arXiv subjects

Simone Melchionna

Publications and source records attributed to Simone Melchionna.

At least 37 records · Page 2Linked to original sources

arXiv2011

Towards a mesoscopic model of water-like fluids with hydrodynamic interactions

We present a mesoscopic lattice model for non-ideal fluid flows with directional interactions, mimicking the effects of hydrogen-bonds in water. The model supports a rich and complex structural dynamics of the orientational order parameter, and exhibits the formation of disordered domains whose size and shape depend on the relative strength of directional order and thermal diffusivity. By letting the directional forces carry an inverse density dependence, the model is able to display a correlation between ordered domains and low density regions, reflecting the idea of water as a denser liquid in the disordered state than in the ordered one.

cond-mat.mes-hall↗

arXiv2011

A model for red blood cells in simulations of large-scale blood flows

Red blood cells (RBCs) are an essential component of blood. A method to include the particulate nature of blood is introduced here with the goal of studying circulation in large-scale realistic vessels. The method uses a combination of the Lattice Boltzmann method (LBM) to account for the plasma motion, and a modified Molecular Dynamics scheme for the cellular motion. Numerical results illustrate the quality of the model in reproducing known rheological properties of blood as much as revealing the effect of RBC structuring on the wall shear stress, with consequences on the development of cardiovascular diseases.

physics.med-ph↗

arXiv2011

Electro-osmotic flows under nanoconfinement: a self-consistent approach

We introduce a theoretical and numerical method to investigate the properties of electro-osmotic flows under conditions of extreme confinement. The present approach, aiming to provide a simple modeling of electrolyte solutions described as ternary mixtures, which comprises two ionic species and a third uncharged component, is an extension of our recent work on binary neutral mixtures. The approach, which combines elements of kinetic theory, density functional theory with Lattice-Boltzmann algorithms, is microscopic and self-consistent and does not require the us e of constitutive equations to determine the fluxes. Numerical solutions are obtained by solving the resulting coupled equations for the one-particle phase-space distributions of the species by means of a Lattice Boltzmann discretization procedure. Results are given for the microscopic density and velocity profiles and for the volumetric and charge flow.

cond-mat.mes-hall↗

arXiv2011

Multicomponent Diffusion in Nanosystems

We present the detailed analysis of the diffusive transport of spatially inhomogeneous fluid mixtures and the interplay between structural and dynamical properties varying on the atomic scale. The present treatment is based on different areas of liquid state theory, namely kinetic and density functional theory and their implementation as an effective numerical method via the Lattice Boltzmann approach. By combining the first two methods it is possible to obtain a closed set of kinetic equations for the singlet phase space distribution functions of each species. The interactions among particles are considered within a self-consistent approximation and the resulting effective molecular fields are analyzed. We focus on multispecies diffusion in systems with short-range hard-core repulsion between particles of unequal sizes and weak attractive long-range interactions. As a result, the attractive part of the potential does not contribute explicitly to viscosity but to diffusivity and the thermodynamic properties. Finally, we obtain a practical scheme to solve the kinetic equations by employing a discretization procedure derived from the Lattice Boltzmann approach. Within this framework, we present numerical data concerning the mutual diffusion properties both in the case of a quiescent bulk fluid and shear flow inducing Taylor dispersion.

cond-mat.mes-hall↗

arXiv2011

Dynamics of Fluid Mixtures in Nanospaces

A multicomponent extension of our recent theory of simple fluids [ U.M.B. Marconi and S. Melchionna, Journal of Chemical Physics, 131, 014105 (2009) ] is proposed to describe miscible and immiscible liquid mixtures under inhomogeneous, non steady conditions typical of confined fluid flows. We first derive from a microscopic level the evolution equations of the phase space distribution function of each component in terms of a set of self consistent fields, representing both body forces and viscous forces (forces dependent on the density distributions in the fluid and on the velocity distributions). Secondly, we solve numerically the resulting governing equations by means of the Lattice Boltzmann method whose implementation contains novel features with respect to existing approaches. Our model incorporates hydrodynamic flow, diffusion, surface tension, and the possibility for global and local viscosity variations. We validate our model by studying the bulk viscosity dependence of the mixture on concentration, packing fraction and size ratio. Finally we consider inhomogeneous systems and study the dynamics of mixtures in slits of molecular thickness and relate structural and flow properties.

cond-mat.stat-mech↗

arXiv2010

Dynamic density functional theory versus Kinetic theory of simple fluids

By combining methods of kinetic and density functional theory, we present a description of molecular fluids which accounts for their microscopic structure and thermodynamic properties as well as for the hydrodynamic behavior. We focus on the evolution of the one particle phase space distribution, rather than on the evolution of the average particle density, which features in dynamic density functional theory. The resulting equation can be studied in two different physical limits: diffusive dynamics, typical of colloidal fluids without hydrodynamic interaction, where particles are subject to overdamped motion resulting from the coupling with a solvent at rest, and inertial dynamics, typical of molecular fluids. Finally, we propose an algorithm to solve numerically and efficiently the resulting kinetic equation by employing a discretization procedure analogous to the one used in the Lattice Boltzmann method.

cond-mat.mes-hall↗

arXiv2009

Quantized biopolymer translocation through nanopores: departure from simple scaling

We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds through multi-folded configurations characterized by a well-defined integer number of folds. As a consequence, the translocation time acquires a dependence on the average folding number, which results in a deviation from the single-exponent power-law characterizing single-file translocation through narrow pores. The mechanism of folding quantization allows polymers above a threshold length (approximately $1,000$ persistence lengths for double-stranded DNA) to exhibit cooperative behavior and as a result to translocate noticeably faster.

physics.bio-ph↗

arXiv2009

A unified framework for dynamic density functional and Lattice Boltzmann methods

Using methods of kinetic theory and liquid state theory we propose a description of the non-equilibrium behavior of molecular fluids which takes into account their microscopic structure and thermodynamic properties. The present work represents an alternative to the recent dynamic density functional theory which can only deal with colloidal fluids and is not apt to describe the hydrodynamic behavior of a molecular fluid. The method is based on a suitable modification of the Boltzmann transport equation for the phase space distribution and provides a detailed description of the local structure of the fluid and of the transport coefficients under inhomogeneous conditions. Finally, we propose a practical scheme to solve numerically and efficiently the resulting kinetic equation by employing a discretization procedure analogous to the one used in the Lattice Boltzmann method.

cond-mat.stat-mech↗

arXiv2009

Numerical simulation of conformational variability in biopolymer translocation through wide nanopores

Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular motion to a mesoscopic fluid solvent. Thousands of events of long polymers (up to 8000 monomers) are monitored as they pass through nanopores. Comparison between the different pore sizes shows that wide pores can host a larger number of multiple biopolymer segments, as compared to smaller pores. The simulations provide clear evidence of folding quantization in the translocation process as the biopolymers undertake multi-folded configurations, characterized by a well-defined integer number of folds. Accordingly, the translocation time is no longer represented by a single-exponent power law dependence on the length, as it is the case for single-file translocation through narrow pores. The folding quantization increases with the biopolymer length, while the rate of translocated beads at each time step is linearly correlated to the number of resident beads in the pore. Finally, analysis of the statistics over the translocation work unravels the importance of the hydrodynamic interactions in the process.

physics.bio-ph↗

arXiv2008

Hydrodynamic correlations in the translocation of 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 $α$ $\approx 1.2$. The actual value of the exponent from the simulations is $α= 1.28 \pm 0.01$, 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.

physics.bio-ph↗

arXiv2008

Quantized current blockade and hydrodynamic correlations in biopolymer translocation through nanopores: evidence from multiscale simulations

We present a detailed description of biopolymer translocation through a nanopore in the presence of a solvent, using an innovative multi-scale methodology which treats the biopolymer at the microscopic scale as combined with a self-consistent mesoscopic description for the solvent fluid dynamics. We report evidence for quantized current blockade depending on the folding configuration and offer detailed information on the role of hydrodynamic correlations in speeding-up the translocation process.

physics.comp-ph↗

arXiv2007

Phase-space approach to dynamical density functional theory

We consider a system of interacting particles subjected to Langevin inertial dynamics and derive the governing time-dependent equation for the one-body density. We show that, after suitable truncations of the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy, and a multiple time scale analysis, we obtain a self-consistent equation involving only the one-body density. This study extends to arbitrary dimensions previous work on a one-dimensional fluid and highlights the subtelties of kinetic theory in the derivation of dynamical density functional theory.

cond-mat.stat-mech↗

arXiv2007

Parallel multiscale modeling of biopolymer dynamics with hydrodynamic correlations

We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic 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. We describe an efficient parallel implementation of the method which exhibits excellent scalability on the Blue Gene platform. We investigate both dynamical and statistical aspects of the translocation process 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.comp-ph↗

arXiv2007

Coupling Lattice Boltzmann with Atomistic Dynamics for the multiscale simulation of nano-biological flows

We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The multiscale approach is based on a simple scheme of exchange of space-time information between the atomistic and mesoscopic scales and is capable of describing self-consistent hydrodynamic effects on molecular motion at a computational cost which scales linearly with both solute size and solvent volume. For an application of our multiscale method, we consider the much studied problem of biopolymer translocation through nanopores: we find that the method reproduces with remarkable accuracy the statistical scaling behavior of the translocation process and provides valuable insight into the cooperative aspects of biopolymer and hydrodynamic motion.

physics.bio-ph↗

arXiv2007

Water confined in nanopores: spontaneous formation of microcavities

Molecular Dynamics simulations of water confined in nanometer sized, hydrophobic channels show that water forms localized cavities for pore diameter ~ 2.0 nm. The cavities present non-spherical shape and lay preferentially adjacent to the confining wall inducing a peculiar form to the liquid exposed surface. The regime of localized cavitation appears to be correlated with the formation of a vapor layer, as predicted by the Lum-Chandler-Weeks theory, implying partial filling of the pore.

cond-mat.soft↗

arXiv2007

Design of quasi-symplectic propagators for Langevin dynamics

A vector field splitting approach is discussed for the systematic derivation of numerical propagators for deterministic dynamics. Based on the formalism, a class of numerical integrators for Langevin dynamics are presented for single and multiple timestep algorithms.

physics.comp-ph↗

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↗