Related papers: The dynamical transition in proteins and non-Gauss…
We used molecular dynamics simulations, the Green-Kubo Modal Analysis (GKMA) method and sonification to study the modal contributions to thermal conductivity in individual polythiophene chains. The simulations suggest that it is possible to…
Quantum molecular dynamics requires an accurate representation of the molecular potential energy surface from a minimal number of electronic structure calculations, particularly for nonadiabatic dynamics where excited states are required.…
Protein dynamics has been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is…
The structural stability and phonon properties of SnSe/SnS superlattices at finite temperatures have been studied using machine learning force field molecular dynamics and the anharmonic phonon approach. The vertical SnSe/SnS superlattice…
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 present a non-perturbative, mean-field theory for the Fermi-Pasta-Ulam-Tsingou model with quartic interaction, capturing the quasiperiodic features shown by the system at all energies in the thermodynamic limit. Starting from the true…
Neutral evolution is the simplest model of molecular evolution and thus it is most amenable to a comprehensive theoretical investigation. In this paper, we characterize the statistical properties of neutral evolution of proteins under the…
A prime example of non-equilibrium or active environment is a biological cell. In order to understand in-vivo functioning of biomolecules such as proteins, chromatins, a description beyond equilibrium is absolutely necessary. In this…
The 1/f-noise is considered which has no relation to long-lasting processes but originates from the same dynamical mechanisms as what are responsible for the loss of memory, fast relaxation and usual shot noise. The universal long-range…
A stochastic differential equation that describes the dynamics of single-domain magnetic particles at any temperature is derived using a classical formalism. The deterministic terms recover existing theory and the stochastic process takes…
Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…
Herein we develop a dynamical foundation for fractional Brownian Motion. A clear relation is established between the asymptotic behaviour of the correlation function and diffusion in a dynamical system. Then, assuming that scaling is…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
Machine learning (ML) methods provide advanced means for understanding inherent patterns within large and complex datasets. Here, we employ the principal component analysis (PCA) and the diffusion map (DM) techniques to evaluate the glass…
The finding that electronic conductance across ultra-thin protein films between metallic electrodes remains nearly constant from room temperature to just a few degrees Kelvin has posed a challenge. We show that a model based on a…
We investigate the behaviour of the lowest nonhydrodynamic modes in a class of holographic models which exhibit an equation of state closely mimicking the one determined from lattice QCD. We calculate the lowest quasinormal mode frequencies…
Low-frequency molecular fluctuations in the translational nonequilibrium zone of one-dimensional strong shock waves are characterised for the first time in a kinetic collisional framework in the Mach number range $2\le M\le 10$. Our…
The Spatial Convolution Model (SCM) analyzes allostery based on the spatial evolution of the docking protein elastic media, whereby convolution of the media in response to wave propagation is solved as a function of Z fluctuations and…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…