Related papers: The dynamical transition in proteins and non-Gauss…
We present a study on the near equilibrium dynamics of two small proteins in the family of truncated hemoglobins, developed under the framework of a Gaussian network approach. Effective beta carbon atoms are taken into account besides…
A paradigm for isothermal, mechanical rectification of stochastic fluctuations is introduced in this paper. The central idea is to transform energy injected by random perturbations into rigid-body rotational kinetic energy. The prototype…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
Normal mode dynamics are ubiquitous underlying the motions of diverse systems from rotating stars to crystal structures. These behaviors are composed of simple collective motions of particles which move with the same frequency and phase,…
Recent experiments using fluorescence spectroscopy have been able to probe the dynamics of conformational fluctuations in proteins. The fluctuations are Gaussian but do not decay exponentially, and are therefore, non-Markovian. We present a…
To sample rare events, dissipation-corrected targeted molecular dynamics (dcTMD) applies a constant velocity constraint along a one-dimensional reaction coordinate $s$, which drives an atomistic system from an initial state into a target…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
A single mechanism, endemic to the standard model of physics, is proposed to explain wavefunction collapse, classical motion, dissipation, equilibration, and the transition from pure quantum mechanics through open system decoherence to the…
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…
Using a large scale molecular dynamics computer simulation we investigate the dynamics of a supercooled melt of SiO_2. We find that with increasing temperature the temperature dependence of the diffusion constants crosses over from an…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…
A modeling framework for the internal conformational dynamics and external mechanical movement of single biological macromolecules in aqueous solution at constant temperature is developed. Both the internal dynamics and external movement…
Linear instability of high-speed boundary layers is routinely examined assuming quiescent edge conditions, without reference to the internal structure of shocks or to instabilities potentially generated in them. Our recent work has shown…
Summary: Coarse-grained normal mode analysis (NMA) is a fast computational technique to study the dynamics of biomolecules. Here we present the Najmanovich Research Group Toolkit for Elastic Networks (NRGTEN). NRGTEN is a Python toolkit…
We present results of a hole burning study with thermal cycling and waiting time spectral diffusion experiments on a modified cytochrome - c protein in its native as well as in its denatured state. The experiments show features which seem…
Heterogeneous diffusion processes are prevalent in various fields, including the motion of proteins in living cells, the migratory movement of birds and mammals, and finance. These processes are often characterized by time-varying dynamics,…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We study low-temperature nucleation in kinetic Ising models by analytical and simulational methods, confirming the general result for the average metastable lifetime, <tau> = A*exp(beta*Gamma) (beta = 1/kT) [E. Jordao Neves and R.H.…
Most material properties of great physical interest are directly related to nuclear dynamics, e.g. the ionic thermal conductivity, Raman/IR vibrational spectra, inelastic X-ray, and Neutron scattering. A theory able to compute from first…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…