Large scale molecular dynamics simulations on graphic processing units (GPUs) are employed to study the scaling behavior of ring polymers with various topological constraints in melts. Typical sizes of rings containing $3_1$, $5_1$ knots and catenanes made up of two unknotted rings scale like $N^{1/3}$ in the limit of large ring sizes $N$. This is […]

December 16, 2014 by hgpu

We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a newly proposed "edge-based" approach, where a thread is started per each potentially non-zero interaction. We find that the former […]

January 23, 2014 by hgpu

A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the computational power of GPUs. In addition, the hierarchical self-assembly of soft anisotropic particles and the problems related to polymerization can […]

October 10, 2013 by hgpu

We present a generalization of the inertial coupling (IC) [Usabiaga et al. J. Comp. Phys. 2013] which permits the resolution of radiation forces on small particles with arbitrary acoustic contrast factor. The IC method is based on a Eulerian-Lagrangian approach: particles move in continuum space while the fluid equations are solved in a regular mesh […]

July 3, 2013 by hgpu

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 [F. Balboa Usabiaga, I. Pagonabarraga, and R. Delgado-Buscalioni, J. Comp. Phys., 235:701-722, 2013]. The coupling consistently includes excess (positive or negative) inertia of the particles relative to the displaced fluid, […]

January 2, 2013 by hgpu

We present an implementation of the analysis of dynamic near field scattering (NFS) data using a graphics processing unit (GPU). We introduce an optimized data management scheme thereby limiting the number of operations required. Overall, we reduce the processing time from hours to minutes, for typical experimental conditions. Previously the limiting step in such experiments, […]

September 18, 2012 by hgpu

We report the first CUDA graphics-processing-unit (GPU) implementation of the polymer field-theoretic simulation framework for determining fully fluctuating expectation values of equilibrium properties for periodic and select aperiodic polymer systems. Our implementation is suitable both for self-consistent field theory (mean-field) solutions of the field equations, and for fully fluctuating simulations using the complex Langevin approach. […]

April 25, 2012 by hgpu

Swarms of self-propelled particles exhibit complex behavior that can arise from simple models, with large changes in swarm behavior resulting from small changes in model parameters. We investigate the steady-state swarms formed by self-propelled Morse particles in three dimensions using molecular dynamics simulations optimized for GPUs. We find a variety of swarms of different overall […]

January 4, 2012 by hgpu

We propose a single chain slip-spring model, which is based on the slip-spring model by Likhtman [A. E. Likhtman, Macromolecules, 38, 6128 (2005)], for fast rheology simulations of entangled polymers on a GPU. We modify the original slip-spring model slightly for efficient calculations on a GPU. Our model is designed to satisfy the detailed balance […]

June 16, 2011 by hgpu

A comparative simulation study of polymer brushes formed by grafting at a planar surface either flexible linear polymers (chain length $N_L$) or (non-catenated) ring polymers (chain length $N_R=2 N_L$) is presented. Two distinct off-lattice models are studied, one by Monte Carlo methods, the other by Molecular Dynamics, using a fast implementation on graphics processing units […]

April 29, 2011 by hgpu

Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD) simulations for system sizes ranging up to about 1 million particles. Particular emphasis is put on the numerical long-time stability in terms […]

January 18, 2011 by hgpu

Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules, under physiologically relevant conditions, is challenging even for distributed computing systems. Graphics Processing Units (GPUs) are emerging as an alternative programming platform to the more traditional CPUs as they provide high raw computational […]

November 12, 2010 by hgpu