arXiv subjects

Sauro Succi

Publications and source records attributed to Sauro Succi.

210 records · Page 12Linked to original sources

arXiv2007

Multiscale modeling of biopolymer translocation through a nanopore

We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the solvent dynamics, explicitly taking into account the interactions of the molecule with the surrounding fluid. Both dynamical and statistical aspects of the translocation process were investigated, by simulating polymers of various initial configurations and lengths. For a representative molecule size, we explore the effects of important parameters that enter in the simulation, paying particular attention to the strength of the molecule-solvent coupling and of the external electric field which drives the translocation process. Finally, we explore the connection between the generic polymers modeled in the simulation and DNA, for which interesting recent experimental results are available.

physics.bio-ph↗

arXiv2007

Exploring DNA translocation through a nanopore via a multiscale Lattice-Boltzmann Molecular-Dynamics methodology

A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of various initial configurations and lengths we map the probability distibutions of the passage times of the DNA through the nanopore. A scaling law behavior for the most probable of these times with respect to length is derived, and shown to exhibit an exponent that is in a good agreement with the experimental findings. The essential features of the DNA dynamics as it passes through the pore are explored.

physics.bio-ph↗

arXiv2007

Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore

We present a multiscale approach to the modeling of polymer dynamics in the presence of a fluid solvent. The approach combines Langevin Molecular Dynamics (MD) techniques with a mesoscopic Lattice-Boltzmann (LB) method for the solvent dynamics. A unique feature of the present approach is that hydrodynamic interactions between the solute macromolecule and the aqueous solvent are handled explicitly, and yet in a computationally tractable way due to the dual particle-field nature of the LB solver. The suitability of the present LB-MD multiscale approach is demonstrated for the problem of polymer fast translocation through a nanopore. We also provide an interpretation of our results in the context of DNA translocation through a nanopore, a problem that has attracted much theoretical and experimental attention recently.

physics.bio-ph↗

arXiv2005

Solving the Fokker-Planck kinetic equation on a lattice

We propose a discrete lattice version of the Fokker-Planck kinetic equation along lines similar to the Lattice-Boltzmann scheme. Our work extends an earlier one-dimensional formulation to arbitrary spatial dimension $D$. A generalized Hermite-Gauss procedure is used to construct a discretized kinetic equation and a Chapman-Enskog expansion is applied to adapt the scheme so as to correctly reproduce the macroscopic continuum equations. The stability of the algorithm with respect to the finite time-step $Δt$ is characterized by the eigenvalues of the collision matrix. A heuristic second-order algorithm in $Δt$ is applied to investigate the time evolution of the distribution function of simple model systems, and compared to known analytical solutions. Preliminary investigations of sedimenting Brownian particles subjected to an orthogonal centrifugal force illustrate the numerical efficiency of the Lattice-Fokker-Planck algorithm to simulate non-trivial situations. Interactions between Brownian particles may be accounted for by adding a standard BGK collision operator to the discretized Fokker-Planck kernel.

cond-mat.stat-mech↗

arXiv2005

A note on the lattice Boltzmann method beyond the Chapman Enskog limits

A non-perturbative analysis of the Bhatnagar-Gross-Krook (BGK) model kinetic equation for finite values of the Knudsen number is presented. This analysis indicates why discrete kinetic versions of the BGK equation, and notably the Lattice Boltzmann method, can provide semi-quantitative results also in the non-hydrodynamic, finite-Knudsen regime, up to $Kn\sim {\cal O}(1)$. This may help the interpretation of recent Lattice Boltzmann simulations of microflows, which show satisfactory agreement with continuum kinetic theory in the moderate-Knudsen regime.

cond-mat.stat-mech↗

arXiv2004

Lattice Boltzmann method at finite-Knudsen numbers

A modified lattice Boltzmann model with a stochastic relaxation mechanism mimicking "virtual'' collisions between free-streaming particles and solid walls is introduced. This modified scheme permits to compute plane channel flows in satisfactory agreement with analytical results over a broad spectrum of Knudsen numbers, ranging from the hydrodynamic regime, all the way to quasi-free flow regimes up to Kn 30.

nlin.CD↗

arXiv2004

Analytical calculation of slip flow in lattice Boltzmann models with kinetic boundary conditions

We present a mathematical formulation of kinetic boundary conditions for Lattice Boltzmann schemes in terms of reflection, slip, and accommodation coefficients. It is analytically and numerically shown that, in the presence of a non-zero slip coefficient, the Lattice Boltzmann flow develops a physical slip flow component at the wall. Moreover, it is shown that the slip coefficient can be tuned in such a way to recover quantitative agreement with analytical and experimental results up to second order in the Knudsen number.

nlin.CG↗

arXiv2004

Kinetic Theory of Turbulence Modeling: Smallness Parameter, Scaling and Microscopic Derivation of Smagorinsky Model

A mean-field approach (filtering out subgrid scales) is applied to the Boltzmann equation in order to derive a subgrid turbulence model based on kinetic theory. It is demonstrated that the only Smagorinsky type model which survives in the hydrodynamic limit on the viscosity time scale is the so-called tensor-diffusivity model. Scaling of the filter-width with Reynolds number and Knudsen number is established. This sets the first rigorous step in deriving turbulence models from kinetic theory.

cond-mat.stat-mech↗

arXiv2002

Galilean-Invariant Lattice-Boltzmann Models with H-Theorem

We demonstrate that the requirement of galilean invariance determines the choice of H function for a wide class of entropic lattice Boltzmann models for the incompressible Navier-Stokes equations. The required H function has the form of the Burg entropy for D=2, and of a Tsallis entropy with q=1-2/D for D>2, where D is the number of spatial dimensions. We use this observation to construct a fully explicit, unconditionally stable, galilean invariant, lattice-Boltzmann model for the incompressible Navier-Stokes equations, for which attainable Reynolds number is limited only by grid resolution.

cond-mat.stat-mech↗

arXiv2002

Role of the H theorem in lattice Boltzmann hydrodynamic simulations

In the last decade, minimal kinetic models, and primarily the Lattice Boltmann equation, have met with significant success in the simulation of complex hydrodynamic phenomena, ranging from slow flows in grossly irregular geometries to fully developed turbulence, to flows with dynamic phase transitions. Besides their practical value as efficient computational tools for the dynamics complex systems, these minimal models may also represent a new conceptual paradigm in modern computational statistical mechanics: instead of proceeding bottom-up from the underlying microdynamic systems, these minimal kinetic models are built top-down starting from the macroscopic target equations. This procedure can provide dramatic advantages, provided the essential physics is not lost along the way. For dissipative systems, one such essential requirement is the compliance with the Second Law of thermodynamics. In this Colloquium, we present a chronological survey of the main ideas behind the Lattice Boltzmann method, with special focus on the role played by the $H$ theorem in enforcing compliance of the method with macroscopic evolutionary constraints (Second Law) as well as in serving as a numerically stable computational tool for fluid flows and other dissipative systems out of equilibrium.

cond-mat.stat-mech↗

arXiv1996

Turbulent channel flow simulations using a coarse-grained extension of the Lattice Boltzmann method

A coarse-grained version of the Lattice Boltzmann (LB) method is developed with the intent of enhancing its geometrical flexibility so as to be able to tackle a wider class of flows of engineering interest. To this purpose, the original uniform LB technique is combined with standard finite-volume techniques based upon a blend of piecewise constant and piecewise linear interpolation schemes. A series of validation tests for the three dimensional channel flow with one-dimensional (cross-channel) statistical behaviour are presented. The main conclusion is that, although the method does indeed mark a significant stride forward with respect to the original uniform LB scheme, better interpolation schemes should be developed before the coarse-grain LB can become fully competitive with modern CFD schemes.

comp-gas↗

arXiv1996

Lattice Boltzmann Equation: Failure or Success?

The lattice Boltzmann equation (LBE) is a microscopically-inspired method designed to solve macroscopic fluid dynamics problems. As a such, it lives at the interface between the microscopic (molecular) and macroscopic (continuum) worlds, hopefully capturing the best of the two. In this paper we shall discuss whether or not, after almost a decade since its inception, LBE has lived up to the initial expectations. Open problems and future research developments are also briefly outlined.

comp-gas↗