Self-learning Multiscale Simulation for Achieving High Accuracy and High Efficiency Simultaneously

We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular system. Based on the resolution exchange simulations between atomistic and CG replicas, a self-learning strategy is introduced to progressively improve the CG potential by an iterative way. Two tests show that, the new method can rapidly improve the CG potential and achieve efficient sampling even starting from an unrealistic CG potential. The resulting free energy agreed well with exact result and the convergence by the method was much faster than that by the replica exchange method. The method is generic and can be applied to many biological as well as non-biological problems.Comment: 14 pages, 6 figure

Massive 4d4d particle with torsion and conformal mechanics

The consequences of coupling of the torsion (highest curvature) term to the Lagrangian of a massive spinless particle in four-dimensional space-time are studied. It is shown that the modified system remains spinless and possesses extended gauge invariance. Though the torsion term does not generate spin, it provides the system with a nontrivial mass spectrum, described by one-dimensional conformal mechanics. Under an appropriate choise of characteristic constants the system has solutions with a discrete mass spectrum.Comment: 9 pages, revised version accepted in Phys.Lett.

Coalescence in low-viscosity liquids

The expected universal dynamics associated with the initial stage of droplet coalescence are difficult to study visually due to the rapid motion of the liquid and the awkward viewing geometry. Here we employ an electrical method to study the coalescence of two inviscid droplets at early times. We measure the growth dynamics of the bridge connecting the two droplets and observe a new asymptotic regime inconsistent with previous theoretical predictions. The measurements are consistent with a model in which the two liquids coalesce with a slightly deformed interface.Comment: 4 pages and 4 figure

An Inverse Scattering Transform for the Lattice Potential KdV Equation

The lattice potential Korteweg-de Vries equation (LKdV) is a partial difference equation in two independent variables, which possesses many properties that are analogous to those of the celebrated Korteweg-de Vries equation. These include discrete soliton solutions, Backlund transformations and an associated linear problem, called a Lax pair, for which it provides the compatibility condition. In this paper, we solve the initial value problem for the LKdV equation through a discrete implementation of the inverse scattering transform method applied to the Lax pair. The initial value used for the LKdV equation is assumed to be real and decaying to zero as the absolute value of the discrete spatial variable approaches large values. An interesting feature of our approach is the solution of a discrete Gel'fand-Levitan equation. Moreover, we provide a complete characterization of reflectionless potentials and show that this leads to the Cauchy matrix form of N-soliton solutions

Conductance through the disclination dipole defect in metallic carbon nanotubes

The electronic transport properties of a metallic carbon nanotube with the five-seven disclination pair characterized by a lattice distortion vector are investigated. The influence of the disclination dipole includes induced curvature and mixing of two sublattices. Both these factors are taken into account via a self-consistent perturbation approach. The conductance and the Fano factor are calculated within the transfer-matrix technique. PACS: 73.63.Fg, 72.80.Rj, 72.10.F

Ariel - Volume 3 Number 2

Editors Richard J. Bonanno Robin A. Edwards Associate Editors Steven Ager Stephen Flynn Tom Williams Lay-out Editor Eugenia Miller Contributing Editors Paul Bialas Milton Packer Robert Breckenridge Lynne Porter Mark Pearlman Terry Burt Mike Leo Editors Emeritus Delvyn C. Case, Jr. Paul M. Fernhof

Species assembly in model ecosystems, II: Results of the assembly process

In the companion paper of this set (Capitan and Cuesta, 2010) we have developed a full analytical treatment of the model of species assembly introduced in Capitan et al. (2009). This model is based on the construction of an assembly graph containing all viable configurations of the community, and the definition of a Markov chain whose transitions are the transformations of communities by new species invasions. In the present paper we provide an exhaustive numerical analysis of the model, describing the average time to the recurrent state, the statistics of avalanches, and the dependence of the results on the amount of available resource. Our results are based on the fact that the Markov chain provides an asymptotic probability distribution for the recurrent states, which can be used to obtain averages of observables as well as the time variation of these magnitudes during succession, in an exact manner. Since the absorption times into the recurrent set are found to be comparable to the size of the system, the end state is quickly reached (in units of the invasion time). Thus, the final ecosystem can be regarded as a fluctuating complex system where species are continually replaced by newcomers without ever leaving the set of recurrent patterns. The assembly graph is dominated by pathways in which most invasions are accepted, triggering small extinction avalanches. Through the assembly process, communities become less resilient (e.g., have a higher return time to equilibrium) but become more robust in terms of resistance against new invasions.Comment: 14 pages, 13 figures. Revised versio

Comparative analysis of rigidity across protein families

We present a comparative study in which 'pebble game' rigidity analysis is applied to multiple protein crystal structures, for each of six different protein families. We find that the main-chain rigidity of a protein structure at a given hydrogen bond energy cutoff is quite sensitive to small structural variations, and conclude that the hydrogen bond constraints in rigidity analysis should be chosen so as to form and test specific hypotheses about the rigidity of a particular protein. Our comparative approach highlights two different characteristic patterns ('sudden' or 'gradual') for protein rigidity loss as constraints are removed, in line with recent results on the rigidity transitions of glassy networks

Earth Occultation Imaging of the Low Energy Gamma-Ray Sky with GBM

The Earth Occultation Technique (EOT) has been applied to Fermi's Gamma-ray Burst Monitor (GBM) to perform all-sky monitoring for a predetermined catalog of hard X-ray/soft gamma-ray sources. In order to search for sources not in the catalog, thus completing the catalog and reducing a source of systematic error in EOT, an imaging method has been developed -- Imaging with a Differential filter using the Earth Occultation Method (IDEOM). IDEOM is a tomographic imaging method that takes advantage of the orbital precession of the Fermi satellite. Using IDEOM, all-sky reconstructions have been generated for ~sim 4 years of GBM data in the 12-50 keV, 50-100 keV and 100-300 keV energy bands in search of sources otherwise unmodeled by the GBM occultation analysis. IDEOM analysis resulted in the detection of 57 sources in the 12-50 keV energy band, 23 sources in the 50-100 keV energy band, and 7 sources in the 100-300 keV energy band. Seventeen sources were not present in the original GBM-EOT catalog and have now been added. We also present the first joined averaged spectra for four persistent sources detected by GBM using EOT and by the Large Area Telescope (LAT) on Fermi: NGC 1275, 3C 273, Cen A, and the Crab