Related papers: H-bonds in Crambin: Coherence in an alpha helix
Through density functional theory and molecular dynamics calculations, we have analysed various metal polyhydrides to understand whether hydrogen is present in its molecular or atomic form - tetrahydrides of Ba,Sr,Ra, Cs and La;…
The closure of cooperative chains of Hydrogen Bonding, HB, to form cycles can enhance cooperativity. Cycles of charge transfer can balance charge into and out of every site, eliminating the charge build-up that limits the cooperativity of…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
Polymerization of fibrin, the primary structural protein of blood clots and thrombi, occurs through binding of knobs 'A' and 'B' in the central nodule of fibrin monomer to complementary holes 'a' and 'b' in the beta- and gamma-nodules,…
This application paper investigates the stability of hydrogen bonds (H-bonds), as characterized by the Quantum Theory of Atoms in Molecules (QTAIM). First, we contribute a database of 4544 electron densities associated to four isomers of…
We use the torsional angles of the protein chain as generalized coordinates in the canonical formalism, derive canonical equations of motion, and investigate the coordinate dependence of the kinetic energy expressed in terms of the…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
Power system coherency refers to the phenomenon that machines in a power network exhibit similar frequency responses after disturbances, and is foundational for model reduction and control design. Despite abundant empirical observations,…
Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind a variety of specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic…
We examine the behaviour of hydrogen ions, atoms and molecules in alpha-boron using density functional calculations. Hydrogen behaves as a negative-U centre, with positive H ions preferring to sit off-center on inter-layer bonds and…
Molecular hydrogen in silicon has been studied by path-integral molecular dynamics simulations in the canonical ensemble. Finite-temperature properties of these point defects were analyzed in the range from 300 to 900 K. Interatomic…
Intermittent density fluctuations of nucleotide molecules (adenine, guanine, cytosine and thymine) along DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
The kinematic constrains on interacting nucleons in Large Hadron Collider (LHC) heavy-ion collisions are investigated in the framework of the Heavy Ion Jet Interaction Generator (HIJING) code incorporated with a collective cascade recipe.…
This paper is focused on the coherent effects that appear in tracer statistics in two-dimensional incompressible turbulence in the presence of an average velocity. We show that this determines strong modifications of the transport and…
We study the distribution of hydrogen and various hydride configurations in realistic models of a-Si:H for two different concentration generated via experimentally constrained molecular relaxation approach (ECMR) [1]. The microstructure…
Modeling of frictional contacts is crucial for investigating mechanical performances of composite materials under varying service environments. The paper considers a linear elasticity system with strongly heterogeneous coefficients and…
We present a study on the near equilibrium dynamics of two small proteins in the family of truncated hemoglobins, developed under the framework of a Gaussian network approach. Effective beta carbon atoms are taken into account besides…
We report a molecular dynamics simulation of selenium, described by a three-body interaction. The temperatures T_g and T_c and the structural properties are in agreement with experiment. The mean nearest neighbor coordination number is 2.1.…
The experimental study of hydrogen bonds and their symmetrisation under extreme conditions is predominantly driven by diffraction methods, despite challenges of localising or probing the hydrogen subsystems directly. Until recently, H-bond…