Related papers: Probing vibrational energy relaxation in proteins …
We use empirical molecular dynamics technique to study the low-energy vibrations in a large 4096 atom model for pure amorphous silicon and a set of models with voids of different size based on it. Numerical vibrational eigenvalues and…
We develop a new approach to robust adaptive beamforming in the presence of signal steering vector errors. Since the signal steering vector is known imprecisely, its presumed (prior) value is used to find a more accurate estimate of the…
A Fermi resonance-algebraic model is proposed for molecular vibrations, where a U(2) algebra is used for describing the vibrations of each bond, and Fermi resonances between stretching and bending modes are taken into account. The model for…
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…
A method for characterising the wave-function of freely-propagating particles would provide a useful tool for developing quantum-information technologies with single electronic excitations. Previous continuous-variable quantum tomography…
We study amorphous solids with strong elastic disorder and find an un-jamming instability that exists, inter alia, in an harmonic model built using Euclidean random matrices (ERM). Employing the Zwanzig-Mori projection operator formalism…
The relaxation of temperatures and velocities of the components of a quasi-equilibrium two-component homogeneous completely ionized plasma is investigated on the basis of a generalization of the Chapman-Enskog method applied to the Landau…
The primary steps of photosynthesis rely on the generation, transport, and trapping of excitons in pigment-protein complexes (PPCs). Generically, PPCs possess highly structured vibrational spectra, combining many discrete intra-pigment…
We present a detailed theoretical study of the ultrafast quasiparticle relaxation dynamics observed in normal metals and heavy fermion materials with femtosecond time-resolved optical pump-probe spectroscopy. For normal metals, a nonthermal…
We study the vibrational spectrum of the protonated water dimer, by means of a divide-and-conquer semiclassical initial value representation of the quantum propagator, as a first step in the study of larger protonated water clusters. We use…
In this article, we develop the $C^1$-nonconforming $C^0$-conforming virtual element method (VEM) for the vanishing moment approximation of the second-order fully nonlinear Monge-Amp\`ere equation in two dimensions. In the vanishing moment…
This work reports numerical experiments intended to clarify the internal equilibration process in large molecules, following vibrational excitation. A model of amorphous and oxygenated hydrocarbon macromolecule (about 500 atoms)--simulating…
A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…
Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these…
We propose a new mathematical tool for the study of transport properties of models for lattice vibrations in crystalline solids. By replication of dynamical degrees of freedom, we aim at a new dynamical system where the "local" dynamics can…
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…
A theory is set up of spherical proteins interacting by screened electrostatics and constant adhesion, in which the effective adhesion parameter is optimized by a variational principle for the free energy. An analytical approach to the…
We use molecular dynamics computer simulations to investigate the relaxation dynamics of a simple model for a colloidal gel at a low volume fraction. We find that due to the presence of the open spanning network this dynamics shows at low…
In this article we introduce a multi-modal variational method to analytically estimate the full number- and corresponding energy-density profile of a spin-1 Bose-Einstein condensate (BEC) for a number of particles as low as 500 under…
Understanding the molecular vibrations underlying each of the unknown infrared emission (UIE) bands (such as those found at 3.3, 3.4, 3.5, 6.2, 6.9, 7.7, 11.3, 15.8, 16.4, 18.9 mm) observed in or towards astronomical objects is a vital link…