Biomedical subjects

Giovanni Bussi

Publications and source records attributed to Giovanni Bussi.

5 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.

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PubMed2006

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics.

We develop a new free-energy method, based on the combination of parallel tempering and metadynamics, and apply this method to the calculation of the free-energy landscape of the folding beta hairpin in explicit water. We show that the combined method greatly improves the performance of both parallel tempering and metadynamics. In particular, we are able to sample the high free-energy regions, which are not accessible with conventional parallel tempering. We use our results to calculate the difference in entropy and enthalpy between the folded and the unfolded state and to characterize the most populated configurations in the relevant free-energy basins.

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PubMed2006

Equilibrium free energies from nonequilibrium metadynamics.

In this Letter we propose a new formalism to map history-dependent metadynamics in a Markovian process. We apply this formalism to model Langevin dynamics and determine the equilibrium distribution of a collection of simulations. We demonstrate that the reconstructed free energy is an unbiased estimate of the underlying free energy and analytically derive an expression for the error. The present results can be applied to other history-dependent stochastic processes, such as Wang-Landau sampling.

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PubMed2004

Excitons in carbon nanotubes: an ab initio symmetry-based approach.

The optical absorption spectrum of the carbon (4,2) nanotube is computed using an ab initio many-body approach which takes into account excitonic effects. We develop a new method involving a local basis set which is symmetric with respect to the screw-symmetry of the tube. Such a method has the advantages of scaling faster than plane-wave methods and allowing for a precise determination of the symmetry character of the single-particle states, two-particle excitations, and selection rules. The binding energy of the lowest, optically active states is approximately 0.8 eV. The corresponding exciton wave functions are delocalized along the circumference of the tube and localized in the direction of the tube axis.

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PubMed2002

Solid state effects on exciton states and optical properties of PPV.

We perform ab initio calculations of optical properties for a typical semiconductor conjugated polymer, poly-para-phenylenevinylene, in both isolated chain and crystalline packing. In order to obtain results for excitonic energies and real-space wave functions we explicitly include electron-hole interaction within the density-matrix formalism. We find that the details of crystalline arrangement crucially affect the optical properties, leading to a richer exciton structure and opening nonradiative decay channels. This has implications for the optical activity and optoelectronic applications of polymer films.

Journal Article↗