相关论文: RNA Secondary Structures: Complex Statics and Glas…
The swap Monte Carlo algorithm allows the preparation of highly stable glassy configurations for a number of glass-formers, but is inefficient for some models, such as the much studied binary Kob-Andersen (KA) mixture. We have recently…
The study of the properties of glass-forming liquids is difficult for many reasons. Analytic solutions of mean field models are usually available only for systems embedded in a space with an unphysically high number of spatial dimensions;…
Finite-dimensional signatures of spinodal criticality are notoriously difficult to come by. The dynamical transition of glass-forming liquids, first described by mode-coupling theory, is a spinodal instability preempted by thermally…
To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the…
Graphity models are characterized by configuration spaces in which states correspond to graphs and Hamiltonians that depend on local properties of graphs such as the degrees of vertices and numbers of short cycles. As statistical systems,…
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…
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…
Metastable structures in macromolecular and colloidal systems are non-equilibrium states that often have long lifetimes and cause difficulties in simulating equilibrium. In order to escape from the long-lived metastable states, we propose a…
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…
The discrete Gaussian model for the surface of a crystal deposited on a disordered substrate is studied by Monte Carlo simulations. A continuous transition is found from a phase with a thermally-induced roughness to a glassy one in which…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
We discuss the status of Monte Carlo simulations of (mainly finite dimensional) spin glass systems. After a short historical note and a brief theoretical introduction we start by discussing the (crucial) 3D case: the warm phase, the…
Two coarse-grained models for polymer chains in dense glass-forming polymer melts are studied by computer simulation: the bond-fluctuation model on a simple cubic lattice, where a bond-length potential favors long bonds, is treated by…
Observations of glassy dynamics in experiments on confluent cellular tissue have inspired a wealth of computational and theoretical research to model their emergent collective behavior. Initial studies of the physical properties of several…
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…
We propose here a method to generate random networked amorphous structure using only readily available short-range properties like bond lengths, bond angles and connectivity of the constituents. This method is a variant of Monte-Carlo (MC)…
The short supercoiled circular DNA molecules are shown to be glassy systems and canonical Metropolis Monte Carlo simulations of the systems tend to get stuck in local metastable energy basins. A novel Monte Carlo algorithm is developed to…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
In this paper we present a dynamical Monte Carlo algorithm which is applicable to systems satisfying a clustering condition: during the dynamical evolution the system is mostly trapped in deep local minima (as happens in glasses, pinning…
A Monte Carlo method based on a density-of-states sampling is proposed for study of arbitrary statistical mechanical ensembles in a continuum. A random walk in the two-dimensional space of particle number and energy is used to estimate the…