相关论文: RNA Secondary Structures: Complex Statics and Glas…
The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte…
We develop a generic strategy and simple numerical models for multi-component metallic glasses for which the swap Monte Carlo algorithm can produce highly stable equilibrium configurations equivalent to experimental systems cooled more than…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
We argue that one can associate a pseudo-time with sequences of configurations generated in the course of classical Monte Carlo simulations for a single-minimum bound state, if the sampling is optimal. Hereby the sampling rates can be,…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
Growth of gallium nitride on GaN(0001) surface is modeled by Monte Carlo method. Simulated growth is conducted in N-rich conditions, hence it is controlled by Ga atoms surface diffusion. It is shown that dominating four-body interactions of…
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…
Nematic liquid crystals confined to geometrically as well as chemically patterned substrate on one end and a flat substrate with strong anchoring on the other is studied using non-Boltzmann Monte Carlo methods. We observe significant…
We study the spacial and temporal multiscale properties of complex systems. We present accelerated algorithms for dilute spin glasses and display explicitly their relation to the effective dynamics of specific collective degrees of freedom…
Structural and static properties of a classical two-dimensional (2D) system consisting of a finite number of charged particles which are laterally confined by a parabolic potential are investigated by Monte Carlo (MC) simulations and the…
In this paper we model several simple biochemical operations on RNA molecules that modify their secondary structure by means of a suitable variation of Gro\ss e-Rhode's Algebra Transformation Systems.
Density tempering (also called density annealing) is a sequential Monte Carlo approach to Bayesian inference for general state models; it is an alternative to Markov chain Monte Carlo. When applied to state space models, it moves a…
The dynamics of strongly disordered systems becomes extremely slow or glassy at low temperatures, which results in a characteristic aging scenario. This means that the outcome of measurements strongly depends on the history of the system…
We applied a multicanonical algorithm (entropic sampling) to a two-dimensional and a three-dimensional Lennard-Jones system with quasicrystalline and glassy ground states. Focusing on the ability of the algorithm to locate low lying energy…
We study a matrix model that has $\phi_a^i\ (a=1,2,\ldots,N,\ i=1,2,\ldots,R)$ as its dynamical variable, whose lower indices are pairwise contracted, but upper ones are not always done so. This matrix model has a motivation from a tensor…
DNA migration in topologically structured microchannels with periodic cavities is investigated experimentally and with Brownian dynamics simulations of a simple bead-spring model. The results are in very good agreement with one another. In…
The swap Monte Carlo algorithm introduces non-physical dynamic rules to accelerate the exploration of the configuration space of supercooled liquids. Its success raises deep questions regarding the nature and physical origin of the slow…
Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks (GRNs). In this view, different phenotypes are associated with alternative states…
Systems with long-range interactions when quenced into a metastable state near the pseudo-spinodal exhibit nucleation processes that are quite different from the classical nucleation seen near the coexistence curve. In systems with…
In this chapter, we describe three related studies of the universal physics of two-component unitary Fermi gases with resonant short-ranged interactions. First we discuss an ab initio auxiliary field quantum Monte Carlo technique for…