Related papers: Thermodynamics of a model for RNA folding
The thermodynamic properties of a spin S=1/2 tetrameric Heisenberg antiferromagnetic chain with alternating interactions AF1-AF2-AF1-F (AF and F denote the antiferromagnetic and ferromagnetic couplings, respectively) are studied by means of…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
In this paper, we study the thermodynamical properties of the classical one-dimensional Klein-Gordan lattice model ($n \ge 2$) by using the cluster variation method with linear response theory. The results of this method are exact in the…
Nested sampling is a Bayesian sampling technique developed to explore probability distributions lo- calised in an exponentially small area of the parameter space. The algorithm provides both posterior samples and an estimate of the evidence…
The DFN (Doyle-Fuller-Newman) model is well know for being accurate and computationally expensive. In situations where temperature gradients are important (eg fast charging) it is desirable to couple the temperature dynamics within a…
We present a unified description of dense matter and neutron-star structure based on simple but physically motivated models. Starting from the thermodynamics of degenerate Fermi gases, we construct an equation of state for cold, catalyzed…
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…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
An important process for antimatter experiments is the cooling of particles in a Penning-Malmberg trap to experimentally useful temperatures. A non-neutral plasma of one species (e.g. antiprotons) can be collisionally cooled on another…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
We investigate the low temperature thermodynamics and correlation functions of one-dimensional spin-1/2 fermions with strong repulsion in an external magnetic field via the thermodynamic Bethe ansatz method. The exact thermodynamics of the…
We present a comprehensive study of the thermodynamic properties of the three-dimensional fermionic Hubbard model, with application to cold fermionic atoms subject to an optical lattice and a trapping potential. Our study is focused on the…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
We study the thermodynamic behavior of the random chain model proposed by Iori, Marinari and Parisi, and how this depends on the actual sequence of interactions along the chain. The properties of randomly chosen sequences are compared to…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica…
We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and $\beta-$sheets in protein, by…
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…