Quantum Diffusive Dynamics of Macromolecular Transitions

We study the role of quantum fluctuations of atomic nuclei in the real-time dynamics of non-equilibrium macro-molecular transitions. To this goal we introduce an extension of the Dominant Reaction Pathways (DRP) formalism, in which the quantum corrections to the classical overdamped Langevin dynamics are rigorously taken into account to order h^2 . We first illustrate our approach in simple cases, and compare with the results of the instanton theory. Then we apply our method to study the C7_eq to C7_ax transition of alanine dipeptide. We find that the inclusion of quantum fluctuations can significantly modify the reaction mechanism for peptides. For example, the energy difference which is overcome along the most probable pathway is reduced by as much as 50%.Comment: Final version, to appear in the Journal of Chemical Physic

Fluctuations in the Ensemble of Reaction Pathways

The dominant reaction pathway (DRP) is a rigorous framework to microscopically compute the most probable trajectories, in non-equilibrium transitions. In the low-temperature regime, such dominant pathways encode the information about the reaction mechanism and can be used to estimate non-equilibrium averages of arbitrary observables. On the other hand, at sufficiently high temperatures, the stochastic fluctuations around the dominant paths become important and have to be taken into account. In this work, we develop a technique to systematically include the effects of such stochastic fluctuations, to order k_B T. This method is used to compute the probability for a transition to take place through a specific reaction channel and to evaluate the reaction rate

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

Parameter free calculation of hadronic masses from instantons

We propose a non-perturbative calculation scheme which is based on the semi-classical approximation of QCD and can be used to evaluate quantities of interest in hadronic physics. As a first application, we evaluate the mass of the pion and of the nucleon. Such masses are related to a particular combination of Green functions which, in some limit, is dominated by the contribution of \emph{very small-sized} instantons. The size distribution of these pseudo-particles is determined by the 't Hooft tunneling amplitude formula and therefore our calculation is free from any model parameters. We prove that instanton forces generate a light pion and a nucleon with realistic mass ($M_n \sim 970 MeV$). In connection with sum-rules approaches, we discuss the overlap of instantons with pion and nucleon resonances

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

Heavy-quarks in the QGP: study of medium effects through euclidean propagators and spectral functions

The heavy-quark spectral function in a hot plasma is reconstructed from the corresponding euclidean propagator. The latter is evaluated through a path-integral simulation. A weak-coupling calculation is also performed, allowing to interpret the qualitative behavior of the spectral function in terms of quite general physical processes.Comment: 4 pages, 3 figures - To appear in the conference proceedings for Quark Matter 2009, March 30 - April 4, Knoxville, Tennesse

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

Protótipo de um lisímetro de pesagem automático para estudos em casa de vegetais.

O prototipo de lisimetro de pesagem automatico foi desenvolvido para medicoes do requerimento de aguas das culturas. O sistema e operado com o auxilio de apenas um computador, na forma de placa, e,e basicamente, feito de um conjunto de extensometros de precisao ("strain gages"), um regulador de voltagem, um conversor de sinal analogico para digital e um conjunto de amplificadores operacionais. Os extensometros transdutores foram colocados, com adesivo epoxy, sobre uma lamina de aluminio e conectados em um circuito de "ponte de wheatstone" para a medicao de variaveis, tais como peso. Um sistema de aquisicao automatica de dados foi criado. Os principais, esboco, montagem e funcionamento da instrumentacao estao descritos. O sistema foi calibrado atraves de carregamento e descarregamento de pesos padrao pre-selecionados na plataforma de pesagem e testado e avaliado em plantas de milho e feijoeiro que foram cultivadas em vasos, em condicoes de casa de vegetacao, na EMBRAPA-CNPMS. Um programa de computador foi desenvolvido para adquirir os dados dos sensores, permitindo os registros de local, data, horario e dados para posicoes especificas da memoria e orientando o usuario para a entrada dos intervalos de tempo. Uma linguagem residente BASIC, contida no microcomputador, foi utilizada na programacao