arXiv subjects

G. De Fabritiis

Publications and source records attributed to G. De Fabritiis.

11 recordsLinked to original sources

arXiv2009

ACEMD: Accelerating bio-molecular dynamics in the microsecond time-scale

The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation program designed specifically for GPUs which is able to achieve supercomputing scale performance of 40 nanoseconds/day for all-atom protein systems with over 23,000 atoms. We illustrate the characteristics of the code, its validation and performance. We also run a microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. This performance on cost effective hardware allows ACEMD to reach microsecond timescales routinely with important implications in terms of scientific applications.

physics.comp-ph↗

arXiv2007

A hybrid method coupling fluctuating hydrodynamics and molecular dynamics for the simulation of macromolecules

We present a hybrid computational method for simulating the dynamics of macromolecules in solution which couples a mesoscale solver for the fluctuating hydrodynamics (FH) equations with molecular dynamics to describe the macromolecule. The two models interact through a dissipative Stokesian term first introduced by Ahlrichs and Dünweg [J. Chem. Phys. {\bf 111}, 8225 (1999)]. We show that our method correctly captures the static and dynamical properties of polymer chains as predicted by the Zimm model. In particular, we show that the static conformations are best described when the ratio $\fracσ{b}=0.6$, where $σ$ is the Lennard-Jones length parameter and $b$ is the monomer bond length. We also find that the decay of the Rouse modes' autocorrelation function is better described with an analytical correction suggested by Ahlrichs and Dünweg. Our FH solver permits us to treat the fluid equation of state and transport parameters as direct simulation parameters. The expected independence of the chain dynamics on various choices of fluid equation of state and bulk viscosity is recovered, while excellent agreement is found for the temperature and shear viscosity dependence of centre of mass diffusion between simulation results and predictions of the Zimm model. We find that Zimm model approximations start to fail when the Schmidt number $Sc \lessapprox 30$. Finally, we investigate the importance of fluid fluctuations and show that using the preaveraged approximation for the hydrodynamic tensor leads to around 3% error in the diffusion coefficient for a polymer chain when the fluid discretization size is greater than $50Å$.

cond-mat.soft↗

arXiv2007

Performance of the Cell processor for biomolecular simulations

The new Cell processor represents a turning point for computing intensive applications. Here, I show that for molecular dynamics it is possible to reach an impressive sustained performance in excess of 30 Gflops with a peak of 45 Gflops for the non-bonded force calculations, over one order of magnitude faster than a single core standard processor.

physics.comp-ph↗

arXiv2006

Fluctuating hydrodynamic modelling of fluids at the nanoscale

A good representation of mesoscopic fluids is required to combine with molecular simulations at larger length and time scales (De Fabritiis {\it et. al}, Phys. Rev. Lett. 97, 134501 (2006)). However, accurate computational models of the hydrodynamics of nanoscale molecular assemblies are lacking, at least in part because of the stochastic character of the underlying fluctuating hydrodynamic equations. Here we derive a finite volume discretization of the compressible isothermal fluctuating hydrodynamic equations over a regular grid in the Eulerian reference system. We apply it to fluids such as argon at arbitrary densities and water under ambient conditions. To that end, molecular dynamics simulations are used to derive the required fluid properties. The equilibrium state of the model is shown to be thermodynamically consistent and correctly reproduces linear hydrodynamics including relaxation of sound and shear modes. We also consider non-equilibrium states involving diffusion and convection in cavities with no-slip boundary conditions.

physics.flu-dyn↗

arXiv2006

Multiscale modelling of liquids with molecular specificity

The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the full molecular nature of the system where it is of interest and coarse-graining it elsewhere. This is made possible by coupling molecular dynamics with a mesoscopic description of realistic liquids based on Landau's fluctuating hydrodynamics. We show that our scheme correctly couples hydrodynamics and that fluctuations, at both the molecular and continuum levels, are thermodynamically consistent. Hybrid simulations of sound waves in bulk water and reflected by a lipid monolayer are presented as illustrations of the scheme.

physics.flu-dyn↗

arXiv2006

Coupled applications on distributed resources

Coupled models are set to become increasingly important in all aspects of science and engineering as tools with which to study complex systems in an integrated manner. Such coupled, hybrid simulations typically communicate data between the component models of which they are comprised relatively infrequently, and so a Grid is expected to present an ideal architecture on which to run them. In the present paper, we describe a simple, flexible and extensible architecture for a two-component hybrid molecular-continuum coupled model (hybrid MD). We discuss its deployment on distributed resources and the extensions to the RealityGrid computational-steering system to handle coupled models.

physics.comp-ph↗

arXiv2006

A stochastic Trotter integration scheme for dissipative particle dynamics

In this article we show in details the derivation of an integration scheme for the dissipative particle dynamic model (DPD) using the stochastic Trotter formula [De Fabritiis et al., Physica A, 361, 429 (2006)]. We explain some subtleties due to the stochastic character of the equations and exploit analyticity in some interesting parts of the dynamics. The DPD-Trotter integrator demonstrates the inexistence of spurious spatial correlations in the radial distribution function for an ideal gas equation of state. We also compare our numerical integrator to other available DPD integration schemes.

cond-mat.soft↗

arXiv2005

Efficient numerical integrators for stochastic models

The efficient simulation of models defined in terms of stochastic differential equations (SDEs) depends critically on an efficient integration scheme. In this article, we investigate under which conditions the integration schemes for general SDEs can be derived using the Trotter expansion. It follows that, in the stochastic case, some care is required in splitting the stochastic generator. We test the Trotter integrators on an energy-conserving Brownian model and derive a new numerical scheme for dissipative particle dynamics. We find that the stochastic Trotter scheme provides a mathematically correct and easy-to-use method which should find wide applicability.

physics.comp-ph↗

arXiv2005

Determination of the chemical potential using energy-biased sampling

An energy-biased method to evaluate ensemble averages requiring test-particle insertion is presented. The method is based on biasing the sampling within the subdomains of the test-particle configurational space with energies smaller than a given value freely assigned. These energy-wells are located via unbiased random insertion over the whole configurational space and are sampled using the so called Hit&Run algorithm, which uniformly samples compact regions of any shape immersed in a space of arbitrary dimensions. Because the bias is defined in terms of the energy landscape it can be exactly corrected to obtain the unbiased distribution. The test-particle energy distribution is then combined with the Bennett relation for the evaluation of the chemical potential. We apply this protocol to a system with relatively small probability of low-energy test-particle insertion, liquid argon at high density and low temperature, and show that the energy-biased Bennett method is around five times more efficient than the standard Bennett method. A similar performance gain is observed in the reconstruction of the energy distribution.

physics.chem-ph↗

arXiv2003

On size and growth of business firms

We study size and growth distributions of products and business firms in the context of a given industry. Firm size growth is analyzed in terms of two basic mechanisms, i.e. the increase of the number of new elementary business units and their size growth. We find a power-law relationship between size and the variance of growth rates for both firms and products, with an exponent between -0.17 and -0.15, with a remarkable stability upon aggregation. We then introduce a simple and general model of proportional growth for both the number of firm independent constituent units and their size, which conveys a good representation of the empirical evidences. This general and plausible generative process can account for the observed scaling in a wide variety of economic and industrial systems. Our findings contribute to shed light on the mechanisms that sustain economic growth in terms of the relationships between the size of economic entities and the number and size distribution of their elementary components.

cond-mat↗

arXiv2003

Dynamical geometry for multiscale dissipative particle dynamics

In this paper, we review the computational aspects of a multiscale dissipative particle dynamics model for complex fluid simulations based on the feature-rich geometry of the Voronoi tessellation. The geometrical features of the model are critical since the mesh is directly connected to the physics by the interpretation of the Voronoi volumes of the tessellation as coarse-grained fluid clusters. The Voronoi tessellation is maintained dynamically in time to model the fluid in the Lagrangian frame of reference, including imposition of periodic boundary conditions. Several algorithms to construct and maintain the periodic Voronoi tessellations are reviewed in two and three spatial dimensions and their parallel performance discussed. The insertion of polymers and colloidal particles in the fluctuating hydrodynamic solvent is described using surface boundaries.

cond-mat.soft↗