arXiv subjects

V. Minicozzi

Publications and source records attributed to V. Minicozzi.

3 recordsLinked to original sources

arXiv2018

EuPRAXIA@SPARC_LAB Design study towards a compact FEL facility at LNF

On the wake of the results obtained so far at the SPARC\_LAB test-facility at the Laboratori Nazionali di Frascati (Italy), we are currently investigating the possibility to design and build a new multi-disciplinary user-facility, equipped with a soft X-ray Free Electron Laser (FEL) driven by a $\sim$1 GeV high brightness linac based on plasma accelerator modules. This design study is performed in synergy with the EuPRAXIA design study. In this paper we report about the recent progresses in the on going design study of the new facility.

physics.acc-ph↗

arXiv2001

A simple atomistic model for the simulation of the gel phase of lipid bilayers

In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive Molecular Dynamics simulations, in the (NVE) micro-canonical ensemble, of two systems of different sizes (2x32 and 2x256 molecules), over a fairly large set of temperatures and densities, using parallel platforms and more standard serial computers. Depending on the dimension of the system, the dynamics was followed for physical times that go from few hundred of picoseconds for the largest system to 5--10 nanoseconds for the smallest one. We find that the bilayer remains stable even in the absence of water and neglecting Coulomb interactions in the whole range of temperatures and densities we have investigated. The extension of the region of physical parameters that we have explored has allowed us to study significant points in the phase diagram of the bilayer and to expose marked structural changes as density and temperature are varied, which are interpreted as the system passing from a crystal to a gel phase.

physics.bio-ph↗

arXiv1997

Parallel computing and molecular dynamics of biological membranes

In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on the possible programming strategies. Liquids can be very satisfactorily simulated using the "systolic" method. For more complex systems, like the biological ones at which we are ultimately interested in, the "domain decomposition" approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of elementary components of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed.

physics.bio-ph↗