Related papers: Quantum conformational transition in biological ma…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
In this report, we explore the use of a quantum optimization algorithm for obtaining low energy conformations of protein models. We discuss mappings between protein models and optimization variables, which are in turn mapped to a system of…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
A deformable body can rotate even with no angular momentum, simply by changing its shape. A good example is a falling cat, how it maneuvers in air to land on its feet. Here a first principles molecular level example of the phenomenon is…
We address the nonadiabatic quantum dynamics of macrosystems with several coupled electronic states, taking into account the possibility of multi-state conical intersections. The general situation of an arbitrary number of states and…
This article covers few selected aspects of quantum theory of molecular rotations and vibrations. Triatomic molecules are the simplest systems, which show qualitative characteristics of larger polyatomic molecules. On the minimal example of…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
Torsional-space Monte Carlo simulations of flexible molecules are usually based on the assumption that all values of dihedral angles have equal probability in the absence of atomic interactions. In the present paper it is shown that this…
The non-Markovian nature of polymer motions is accounted for in folding kinetics, using frequency-dependent friction. Folding, like many other problems in the physics of disordered systems, involves barrier crossing on a correlated energy…
We investigate the transient effects occurring in a molecular quantum dot described by an Anderson-Holstein Hamiltonian which is instantly coupled to two fermionic leads biased by a finite voltage. In the limit of weak electron-phonon…
We investigate the influence of thermally activated internal molecular dynamics on the phase shifts of matter waves inside a molecule interferometer. While de Broglie physics generally describes only the center-of-mass motion of a quantum…
The aim of the present paper is to provide a preliminary investigation of the thermodynamics of particles obeying monotone statistics. To render the potential physical applications realistic, we propose a modified scheme called…
We study the model of a molecular switch comprised of a molecule with a soft vibrational degree of freedom coupled to metallic leads. In the presence of strong electron-ion interaction, different charge states of the molecule correspond to…
The change of the vibrational energy within a molecule after collisions with another molecule plays an essential role in the evolution of molecular internal energy distributions, which is also the limiting process in the relaxation of the…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
In the geometry of quantum-mechanical processes, the time-varying curvature coefficient of a quantum evolution is specified by the magnitude squared of the covariant derivative of the tangent vector to the state vector. In particular, the…
A quantum system can undergo a continuous phase transition at the absolute zero of temperature as some parameter entering its Hamiltonian is varied. These transitions are particularly interesting for, in contrast to their classical finite…