相关论文: Thermodynamics of a model for RNA folding

In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…

Ribonucleic Acid (RNA) can fold into shapes that perform functions in the cell. These foldings are governed by Watson-Crick base pairing, namely Adenine to Uracil and Cytosine to Guanine (A-U and G-C). The properties of the H-P…

We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…

A one dimensional experiment in granular dynamics is carried out to test the thermodynamic theory of weakly excited granular systems [Hayakawa and Hong, Phys. Rev. Lett. {\bf 78}, 2764(1997)] where granular particles are treated as spinless…

Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed…

A new approach to modelling the behaviour of simple fluids is presented. Starting from the usual expression of the partition function of N molecules, a Fourier transformation is performed. It is argued that the N(N-1)/2 dynamical variables…

The thermodynamics of the O(N) nonlinear sigma model in 1+1 dimensions is studied. We calculate the finite temperature effective potential in leading order in the 1/N expansion and show that at this order the effective potential can be made…

Inspired by some recent experiments and numerical works related to nanoresonators, we perform classical molecular dynamics simulations to investigate the thermal expansion and the ability of the device to act as a strain sensor assisted by…

Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…

The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical…

In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…

Detailed thermodynamic analysis of complex systems with multiple stable configurational states allows for insight into the cooperativity of each individual transition. In this work we derive a heat capacity decomposition comprising…

The folding of a peptide chain into a three dimensional structure is a thermodynamically driven process such that the chain naturally evolves to form domains of similar amino acids. The formation of this domain occurs by curling the one…

The new mathematical framework based on the free energy of pure classical fluids presented in [R. D. Rohrmann, Physica A 347, 221 (2005)] is extended to multi-component systems to determine thermodynamic and structural properties of…

A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…

The thermodynamical properties are calculated for a three-dimensional model of $N$ harmonically interacting spin-polarized fermions in a parabolic potential well. The obtained dependences of the chemical potential and of the internal energy…

We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…

Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…

We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…

The dynamics of biological polymers, including proteins, RNA, and DNA, occur in very high-dimensional spaces. Many naturally-occurring polymers can navigate a vast phase space and rapidly find their lowest free energy (folded) state. Thus,…