Ab-initio Dynamics of Rare Thermally Activated Reactions

We introduce a framework to investigate ab-initio the dynamics of rare thermally activated reactions. The electronic degrees of freedom are described at the quantum-mechanical level in the Born-Oppenheimer approximation, while the nuclear degrees of freedom are coupled to a thermal bath, through a Langevin equation. This method is based on the path integral representation for the stochastic dynamics and yields the time evolution of both nuclear and electronic degrees of freedom, along the most probable reaction pathways, without spending computational time to explore metastable states. This approach is very efficient and allows to study thermally activated reactions which cannot be simulated using ab-initio molecular dynamics techniques. As a first illustrative application, we characterize the dominant pathway in the cyclobutene to butadiene reaction.Comment: 4 pages, 4 figure

Investigating Biological Matter with Theoretical Nuclear Physics Methods

The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such systems, collective excitations, cooperative transitions and phase transitions emerge as the result of the interplay of strong correlations with quantum or thermal fluctuations. In view of such an observation, some theoretical methods initially developed in the context of theoretical nuclear physics have been adapted to investigate the dynamics of biomolecules. In this talk, we review some of our recent studies performed along this direction. In particular, we discuss how the path integral formulation of the molecular dynamics allows to overcome some of the long-standing problems and limitations which emerge when simulating the protein folding dynamics at the atomistic level of detail.Comment: Prepared for the proceedings of the "XII Meeting on the Problems of Theoretical Nuclear Physics" (Cortona11

Dominant Reaction Pathways in High Dimensional Systems

This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multi-dimensional systems obeying Langevin dynamics. We show how to obtain the set of most probable reaction pathways and compute the corrections due to quadratic thermal fluctuations around such trajectories. We discuss how to obtain predictions for the evolution of arbitrary observables and how to generate conformations which are representative of the transition state ensemble. We present an illustrative implementation of our method by studying the diffusion of a point particle in a 2-dimensional funneled external potential.Comment: 18 pages, 7 figures. Improvement in the text and in the figures. Version submitted for publicatio

Instanton Contribution to the Pion Electro-Magnetic Formfactor at Q^2 > 1 GeV^2

We study the effects of instantons on the charged pion electro-magnetic formfactor at intermediate momenta. In the Single Instanton Approximation (SIA), we predict the pion formfactor in the kinematic region Q^2=2-15 GeV^2. By developing the calculation in a mixed time-momentum representation, it is possible to maximally reduce the model dependence and to calculate the formfactor directly. We find the intriguing result that the SIA calculation coincides with the vector dominance monopole form, up to surprisingly high momentum transfer Q^2~10 GeV^2. This suggests that vector dominance for the pion holds beyond low energy nuclear physics.Comment: 8 pages, 5 figures, minor revision

Quantum Charge Transport and Conformational Dynamics of Macromolecules

We study the dynamics of quantum excitations inside macromolecules which can undergo conformational transitions. In the first part of the paper, we use the path integral formalism to rigorously derive a set of coupled equations of motion which simultaneously describe the molecular and quantum transport dynamics, and obey the fluctuation/dissipation relationship. We also introduce an algorithm which yields the most probable molecular and quantum transport pathways in rare, thermally-activated reactions. In the second part of the paper, we apply this formalism to simulate the propagation of a charge during the collapse of a polymer from an initial stretched conformation to a final globular state. We find that the charge dynamics is quenched when the chain reaches a molten globule state. Using random matrix theory we show that this transition is due to an increase of quantum localization driven by dynamical disorder.Comment: 11 pages, 2 figure

Quantitative Protein Dynamics from Dominant Folding Pathways

We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding problem are removed and simulating the entire reaction in atomistic details using existing computers becomes feasible. In addition, this formalism provides a natural framework to investigate the relationships between thermodynamical and kinetic aspects of the folding. For example, it is possible to show that, in order to have a large probability to remain unchanged under Langevin diffusion, the native state has to be characterized by a small conformational entropy. We discuss how to determine the most probable folding pathway, to identify configurations representative of the transition state and to compute the most probable transition time. We perform an illustrative application of these ideas, studying the conformational evolution of alanine di-peptide, within an all-atom model based on the empiric GROMOS96 force field.Comment: 4 pages, 1 figur

A Comment on "Semiquantum Chaos"

The identification of the particle creation and distruction operators is discussed.Comment: 4 pages (latex), 1 figure (postscript

Clonal variability of several grapevine cultivars (V. vinifera L.) grown in the Emilia-Romagna

Clonal selection has been performed over the past 2 decades by the University of Bologna to maintain the traditional grapevine cultivars grown in the Emilia-Romagna. Around 1980 budwood canes from several biotypes of the cvs Lambrusco di Sorbara, Lambrusco Salamino, Lambrusco Grasparossa, Lambrusco Maestri and Fortana were collected from old vineyards and used to establish a preliminary trial. The vines were tested for their virus status and compared for yield, grape quality, leaf characters and phenological phases in order to evaluate the biotype variability and clonal repeatability within each cultivar. L. Salamino, L. Grasparossa and L. Maestri showed very low degrees of genetic determination for yield and quality, while Fortana and L Sorbara exhibited quite high degrees. The results in both cases were independent on the virus status of the vines. While for cvs L. Salamino, L. Maestri and L. Grasparossa selection can be made only on the basis of virus status, good selection potentials were found with cvs L. Sorbara and Fortana. Fortana also exhibited marked differences in leaf morphology and phenological phases. Further investigations are needed to better characterize the diversity among biotypes of this variety, since the delimitation between cultivars and clones remains questionable