5,171 research outputs found
Dynamics of short polymer chains in solution
We present numerical and analytical results describing the effect of
hydrodynamic interactions on the dynamics of a short polymer chain in solution.
A molecular dynamics algorithm for the polymer is coupled to a direct
simulation Monte Carlo algorithm for the solvent. We give an explicit
expression for the velocity autocorrelation function of the centre of mass of
the polymer which agrees well with numerical results if Brownian dynamics,
hydrodynamic correlations and sound wave scattering are included
Coarse Grained Simulations of a Small Peptide: Effects of Finite Damping and Hydrodynamic Interactions
In the coarse grained Brownian Dynamics simulation method the many solvent
molecules are replaced by random thermal kicks and an effective friction acting
on the particles of interest. For Brownian Dynamics the friction has to be so
strong that the particles' velocities are damped much faster than the duration
of an integration timestep. Here we show that this conceptual limit can be
dropped with an analytic integration of the equations of damped motion. In the
resulting Langevin integration scheme our recently proposed approximate form of
the hydrodynamic interactions between the particles can be incorparated
conveniently, leading to a fast multi-particle propagation scheme, which
captures more of the short-time and short-range solvent effects than standard
BD. Comparing the dynamics of a bead-spring model of a short peptide, we
recommend to run simulations of small biological molecules with the Langevin
type finite damping and to include the hydrodynamic interactions.Comment: 7 pages, 6 figures, submitted to J Chem Phy
GPU-accelerated simulation of colloidal suspensions with direct hydrodynamic interactions
Solvent-mediated hydrodynamic interactions between colloidal particles can
significantly alter their dynamics. We discuss the implementation of Stokesian
dynamics in leading approximation for streaming processors as provided by the
compute unified device architecture (CUDA) of recent graphics processors
(GPUs). Thereby, the simulation of explicit solvent particles is avoided and
hydrodynamic interactions can easily be accounted for in already available,
highly accelerated molecular dynamics simulations. Special emphasis is put on
efficient memory access and numerical stability. The algorithm is applied to
the periodic sedimentation of a cluster of four suspended particles. Finally,
we investigate the runtime performance of generic memory access patterns of
complexity for various GPU algorithms relying on either hardware cache
or shared memory.Comment: to appear in a special issue of Eur. Phys. J. Special Topics on
"Computer Simulations on GPUs
Inertial Coupling Method for particles in an incompressible fluctuating fluid
We develop an inertial coupling method for modeling the dynamics of
point-like 'blob' particles immersed in an incompressible fluid, generalizing
previous work for compressible fluids. The coupling consistently includes
excess (positive or negative) inertia of the particles relative to the
displaced fluid, and accounts for thermal fluctuations in the fluid momentum
equation. The coupling between the fluid and the blob is based on a no-slip
constraint equating the particle velocity with the local average of the fluid
velocity, and conserves momentum and energy. We demonstrate that the
formulation obeys a fluctuation-dissipation balance, owing to the
non-dissipative nature of the no-slip coupling. We develop a spatio-temporal
discretization that preserves, as best as possible, these properties of the
continuum formulation. In the spatial discretization, the local averaging and
spreading operations are accomplished using compact kernels commonly used in
immersed boundary methods. We find that the special properties of these kernels
make the discrete blob a particle with surprisingly physically-consistent
volume, mass, and hydrodynamic properties. We develop a second-order
semi-implicit temporal integrator that maintains discrete
fluctuation-dissipation balance, and is not limited in stability by viscosity.
Furthermore, the temporal scheme requires only constant-coefficient Poisson and
Helmholtz linear solvers, enabling a very efficient and simple FFT-based
implementation on GPUs. We numerically investigate the performance of the
method on several standard test problems...Comment: Contains a number of corrections and an additional Figure 7 (and
associated discussion) relative to published versio
Spectral Ewald Acceleration of Stokesian Dynamics for polydisperse suspensions
In this work we develop the Spectral Ewald Accelerated Stokesian Dynamics
(SEASD), a novel computational method for dynamic simulations of polydisperse
colloidal suspensions with full hydrodynamic interactions. SEASD is based on
the framework of Stokesian Dynamics (SD) with extension to compressible
solvents, and uses the Spectral Ewald (SE) method [Lindbo & Tornberg, J.
Comput. Phys. 229 (2010) 8994] for the wave-space mobility computation. To meet
the performance requirement of dynamic simulations, we use Graphic Processing
Units (GPU) to evaluate the suspension mobility, and achieve an order of
magnitude speedup compared to a CPU implementation. For further speedup, we
develop a novel far-field block-diagonal preconditioner to reduce the far-field
evaluations in the iterative solver, and SEASD-nf, a polydisperse extension of
the mean-field Brownian approximation of Banchio & Brady [J. Chem. Phys. 118
(2003) 10323]. We extensively discuss implementation and parameter selection
strategies in SEASD, and demonstrate the spectral accuracy in the mobility
evaluation and the overall computation scaling. We
present three computational examples to further validate SEASD and SEASD-nf in
monodisperse and bidisperse suspensions: the short-time transport properties,
the equilibrium osmotic pressure and viscoelastic moduli, and the steady shear
Brownian rheology. Our validation results show that the agreement between SEASD
and SEASD-nf is satisfactory over a wide range of parameters, and also provide
significant insight into the dynamics of polydisperse colloidal suspensions.Comment: 39 pages, 21 figure
A fluctuating boundary integral method for Brownian suspensions
We present a fluctuating boundary integral method (FBIM) for overdamped
Brownian Dynamics (BD) of two-dimensional periodic suspensions of rigid
particles of complex shape immersed in a Stokes fluid. We develop a novel
approach for generating Brownian displacements that arise in response to the
thermal fluctuations in the fluid. Our approach relies on a first-kind boundary
integral formulation of a mobility problem in which a random surface velocity
is prescribed on the particle surface, with zero mean and covariance
proportional to the Green's function for Stokes flow (Stokeslet). This approach
yields an algorithm that scales linearly in the number of particles for both
deterministic and stochastic dynamics, handles particles of complex shape,
achieves high order of accuracy, and can be generalized to three dimensions and
other boundary conditions. We show that Brownian displacements generated by our
method obey the discrete fluctuation-dissipation balance relation (DFDB). Based
on a recently-developed Positively Split Ewald method [A. M. Fiore, F. Balboa
Usabiaga, A. Donev and J. W. Swan, J. Chem. Phys., 146, 124116, 2017],
near-field contributions to the Brownian displacements are efficiently
approximated by iterative methods in real space, while far-field contributions
are rapidly generated by fast Fourier-space methods based on fluctuating
hydrodynamics. FBIM provides the key ingredient for time integration of the
overdamped Langevin equations for Brownian suspensions of rigid particles. We
demonstrate that FBIM obeys DFDB by performing equilibrium BD simulations of
suspensions of starfish-shaped bodies using a random finite difference temporal
integrator.Comment: Submitted to J. Comp. Phy
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