相关论文: RNA Secondary Structures: Complex Statics and Glas…
We present a new Monte Carlo algorithm that produces results of high accuracy with reduced simulational effort. Independent random walks are performed (concurrently or serially) in different, restricted ranges of energy, and the resultant…
In this paper, we use the biological domain knowledge incorporated into stochastic models for ab initio RNA secondary-structure prediction to improve the state of the art in joint compression of RNA sequence and structure data (Liu et al.,…
We describe an efficient Monte Carlo algorithm using a random walk in energy space to obtain a very accurate estimate of the density of states for classical statistical models. The density of states is modified at each step when the energy…
Using a distinguishable-particle lattice model based on void-induced dynamics, we successfully reproduce the well-known linear relation between heat capacity and temperature at very low temperatures. The heat capacity is dominated by…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
We use a standard Monte-Carlo algorithm to study the slow dynamics of a binary Lennard-Jones glass-forming mixture at low temperature. We find that Monte-Carlo is by far the most efficient way to simulate a stochastic dynamics since…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
We use replica exchange Monte-Carlo simulations to measure the equilibrium equation of state of the disordered fluid state for a binary hard sphere mixture up to very large densities where standard Monte-Carlo simulations do not easily…
We introduce and study a model which admits a complex landscape without containing quenched disorder. Continuing our previous investigation we introduce a disordered model which allows us to reconstruct all the main features of the original…
Simulating percolation and critical phenomena of labelled species inside films composed of single-component linear homogeneous macromolecules using molecular Monte Carlo method in 3 dimensions, we study dependence of these conducting…
We present a model for the dynamics in energy space of multicanonical simulation methods that lends itself to a rather complete analytic characterization. The dynamics is completely determined by the density of states. In the \pm J 2D spin…
Across many scientific and engineering disciplines, it is important to consider how much the output of a given system changes due to perturbations of the input. Here, we investigate the glassy phase of $\pm J$ spin glasses at zero…
Glassy systems are disordered systems characterized by extremely slow dynamics. Examples are supercooled liquids, whose dynamics slow down under cooling. The specific pattern of slowing-down depends on the material considered. This…
We present a simple mathematical framework for the description of the dynamics of glassy systems in terms of a random walk in a complex energy landscape pictured as a network of minima. We show how to use the tools developed for the study…
We study, using simulations the dynamical properties of complex ferromagnetic granular materials. The system of grains is modeled by a disordered two-dimensional lattice in which the grains are embedded, while the magnitude and direction of…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
We study the dynamics of a glassy model with infinite range interactions externally driven by an oscillatory force. We find a well-defined transition in the (Temperature-Amplitude-Frequency) phase diagram between (i) a `glassy' state…
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…
Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental approaches, a promising candidate is the "chemical modification…
We use a Monte Carlo bond-switching method to study systematically the thermodynamic properties of a "continuous random network" model, the canonical model for such amorphous systems as a-Si and a-SiO$_2$. Simulations show first-order…