Sauro Succi

MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations

We present a parallel version of MUPHY, a multi-physics/scale code based upon the combination of microscopic Molecular Dynamics (MD) with a hydro-kinetic Lattice Boltzmann (LB) method. The features of the parallel version of MUPHY are hereby demonstrated for the case of translocation of biopolymers through nanometer-sized, multi-pore configurations, taking into explicit account the hydrodynamic interactions of the translocating molecules with the surrounding fluid. The parallel implementation exhibits excellent scalability on the IBM BlueGene platform and includes techniques which may improve the flexibility and efficiency of other complex multi-physics parallel applications, such as hemodynamics, targeted-drug delivery and others.

Hydrodynamic correlations in the translocation of a biopolymer through a nanopore : Theory and multiscale simulations

We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that the coupling of the correlated molecular motion to hydrodynamics results in significant acceleration of the translocation process. Based on these results, we construct a phenomenological model which incorporates the statistical and dynamical features of the translocation process and predicts a power-law dependence of the translocation time on the polymer length with an exponent alpha approximately 1.2. The actual value of the exponent from the simulations is alpha=1.28+/-0.01, which is in excellent agreement with experimental measurements of DNA translocation through a nanopore, and is not sensitive to the choice of parameters in the simulation. The mechanism behind the emergence of such a robust exponent is related to the interplay between the longitudinal and transversal dynamics of both translocated and untranslocated segments. The connection to the macroscopic picture involves separating the contributions from the blob shrinking and shifting processes, which are both essential to the translocation dynamics.

Lattice Boltzmann 2038

Based on the past twenty-five years of lattice Boltzmann research, we venture into a far-flung prediction for the next twenty-five, with past and future privileged over the present state of affairs.

Prediction of coronary artery plaque progression and potential rupture from 320-detector row prospectively ECG-gated single heart beat CT angiography: Lattice Boltzmann evaluation of endothelial shear stress

Advances in MDCT will extend coronary CTA beyond the morphology data provided by systems that use 64 or fewer detector rows. Newer coronary CTA technology such as prospective ECG-gating will also enable lower dose examinations. Since the current standard of care for coronary diagnoses is catheterization, CT will continue to be benchmarked against catheterization reference points, in particular temporal resolution, spatial resolution, radiation dose, and volume coverage. This article focuses on single heart beat cardiac acquisitions enabled by 320-detector row CT. Imaging with this system can now be performed with patient radiation doses comparable to catheterization. The high image quality, excellent contrast opacification, and absence of stair-step artifact provide the potential to evaluate endothelial shear stress (ESS) noninvasively with CT. Low ESS is known to lead to the development and progression of atherosclerotic plaque culminating in high-risk vulnerable plaque likely to rupture and cause an acute coronary event. The magnitude of local low ESS, in combination with the local remodeling response and the severity of systemic risk factors, determines the natural history of each plaque. This paper describes the steps required to derive an ESS map from 320-detector row CT data using the Lattice Boltzmann method to include the complex geometry of the coronary arterial tree. This approach diminishes the limitations of other computational fluid dynamics methods to properly evaluate multiple coronary arteries, including the complex geometry of coronary bifurcations where lesions tend to develop.

Hydrokinetic approach to large-scale cardiovascular blood flow

We present a computational method for commodity hardware-based clinical cardiovascular diagnosis based on accurate simulation of cardiovascular blood flow. Our approach leverages the flexibility of the Lattice Boltzmann method to implementation on high-performance, commodity hardware, such as Graphical Processing Units. We developed the procedure for the analysis of real-life cardiovascular blood flow case studies, namely, anatomic data acquisition, geometry and mesh generation, flow simulation and data analysis and visualization. We demonstrate the usefulness of our computational tool through a set of large-scale simulations of the flow patterns associated with the arterial tree of a patient which involves two hundred million computational cells. The simulations show evidence of a very rich and heterogeneous endothelial shear stress pattern (ESS), a quantity of recognized key relevance to the localization and progression of major cardiovascular diseases, such as atherosclerosis, and set the stage for future studies involving pulsatile flows.

Mapping reactive flow patterns in monolithic nanoporous catalysts

Abstract The development of high-efficiency porous catalyst membranes critically depends on our understanding of where the majority of the chemical conversions occur within the porous structure. This requires mapping of chemical reactions and mass transport inside the complex nanoscale architecture of porous catalyst membranes which is a multiscale problem in both the temporal and spatial domains. To address this problem, we developed a multiscale mass transport computational framework based on the lattice Boltzmann method that allows us to account for catalytic reactions at the gas–solid interface by introducing a new boundary condition. In good agreement with experiments, the simulations reveal that most catalytic reactions occur near the gas-flow facing side of the catalyst membrane if chemical reactions are fast compared to mass transport within the porous catalyst membrane.

Multiscale Simulation of Cardiovascular flows on the IBM Bluegene/P: Full Heart-Circulation System at Red-Blood Cell Resolution

We present the first large-scale simulation of blood flow in the coronary artieries and other vessels supplying blood to the heart muscle, with a realistic description of human arterial geometry at spatial resolutions from centimeters down to 10 microns (near the size of red blood cells). This multiscale simulation resolves the fluid into a billion volume units, embedded in a bounding space of 300 billion voxels, coupled with the concurrent motion of 300 million red blood cells, which interact with one another and with the surrounding fluid. The level of detail is sufficient to describe phenomena of potential physiological and clinical significance, such as the development of atherosclerotic plaques. The simulation achieves excellent scalability on up to 294, 912 Blue Gene/P computational cores.

Effects of Knudsen diffusivity on the effective reactivity of nanoporous catalyst media

Abstract We investigate the non-equilibrium hydrodynamic effects on the reactivity of a nanoporous catalytic sample. Numerical simulations using the Lattice Boltzmann Method (LBM) show that non-equilibrium effects enhance the reactivity of the porous sample, in agreement with theoretical predictions [1] . In addition, we provide a quantitative assessment of the reactivity in terms of the thickness of the reactive layer inside the nanoporous catalytic sample. Such an assessment constitutes a first step towards integrated simulations encompassing nanoscale reactivity and transport coefficients within a macroscale description of experimental relevance.

Fluctuation correlations in reaction-diffusion systems: Reactive lattice gas automata approach

We model reaction-diffusion systems with reactive lattice gas automata, which possess intrinsic microscopic fluctuations. We show that, within the limits of linear theory, the commonly accepted Landau equation describes correctly the measured effects of the fluctuations, as evidenced by the density autocorrelation function. We suggest that the reactive lattice gas automata constitute a powerful method for investigating reaction-diffusion systems where intrinsic fluctuations play an important role.

Extended friction elucidates the breakdown of fast water transport in graphene oxide membranes

The understanding of water transport in graphene oxide (GO) membranes stands out as a major theoretical problem in graphene research. Notwithstanding the intense efforts devoted to the subject in the recent years, a consolidated picture of water transport in GO membranes is yet to emerge. By performing mesoscale simulations of water transport in ultrathin GO membranes, we show that even small amounts of oxygen functionalities can lead to a dramatic drop of the GO permeability, in line with experimental findings. The coexistence of bulk viscous dissipation and spatially extended molecular friction results in a major decrease of both slip and bulk flow, thereby suppressing the fast water transport regime observed in pristine graphene nanochannels. Inspection of the flow structure reveals an inverted curvature in the near-wall region, which connects smoothly with a parabolic profile in the bulk region. Such inverted curvature is a distinctive signature of the coexistence between single-particle Langevin friction and collective hydrodynamics. The present mesoscopic model with spatially extended friction may offer a computationally efficient tool for future simulations of water transport in nanomaterials.