相关论文: The Role of Weak Interactions in Characterizing Pe…
The conformations available to polypeptides are determined by the interatomic forces acting on the peptide units, whereby backbone torsion angles are restricted as described by the Ramachandran plot. Although typical proteins are composed…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
The paper considers quantum electrodynamics (QED) and weak interaction of elementary particles in the lower orders of the perturbation theory using nonlocal Hamiltonian in the Foldy-Wouthuysen (FW) representation. Feynman rules in the FW…
Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as $\alpha$-helices and $\beta$-sheets. Secondary structure is characterized by the local rotational state of the protein…
We introduce a vector-based interpretation of the chemical bond within the quantum theory of atoms in molecules (QTAIM), the bond-path framework set $\mathbb{B} = \{p, q, r\}$, to follow variations in the 3-D morphology of all bonds for the…
A deep understanding of the intricate interactions between particles within a system is a key approach to revealing the essential characteristics of the system, whether it is an in-depth analysis of molecular properties in the field of…
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…
We use a new interpretation of the chemical bond within QTAIM. The bond-path framework set $\mathbb{B} = \{p, q, r\}$ with associated linkages with lengths $\mathbb{H}^*,m\mathbb{H}$ and the familiar bond-path length is used to describe a…
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…
Understanding interactions between membranes requires measurements on well-controlled systems close to natural conditions, in which fluctuations play an important role. We have determined, by grazing incidence X-ray scattering, the…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha-helices and beta-strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe…
The multi-component quantum theory of atoms in molecules (MC-QTAIM) analysis is done on methane, ethylene, acetylene and benzene as selected basic hydrocarbons. This is the first report on applying the MC-QTAIM analysis on polyatomic…
Experiments have observed superconductivity in atomically-thin metallic layers deposited on semiconducting substrates. As in any superconductor, it is important to determine the structure of the superconducting pairing function in order to…
Thin-walled structures clamped by friction joints, such as aircraft skin panels are exposed to bending-stretching coupling and frictional contact. We propose an original sub-structuring approach, where the system is divided into thin-walled…
The qualitative solvent- and temperature-dependent conformational behavior of a peptide in the proximity of solid substrates with different adsorption properties is investigated by means of a simple lattice model. The resulting pseudophase…
Waveguide quantum electrodynamics (WQED) provides a powerful platform for exploring quantum optical phenomena by enhancing atom-photon interactions through photon confinement in a waveguide. Here we investigate the photon-scattering…
Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present PepFlow, the first…
The nonleptonic weak $|\Delta S|=1$ $\Lambda N$ interaction, responsible for the dominant, nonmesonic decay of all but the lightest hypernuclei, is studied in the framework of an effective field theory. The long-range physics is described…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…