skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Computationally efficient algorithms for Brownian dynamics simulation of long flexible macromolecules modeled as bead-rod chains

Authors:
;
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1344193
Grant/Contract Number:
FG02-08ER46528
Resource Type:
Journal Article: Publisher's Accepted Manuscript
Journal Name:
Physical Review Fluids
Additional Journal Information:
Journal Volume: 2; Journal Issue: 2; Related Information: CHORUS Timestamp: 2017-02-17 22:09:13; Journal ID: ISSN 2469-990X
Publisher:
American Physical Society
Country of Publication:
United States
Language:
English

Citation Formats

Moghani, Mahdy Malekzadeh, and Khomami, Bamin. Computationally efficient algorithms for Brownian dynamics simulation of long flexible macromolecules modeled as bead-rod chains. United States: N. p., 2017. Web. doi:10.1103/PhysRevFluids.2.023303.
Moghani, Mahdy Malekzadeh, & Khomami, Bamin. Computationally efficient algorithms for Brownian dynamics simulation of long flexible macromolecules modeled as bead-rod chains. United States. doi:10.1103/PhysRevFluids.2.023303.
Moghani, Mahdy Malekzadeh, and Khomami, Bamin. Fri . "Computationally efficient algorithms for Brownian dynamics simulation of long flexible macromolecules modeled as bead-rod chains". United States. doi:10.1103/PhysRevFluids.2.023303.
@article{osti_1344193,
title = {Computationally efficient algorithms for Brownian dynamics simulation of long flexible macromolecules modeled as bead-rod chains},
author = {Moghani, Mahdy Malekzadeh and Khomami, Bamin},
abstractNote = {},
doi = {10.1103/PhysRevFluids.2.023303},
journal = {Physical Review Fluids},
number = 2,
volume = 2,
place = {United States},
year = {Fri Feb 17 00:00:00 EST 2017},
month = {Fri Feb 17 00:00:00 EST 2017}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1103/PhysRevFluids.2.023303

Citation Metrics:
Cited by: 1work
Citation information provided by
Web of Science

Save / Share:
  • We derive an exact nonequilibrium expression for the probability density of the scalar extension of an arbitrary section of a Rouse chain in dilute solution. We use this new result to assess the accuracy of a new non-equilibrium Brownian dynamics (NEBD) computer simulation method for macromolecular fluids. The NEBD method allows the examination of systems which, because of their complexity, are intractable to analytical methods. Comparison of simulation results for Rouse chains in shear flow with analytical results for the distribution of the end-to-end distance and the distribution of individual chain segment extensions shows that NEBD does indeed produce reliablemore » results.« less
  • With the advent of positron emission tomography (PET), a variety of techniques have been developed to measure local cerebral blood flow (LCBF) noninvasively in humans. It is essential that the techniques developed should be statistically reliable and computationally efficient. A potential class of techniques, which includes linear least squares (LS), linear weighted least squares (WLS), linear generalized least squares (GLS), and linear generalized weighted least squares (GWLS), is proposed. The statistical characteristics of the new methods were examined by computer simulation. The authors present a comparison of these four methods with two other rapid estimation techniques developed by Huang etmore » al. and Alpert, and two classical methods, the unweighted and weighted nonlinear least squares regression which are supposed to have optimal statistical properties. The results show that the new methods can take full advantage of the contribution from the fine temporal sampling data of modern tomographs, and thus provide statistically reliable estimates that are comparable to those obtained from nonlinear least squares regression. The new methods also have high computational efficiency, and the parameters can be estimated directly from operational equations in one single step. Therefore, they can potentially be used in image-wide estimation of local cerebral blood flow and distribution volume with positron emission tomography.« less
  • The role of the bead-solvent interaction has been studied for its influence on the dynamics of an N-bead macromolecule which is immersed into a solution. Using a Fokker-Planck equation for the phase-space distribution function of the macromolecule, we show that all the effects of the solution can be treated entirely in terms of the friction tensors which are assigned to each pair of interacting beads in the chain. For the high-density as well as for the critical solvent, the properties of these tensors are discussed in detail and are calculated by using several (realistic) choices of the bead-solvent potential. Frommore » the friction tensors, moreover, an expression for the center-of-mass friction coefficient of a (N-bead) chain macromolecule is derived. Numerical data for this coefficient for 'truncated' Lennard-Jones bead-solvent potential are compared with results from molecular dynamic simulations and from the phenomenological theoretical data as found in the literature.« less
  • An improved version of a recently developed stochastic cluster dynamics (SCD) method (Marian and Bulatov, 2012) [6] is introduced as an alternative to rate theory (RT) methods for solving coupled ordinary differential equation (ODE) systems for irradiation damage simulations. SCD circumvents by design the curse of dimensionality of the variable space that renders traditional ODE-based RT approaches inefficient when handling complex defect population comprised of multiple (more than two) defect species. Several improvements introduced here enable efficient and accurate simulations of irradiated materials up to realistic (high) damage doses characteristic of next-generation nuclear systems. The first improvement is a proceduremore » for efficiently updating the defect reaction-network and event selection in the context of a dynamically expanding reaction-network. Next is a novel implementation of the τ-leaping method that speeds up SCD simulations by advancing the state of the reaction network in large time increments when appropriate. Lastly, a volume rescaling procedure is introduced to control the computational complexity of the expanding reaction-network through occasional reductions of the defect population while maintaining accurate statistics. The enhanced SCD method is then applied to model defect cluster accumulation in iron thin films subjected to triple ion-beam (Fe{sup 3+}, He{sup +} and H{sup +}) irradiations, for which standard RT or spatially-resolved kinetic Monte Carlo simulations are prohibitively expensive.« less