8,905 research outputs found
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
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
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
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
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
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
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 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 , 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 , 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
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Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.
The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing
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
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