Massimo Marchi

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This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for(More)
In this communication, we provide theoretical evidence that the folded structure of a simple peptide, alanine zwitterionic octapeptide, or A8, unstable in solution, becomes stable in a reverse micelle (RM) of appropriate size. Our molecular dynamics simulations were carried out for realistic models of sodium 2-ethylhexylsulfosuccinate RM in isooctane,(More)
We describe a modified grid architecture that allows the specification and enforcement connection policies to grid on Web Services. This is accomplished by interposing a policy enforcement engine between a calling application and the relative client stubs. Only service requests need be analyzed and filtered. Connection policies are conveniently expressed in(More)
This paper is concerned with the dynamics of water around a small globular protein. Dipolar second-rank relaxation time and diffusion properties of surface water were computed by extensive molecular dynamics simulations of lysozyme in water which lasted a total of 28 ns. Our results indicate that the rotational relaxation of water in the vicinity of(More)
This paper presents some preliminary results obtained in the development of a new branch-and-bound algorithm for Answer Set Programming. We exploit the intrinsic parallelism of branch-and-bound to distribute the computation among agents that cooperate to find an answer set for the problem instance at hand. The effectiveness of our solution in extracting(More)
This paper reports on molecular dynamics simulations of two hydrated micelles composed of C12E6 and LDAO surfactants. The simulations results provide a quantitative picture of the dynamics of the hydration water at the water/micelle interface. Both the residence time of water near the micelle surface and its retardation with respect to the bulk have been(More)
This paper deals with the development and validation of new potential parameter sets, based on the CHARMM36 and GLYCAM06 force fields, to simulate micelles of the two anomeric forms (α and β) of N-dodecyl-β-maltoside (C(12)G(2)), a surfactant widely used in the extraction and purification of membrane proteins. In this context, properties such as size,(More)
To assess the feasibility of high-pressure simulation of biomolecular systems, we discuss some practical aspects of molecular dynamics simulation techniques at constant pressure and temperature. We compare the extended Lagrangian (EL) method, initially developed by Andersen1 for sampling from well-defined statistical mechanical ensembles, with the method by(More)
Water around biomolecules slows down with respect to pure water, and both rotation and translation exhibit anomalous time dependence in the hydration shell. The origin of such behavior remains elusive. We use molecular dynamics simulations of water dynamics around several designed protein models to establish the connection between the appearance of the(More)
We present the first comparative molecular dynamics investigation for a dodecylphosphocholine (DPC) micelle performed in condensed phase using the CHARMM36, GROMOS53A6, GROMOS54A7, and GROMOS53A6/Berger force fields and a set of parameters developed anew. Our potential consists of newly derived RESP atomic charges, which are associated with the Amber99SB(More)