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

Finite-range effects in dilute Fermi gases at unitarity

We develop a theoretical method going beyond the contact-interaction approximation frequently used in mean-field theories of many-fermion systems, based on the low-energy T-matrix of the pair potential to rigorously define the effective radius of the interaction. One of the main consequences of our approach is the possibility to investigate finite-density effects, which are outside the range of validity of approximations based on delta-like potentials. We apply our method to the calculation of density dependent properties of an ultracold gas of 6Li atoms at unitarity, whose two-body interaction potential is calculated using ab initio quantum chemistry methods. We find that density effects will be significant in ultracold gases with densities one order of magnitude higher than those attained in current experiments.Comment: 7 pages, 3 figures. v2: Corrected typos in the main text and in the reference

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

Heavy quark bound states in a quark-gluon plasma: dissociation and recombination

We present a comprehensive approach to the dynamics of heavy quarks in a quark gluon plasma, including the possibility of bound state formation and dissociation. In this exploratory paper, we restrict ourselves to the case of an Abelian plasma, but the extension of the techniques used to the non Abelian case is straightforward. A chain of well defined approximations leads eventually to a generalized Langevin equation, where the force and the noise terms are determined from a correlation function of the equilibrium plasma, and depend explicitly on the configuration of the heavy quarks. We solve the Langevin equation for various initial conditions, various numbers of heavy quark-antiquark pairs, and various temperatures of the plasma. Results of simulations illustrate various expected phenomena: dissociation of bound states as a result of combined effects of screening of the potential and collisions with the plasma constituent, formation of bound pairs (recombination) that occurs when enough heavy quarks are present in the system

Path-integral calculation of the third virial coefficient of quantum gases at low temperatures

We derive path-integral expressions for the second and third virial coefficients of monatomic quantum gases. Unlike previous work that considered only Boltzmann statistics, we include exchange effects (Bose-Einstein or Fermi-Dirac statistics). We use state-of-the-art pair and three-body potentials to calculate the third virial coefficient of 3He and 4He in the temperature range 2.6-24.5561 K. We obtain uncertainties smaller than those of the limited experimental data. Inclusion of exchange effects is necessary to obtain accurate results below about 7 K.Comment: The following article has been accepted by The Journal of Chemical Physics. After it is published, it will be found at http://jcp.aip.org/ Version 2 includes the corrections detailed in the Erratu

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

Thyroid ultrasonography reporting: consensus of Italian Thyroid Association (AIT), Italian Society of Endocrinology (SIE), Italian Society of Ultrasonography in Medicine and Biology (SIUMB) and Ultrasound Chapter of Italian Society of Medical Radiology (SIRM)

Thyroid ultrasonography (US) is the gold standard for thyroid imaging and its widespread use is due to an optimal spatial resolution for superficial anatomic structures, a low cost and the lack of health risks. Thyroid US is a pivotal tool for the diagnosis and follow-up of autoimmune thyroid diseases, for assessing nodule size and echostructure and defining the risk of malignancy in thyroid nodules. The main limitation of US is the poor reproducibility, due to the variable experience of the operators and the different performance and settings of the equipments. Aim of this consensus statement is to standardize the report of thyroid US through the definition of common minimum requirements and a correct terminology. US patterns of autoimmune thyroid diseases are defined. US signs of malignancy in thyroid nodules are classified and scored in each nodule. We also propose a simplified nodule risk stratification, based on the predictive value of each US sign, classified and scored according to the strength of association with malignancy, but also to the estimated reproducibility among different operators

Silk reinforced with graphene or carbon nanotubes spun by spiders

Here, we report the production of silk incorporating graphene and carbon nanotubes directly by spider spinning, after spraying spiders with the corresponding aqueous dispersions. We observe a significant increment of the mechanical properties with respect to the pristine silk, in terms of fracture strength, Young's and toughness moduli. We measure a fracture strength up to 5.4 GPa, a Young's modulus up to 47.8 GPa and a toughness modulus up to 2.1 GPa, or 1567 J/g, which, to the best of our knowledge, is the highest reported to date, even when compared to the current toughest knotted fibres. This approach could be extended to other animals and plants and could lead to a new class of bionic materials for ultimate applications