Related papers: Critical fluctuations in proteins native states
The local statistical fluctuations in Brownian ensembles, the intermediate state of perturbation of one classical ensemble by another one, are system-size invariant if the perturbation parameter has the same size-dependence as that of the…
We determine the uncorrelated modes that characterize the fluctuations in a semi-realistic model for the initial state of high-energy nuclear collisions, consisting of hot spots whose positions are distributed independently. Varying the…
Dynamical fluctuations in global conserved quantities such as baryon number, strangeness, or charge may be observed near a QCD critical point. Results from new measurements of dynamical $K/\pi$ and $p/\pi$ ratio fluctuations are presented.…
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their…
Experimental investigations of the biosynthesis of a number of proteins have pointed out that part of the native structure can be acquired already during translation. We carried out a comprehensive statistical analysis of some average…
The conformational behavior of a polymer in a critical binary solvent confined in a porous medium is studied. The size of the polymer in bulk, which is mainly governed by the correlation length of the solvent density fluctuations, depends…
We discuss a model of protein conformations where the conformations are combinations of short fragments from some small set. For these fragments we consider a distribution of frequencies of occurrence of pairs (sequence of amino acids,…
Jammed packings' mechanical properties depend sensitively on their detailed local structure. Here we provide a complete characterization of the pair correlation close to contact and of the force distribution of jammed frictionless spheres.…
The modeling of the elastic properties of disordered or nanoscale solids requires the foundations of the theory of elasticity to be revisited, as one explores scales at which this theory may no longer hold. The only cases for which…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
We report that protein confinement within nanoscopic vesicular compartments corresponds to a liquid-liquid phase transition with the protein/water within vesicle lumen interacting very differently than in bulk. We show this effect leads to…
Protein variability in single cells has been studied extensively in populations, but little is known about temporal protein fluctuations in a single cell over extended times. We present here traces of protein copy number measured in…
The reorientation dynamics of local tangent vectors of chains in isotropic amorphous melts containing semiflexible model polymers was studied by molecular dynamics simulations. The reorientation is strongly influenced both by the local…
There is mounting empirical evidence that many communities of living organisms display key features which closely resemble those of physical systems at criticality. We here introduce a minimal model framework for the dynamics of a community…
Proteins are composed of chains of amino acids that fold into complex three-dimensional structures. Several key features, such as the radius of gyration, fraction of core amino acids $f_{\rm core}$, packing fraction $\langle \phi\rangle$ of…
Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute-residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach…
Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a…
The sensitivity of the native states of protein-like heteropolymers to mutations modelled as perturbations in the interaction potential between amino acids is studied. The stability threshold against mutations is shown to be zero for random…
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…