相关论文: Dependence of RNA secondary structure on the energ…

We analyze different microscopic RNA models at zero temperature. We discuss both the most simple model, that suffers a large degeneracy of the ground state, and models in which the degeneracy has been remove, in a more or less severe…

We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large…

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…

RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…

The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…

The microscopic model in which nodes interacting with each other are statistical systems is introduced. The nodes conditions are connected with a string of distinct microscopic configurations and depend on external parameters (pressure and…

Thermodynamical features of Xe system is investigated as functions of temperature and freeze-out density in the frame of lattice gas model. The calculation shows different temperature dependence of physical observables at different…

We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…

Both simple and sophisticated models are frequently used in an attempt to understand how real nuclei breakup when subjected to large excitation energies, a process known as nuclear multifragmentation. Many of these models assume…

Folding of RNA is subject to a competition between entropy, relevant at high temperatures, and the random, or random looking, sequence, determining the low- temperature phase. It is known from numerical simulations that for random as well…

We investigate the possibility of extending the notion of temperature in a stochastic model for the RNA/protein folding driven out of equilibrium. We simulate the dynamics of a small RNA hairpin subject to an external pulling force, which…

Phase transitions of small isolated systems are signaled by the shape of the caloric equation of state e^*(T), the relationship between the excitation energy per nucleon e^* and temperature. In this work we compare the experimentally…

The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on…

We extend recent methods for parametric sequence alignment to the parameter space for scoring RNA folds. This involves the construction of an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common…

Loops are abundant in native RNA structures and proliferate close to the unfolding transition. By including a statistical weight ~ l^{-c} for loops of length l in the recursion relation for the partition function, we show that the…

We address the question of the quantitative relationship between thermodynamic phase transitions and topological changes in the potential energy manifold analyzing two classes of one dimensional models, the Burkhardt solid-on-solid model…

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…

RNA molecules form a sequence-specific self-pairing pattern at low temperatures. We analyze this problem using a random pairing energy model as well as a random sequence model that includes a base stacking energy in favor of helix…

Phase transitions are ubiquitous across life, yet hard to quantify and describe accurately. In this work, we develop an approach for characterizing generic attributes of phase transitions from very limited observations made deep within…

The thesis consists of two projects. In the first project, we present a software that analyses RNA secondary structures and compares them. The goal of this software is to find the differences between two secondary structures (experimental…