Fluctuation Pressure of a Stack of Membranes

We calculate the universal pressure constants of a stack of N membranes between walls by strong-coupling theory. The results are in very good agreement with values from Monte-Carlo simulations.Comment: Author Information under http://www.physik.fu-berlin.de/~kleinert/institution.html Latest update of paper also at http://www.physik.fu-berlin.de/~kleinert/31

Optimal Energy Estimation in Path-Integral Monte Carlo Simulations

We investigate the properties of two standard energy estimators used in path-integral Monte Carlo simulations. By disentangling the variance of the estimators and their autocorrelation times we analyse the dependence of the performance on the update algorithm and present a detailed comparison of refined update schemes such as multigrid and staging techniques. We show that a proper combination of the two estimators leads to a further reduction of the statistical error of the estimated energy with respect to the better of the two without extra cost.Comment: 45 pp. LaTeX, 22 Postscript Figure

Two-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins

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 permutations of each other. Despite the simplicity of the model, the knowledge of the free-energy landscape in dependence of a suitable system order parameter enables us to reveal complex folding characteristics known from real bioproteins and synthetic peptides, such as two-state folding, folding through weakly stable intermediates, and glassy metastability.Comment: 10 pages, 1 figur

Condensation of vortices in the X-Y model in 3d: a disorder parameter

A disorder parameter is constructed which signals the condensation of vortices. The construction is tested by numerical simulations.Comment: 9 pages, 5 postscript figures, typset using REVTE

Multicanonical Study of Coarse-Grained Off-Lattice Models for Folding Heteropolymers

We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with two simple effective, coarse-grained off-lattice models to study the influence of specific interactions in the models on conformational transitions of selected sequences with 20 monomers. Another aspect of the investigation was the comparison with the purely hydrophobic homopolymer and the study of general conformational properties induced by the "disorder" in the sequence of a heteropolymer. Furthermore, we applied an optimization algorithm to sequences with up to 55 monomers and compared the global-energy minimum found with lowest-energy states identified within the multicanonical simulation. This was used to find out how reliable the multicanonical method samples the free-energy landscape, in particular for low temperatures.Comment: 11 pages, RevTeX, 10 Postscript figures, Author Information under http://www.physik.uni-leipzig.de/index.php?id=2

Monte Carlo study of the evaporation/condensation transition on different Ising lattices

In 2002 Biskup et al. [Europhys. Lett. 60, 21 (2002)] sketched a rigorous proof for the behavior of the 2D Ising lattice gas, at a finite volume and a fixed excess \delta M of particles (spins) above the ambient gas density (spontaneous magnetisation). By identifying a dimensionless parameter \Delta (\delta M) and a universal constant \Delta_c, they showed in the limit of large system sizes that for \Delta < \Delta_c the excess is absorbed in the background (``evaporated'' system), while for \Delta > \Delta_c a droplet of the dense phase occurs (``condensed'' system). To check the applicability of the analytical results to much smaller, practically accessible system sizes, we performed several Monte Carlo simulations for the 2D Ising model with nearest-neighbour couplings on a square lattice at fixed magnetisation M. Thereby, we measured the largest minority droplet, corresponding to the condensed phase, at various system sizes (L=40, >..., 640). With analytic values for for the spontaneous magnetisation m_0, the susceptibility \chi and the Wulff interfacial free energy density \tau_W for the infinite system, we were able to determine \lambda numerically in very good agreement with the theoretical prediction. Furthermore, we did simulations for the spin-1/2 Ising model on a triangular lattice and with next-nearest-neighbour couplings on a square lattice. Again, finding a very good agreement with the analytic formula, we demonstrate the universal aspects of the theory with respect to the underlying lattice. For the case of the next-nearest-neighbour model, where \tau_W is unknown analytically, we present different methods to obtain it numerically by fitting to the distribution of the magnetisation density P(m).Comment: 14 pages, 17 figures, 1 tabl

Application of Multicanonical Multigrid Monte Carlo Method to the Two-Dimensional ϕ4\phi^4-Model: Autocorrelations and Interface Tension

We discuss the recently proposed multicanonical multigrid Monte Carlo method and apply it to the scalar $\phi^4$-model on a square lattice. To investigate the performance of the new algorithm at the field-driven first-order phase transitions between the two ordered phases we carefully analyze the autocorrelations of the Monte Carlo process. Compared with standard multicanonical simulations a real-time improvement of about one order of magnitude is established. The interface tension between the two ordered phases is extracted from high-statistics histograms of the magnetization applying histogram reweighting techniques.Comment: 49 pp. Latex incl. 14 figures (Fig.7 not included, sorry) as uuencoded compressed tar fil

Error estimation and reduction with cross correlations

Besides the well-known effect of autocorrelations in time series of Monte Carlo simulation data resulting from the underlying Markov process, using the same data pool for computing various estimates entails additional cross correlations. This effect, if not properly taken into account, leads to systematically wrong error estimates for combined quantities. Using a straightforward recipe of data analysis employing the jackknife or similar resampling techniques, such problems can be avoided. In addition, a covariance analysis allows for the formulation of optimal estimators with often significantly reduced variance as compared to more conventional averages.Comment: 16 pages, RevTEX4, 4 figures, 6 tables, published versio

Monte Carlo Study of Cluster-Diameter Distribution: A New Observable to Estimate Correlation Lengths

We report numerical simulations of two-dimensional $q$-state Potts models with emphasis on a new quantity for the computation of spatial correlation lengths. This quantity is the cluster-diameter distribution function $G_{diam}(x)$, which measures the distribution of the diameter of stochastically defined cluster. Theoretically it is predicted to fall off exponentially for large diameter $x$, $G_{diam} \propto \exp(-x/\xi)$, where $\xi$ is the correlation length as usually defined through the large-distance behavior of two-point correlation functions. The results of our extensive Monte Carlo study in the disordered phase of the models with $q=10$, 15, and $20$ on large square lattices of size $300 \times 300$, $120 \times 120$, and $80 \times 80$, respectively, clearly confirm the theoretically predicted behavior. Moreover, using this observable we are able to verify an exact formula for the correlation length $\xi_d(\beta_t)$ in the disordered phase at the first-order transition point $\beta_t$ with an accuracy of about $1$ for all considered values of $q$. This is a considerable improvement over estimates derived from the large-distance behavior of standard (projected) two-point correlation functions, which are also discussed for comparison.Comment: 20 pages, LaTeX + 13 postscript figures. See also http://www.cond-mat.physik.uni-mainz.de/~janke/doc/home_janke.htm

Coarse-Grained Modeling of Genetic Circuits as a Function of the Inherent Time Scales

From a coarse-grained perspective the motif of a self-activating species, activating a second species which acts as its own repressor, is widely found in biological systems, in particular in genetic systems with inherent oscillatory behavior. Here we consider a specific realization of this motif as a genetic circuit, in which genes are described as directly producing proteins, leaving out the intermediate step of mRNA production. We focus on the effect that inherent time scales on the underlying fine-grained scale can have on the bifurcation patterns on a coarser scale in time. Time scales are set by the binding and unbinding rates of the transcription factors to the promoter regions of the genes. Depending on the ratio of these rates to the decay times of the proteins, the appropriate averaging procedure for obtaining a coarse-grained description changes and leads to sets of deterministic equations, which differ in their bifurcation structure. In particular the desired intermediate range of regular limit cycles fades away when the binding rates of genes are of the same order or less than the decay time of at least one of the proteins. Our analysis illustrates that the common topology of the widely found motif alone does not necessarily imply universal features in the dynamics.Comment: 29 pages, 16 figure