Related papers: The dynamical transition in proteins and non-Gauss…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
We present a detailed description of semi-quantum molecular dynamics simulation of stochastic dynamics of a system of interacting particles. Within this approach, the dynamics of the system is described with the use of classical Newtonian…
Phase transitions occur when a macroscopic number of local degrees of freedom coherently change their behavior. In ground states of quantum many-body systems, phase transitions due to quantum fluctuations are observed as non-analytic…
We implement a standard Monte Carlo algorithm to study the slow, equilibrium dynamics of a silica melt in a wide temperature regime, from 6100 K down to 2750 K. We find that the average dynamical behaviour of the system is in quantitative…
Dynamical mechanical analysis (DMA)(f=0.2 - 100 Hz) is used to study the dynamics of confined water in mesoporous Gelsil (2.6 nm and 5 nm pores) and Vycor (10 nm) in the temperature range from T=80 K to 300 K. Confining water into nanopores…
In conventional glassformers at sufficiently short times and low enough temperatures, molecules are mutually caged by the intermolecular potential. The fluctuation and dissipation from motion of caged molecules when observed by elastic…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
In a recently developed microscopic mean field theory, we have shown that the dynamics of a system, when described only in terms of its pair structure, can predict the correct dynamical transition temperature. Further, the theory predicted…
A single-column model is used to investigate regime transitions within the stable atmospheric boundary layer, focusing on the role of small-scale fluctuations in wind and temperature dynamics and of turbulence intermittency as triggers for…
Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native…
The dynamical behavior of a harmonic chain in a spatially periodic potential (Frenkel-Kontorova model, discrete sine-Gordon equation) under the influence of an external force and a velocity proportional damping is investigated. We do this…
Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a variety of chemical, physical, and biological systems. In the standard approach in physical and chemical systems, the key properties that make these…
While the origin of temporal correlations in Langevin dynamics have been thoroughly researched, the understanding of Spatially Correlated Noise (SCN) is rather incomplete. In particular, very little is known about the relation between…
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in enzyme simulation. Over ten convergence studies of QM/MM methods have revealed over the past several years that key energetic and structural properties…
The dynamics of lysozyme is probed by attaching -SCN to all alanine-residues. The 1-dimensional infrared spectra exhibit frequency shifts in the position of the maximum absorption by 4 cm$^{-1}$ which is consistent with experiments in…
Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple…
Anomalous diffusion is frequently described by scaled Brownian motion (SBM), a Gaussian process with a power-law time dependent diffusion coefficient. Its mean squared displacement is $\langle x^2(t)\rangle\simeq\mathscr{K}(t)t$ with…
We study the dynamics of a simple adaptive system in the presence of noise and periodic damping. The system is composed by two paths connecting a source and a sink, the dynamics is governed by equations that usually describe food search of…
Heat-induced mobility of nucleosomes along DNA is an experimentally well-studied phenomenon. A recent experiment shows that the repositioning is modified in the presence of minor-groove binding DNA ligands. We present here a stochastic…
We describe how we can precisely measure variations in the entropy S of small solid samples below room temperature, as a function the temperature T or the external magnetic field H, respectively. A simple differential-thermal analysis (DTA)…