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

Trajectory Deflection of Spinning Magnetic Microparticles, the Magnus Effect at the Microscale

The deflection due to the Magnus force of magnetic particles with a diameter of 80 micrometer dropping through fluids and rotating in a magnetic field was measured. With Reynolds number for this experiment around 1, we found trajectory deflections of the order of 1 degree, in agreement within measurement error with theory. This method holds promise for the sorting and analysis of the distribution in magnetic moment and particle diameter of suspensions of microparticles, such as applied in catalysis, or objects loaded with magnetic particles.Comment: 12 pages, 3 figures. Appendix with 6 figure

Generalized-ensemble Monte carlo method for systems with rough energy landscape

We present a novel Monte Carlo algorithm which enhances equilibrization of low-temperature simulations and allows sampling of configurations over a large range of energies. The method is based on a non-Boltzmann probability weight factor and is another version of the so-called generalized-ensemble techniques. The effectiveness of the new approach is demonstrated for the system of a small peptide, an example of the frustrated system with a rugged energy landscape.Comment: Latex; ps-files include

Testing Error Correcting Codes by Multicanonical Sampling of Rare Events

The idea of rare event sampling is applied to the estimation of the performance of error-correcting codes. The essence of the idea is importance sampling of the pattern of noises in the channel by Multicanonical Monte Carlo, which enables efficient estimation of tails of the distribution of bit error rate. The idea is successfully tested with a convolutional code

The smallest eigenvalue of Hankel matrices

Let H_N=(s_{n+m}),n,m\le N denote the Hankel matrix of moments of a positive measure with moments of any order. We study the large N behaviour of the smallest eigenvalue lambda_N of H_N. It is proved that lambda_N has exponential decay to zero for any measure with compact support. For general determinate moment problems the decay to 0 of lambda_N can be arbitrarily slow or arbitrarily fast. In the indeterminate case, where lambda_N is known to be bounded below by a positive constant, we prove that the limit of the n'th smallest eigenvalue of H_N for N tending to infinity tends rapidly to infinity with n. The special case of the Stieltjes-Wigert polynomials is discussed

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

Effects of thermal fluctuation and the receptor-receptor interaction in bacterial chemotactic signalling and adaptation

Bacterial chemotaxis is controlled by the conformational changes of the receptors, in response to the change of the ambient chemical concentration. In a statistical mechanical approach, the signalling due to the conformational changes is a thermodynamic average quantity, dependent on the temperature and the total energy of the system, including both ligand-receptor interaction and receptor-receptor interaction. This physical theory suggests to biology a new understanding of cooperation in ligand binding and receptor signalling problems. How much experimental support of this approach can be obtained from the currently available data? What are the parameter values? What is the practical information for experiments? Here we make comparisons between the theory and recent experimental results. Although currently comparisons can only be semi-quantitative or qualitative, consistency is clearly shown. The theory also helps to sort a variety of data.Comment: 26 pages, revtex. Journal version. Analysis on another set of data on adaptation time is adde

Superconductivity in zigzag CuO chains

Superconductivity has recently been discovered in Pr$_{2}$Ba$_{4}$Cu$_{7}$O$_{15-\delta}$ with a maximum $T_c$ of about 15K. Since the CuO planes in this material are believed to be insulating, it has been proposed that the superconductivity occurs in the double (or zigzag) CuO chain layer. On phenomenological grounds, we propose a theoretical interpretation of the experimental results in terms of a new phase for the zigzag chain, labelled by C$_1$S$_{3/2}$. This phase has a gap for some of the relative spin and charge modes but no total spin gap, and can have a divergent superconducting susceptibility for repulsive interactions. A microscopic model for the zigzag CuO chain is proposed, and on the basis of density matrix renormalization group (DMRG) and bosonization studies of this model, we adduce evidence that supports our proposal.Comment: 10 pages, 5 figures; Journal-ref. adde

Out of Equilibrium Solutions in the XYXY-Hamiltonian Mean Field model

Out of equilibrium magnetised solutions of the $XY$-Hamiltonian Mean Field ($XY$-HMF) model are build using an ensemble of integrable uncoupled pendula. Using these solutions we display an out-of equilibrium phase transition using a specific reduced set of the magnetised solutions

Ground Truths in the Humanities

Ensuring a faithful interaction with data and its representation for humanities can and should depend on expert-constructed ground truths