Constrained Molecular Dynamics II: a N-body approach to nuclear systems

In this work we illustrate the basic development of the constrained molecular dynamics applied to the N-body problem in nuclear physics. The heavy computational taskes related to quantum effects, to the presence of the "hard core" repulsive interaction have been worked out by defining a set of transformations based on the concept of impulsive forces. In particular in the implemented version II of the Constrained Molecular Dynamics model the problem related to the non conservation of the total angular momentum has been solved. This problem can affect others semiclassical microscopic approaches as due to the "hard core" repulsive interaction or to the use of stochastic forces. The effect of the restored conservation law on the fusion cross section for 40Ca+40Ca system is also briefly discussed.Comment: Tex version 3.1459 (Web2C 7.3.1);main text+fig.cap in .tex 13 page; +4 figures .ps;the order and the numerical label of the figure files reflect the figure numbers in the main tex and captions, Submited to Journal of computational physic

Microscopic approaches for nuclear Many-Body dynamics: applications to nuclear reactions

These lecture notes are addressed to PhD student and/or researchers who want a general overview of microscopic approaches based on mean-field and applied to nuclear dynamics. Our goal is to provide a good description of low energy heavy-ion collisions. We present both formal aspects and practical applications of the time-dependent Hartree-Fock (TDHF) theory. The TDHF approach gives a mean field dynamics of the system under the assumption that particles evolve independently in their self-consistent average field. As an example, we study the fusion of both spherical and deformed nuclei with TDHF. We also focus on nucleon transfer which may occur between nuclei below the barrier. These studies allow us to specify the range of applications of TDHF in one hand, and, on the other hand, its intrinsic limitations: absence of tunneling below the Coulomb barrier, missing dissipative effects and/or quantum fluctuations. Time-dependent mean-field theories should be improved to properly account for these effects. Several approaches, generically named "beyond TDHF" are presented which account for instance for pairing and/or direct nucleon-nucleon collisions. Finally we discuss recent progresses in exact ab-initio methods based on the stochastic mean-field concept.Comment: 55 pages. Lecture given at the "Joliot Curie" school, Maubuisson, september 17-22, 2007. A french version is available at http://www.cenbg.in2p3.fr/heberge/EcoleJoliotCurie/coursannee/cours/CoursSimenel.pd

Pseudorapidity shape of elliptic flow as signature for fast equilibration in relativistic heavy-ion collisions at energies up to sqrt(s) = 200 GeV

The implications of parton recombination processes on the dynamics of ultrarelativistic heavy-ion reactions are investigated. To do so, the quark-gluon string transport model has been extended for partonic recombination and fusion processes. Parton recombination leads to short equilibration times and improves significantly on the theoretical description of measured directed and elliptic flow, i.e., v_1 and v_2, distributions in Au+Au collisions at sqrt(s) = 200 GeV, in particular what concerns their pseudorapidity dependence. The shape of v_2(eta) is found to be closely related to fast thermalization.Comment: 7 pages (revtex4) with 4 figures, v3: substantially extended description and discussion of the model and its results, accepted for publication in Phys. Rev.

Reactive direction control for a mobile robot: A locust-like control of escape direction emerges when a bilateral pair of model locust visual neurons are integrated

Locusts possess a bilateral pair of uniquely identifiable visual neurons that respond vigorously to the image of an approaching object. These neurons are called the lobula giant movement detectors (LGMDs). The locust LGMDs have been extensively studied and this has lead to the development of an LGMD model for use as an artificial collision detector in robotic applications. To date, robots have been equipped with only a single, central artificial LGMD sensor, and this triggers a non-directional stop or rotation when a potentially colliding object is detected. Clearly, for a robot to behave autonomously, it must react differently to stimuli approaching from different directions. In this study, we implement a bilateral pair of LGMD models in Khepera robots equipped with normal and panoramic cameras. We integrate the responses of these LGMD models using methodologies inspired by research on escape direction control in cockroaches. Using ‘randomised winner-take-all’ or ‘steering wheel’ algorithms for LGMD model integration, the khepera robots could escape an approaching threat in real time and with a similar distribution of escape directions as real locusts. We also found that by optimising these algorithms, we could use them to integrate the left and right DCMD responses of real jumping locusts offline and reproduce the actual escape directions that the locusts took in a particular trial. Our results significantly advance the development of an artificial collision detection and evasion system based on the locust LGMD by allowing it reactive control over robot behaviour. The success of this approach may also indicate some important areas to be pursued in future biological research

A solvable model of Vlasov-kinetic plasma turbulence in Fourier-Hermite phase space

A class of simple kinetic systems is considered, described by the 1D Vlasov-Landau equation with Poisson or Boltzmann electrostatic response and an energy source. Assuming a stochastic electric field, a solvable model is constructed for the phase-space turbulence of the particle distribution. The model is a kinetic analog of the Kraichnan-Batchelor model of chaotic advection. The solution of the model is found in Fourier-Hermite space and shows that the free-energy flux from low to high Hermite moments is suppressed, with phase mixing cancelled on average by anti-phase-mixing (stochastic plasma echo). This implies that Landau damping is an ineffective route to dissipation (i.e., to thermalisation of electric energy via velocity space). The full Fourier-Hermite spectrum is derived. Its asymptotics are $m^{-3/2}$ at low wave numbers and high Hermite moments ($m$) and $m^{-1/2}k^{-2}$ at low Hermite moments and high wave numbers ($k$). These conclusions hold at wave numbers below a certain cut off (analog of Kolmogorov scale), which increases with the amplitude of the stochastic electric field and scales as inverse square of the collision rate. The energy distribution and flows in phase space are a simple and, therefore, useful example of competition between phase mixing and nonlinear dynamics in kinetic turbulence, reminiscent of more realistic but more complicated multi-dimensional systems that have not so far been amenable to complete analytical solution.Comment: 35 pages, minor edits, final version accepted by JP

Phase mixing vs. nonlinear advection in drift-kinetic plasma turbulence

A scaling theory of long-wavelength electrostatic turbulence in a magnetised, weakly collisional plasma (e.g., ITG turbulence) is proposed, with account taken both of the nonlinear advection of the perturbed particle distribution by fluctuating ExB flows and of its phase mixing, which is caused by the streaming of the particles along the mean magnetic field and, in a linear problem, would lead to Landau damping. It is found that it is possible to construct a consistent theory in which very little free energy leaks into high velocity moments of the distribution function, rendering the turbulent cascade in the energetically relevant part of the wave-number space essentially fluid-like. The velocity-space spectra of free energy expressed in terms of Hermite-moment orders are steep power laws and so the free-energy content of the phase space does not diverge at infinitesimal collisionality (while it does for a linear problem); collisional heating due to long-wavelength perturbations vanishes in this limit (also in contrast with the linear problem, in which it occurs at the finite rate equal to the Landau-damping rate). The ability of the free energy to stay in the low velocity moments of the distribution function is facilitated by the "anti-phase-mixing" effect, whose presence in the nonlinear system is due to the stochastic version of the plasma echo (the advecting velocity couples the phase-mixing and anti-phase-mixing perturbations). The partitioning of the wave-number space between the (energetically dominant) region where this is the case and the region where linear phase mixing wins its competition with nonlinear advection is governed by the "critical balance" between linear and nonlinear timescales (which for high Hermite moments splits into two thresholds, one demarcating the wave-number region where phase mixing predominates, the other where plasma echo does).Comment: 45 pages (single-column), 3 figures, replaced with version published in JP

An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics

The use of protein tagging to facilitate detailed characterization of target proteins has not only revolutionized cell biology, but also enabled biochemical analysis through efficient recovery of the protein complexes wherein the tagged proteins reside. The endogenous use of these tags for detailed protein characterization is widespread in lower organisms that allow for efficient homologous recombination. With the recent advances in genome engineering, tagging of endogenous proteins is now within reach for most experimental systems, including mammalian cell lines cultures. In this work, we describe the selection of peptides with ideal mass spectrometry characteristics for use in quantification of tagged proteins using targeted proteomics. We mined the proteome of the hyperthermophile Pyrococcus furiosus to obtain two peptides that are unique in the proteomes of all known model organisms (proteotypic) and allow sensitive quantification of target proteins in a complex background. By combining these 'Proteotypic peptides for Quantification by SRM' (PQS peptides) with epitope tags, we demonstrate their use in co-immunoprecipitation experiments upon transfection of protein pairs, or after introduction of these tags in the endogenous proteins through genome engineering. Endogenous protein tagging for absolute quantification provides a powerful extra dimension to protein analysis, allowing the detailed characterization of endogenous proteins