Concurrent Molecular Dynamics Simulation of ST2 Water on a Transputer Array

Abstract A concurrent implementation of a Molecular Dynamics program for ST2 water molecules is presented, which exploits the great potentialities of the Transputer arrays for statistical mechanical calculations. High load-balance efficiency is obtained using a new task decomposition algorithm which evenly distributes particles and interaction calculations among the processors. This approach can also help to solve efficiently the more general problem of task distribution in parallel computing of symmetric pairwise system properties.

One-dimensional hydrodynamic modeling of coronal plasmas on transputer arrays

Abstract We describe a concurrent implementation of the Palermo-Harvard hydrodynamic code on cost-effective and modularity expandable transputer arrays. We have tested the effectiveness of our approach by simulating an already well-studied compact solar-flare model on different transputer configurations and compared their performances with those of other machines. We have found that the speed of the concurrent program on a 16-T800 transputers array is ~1/9 of that of the equivalent code optimized for a CRAY X-MP/48. This work clearly shows that transputer-based arrays provide locally available high computing-power tools to extend the investigation of compact solar flares and similar astroph…

Influence of TFE on the proteins interactions of a lysozyme solution: a small angle X-ray scattering study

Protein diffusion in ovo

Protein diffusion, stability and activity in crowded media

Functional and dysfunctional isoforms of human neuroserpin

Neuroserpin (NS) is a serine protease inhibitor (SERPIN) involved in different neurological pathologies, including the Familial Encephalopathy with Neuroserpin Inclusion Bodies (FENIB), related to the aberrant polymerization of NS mutants. Here we present an in vitro and in silico characterization of native NS and its dysfunctional conformation isoforms: the proteolytically cleaved conformer, the inactive latent conformer, and the polymeric conformer. Using circular dichroism and fluorescence spectroscopy, we present an experimental validation of the latent model and highlight the main structural features of the different conformers. In par- ticular, emission spectra of aromatic residues yi…

Contributory presentations/posters

Interaction of explicit solvent with hydrophobic/philic/charged residues of a protein: Residue character vs. conformational context

Molecular dynamics simulations of model solutes in explicit molecular water have recently elicited novel aspects of the strong nonpair additivity of the potential of mean force (PMF) and related solvent-induced forces (SIFs) and hydration. Here we present the results of the same type of work on SIFs acting on bovine pancreatic trypsin inhibitor (BPTI) at single residue/sidechain resolution. In this system, nonpair additivity and the consequent dependence of SIFs on the protein conformational context are sufficiently strong to overturn SIFs on some individual residues, relative to expectations based on their individual characters. This finding calls for a revisitation and offers a richer and…