Related papers: The dynamical transition in proteins and non-Gauss…
Recently we have shown experimental evidence for a fragile-to-strong dynamic crossover (FSC) phenomenon in hydration water around a globular protein (lysozyme) at ambient pressure. In this letter we show that when applying pressure to the…
We apply the self-consistent harmonic approximation (SCHA) to study static and dynamic properties of the two-dimensional classical Heisenberg model with easy-axis anisotropy. The static properties obtained are magnetization and spin wave…
We study the stochastic motion of active particles that undergo spontaneous transitions between two distinct modes of motion. Each mode is characterized by a velocity distribution and an arbitrary (anti-)persistence. We present an…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
We analyse mobile-immobile transport of particles that switch between the mobile and immobile phases with finite rates. Despite this seemingly simple assumption of Poissonian switching we unveil a rich transport dynamics including…
We study the viscoelastic response of amorphous polymers using theory and simulations. By accounting for internal stresses and considering instantaneous normal modes (INMs) within athermal non-affine theory, we make parameter-free…
The change of the vibrational energy within a molecule after collisions with another molecule plays an essential role in the evolution of molecular internal energy distributions, which is also the limiting process in the relaxation of the…
The frequencies of the analytic normal modes for N identical particles are studied as a function of system parameters from the weakly interacting BCS regime to the strongly interacting unitary regime. The normal modes were obtained…
Using an Ising-like model of protein mechanical unfolding, we introduce a diffusive dynamics on its exactly known free energy profile, reducing the nonequilibrium dynamics of the model to a biased random walk. As an illustration, the model…
Nuclear magnetic resonance (NMR) is sensitive to dynamics on a wide range of correlation times. Recently, we have shown that analysis of relaxation rates via fitting to a correlation function with a small number of exponential terms could…
This paper is concerned with the stochastic thermodynamics of non-equilibrium Gaussian processes that can exhibit anomalous diffusion. In the systems considered, the noise correlation function is not necessarily related to friction. Thus,…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
A recent theory described strange metal behavior in a model of a Fermi surface coupled a two-dimensional quantum critical bosonic field with a spatially random Yukawa coupling. With the assumption of self-averaging randomness, similar to…
In this paper, we examine the thermodynamic behavior of a quantum harmonic oscillator with a position-dependent mass (PDM), where spatial inhomogeneity is modeled through a deformation parameter {\alpha}. Based on the exact energy spectrum,…
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
The non-Markovian nature of polymer motions is accounted for in folding kinetics, using frequency-dependent friction. Folding, like many other problems in the physics of disordered systems, involves barrier crossing on a correlated energy…
Mean square displacements of hydrogen atoms in glass-forming materials and proteins, as reported by incoherent elastic neutron scattering, show kinks in their temperature dependence. This crossover, known as the dynamical transition,…