Manuela Minozzi | Link Campus University (original) (raw)

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Papers by Manuela Minozzi

Philosophical Magazine, 2020

Trehalose aqueous solutions are relevant in many technological applications, for example in cryop... more Trehalose aqueous solutions are relevant in many technological applications, for example in cryopreservation of biomolecules. It is known that the presence of this disaccharide is able to slow down the dynamics of nearby water molecules and to modify their spatial rearrangement, nevertheless, a complete understanding of the properties of water-trehalose solutions and of trehalose cryoprotective properties is still lacking. Here we discuss recent molecular dynamics simulation results of water-trehalose solutions, performed at different temperatures upon cooling, and we compare the results with the behavior of the bulk phase. In particular we focus on the dynamical properties of hydration water, i.e., the water molecules in the hydration shell of the disaccharide. Hydration water shows a sub-diffusive behavior with respect to bulk water, the same structural relaxation typical of glass formers liquids, albeit slightly slower than in the bulk, and an additional relaxation process at lon...

Theoretical Chemistry Accounts, 2007

Classical molecular dynamics (MD) and non-equilibrium steered molecular dynamics (SMD) simulation... more Classical molecular dynamics (MD) and non-equilibrium steered molecular dynamics (SMD) simulations were performed on the molecular structure of the potassium channel KcsA using the GROMOS 87 force fields. Our simulations focused on mechanistic and dynamic properties of the permeation of potassium ions through the selectivity filter of the channel. According to the SMD simulations a concerted movement of ions inside the selectivity filter from the cavity to extracellular side depends on the conformation of the peptide linkage between Val76 and Gly77 residues in one subunit of the channel. In SMD simulations, if the carbonyl oxygen of Val76 is positioned toward the ion bound at the S3 site (gate-opened conformation) the net flux of ions through the filter is observed. When the carbonyl oxygen leaped out from the filter (gate-closed conformation), ions were blocked at the S3 site and no flux occurred. A reorientation of the Thr75-Val76 linkage indicated by the CHARMM-based MD simulations per

The Journal of Physical Chemistry B, 2012

Predicting the permeability coefficient (P) of drugs permeating through the cell membrane is of p... more Predicting the permeability coefficient (P) of drugs permeating through the cell membrane is of paramount importance in drug discovery. We here propose an approach for calculating P based on bias-exchange metadynamics. The approach allows constructing from atomistic simulations a model of permeation taking explicitly into account not only the "trivial" reaction coordinate, the position of the drug along the direction normal to the lipid membrane plane, but also other degrees of freedom, for example, the torsional angles of the permeating molecule, or variables describing its solvation/ desolvation. This allows deriving an accurate picture of the permeation process, and constructing a detailed molecular model of the transition state, making a rational control of permeation properties possible. We benchmarked this approach on the permeation of ethanol molecules through a POPC membrane, showing that the value of P calculated with our model agrees with the one calculated by a long unbiased molecular dynamics of the same system.

Physical Review E, 2007

We develop a series of molecular dynamics computer simulations of liquid water, performed with a ... more We develop a series of molecular dynamics computer simulations of liquid water, performed with a polarizable potential model, to calculate the spinodal line and the curve of maximum density inside the metastable supercooled region. After analysing the structural properties, the liquid spinodal line is followed down to T = 210 K. A monotonic decrease is found in the explored region. The curve of maximum density bends on approaching the spinodal line. These results, in agreement with similar studies on non polarizable models of water, are consistent with the existence of a second critical point for water.

Journal of Molecular Liquids, 2006

The behaviour of supercooled water in an extended region of the phase diagram, from ambient condi... more The behaviour of supercooled water in an extended region of the phase diagram, from ambient conditions to negative pressure and low temperatures, is studied by computer simulation employing a polarizable water potential. The structural analysis of the system shows that the polarizable potential chosen well reproduces the water properties even in extreme conditions and allows us to perform a more

$Research paper thumbnail of Dynamic fracture model for acoustic emission$

The European Physical Journal B - Condensed Matter, 2003

PLoS ONE, 2011

Bacteria express beta-lactamases to counteract the beneficial action of antibiotics. Benzo[b]-thi... more Bacteria express beta-lactamases to counteract the beneficial action of antibiotics. Benzo[b]-thiophene-2-boronic acid (BZB) derivatives are b-lactamase inhibitors and, as such, promising compounds to be associated with b-lactam antibacterial therapies. The uncharged form of BZB, in particular, is suggested to diffuse through the outer membrane of Gram negative bacteria. In this study, through the combination of electrophysiological experiments across reconstituted PC/n-decane bilayers and metadynamics-based free energy calculations, we investigate the permeation mechanism of boronic compounds. Our experimental data establish that BZB passes through the membrane, while computer simulations provide hints for the existence of an aqueous, water-filled monomolecular channel. These findings provide new perspectives for the design of boronic acid derivatives with high membrane permeability.

We studied the time evolution problem driven by growth for a non-Euclidean ball which at its init... more We studied the time evolution problem driven by growth for a non-Euclidean ball which at its initial state is equipped with a non-compatible distortion field. The problem is set within the framework of non-linear elasticity with large growing distortions. No bulk accretive forces are considered, and growth is only driven by the stress state. We showed that, when stress-driven growth is considered, distortions can evolve along different trajectories which share a common attracting manifold; moreover, they eventually attain a steady and compatible form, to which there corresponds a stress-free state of the ball.