Simone Melchionna

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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 their hydrodynamic behavior. We focus on the evolution of the one-particle phase space distribution, rather than on the evolution of the average particle density(More)
Heart disease is the number one killer in the United States, and finding indicators of the disease at an early stage is critical for treatment and prevention. In this paper we evaluate visualization techniques that enable the diagnosis of coronary artery disease. A key physical quantity of medical interest is endothelial shear stress (ESS). Low ESS has been(More)
1Istituto Applicazioni Calcolo, CNR, Viale Manzoni, 30-00185 Rome, Italy 2Nvidia Corporation, 2701 San Tomas Expressway, Santa Clara, CA 95050, U.S.A. 3SOFT, Istituto Nazionale Fisica della Materia, CNR, P.le A. Moro, 2-00185 Rome, Italy 4Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, U.S.A.(More)
A new multiscale approach for simulating nanobiological flows uses concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The approach is based on a simple scheme of space- time information exchange between the atomistic and mesoscopic scales.
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(More)
Two mesophilic/thermophilic variants of the G-domain of the elongation factor Tu were studied via molecular dynamics simulations. By analyzing the simulation data via the Voronoi space tessellation, we have found that the two proteins have the same macromolecular packing, while the water-exposed surface area is larger for the thermophile. A larger(More)
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(More)
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we(More)
We present a computational framework for multi-scale simulations of real-life biofluidic problems. The framework allows to simulate suspensions composed by hundreds of millions of bodies interacting with each other and with a surrounding fluid in complex geometries. We apply the methodology to the simulation of blood flow through the human coronary arteries(More)
The selectivity of micropores and ion channels is examined for simple pore topologies within the framework of density functional theory of highly confined fluids. In an infinite cylindrical pore purely steric (excluded volume) effects are shown to lead to strong, nontrivial size selectivity, which is highly sensitive to the pore radius. A crude modeling of(More)