Related papers: The protein dynamical transition is independent of…
Water is vital for life, and without it biomolecules and cells cannot maintain their structures and functions. The remarkable properties of water originate from its ability to form hydrogen-bonding networks and dynamics, which the…
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by softening of the vibrational force constant by electrostatic and van der Waals forces…
Multi-molecular excited states accompanied by an intra- and inter-molecular geometric relaxation are commonly encountered in optical and electrooptical studies and applications of organic semiconductors as, for example excimers or charge…
We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…
Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the…
Domain phases in ultrathin Fe/Ni/W(110) films with perpendicular anisotropy have been studied using the ac magnetic susceptibility. Dynamics on time scales of minutes to hours were probed by quenching the system from high temperature to the…
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…
Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and characterization of microparticles in biomedical and nanoelectronics research. In…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
We review recent rigorous mathematical results about the macroscopic behaviour of harmonic chains with the dynamics perturbed by a random exchange of velocities between nearest neighbor particles. The random exchange models the effects of…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…
We present a study of static and frequency-dependent diffusion with anisotropic thermally activated transition rates in a two-dimensional bond percolation system. The approach accounts for temperature effects on diffusion coefficients in…
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…
Thin layers of water on biomolecular and other nanostructured surfaces can be supercooled to temperatures not accessible with bulk water. Chen et al. [PNAS 103, 9012 (2006)] suggested that anomalies near 220 K observed by quasi-elastic…
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…
Membrane phase behavior induced by the binding of curvature-inducing proteins is studied by a combination of analytical and numerical approaches. In thermal equilibrium under the detailed balance between binding and unbinding, the membrane…
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…
Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast ($\sim$ pico-nanosecond, ps-ns) and small-amplitude ($\sim$ \AA )…
2H NMR is used to study the mechanisms for the reorientation of protein hydration water. In the past, crossovers in temperature-dependent correlation times were reported at T_x1=225K (X1) and T_x2=200K (X2). We show that neither X1 nor X2…