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Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…
Fluctuating environments are situations where the spatio-temporal stochasticity plays a significant role in the evolutionary dynamics. The study of the evolution of cooperation in these environments typically assumes a homogeneous, well…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
The original ideas of Cooper and Dryden, that allosteric signalling can be induced between distant binding sites on proteins without any change in mean structural conformation, has proved to be a remarkably prescient insight into the rich…
Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent…
Increasing shares of fluctuating renewable energy sources induce higher and higher power flow variability at the transmission level. The question arises as to what extent existing networks can absorb additional fluctuating power injection…
The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are…
Allosteric regulation in proteins is often accompanied by conformational changes that facilitate transmission of mechanical signals between distant ligand binding sites. Typically, these deformations are classified in terms of specific…
Protein functions in cells may be activated or modified by the attachment of several kinds of chemical groups. While protein phosphorylation, i.e. the attachment of a phosphoryl (PO$_3^-$) group, is the most studied form of protein…
Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well-defined internal mechanical motions to various initial deformations and that these…
Elastocaloric cooling has been identified as a promising alternative to high global warming potential vapor compression cooling. Two key bottlenecks to adoption are the need for bulky/expensive actuators to provide sufficient uniaxial…
We study the effects of thermal fluctuations on a small elastic ring. We derive analytical expressions for the correlation functions of the Euler angles, for the real space two--point correlation functions and for the probability…
Data is scaling exponentially in fields ranging from genomics to neuroscience to economics. A central question is: can modern machine learning methods be applied to construct predictive models of natural systems like cells and brains based…
We report a detailed computational study by Brownian Dynamics simulations of the structure and dynamics of a liquid of patchy particles which develops an amorphous tetrahedral network upon decreasing temperature. The highly directional…
As liquids approach the glass transition temperature, dynamical heterogeneity emerges as a crucial universal feature of their behavior. Dynamic facilitation, where local motion triggers further motion nearby, plays a major role in this…
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…
We study finite-temperature properties of strongly correlated fermions in two-dimensional optical lattices by means of numerical linked cluster expansions, a computational technique that allows one to obtain exact results in the…
The thermally activated motion of dislocations across fields of obstacles distributed at random and in a correlated manner, in separate models, is studied by means of computer simulations. The strain rate sensitivity and strength are…
Proteins often regulate their activities via allostery - or action at a distance - in which the binding of a ligand at one binding site influences the affinity for another ligand at a distal site. Although less studied than in proteins,…
A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…