Related papers: Analysis of PIN1 WW domain through a simple Statis…
Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very…
Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate…
We study the statistics of domain wall excitations in quantum spin chains. We focus on systems with finite symmetry groups represented by matrix product unitaries (MPUs), i.e. finite depth quantum circuits. Such symmetries can be anomalous,…
This article reviews theoretical and experimental developments for one-dimensional Fermi gases. Specifically, the experimentally realized two-component delta-function interacting Fermi gas -- the Gaudin-Yang model -- and its generalisations…
Extreme scaling for purposes of achieving higher density and lower energy continues to increase the probability of memory faults. For domain wall (DW) memories, misalignment faults arise when aligning domains with access points. A…
We model protein folding as a physical stochastic process as follows. The unfolded protein chain is treated as a random coil described by SAW (self-avoiding walk). Folding is induced by hydrophobic forces and other interactions, such as…
A model of disordered spin-Peierls system is considered, where domain walls are randomly distributed as a telegraph noise. For this realization of the disorder in an XX spin chain, we calculate exactly the density of states as well as…
We further study the stochastic model discussed in Ref.[2] in which positive and negative particles diffuse in an asymmetric, CP invariant way on a ring. The positive particles hop clockwise, the negative counter-clockwise and…
We studied the structural, dynamical properties and melting of a quasi-one-dimensional system of charged particles, interacting through a screened Coulomb potential. The ground state energy was calculated and, depending on the density and…
Global expression analyses using microarray technologies are becoming more common in genomic research, therefore, new statistical challenges associated with combining information from multiple studies must be addressed. In this paper we…
We present a quantitative comparison between extensive Monte Carlo simulations and self-consistent field calculations on the phase diagram and wetting behavior of a symmetric, binary (AB) polymer blend confined into a film. The flat walls…
Frustrated spin systems generically suffer from the negative sign problem inherent to Monte Carlo methods. Since the severity of this problem is formulation dependent, optimization strategies can be put forward. We introduce a phase pinning…
Experimental observations suggest that proteins follow different pathways under different environmental conditions. We perform molecular dynamics simulations of a model of the SH3 domain over a broad range of temperatures, and identify…
Calculations of the binding energy of the transition metal oxide molecules TiO and MnO are presented, using a recently developed phaseless auxiliary field quantum Monte Carlo approach. This method maps the interacting many-body problem onto…
Monte Carlo simulations are performed for the S = 1/2 XY and ferro- and antiferromagnetic Heisenberg model in two dimensions using the loop algorithm. Thermodynamic properties of all these models are investigated in wide temperature range.…
Probabilistic inversion methods based on Markov chain Monte Carlo (MCMC) simulation are well suited to quantify parameter and model uncertainty of nonlinear inverse problems. Yet, application of such methods to CPU-intensive forward models…
We present a quantitative investigation of magnetic domain wall pinning in thin magnets with perpendicular anisotropy. A self-consistent description exploiting the universal features of the depinning and thermally activated sub-threshold…
Normal mode analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent normal modes capture the salient features of the…
We study spectral statistics of one-dimensional quasi-periodic systems at the metal-insulator transition. Several types of spectral statistics are observed at the critical points, lines, and region. On the critical lines, we find the…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P. Grassberger, Phys. Rev. E, in press (1997)) leads to extremely efficient algorithms for the folding of simple model proteins. We test it on several models…