Related papers: Probing vibrational energy relaxation in proteins …
We consider the approximation of the 2D frictionless contact problem in elasticity using the Virtual Element Methods (VEMs). To overcome the volumetric locking phenomenon in the nearly incompressible case, we adopt a mixed…
We investigate the collective excitations of a harmonically trapped two-dimensional Fermi gas from the collisionless (zero sound) to the hydrodynamic (first sound) regime. The breathing mode, which is sensitive to the equation of state, is…
Some of us have recently reported in Science 321 232 (2008) vibrational cooling of translationally cold Cs_2 molecules into the lowest vibrational level v=0 of the singlet X 1Sigma_g ground electronic state. Starting from a sample of cold…
We show that viscoelastic effects play a crucial role in the damping of vibrational modes in harmonic amorphous solids. The relaxation of a given plane wave is described by a memory function of a semi-infinite one-dimensions mass-spring…
Biomolecular thermodynamics and spectroscopy depend on relative conformer energies, local curvatures, and collective dipole fluctuations on the potential-energy surface. Conventional molecular mechanics force fields enable large-scale…
The use of free energy perturbation (FEP) methods to study protein-ligand complexes is one of the most important tools in structure-based drug design. Because FEP methods typically rely on force fields, they may suffer from force field…
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…
We consider the equilibration rate for fermions in Bose-Fermi mixtures undergoing cross-dimensional rethermalization. Classical Monte Carlo simulations of the relaxation process are performed over a wide range of parameters, focusing on the…
Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…
Descent extensions of the soft-wall model are used to accommodate two variants of Regge trajectories of vector meson excitations. At non-zero temperatures, various options for either sequential or instantaneous disappearance of vector…
We apply adaptive feedback for the partial refrigeration of a mechanical resonator, i.e. with the aim to simultaneously cool the classical thermal motion of more than one vibrational degree of freedom. The feedback is obtained from a neural…
We analyse the Virtual Element Methods (VEM) on a simple elliptic model problem, allowing for more general meshes than the one typically considered in the VEM literature. For instance, meshes with arbitrarily small edges (with respect to…
In this paper, we derive a series of exact analytical closed expressions to calculate the complex eigenfrequencies and the displacement for the corresponding eigenmodes of a viscoelastic (nano-)sphere in the presence of linear damping.…
We present an embedded-atom-method (EAM) model that is specifically designed to accurately describe vibrations in bcc alkali metals. Using this model, we study bulk vibrational structure of Li, Na, K, and Rb when configured in bcc and the…
The damping of vortex cyclotron modes is investigated within a generalized quantum theory of vortex waves. Similarly to the case of Kelvin modes, the friction coefficient turns out to be essentially unchanged under such oscillations, but it…
We develop a formalism to directly evaluate the matrix of force constants within a Quantum Monte Carlo calculation. We utilize the matrix of force constants to accurately relax the positions of atoms in molecules and determine their…
The time evolution of the distribution function for a particle-hole excitation in a Fermi system was calculated using the direct numerical solution of a nonlinear diffusion equation in momentum space. A phenomenological expression for…
This short note reports a new derivation of the optimal order of the a priori error estimates for conforming virtual element methods (VEM) on 3D polyhedral meshes based on an error equation. The geometric assumptions, which are necessary…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
This paper introduces an axiomatic basis for measuring the energy characteristic of vibrating dynamical systems. The basic approach is to compare non-modulated vs. modulated waveforms in measuring energy during the vibratory motion $m(t)$…