Related papers: RNA Secondary Structures: Complex Statics and Glas…
We investigate dynamic scaling properties of the two-dimensional gauge glass model for the vortex glass phase in superconductors with quenched disorder. From extensive Monte Carlo simulations we obtain static and dynamic finite size scaling…
Monte Carlo sampling of any system may be analyzed in terms of an associated glass model -- a variant of the Random Energy Model -- with, whenever there is a sign problem, complex fields. This model has three types of phases (liquid, frozen…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
A random matrix approach to glassy physics is introduced. It leads to a class of models which exhibit both, glassy low-temperature phases, and double-- and single-well configurations in their potential energy. The distribution of parameters…
The dynamics of glass formation in monatomic and binary liquids are studied numerically using a microscopic field theory for the evolution of the time-averaged atomic number density. A stochastic framework combining phase field crystal free…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
These lecture notes introduce quantum spin systems and several computational methods for studying their ground-state and finite-temperature properties. Symmetry-breaking and critical phenomena are first discussed in the simpler setting of…
We present a formalism of the transition matrix Monte Carlo method. A stochastic matrix in the space of energy can be estimated from Monte Carlo simulation. This matrix is used to compute the density of states, as well as to construct…
Model chains are studied via Monte Carlo simulations which are deposited with a fixed flux on a substrate. They may represent, e.g., stiff lipophilic chains with an head group and tail groups mimicking the alkyl chain. After some subsequent…
We investigate numerically the low temperature equilibration of glassy systems via non-local Monte Carlo methods. We re-examine several systems that have been studied previously and investigate new systems in order to test the performance…
Continuum Monte-Carlo simulations at constant pressure are performed on short chain molecules at surfaces. The rodlike chains, consisting of seven effective monomers, are attached at one end to a flat twodimensional substrate. It is found…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, "replica" ensemble of walkers, whose population evolves in…
Although coarse-grained models have been widely used to explain exotic phenomena in complex fluids, such as droplet formation in living cells, these conventional approaches often fail to capture the intricate microscopic degrees of freedom…
We perform kinetic Monte Carlo simulations of a distinguishable-particle lattice model of structural glasses with random particle interactions. By varying the interaction distribution and the average particle hopping energy barrier, we…
We analyze numerically the training dynamics of deep neural networks (DNN) by using methods developed in statistical physics of glassy systems. The two main issues we address are (1) the complexity of the loss landscape and of the dynamics…
The basic problem in equilibrium statistical mechanics is to compute phase space average, in which Monte Carlo method plays a very important role. We begin with a review of nonlocal algorithms for Markov chain Monte Carlo simulation in…
An ideal atomistic model of a disordered material should contradict no experiments,and should also be consistent with accurate force fields (either {\it ab initio}or empirical). We make significant progress toward jointly satisfying {\it…
We study the low temperature dynamics of a two dimensional short-range spin system with uniform ferromagnetic interactions, which displays glassiness at low temperatures despite the absence of disorder or frustration. The model has a dual…
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…