Related papers: Thermodynamics of a model for RNA folding
We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
The thermodynamics of the inhomogeneous one-dimensional repulsive fermionic Hubbard model with parabolic confinement is studied by a density-functional theory approach, based on Mermin's generalization to finite temperatures. A…
The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon…
We propose a simple approach, based on the minimization of the total (entropic plus unfolding) energy of a two-state system, describing the stretch-induced unfolding of macromolecules (proteins, silks, nanopolymers, DNA/RNA). The model is…
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…
The SU(2) symmetric Fermi-Hubbard model (FHM) plays an essential role in strongly correlated fermionic many-body systems. In the one particle per site and strongly interacting limit ${U/t \gg 1}$, it is effectively described by the…
Establishing a description for confinement is not something simple. In order to try to understand a little about this phenomenon, we will explore the thermodynamics of models that try to describe it in terms of propagators with violation of…
We extend to finite temperature a Green's function method that was previously proposed to evaluate ground-state properties of mesoscopic clouds of non-interacting fermions moving under harmonic confinement in one dimension. By calculations…
We suggest a new mean field method for studying the thermodynamic competition between magnetic and superconducting phases in a two-dimensional square lattice. A partition function is constructed by writing microscopic interactions that…
Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time…
As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($\phi_F$) reaches the folded state while the remaining fraction of…
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. 78, 2764(1997)] where granular particles are treated as spinless…
We use a simplified model which is based on the same physics as inherent in most statistical models for nuclear multifragmentation. The simplified model allows exact calculations for thermodynamic properties of systems of large number of…
We describe a simple ansatz to approximate the low temperature behavior of proteins and peptides by a mean-field-like model which is analytically solvable. For a small peptide some thermodynamic quantities are calculated and compared with…
Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction…
We propose a new and effective means for designing stable and fast-folding polypeptide sequences using a cumulant expansion of the molecular partition function. This method is unique in that $T_{Z}$, the ``cumulant design temperature''…
We construct a simple thermodynamic model to describe the melting of a supported metal nanoparticle with a spherically curved free surface both with and without surface melting. We use the model to investigate the results of recent…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
Thermodynamic properties of the particles interacting through smooth version of Stell-Hemmer interaction were studied using Wertheim's thermodynamic perturbation theory. The temperature dependence of molar volume, heat capacity, isothermal…