Related papers: Protein conformational dynamics and electronic str…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
Terahertz time-domain spectroscopy and differential scanning calorimetry were used to study the role of the dynamics of biomolecules decoupled from solvent effects. Lyophilised sucrose exhibited steadily increasing absorption with…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
Theory of exciton fine structure in semiconductor quantum dots and its dependence on quantum dot anisotropy and external lateral electric field is presented. The effective exciton Hamiltonian including long range electron-hole exchange…
Lattice protein models, as the Hydrophobic-Polar (HP) model, are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the…
The path integral formalism is applied to derive the full partition function of a generalized Su-Schrieffer-Heeger Hamiltonian describing a particle motion in a bath of oscillators. The electronic correlations are computed versus…
Intricate comparison between two given tertiary structures of proteins is as important as the comparison of their functions. Several algorithms have been devised to compute the similarity and dissimilarity among protein structures. But,…
The interplay of the excitoniclike polariton, polariton, and photoniclike polariton coherent states in mass-imbalanced electron-hole systems within optical microcavities is theoretically examined. Utilizing the unrestricted Hartree-Fock…
The properties of hydrogen at warm dense matter (WDM) conditions are of high importance for the understanding of astrophysical objects and technological applications such as inertial confinement fusion. In this work, we present extensive…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
An overview of recent data on electromagnetic hadron form factors is presented and discussed in terms of selected nucleon models in space-like and time-like regions. Model independent properties connecting scattering and annihilation…
The damping on the fluctuation spectrum and the presence of thermal velocities as properties of warm dark matter particles like sterile neutrinos imprint a distinct signature found from the structure formation mechanisms to the internal…
We consider a Hamiltonian description of the vibrations of a clamped, elastic circular plate. The Hamiltonian of this system features a potential energy with two distinct contributions: one that depends on the local mean curvature of the…
We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…
A simple and surprisingly accurate description of spectral diffusion in deeply frozen globular proteins is constructed directly using the concept of ultrametricity of protein dynamics. Earlier the similar concept has been used for…
Strong coupling between excitons and confined modes of light presents a promising pathway to tunable and enhanced energy transport in organic materials. By forming hybrid light-matter quasiparticles, exciton-polaritons, electronic…
The relaxation of Fourier modes of hamiltonian chains close to equilibrium is studied in the framework of a simple mode-coupling theory. Explicit estimates of the dependence of relevant time scales on the energy density (or temperature) and…
Nucleon and pion electromagnetic form factors are evaluated in the spacelike region within a light-front constituent quark model, where eigenfunctions of a mass operator, reproducing a large set of hadron energy levels, are adopted and…
The electronic structure of plutonium metal and its compounds pose a grand challenge for a fundamental understanding of the Pu-5$f$ electron character. For 30 years the plutonium chalcogenides have been especially challenging, and multiple…