Parallel O(N) Stokes' solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries.

No abstract is available for this paper.

• Publication year

  2017

• Venue

  Journal of Chemical Physics

• Publication date

  2017-06-29

• Fields of study

  Medicine, Physics, Computer Science, Engineering

• Identifiers
  DOI 10.1063/1.4989545PMID 28668032
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• PETSc Users Manual: Revision 3.11

  2019cited by this paper
• PETSc Users Manual Revision 3.4

  2016cited by this paper
• An efficient smoothed profile-lattice Boltzmann method for the simulation of forced and natural convection flows in complex geometries

  2015cited by this paper
• Self-consistent description of electrokinetic phenomena in particle-based simulations.

  2015cited by this paper
• Hydrodynamics of diamond-shaped gradient nanopillar arrays for effective DNA translocation into nanochannels.

  2015cited by this paper
• Towards a Unified Description of the Rheology of Hard-Particle Suspensions.

  2015cited by this paper
• DNA translocation through short nanofluidic channels under asymmetric pulsed electric field.

  2014cited by this paper
• Macromolecular crowding as a regulator of gene transcription.

  2014cited by this paper
• Simulation of diffusion in a crowded environment.

  2013cited by this paper
• Dynamics of confined depletion mixtures of polymers and bidispersed colloids

  2013cited by this paper
• Presentation of large DNA molecules for analysis as nanoconfined dumbbells.

  2013cited by this paper
• Anomalous transport in the crowded world of biological cells

  2013cited by this paper
• Mechanism of margination in confined flows of blood and other multicomponent suspensions.

  2012cited by this paper
• Numerische Bestimmung der Durchgangsrate von Partikeln durch eine Porengeometrie

  2011cited by this paper
• Effects of macromolecular crowding on genetic networks.

  2011cited by this paper
• The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics

  2011cited by this paper
• Mixed and Hybrid Finite Element Methods

  2011cited by this paper
• Pair collisions of fluid-filled elastic capsules in shear flow: Effects of membrane properties and polymer additives

  2010cited by this paper
• Comparison of lattice-Boltzmann and brownian-dynamics simulations of polymer migration in confined flows.

  2010cited by this paper
• Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

  2010cited by this paper
• Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

  2010cited by this paper
• Continuous separation of cells and particles in microfluidic systems.

  2010cited by this paper
• Hydrodynamic effects on the translocation rate of a polymer through a pore.

  2009cited by this paper
• Dipole-induced self-assembly of helical beta-peptides.

  2008cited by this paper
• Dynamics of confined suspensions of swimming particles

  2008cited by this paper
• The effect of hydrodynamic interactions on the dynamics of DNA translocation through pores.

  2008cited by this paper
• Diffusion and spatial correlations in suspensions of swimming particles.

  2008cited by this paper
• Non-equilibrium sedimentation of colloids: confocal microscopy and Brownian dynamics simulations

  2008cited by this paper
• Two-relaxation-time Lattice Boltzmann scheme: About parametrization, velocity, pressure and mixed boundary conditions

  2008cited by this paper
• Fast computation of many-particle hydrodynamic and electrostatic interactions in a confined geometry.

  2007cited by this paper
• Modeling adsorption and order formation by colloidal particles on a solid surface : A Brownian dynamics study

  2006cited by this paper
• Double-Stranded DNA Diffusion in Slitlike Nanochannels

  2006cited by this paper
• N log N method for hydrodynamic interactions of confined polymer systems: Brownian dynamics.

  2006cited by this paper
• Cross-stream-line migration in confined flowing polymer solutions: Theory and simulation

  2006cited by this paper
• Library for Parallel Adaptive Mesh Refinement / Coarsening Simulations

  2006cited by this paper
• Microfluidics: Fluid physics at the nanoliter scale

  2005cited by this paper
• Theory of shear-induced migration in dilute polymer solutions near solid boundaries

  2005cited by this paper
• The method of regularized Stokeslets in three dimensions : Analysis, validation, and application to helical swimming

  2005cited by this paper
• Transport and collective dynamics in suspensions of confined swimming particles.

  2005cited by this paper
• SLEPc: A scalable and flexible toolkit for the solution of eigenvalue problems

  2005cited by this paper
• Electrorheology in nanopores via lattice Boltzmann simulation.

  2004cited by this paper
• Conformation and dynamics of single DNA molecules in parallel-plate slit microchannels.

  2004cited by this paper
• Shear-induced migration in flowing polymer solutions: simulation of long-chain DNA in microchannels [corrected].

  2004cited by this paper
• A model for velocity fluctuations in sedimentation

  2004cited by this paper
• Effect of confinement on DNA dynamics in microfluidic devices

  2003cited by this paper
• Preconditioning Techniques for Newton's Method for the Incompressible Navier–Stokes Equations

  2003cited by this paper
• Modeling hydrodynamic interaction in Brownian dynamics: simulations of extensional flows of dilute solutions of DNA and polystyrene

  2003cited by this paper
• Accelerated Stokesian dynamics: Brownian motion

  2003cited by this paper
• DNA dynamics in a microchannel.

  2003cited by this paper
• SuperLU_DIST: A scalable distributed-memory sparse direct solver for unsymmetric linear systems

  2003cited by this paper
• The immersed boundary method

  2002cited by this paper
• Brownian dynamics simulations of bead-rod and bead-spring chains: numerical algorithms and coarse-graining issues

  2002cited by this paper
• Foaming mechanisms in surfactant free particle suspensions

  2002cited by this paper
• Stochastic simulations of DNA in flow: Dynamics and the effects of hydrodynamic interactions

  2002cited by this paper
• The Method of Regularized Stokeslets

  2001cited by this paper
• Large scale and mesoscopic hydrodynamics for dissipative particle dynamics

  2001cited by this paper
• Macromolecular crowding: obvious but underappreciated.

  2001cited by this paper
• Localized force representations for particles sedimenting in Stokes flow

  2001cited by this paper
• Accelerated Stokesian Dynamics simulations

  2001cited by this paper
• Hydrodynamic interactions in long chain polymers: Application of the Chebyshev polynomial approximation in stochastic simulations

  2000cited by this paper
• Brownian dynamics simulations of single DNA molecules in shear flow

  2000cited by this paper
• Simulation of a single polymer chain in solution by combining lattice Boltzmann and molecular dynamics

  1999cited by this paper
• Brownian dynamics simulations of linear polymers under shear flow

  1999cited by this paper
• Collective effects in dissipative particle dynamics

  1999cited by this paper
• A Supernodal Approach to Sparse Partial Pivoting

  1999cited by this paper
• Single-polymer dynamics in steady shear flow.

  1999cited by this paper
• Single polymer dynamics in an elongational flow.

  1997cited by this paper
• An Asynchronous Parallel Supernodal Algorithm for Sparse Gaussian Elimination

  1997cited by this paper
• Stochastic Processes in Polymeric Fluids

  1996cited by this paper
• Bending and Twisting Elasticity of DNA

  1994cited by this paper
• Brownian dynamics simulations of model hard-sphere suspensions

  1993cited by this paper
• Construction of Langevin forces in the simulation of hydrodynamic interaction

  1986cited by this paper
• Implicit algorithm for Brownian dynamics of polymers

  1986cited by this paper
• Simulation of polymer dynamics. I. General theory

  1978cited by this paper
• Brownian dynamics with hydrodynamic interactions

  1978cited by this paper
• Macromolecular crowding : obvious but underappreciated

  year unknowncited by this paper

• Steric effects in induced-charge electro-osmosis for strong electric fields

  2023cites this paper
• Single-particle dynamics in a low-Reynolds-number fluid under spherical confinement

  2023cites this paper
• Fast Ewald summation for Stokes flow with arbitrary periodicity

  2022cites this paper
• Modeling electrokinetic flows with the discrete ion stochastic continuum overdamped solvent algorithm.

  2022cites this paper
• Discrete ion stochastic continuum overdamped solvent algorithm for modeling electrolytes

  2021cites this paper
• DISCOS for Electrolytes A Discrete Ion Stochastic Continuum Overdamped Solvent Algorithm for Modeling Electrolytes

  2020cites this paper
• Shape induced segregation and anomalous particle transport under spherical confinement

  2020cites this paper
• Structure and dynamics of hydrodynamically interacting finite-size Brownian particles in a spherical cavity: Spheres and cylinders.

  2020cites this paper
• Dynamics and rheology of ring-linear blend semidilute solutions in extensional flow. Part I: Modeling and molecular simulations

  2020cites this paper
• A Discrete Ion Stochastic Continuum Overdamped Solvent Algorithm for Modeling Electrolytes.

  2020influential citation
• Structure and proton conduction in sulfonated poly(ether ether ketone) semi-permeable membranes: a multi-scale computational approach.

  2019cites this paper
• Discrete and Continuum Models for the Salt in Crowded Environments of Suspended Charged Particles.

  2018cites this paper
• Evolutionary strategy for inverse charge measurements of dielectric particles.

  2018cites this paper
• A boundary integral method with volume-changing objects for ultrasound-triggered margination of microbubbles

  2016cites this paper