Biomedical subjects

Davide Donadio

Publications and source records attributed to Davide Donadio.

4 recordsLinked to original sources

PubMed2007

Canonical sampling through velocity rescaling.

The authors present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. The authors illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent of the thermostat parameter also with regard to the dynamic properties.

Journal Article↗

PubMed2006

Freezing of a Lennard-Jones fluid: from nucleation to spinodal regime.

Using molecular dynamics, we investigate the crystal nucleation in a Lennard-Jones fluid as a function of the degree of supercooling. At moderate supercooling, a nucleation picture applies, while for deeper quenches, the phenomenon progressively acquires a spinodal character. We show that in the nucleation regime, the freezing is a two-step process. The formation of the critical nucleus is indeed preceded by the abrupt formation of a precritical crystallite from a density fluctuation in the fluid. In contrast, as the degree of supercooling is increased, crystallization proceeds in a more continuous and collective fashion and becomes more spatially diffuse, indicating that the liquid is unstable and crystallizes by a spinodal mechanism.

Journal Article↗

PubMed2006

Crystal structure transformations in SiO2 from classical and ab initio metadynamics.

Silica is the main component of the Earth's crust and is also of great relevance in many branches of materials science and technology. Its phase diagram is rather intricate and exhibits many different crystalline phases. The reported propensity to amorphization and the strong influence on the outcome of the initial structure and of the pressurization protocol indicate the presence of metastability and large kinetic barriers. As a consequence, theory is also faced with great difficulties and our understanding of the complex transformation mechanisms is still very sketchy despite a large number of simulations. Here, we introduce a substantial improvement of the metadynamics method, which finally brings simulations in close agreement with experiments. We unveil the subtle and non-intuitive stepwise mechanism of the pressure-induced transformation of fourfold-coordinated alpha-quartz into sixfold-coordinated stishovite at room temperature. We also predict that on compression fourfold-coordinated coesite will transform into the post-stishovite alpha-PbO2-type phase. The new method is far more efficient than previous methods, and for the first time the study of complex structural phase transitions with many intermediates is within the reach of molecular dynamics simulations. This insight will help in designing new experimental protocols capable of steering the system towards the desired transition.

Journal Article↗

PubMed2005

Topological defects and bulk melting of hexagonal ice.

We use classical molecular dynamics combined with the recently developed metadynamics method [Laio, A.; Parrinello, M. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 20] to study the process of bulk melting in hexagonal ice. Our simulations show that bulk melting is mediated by the formation of topological defects which preserve the coordination of the tetrahedral network. Such defects cluster to form a defective region involving about 50 molecules with a surprisingly long lifetime. The subsequent formation of coordination defects triggers the transition to the liquid state.

Ice↗