Related papers: Sidechain Dynamics and Protein Folding
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…
In the present work, we provide a dielectric study on two differently concentrated aqueous lysozyme solutions in the frequency range from 1 MHz to 40 GHz and for temperatures from 275 to 330 K. We analyze the three dispersion regions,…
Upon cooling, glass-forming liquids experience a two-step relaxation associated to the cage rattling and the escape from the cage, and the following decoupling between the \b{eta}- and the {\alpha}-relaxations. The found decoupling…
Assuming that mutation and fixation processes are reversible Markov processes, we prove that the equilibrium ensemble of sequences obeys a Boltzmann distribution with $\exp(4N_e m(1 - 1/(2N)))$, where $m$ is Malthusian fitness and $N_e$ and…
We study the kinetics of the first order phase separation transition in boson-fermion cold-atom mixtures. At sufficiently low temperatures such a transition is driven by quantum fluctuations responsible for the formation of critical nuclei…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
We review the non-zero temperature relaxational dynamics of quantum systems near a zero temperature, second-order phase transition. We begin with the quantum Ising chain, for which universal and exact results for the relaxation rates can be…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
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…
The relaxation process of a diffusive ring becomes under-damped if the bias (so called affinity) exceeds a critical threshold value, aka delocalization transition. This is related to the spectral properties of the pertinent stochastic…
The dynamical behavior of a kind of models with hierarchically constrained dynamics is investigated. The models exhibit many properties resembling real structural glasses. In particular, we focus on the study of time-dependent temperature…
It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…
We investigate the possibility of extending the notion of temperature in a stochastic model for the RNA/protein folding driven out of equilibrium. We simulate the dynamics of a small RNA hairpin subject to an external pulling force, which…
The dynamics of structural relaxation in a model polymer glass subject to spatially-homogeneous, time-periodic shear deformation is investigated using molecular dynamics simulations. We study a coarse-grained bead-spring model of short…
Critical slowing down (CSD) has been a trademark of critical dynamics for equilibrium phase transitions of a many-body system, where the relaxation time for the system to reach thermal equilibrium or quantum ground state diverges with…
A simple spin system is studied as an analog for proteins. We investigate how the introduction of randomness and frustration into the system effects the designability and stability of ground state configurations. We observe that the spin…
Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…
We study the relaxation dynamics of a binary liquid mixture near a light-absorbing Janus particle after switching on and off illumination using experiments and theoretical models. The dynamics is controlled by the temperature gradient…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…