to study their properties that determine folding to the native state. The protein chain is modeled as a sequence of $N$ beads. The interactions between beads are taken from a…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
When probing nuclear spins in materials on the nanometer scale, random fluctuations of the spin polarization will exceed the mean Boltzmann polarization for sample volumes below about (100nm)^3. In this work, we use magnetic resonance force…
We investigate sample-to-sample fluctuations of the shear modulus in ensembles of particle packings near the jamming transition. Unlike the average modulus, which exhibits distinct scaling behaviours depending on the interparticle…
The aim of this work is to elucidate how physical principles of protein design are reflected in natural sequences that evolved in response to the thermal conditions of the environment. Using an exactly solvable lattice model, we design…
The past decade has witnessed the development and success of coarse-grained network models of proteins for predicting many equilibrium properties related to collective modes of motion. Curiously, the results are usually robust towards the…
We investigate simultaneous effects of finite system size and global charge conservation on thermal fluctuations in the vicinity of a critical point. For that we consider a finite interacting system which exchanges particles with a finite…
The search for the QCD critical end point (CEP) is a major objective of contemporary heavy-ion physics, motivating the study of fluctuation observables that are sensitive to critical dynamics. In particular, baryon-number fluctuations…
We elucidate the physics of the dynamical transition via 10-100ns molecular dynamics simulations at temperatures spanning 160-300K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a cross-over…
We study fluctuations of particle number in the presence of critical point by utilizing molecular dynamics simulations of the classical Lennard-Jones fluid in a periodic box. The numerical solution of the $N$-body problem naturally…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
Micro and nanoscale materials have remarkable mechanical properties, such as enhanced strength and toughness, but usually display sample-to-sample fluctuations and non-trivial size effects, a nuisance for engineering applications and an…
Systems driven far from equilibrium may exhibit anomalous density fluctuations: active matter with orientational order display giant density fluctuations at large scale, while systems of interacting particles close to an absorbing phase…
We analyze two-particle pseudorapidity correlations in a simple model, where strings of fluctuating length are attached to wounded nucleons.The obtained straightforward formulas allow us to understand the anatomy of the correlations, i.e.,…
An approach is suggested for treating multiscale fluctuations in macromolecular systems. The emphasis is on the statistical properties of such fluctuations. The approach is illustrated by a macromolecular system with mesoscopic fluctuations…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
Autocatalytic fibril nucleation has recently been proposed to be a determining factor for the spread of neurodegenerative diseases, but the same process could also be exploited to amplify minute quantities of protein aggregates in a…
Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain.…
We study the behavior of a moving wall in contact with a particle gas and subjected to an external force. We compare the fluctuations of the system observed in the microcanonical and canonical ensembles, at varying the number of particles.…