19,500 research outputs found
Rocking Subdiffusive Ratchets: Origin, Optimization and Efficiency
We study origin, parameter optimization, and thermodynamic efficiency of
isothermal rocking ratchets based on fractional subdiffusion within a
generalized non-Markovian Langevin equation approach. A corresponding
multi-dimensional Markovian embedding dynamics is realized using a set of
auxiliary Brownian particles elastically coupled to the central Brownian
particle (see video on the journal web site). We show that anomalous
subdiffusive transport emerges due to an interplay of nonlinear response and
viscoelastic effects for fractional Brownian motion in periodic potentials with
broken space-inversion symmetry and driven by a time-periodic field. The
anomalous transport becomes optimal for a subthreshold driving when the driving
period matches a characteristic time scale of interwell transitions. It can
also be optimized by varying temperature, amplitude of periodic potential and
driving strength. The useful work done against a load shows a parabolic
dependence on the load strength. It grows sublinearly with time and the
corresponding thermodynamic efficiency decays algebraically in time because the
energy supplied by the driving field scales with time linearly. However, it
compares well with the efficiency of normal diffusion rocking ratchets on an
appreciably long time scale
Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures
Coarse grain (CG) molecular models have been proposed to simulate complex sys- tems with lower computational overheads and longer timescales with respect to atom- istic level models. However, their acceleration on parallel architectures such as Graphic Processing Units (GPU) presents original challenges that must be carefully evaluated. The objective of this work is to characterize the impact of CG model features on parallel simulation performance. To achieve this, we implemented a GPU-accelerated version of a CG molecular dynamics simulator, to which we applied specic optimizations for CG models, such as dedicated data structures to handle dierent bead type interac- tions, obtaining a maximum speed-up of 14 on the NVIDIA GTX480 GPU with Fermi architecture. We provide a complete characterization and evaluation of algorithmic and simulated system features of CG models impacting the achievable speed-up and accuracy of results, using three dierent GPU architectures as case studie
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
GROMACS is a widely used package for biomolecular simulation, and over the
last two decades it has evolved from small-scale efficiency to advanced
heterogeneous acceleration and multi-level parallelism targeting some of the
largest supercomputers in the world. Here, we describe some of the ways we have
been able to realize this through the use of parallelization on all levels,
combined with a constant focus on absolute performance. Release 4.6 of GROMACS
uses SIMD acceleration on a wide range of architectures, GPU offloading
acceleration, and both OpenMP and MPI parallelism within and between nodes,
respectively. The recent work on acceleration made it necessary to revisit the
fundamental algorithms of molecular simulation, including the concept of
neighborsearching, and we discuss the present and future challenges we see for
exascale simulation - in particular a very fine-grained task parallelism. We
also discuss the software management, code peer review and continuous
integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin
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