相关论文: How superlocalization affects Vibrational Energy E…
Collective protein modes are expected to be important for facilitating energy transfer in the Fenna-Matthews-Olson (FMO) complex, however to date little work has focussed on the microscopic details of these vibrations. The nonlinear network…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
The short time behavior of a disturbed system is influenced by off-shell motion and best characterized by the reduced density matrix possessing high energetic tails. We present analytically the formation of correlations due to collisions in…
The emergence of biochemical activities in a protein seem to commence with the onset of atomic mean-square displacements along the protein lattice. The ensuing protein dynamical transition has been discussed extensively in the literature,…
The problem of the ultraviolet divergences that arise in describing the nucleon dynamics at low energies is considered. By using the example of an exactly solvable model it is shown that after renormalization the interaction generating…
The diffusional dynamics and vibrational spectroscopy of molecular hydrogen (H$_2$) in myoglobin (Mb) is characterized. Hydrogen has been implicated in a number of physiologically relevant processes, including cellular aging or…
We consider a class of nonconvex energy functionals that lies in the framework of the peridynamics model of continuum mechanics. The energy densities are functions of a nonlocal strain that describes deformation based on pairwise…
Numerical studies of amorphous silicon in harmonic approximation show that the highest 3.5% of vibrational normal modes are localized. As vibrational frequency increases through the boundary separating localized from delocalized modes, near…
Motivated by subdiffusive motion of bio-molecules observed in living cells we study the stochastic properties of a non-Brownian particle whose motion is governed by either fractional Brownian motion or the fractional Langevin equation and…
Intramolecular energy transfer driven by near-field effects plays an important role in applications ranging from biophysics and chemistry to nano-optics and quantum communications. Advances in strong light-matter coupling in molecular…
In the full-orbit particle simulations of energetic particle transport in plasmas, the plasma turbulence is typically described as a homogeneous superposition of linear Fourier modes. The turbulence evolution is, however, typically a…
This study investigates the potential impact of intramolecular excitations on the active regions of biomolecular chains, which may play a role in physiological processes within living cells. We assumed that an excitation localized in a…
Evaluating accessible conformational space is computationally expensive and thermal motions are partly neglected in computer models of molecular interactions. This produces error into the estimates of binding strength. We introduce a method…
We investigate the extent to which the commonly used standard pairwise contact potential can be used to identify the native fold of a protein. Ideally one would hope that a universal energy function exists, for which the native folds of all…
Most widely used ligand docking methods assume a rigid protein structure. This leads to problems when the structure of the target protein deforms upon ligand binding. In particular, the ligand's true binding pose is often scored very…
Localized Structures often behave as quasi-particles and they may form molecules characterized by well-defined bond distances. In this paper we show that pointwise nonlocality may lead to a new kind of molecule where bonds are not rigid.…
In the transient state of d-wave superconductors, we investigate the temporal variation of photoinduced changes in the superfluid weight. We derive the formula that relates the nonlinear response function to the nonequilibrium distribution…
Understanding the vibrational and thermal properties of amorphous solids is one of the most discussed and long-standing issues in condensed matter physics. Recent works have made significant steps towards understanding harmonic vibrational…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
Statistical thermodynamics basis of energy and residue position fluctuations is explained for native proteins. The protein and its surroundings are treated as a canonical system with emphasis on the effects of energy exchange between the…