Structure of the Energy Landscape of Short Peptides

We have simulated, as a showcase, the pentapeptide Met-enkephalin (Tyr-Gly-Gly-Phe-Met) to visualize the energy landscape and investigate the conformational coverage by the multicanonical method. We have obtained a three-dimensional topographic picture of the whole energy landscape by plotting the histogram with respect to energy(temperature) and the order parameter, which gives the degree of resemblance of any created conformation with the global energy minimum (GEM).Comment: 17 pages, 4 figure

Non-Perturbative U(1) Gauge Theory at Finite Temperature

For compact U(1) lattice gauge theory (LGT) we have performed a finite size scaling analysis on $N_{\tau} N_s^3$ lattices for $N_{\tau}$ fixed by extrapolating spatial volumes of size $N_s\le 18$ to $N_s\to\infty$. Within the numerical accuracy of the thus obtained fits we find for $N_{\tau}=4$, 5 and~6 second order critical exponents, which exhibit no obvious $N_{\tau}$ dependence. The exponents are consistent with 3d Gaussian values, but not with either first order transitions or the universality class of the 3d XY model. As the 3d Gaussian fixed point is known to be unstable, the scenario of a yet unidentified non-trivial fixed point close to the 3d Gaussian emerges as one of the possible explanations.Comment: Extended version after referee reports. 6 pages, 6 figure

Density of states and Fisher's zeros in compact U(1) pure gauge theory

We present high-accuracy calculations of the density of states using multicanonical methods for lattice gauge theory with a compact gauge group U(1) on 4^4, 6^4 and 8^4 lattices. We show that the results are consistent with weak and strong coupling expansions. We present methods based on Chebyshev interpolations and Cauchy theorem to find the (Fisher's) zeros of the partition function in the complex beta=1/g^2 plane. The results are consistent with reweighting methods whenever the latter are accurate. We discuss the volume dependence of the imaginary part of the Fisher's zeros, the width and depth of the plaquette distribution at the value of beta where the two peaks have equal height. We discuss strategies to discriminate between first and second order transitions and explore them with data at larger volume but lower statistics. Higher statistics and even larger lattices are necessary to draw strong conclusions regarding the order of the transition.Comment: 14 pages, 16 figure

On the Wang-Landau Method for Off-Lattice Simulations in the "Uniform" Ensemble

We present a rigorous derivation for off-lattice implementations of the so-called "random-walk" algorithm recently introduced by Wang and Landau [PRL 86, 2050 (2001)]. Originally developed for discrete systems, the algorithm samples configurations according to their inverse density of states using Monte-Carlo moves; the estimate for the density of states is refined at each simulation step and is ultimately used to calculate thermodynamic properties. We present an implementation for atomic systems based on a rigorous separation of kinetic and configurational contributions to the density of states. By constructing a "uniform" ensemble for configurational degrees of freedom--in which all potential energies, volumes, and numbers of particles are equally probable--we establish a framework for the correct implementation of simulation acceptance criteria and calculation of thermodynamic averages in the continuum case. To demonstrate the generality of our approach, we perform sample calculations for the Lennard-Jones fluid using two implementation variants and in both cases find good agreement with established literature values for the vapor-liquid coexistence locus.Comment: 21 pages, 4 figure

Multi-Overlap Simulations for Transitions between Reference Configurations

We introduce a new procedure to construct weight factors, which flatten the probability density of the overlap with respect to some pre-defined reference configuration. This allows one to overcome free energy barriers in the overlap variable. Subsequently, we generalize the approach to deal with the overlaps with respect to two reference configurations so that transitions between them are induced. We illustrate our approach by simulations of the brainpeptide Met-enkephalin with the ECEPP/2 energy function using the global-energy-minimum and the second lowest-energy states as reference configurations. The free energy is obtained as functions of the dihedral and the root-mean-square distances from these two configurations. The latter allows one to identify the transition state and to estimate its associated free energy barrier.Comment: 12 pages, (RevTeX), 14 figures, Phys. Rev. E, submitte

Entropy-based analysis of the number partitioning problem

In this paper we apply the multicanonical method of statistical physics on the number-partitioning problem (NPP). This problem is a basic NP-hard problem from computer science, and can be formulated as a spin-glass problem. We compute the spectral degeneracy, which gives us information about the number of solutions for a given cost $E$ and cardinality $m$. We also study an extension of this problem for $Q$ partitions. We show that a fundamental difference on the spectral degeneracy of the generalized ($Q>2$) NPP exists, which could explain why it is so difficult to find good solutions for this case. The information obtained with the multicanonical method can be very useful on the construction of new algorithms.Comment: 6 pages, 4 figure

A comparison of extremal optimization with flat-histogram dynamics for finding spin-glass ground states

We compare the performance of extremal optimization (EO), flat-histogram and equal-hit algorithms for finding spin-glass ground states. The first-passage-times to a ground state are computed. At optimal parameter of tau=1.15, EO outperforms other methods for small system sizes, but equal-hit algorithm is competitive to EO, particularly for large systems. Flat-histogram and equal-hit algorithms offer additional advantage that they can be used for equilibrium thermodynamic calculations. We also propose a method to turn EO into a useful algorithm for equilibrium calculations. Keywords: extremal optimization. flat-histogram algorithm, equal-hit algorithm, spin-glass model, ground state.Comment: 10 LaTeX pages, 2 figure

Glauber dynamics of phase transitions: SU(3) lattice gauge theory

Motivated by questions about the QCD deconfining phase transition, we studied in two previous papers Model A (Glauber) dynamics of 2D and 3D Potts models, focusing on structure factor evolution under heating (heating in the gauge theory notation, i.e., cooling of the spin systems). In the present paper we set for 3D Potts models (Ising and 3-state) the scale of the dynamical effects by comparing to equilibrium results at first and second order phase transition temperatures, obtained by re-weighting from a multicanonical ensemble. Our finding is that the dynamics entirely overwhelms the critical and non-critical equilibrium effects. In the second half of the paper we extend our results by investigating the Glauber dynamics of pure SU(3) lattice gauge on $N_{\tau} N_{\sigma}^3$ lattices directly under heating quenches from the confined into the deconfined regime. The exponential growth factors of the initial response are calculated, which give Debye screening mass estimates. The quench leads to competing vacuum domains of distinct $Z_3$ triality, which delay equilibration of pure gauge theory forever, while their role in full QCD remains a subtle question. As in spin systems we find for pure SU(3) gauge theory a dynamical growth of structure factors, reaching maxima which scale approximately with the volume of the system, before settling down to equilibrium. Their influence on various observables is studied and different lattice sizes are simulated to illustrate an approach to a finite volume continuum limit. Strong correlations are found during the dynamical process, but not in the deconfined phase at equilibrium.Comment: 12 pages, 18 figure

Monotonicity and logarithmic convexity relating to the volume of the unit ball

Let $\Omega_n$ stand for the volume of the unit ball in $\mathbb{R}^n$ for $n\in\mathbb{N}$. In the present paper, we prove that the sequence $\Omega_{n}^{1/(n\ln n)}$ is logarithmically convex and that the sequence $\frac{\Omega_{n}^{1/(n\ln n)}}{\Omega_{n+1}^{1/[(n+1)\ln(n+1)]}}$ is strictly decreasing for $n\ge2$. In addition, some monotonic and concave properties of several functions relating to $\Omega_{n}$ are extended and generalized.Comment: 12 page

Thermodynamics of two lattice ice models in three dimensions

In a recent paper we introduced two Potts-like models in three dimensions, which share the following properties: (A) One of the ice rules is always fulfilled (in particular also at infinite temperature). (B) Both ice rules hold for groundstate configurations. This allowed for an efficient calculation of the residual entropy of ice I (ordinary ice) by means of multicanonical simulations. Here we present the thermodynamics of these models. Despite their similarities with Potts models, no sign of a disorder-order phase transition is found.Comment: 5 pages, 7 figure