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

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

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

Observations of HONO by laser-induced fluorescence at the South Pole during ANTCI 2003

Observations of nitrous acid (HONO) by laser-induced fluorescence (LIF) at the South Pole taken during the Antarctic Troposphere Chemistry Investigation (ANTCI), which took place over the time period of Nov. 15, 2003 to Jan. 4, 2004, are presented here. The median observed mixing ratio of HONO 10 m above the snow was 5.8 pptv (mean value 6.3 pptv) with a maximum of 18.2 pptv on Nov 30th, Dec 1st, 3rd, 15th, 17th, 21st, 22nd, 25th, 27th and 28th. The measurement uncertainty is ±35%. The LIF HONO observations are compared to concurrent HONO observations performed by mist chamber/ion chromatography (MC/IC). The HONO levels reported by MC/IC are about 7.2 ± 2.3 times higher than those reported by LIF. Citation: Liao, W., A. T. Case, J. Mastromarino, D. Tan, and J. E. Dibb (2006), Observations of HONO by laser-induced fluorescence at the South Pole during ANTCI 2003, Geophys. Res. Lett., 33, L09810, doi:10.1029/2005GL025470

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

Accuracy of the QUAD4 thick shell element

The accuracy of the relatively new QUAD4 thick shell element is assessed via comparison with a theoretical solution for thick homogeneous and honeycomb flat simply supported plates under the action of a uniform pressure load. The theoretical thick plate solution is based on the theory developed by Reissner and includes the effects of transverse shear flexibility which are not included in the thin plate solutions based on Kirchoff plate theory. In addition, the QUAD4 is assessed using a set of finite element test problems developed by the MacNeal-Schwendler Corp. (MSC). Comparison of the COSMIC QUAD4 element as well as those from MSC and Universal Analytics, Inc. (UAI) for these test problems is presented. The current COSMIC QUAD4 element is shown to have excellent comparison with both the theoretical solutions and also those from the two commercial versions of NASTRAN that it was compared to

New measurements of total ionizing dose in the lunar environment

[1] We report new measurements of solar minimum ionizing radiation dose at the Moon onboard the Lunar Reconnaissance Orbiter (LRO) from June 2009 through May 2010. The Cosmic Ray Telescope for the Effects of Radiation (CRaTER) instrument on LRO houses a compact and highly precise microdosimeter whose design allows measurements of dose rates below 1 micro-Rad per second in silicon achieved with minimal resources (20 g, ∼250 milliwatts, and ∼3 bits/second). We envision the use of such a small yet accurate dosimeter in many future spaceflight applications where volume, mass, and power are highly constrained. As this was the first operation of the microdosimeter in a space environment, the goal of this study is to verify its response by using simultaneous measurements of the galactic cosmic ray ionizing environment at LRO, at L1, and with other concurrent dosimeter measurements and model predictions. The microdosimeter measured the same short timescale modulations in the galactic cosmic rays as the other independent measurements, thus verifying its response to a known source of minimum-ionizing particles. The total dose for the LRO mission over the first 333 days was only 12.2 Rads behind ∼130 mils of aluminum because of the delayed rise of solar activity in solar cycle 24 and the corresponding lack of intense solar energetic particle events. The dose rate in a 50 km lunar orbit was about 30 percent lower than the interplanetary rate, as one would expect from lunar obstruction of the visible sky

Dimensional renormalization: ladders to rainbows

Renormalization factors are most easily extracted by going to the massless limit of the quantum field theory and retaining only a single momentum scale. We derive factors and renormalized Green functions to all orders in perturbation theory for rainbow graphs and vertex (or scattering diagrams) at zero momentum transfer, in the context of dimensional renormalization, and we prove that the correct anomalous dimensions for those processes emerge in the limit D -> 4.Comment: RevTeX, no figure

Stochastic evolution of four species in cyclic competition

We study the stochastic evolution of four species in cyclic competition in a well mixed environment. In systems composed of a finite number $N$ of particles these simple interaction rules result in a rich variety of extinction scenarios, from single species domination to coexistence between non-interacting species. Using exact results and numerical simulations we discuss the temporal evolution of the system for different values of $N$, for different values of the reaction rates, as well as for different initial conditions. As expected, the stochastic evolution is found to closely follow the mean-field result for large $N$, with notable deviations appearing in proximity of extinction events. Different ways of characterizing and predicting extinction events are discussed.Comment: 19 pages, 6 figures, submitted to J. Stat. Mec

Random Walks on a Fluctuating Lattice: A Renormalization Group Approach Applied in One Dimension

We study the problem of a random walk on a lattice in which bonds connecting nearest neighbor sites open and close randomly in time, a situation often encountered in fluctuating media. We present a simple renormalization group technique to solve for the effective diffusive behavior at long times. For one-dimensional lattices we obtain better quantitative agreement with simulation data than earlier effective medium results. Our technique works in principle in any dimension, although the amount of computation required rises with dimensionality of the lattice.Comment: PostScript file including 2 figures, total 15 pages, 8 other figures obtainable by mail from D.L. Stei