Related papers: Structural transitions in biomolecules - a numeric…
We compare two recently proposed methods for the characterization of phase transitions in small systems. The validity and usefulness of these approaches are studied for the case of the q=4 and q=5 Potts model, i.e. systems where a…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
The identification and classification of phases in small systems, e.g. nuclei, social and financial networks, clusters, and biological systems, where the traditional definitions of phase transitions are not applicable, is important to…
We investigate, in an exact manner, the phase structure of the micromaser system in terms of the physical parameters at hand like the atom cavity transit time, the atom-photon frequency detuning, the number of thermal photons and the…
Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of…
This paper explores the connection between dynamical system properties and statistical physics of ensembles of such systems. Simple models are used to give novel phase transitions; particularly for finite N particle systems with many…
We describe here in detail the recently introduced methodology for simulation of structural transitions in crystals. The applications of the new scheme are illustrated on various kinds of crystals and the advantages with respect to previous…
In this paper we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix-random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method…
We study the spatial patterns formed by interacting biological populations or reacting chemicals under the influence of chaotic flows. Multiple species and nonlinear interactions are explicitly considered, as well as cases of smooth and…
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…
We consider a model for substrate-depletion oscillations in genetic systems, based on a stochastic differential equation with a slowly evolving external signal. We show the existence of critical transitions in the system. We apply two…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
This work reports a new methodology aimed at describing characteristics of protein structural shapes, and suggests a framework in which to resolve or classify automatically such structures into known families. This new approach to protein…
We discuss several pairing-related phenomena in nuclear systems, ranging from superfluidity in neutron stars to the gradual breaking of pairs in finite nuclei. We describe recent experimental evidence that points to a relation between…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
We investigate the dynamical and structural properties of absorbing phase transitions (APTs) within granular systems. Specifically, we examine a model for vibrofluidized systems of spherical grains, which undergo a transition from a state…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
A microscopic theory is presented for identifying shape-phase structures and transitions in interacting fermion systems. The method provides a microscopic description for collective shape-phases, and reveals detailed dependence of such…