Related papers: Backbone and Sidechain Ordering in a small Protein
We propose a new criterion to analyse the order of phase transitions within a finite size scaling analysis. It refers to response functions like order parameter susceptibilities and the specific heat and states different monotony behaviour…
We consider two types of strongly disordered one-dimensional Hamiltonian systems coupled to baths (energy or particle reservoirs) at the boundaries: strongly disordered quantum spin chains and disordered classical harmonic oscillators.…
Coexisting fluctuations towards various ordered states are ubiquitous in strongly correlated electronic systems. In particular, measurements of underdoped cuprate high-temperature superconductors reveal evidence for short range charge order…
H-bonds are known to play an important role in the folding of proteins into three-dimensional structures, which in turn determine their diverse functions. The conformations around H-bonds are important, in that they can be non-local along…
The formation of fibrillar aggregates seems to be a common characteristic of polypeptide chains, although the observation of these aggregates may depend on appropriate experimental conditions. Partially folded intermediates seem to have an…
Emergence of new protein structures has proved difficult to trace in nature and engineer in the laboratory. However, one aspect of structure evolution has proved immensely helpful for determining the three-dimensional structure of proteins…
The paper considers heat conduction in a model chain of composite particles with hard core and elastic external shell. Such model mimics three main features of realistic interatomic potentials - hard repulsive core, quasilinear behavior in…
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…
Proteins are large biomolecules that regulate all living organisms and consist of one or several chains. The primary structure of a protein chain is a sequence of amino acid residues whose three main atoms (alpha-carbon, nitrogen, and…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both…
Heuristic insights into a physical picture of Davydov's solitonic model of the one-dimensional protein chain are presented supporting the idea of a non-equilibrium competition between the Davydov phase and a complementary, dynamical-…
Self-organization and nonequilibrium phase transitions are well known to occur in two- and three- dimensional dissipative systems. Here, instead, we provide numerical evidence that these phenomena also occur in a one-dimensional Hamiltonian…
We have studied folding mechanisms of three small globular proteins: crambin (CRN), chymotrypsin inhibitor 2 (CI2) and the fyn Src Homology 3 domain (SH3) which are modelled by a Go-like Hamiltonian with the Lennard-Jones interactions. It…
Protein-protein interaction networks are useful for studying human diseases and to look for possible health care through a holistic approach. Networks are playing an increasing and important role in the understanding of physiological…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
The emergence of biochemical activities in a protein seem to commence with the onset of atomic mean-square displacements along the protein lattice. The ensuing protein dynamical transition has been discussed extensively in the literature,…
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…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…