Replica-Exchange Method in van der Waals Radius Space: Overcoming Steric Restrictions for Biomolecules

We present a new type of the Hamiltonian replica-exchange method, in which not temperatures but the van der Waals radius parameter is exchanged. By decreasing the van der Waals radii that control spatial sizes of atoms, this Hamiltonian replica-exchange method overcomes the steric restrictions and energy barriers. Furthermore, the simulation based on this method escapes from the local-minimum free-energy states and realizes effective sampling in the conformational space. We applied this method to an alanine dipeptide in aqueous solution and showed the effectiveness of the method by comparing the results with those obtained from the conventional canonical method.Comment: 14 pages, (Revtex4), 11 figure

Food Webs: Experts Consuming Families of Experts

The question what determines the structure of natural food webs has been listed among the nine most important unanswered questions in ecology. It arises naturally from many problems related to ecosystem stability and resilience. The traditional view is that population-dynamical stability is crucial for understanding the observed structures. But phylogeny (evolutionary history) has also been suggested as the dominant mechanism. Here we show that observed topological features of predatory food webs can be reproduced to unprecedented accuracy by a mechanism taking into account only phylogeny, size constraints, and the heredity of the trophically relevant traits of prey and predators. The analysis reveals a tendency to avoid resource competition rather than apparent competition. In food webs with many parasites this pattern is reversed.Comment: 16 pages, 3 figures, 1 table + Appendix of 36 pages, 18 figures. movie available from http://ag.rossberg.net/matching.mp

Novel Approach to Super Yang-Mills Theory on Lattice - Exact fermionic symmetry and "Ichimatsu" pattern -

We present a lattice theory with an exact fermionic symmetry, which mixes the link and the fermionic variables. The staggered fermionic variables may be reconstructed into a Majorana fermion in the continuum limit. The gauge action has a novel structure. Though it is the ordinary plaquette action, two different couplings are assigned in the ``Ichimatsu pattern'' or the checkered pattern. In the naive continuum limit, the fermionic symmetry survives as a continuum (or an $O(a^0)$) symmetry. The transformation of the fermion is proportional to the field strength multiplied by the difference of the two gauge couplings in this limit. This work is an extension of our recently proposed cell model toward the realization of supersymmetric Yang-Mills theory on lattice.Comment: 26 pages, 4 figure

Neutrino energy loss rate in a stellar plasma

We review the purely leptonic neutrino emission processes, contributing to the energy loss rate of the stellar plasma. We perform a complete analysis up to the first order in the electromagnetic coupling constant. In particular the radiative electromagnetic corrections, at order $\alpha$, to the process $e^+ e^- -> \nu \bar{\nu}$ at finite density and temperature have been computed. This process gives one of the main contributions to the cooling of stellar interior in the late stages of star evolution. As a result of the analysis we find that the corrections affect the energy loss rate, computed at tree level, by a factor $(-4 \div 1)$ in the temperature and density region where the pair annihilation is the most efficient cooling mechanism.Comment: 41 pages, 11 eps figure

Probing phase coexistence and stabilization of the spin-ordered ferrimagnetic state by Calcium addition in the YBa_{1-x}Ca_{x}Co_{2}O_{5.5} layered cobaltites using neutron diffraction

In this article we study the effects of a partial substitution of Ba with the smaller cation Ca in the layered cobaltites YBaCo_2O_{5+\delta} for \delta \approx 0.5. Neutron thermodiffractograms are reported for the compounds YBa_{0.95}Ca_{0.05}Co_2O_{5.5} (x_{Ca}=0.05) and YBa_{0.90}Ca_{0.10}Co_2O_{5.5} (x_{Ca}=0.10) in the temperature range 20 K \leq T \leq 300 K, as well as high resolution neutron diffraction experiments at selected temperatures for the samples x_{Ca}=0.05, x_{Ca}=0.10 and the parent compound x_{Ca}=0. We have found the magnetic properties to be strongly affected by the cationic substitution. Although the "122" perovskite structure seems unaffected by Ca addition, the magnetic arrangements of Co ions are drastically modified: the antiferromagnetic (AFM) long-range order is destroyed, and a ferrimagnetic phase with spin state order is stabilized below T \sim 290 K. For the sample with x_{Ca}=0.05 a fraction of AFM phase coexists with the ferrimagnetic one below T \sim 190 K, whereas for x_{Ca}=0.10 the AFM order is completely lost. The systematic refinement of the whole series has allowed for a better understanding of the observed low-temperature diffraction patterns of the parent compound, YBaCo_2O_{5.5}, which had not yet been clarified. A two-phase scenario is proposed for the x_{Ca}=0 compound which is compatible with the phase coexistence observed in the x_{Ca}=0.05 sample

Effective Sampling in the Configurational Space by the Multicanonical-Multioverlap Algorithm

We propose a new generalized-ensemble algorithm, which we refer to as the multicanonical-multioverlap algorithm. By utilizing a non-Boltzmann weight factor, this method realizes a random walk in the multi-dimensional, energy-overlap space and explores widely in the configurational space including specific configurations, where the overlap of a configuration with respect to a reference state is a measure for structural similarity. We apply the multicanonical-multioverlap molecular dynamics method to a penta peptide, Met-enkephalin, in vacuum as a test system. We also apply the multicanonical and multioverlap molecular dynamics methods to this system for the purpose of comparisons. We see that the multicanonical-multioverlap molecular dynamics method realizes effective sampling in the configurational space including specific configurations more than the other two methods. From the results of the multicanonical-multioverlap molecular dynamics simulation, furthermore, we obtain a new local-minimum state of the Met-enkephalin system.Comment: 15 pages, (Revtex4), 9 figure

Resolving Exceptional Configurations

In lattice QCD with Wilson fermions, exceptional configurations arise in the quenched approximation at small quark mass. The origin of these large previously uncontrolled lattice artifacts is identified. A simple well-defined procedure (MQA) is presented which removes the artifacts while preserving the correct continuum limit.Comment: Talk presented by E. Eichten at Lattice 97, Edinburgh(UK), July97. 6 pages, LaTeX, 1 table, 5 figure