Exploring the Free Energy Landscape: From Dynamics to Networks and Back

The knowledge of the Free Energy Landscape topology is the essential key to understand many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers are, how the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times or rate constants, and the hierarchical relationship among basins, complete the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, the dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.Comment: PLoS Computational Biology (in press

Modified f(R) gravity from scalar-tensor theory and inhomogeneous EoS dark energy

The reconstruction of f(R)-gravity is showed by using an auxiliary scalar field in the context of cosmological evolution, this development provide a way of reconstruct the form of the function f (R) for a given evolution of the Hubble parameter. In analogy, f(R)-gravity may be expressed by a perfect fluid with an inhomogeneous equation of state that depends on the Hubble parameter and its derivatives. This mathematical equivalence that may confuse about the origin of the mechanism that produces the current acceleration, and possibly the whole evolution of the Hubble parameter, is shown here.Comment: 8 page

Synchronization In Networks Of Noisy Interneurons

this paper we present some of our preliminary results on a system of ten clusters each with ten interneurons. METHOD

Depolarization of Magnetically Confined Plasmas

In a tokamak plasma, reaching the critical energy balance for ignition, for which the gain factor Q =energy output/energy input= ∞, or even the Q ∼ 40 − 50 value needed for reactor operation, is a very challenging task—for example, a plasma 4 temperature of the order of hundreds of million degrees is needed, a value much higher than the core temperature of the sun. The help that can come from a fusion cross section enhancement due to the appropriate polarization of the reacting nuclei could be instrumental in achieving the goal. Two works carried out in the 80s have provided insight on the effective ability of a spin-polarized D–T thermonuclear plasma to preserve the polarization status of the fuel nuclei (Kulsrud et al., Phys Rev Lett, 49:1248, 1982, [1], and Coppi et al., Phys Rev Lett 51:892, 1983, [2]). The conclusions are both encouraging and cautious. While Kulsrud’s work shows that many of the potential mechanisms for depolarization are weak, Coppi’s work points out that the presence of energetic alpha particles, products of the D–T fusion reaction, could generate collective modes able to depolarize the fuel. In the present contribution, we review the arguments and the main results of the two above-mentioned papers, while contextualizing them to present-day tokamak devices. In particular, we consider plasma regimes characteristic of ITER and IGNITOR, two tokamaks under construction and in advanced state of design, respectively, and which represent different approaches to magnetic fusion research. The depolarization rates estimated for these two devices indicate that polarization may not be maintained long enough for fusion reactions to occur, unless ion cyclotron resonances provide an effective damping mechanism for the excited modes. Only a targeted experimental campaign could provide a final answer on the feasibility of polarized fusion in tokamaks

Prospects for direct in situ tests of polarization survival in a tokamak

The cross section for the primary fusion fuel in a tokamak reactor, D+T→α+n, would be increased by a factor of 1.5, if the fuels were spin polarized parallel to the local field. The potential realization of such benefits rests on the crucial question of the survival of spin polarization for periods comparable to the energy containment time. While calculations from the 1980s predicted that polarizations could in fact survive a plasma environment, concerns were raised regarding the impacts of wall recycling. In addition, the technical challenges in preparing and handling polarized materials had long prevented any direct tests. Over the last several decades, this situation has dramatically changed. Detailed simulations of the ITER plasma have projected negligible wall recycling in a high power reactor. In addition, a combination of advances in three areas—polarized material technologies developed for nuclear and particle physics as well as medical imaging, polymer pellets developed for Inertial Confinement, and cryogenic injection guns developed for fueling tokamaks—have matured to the point where a direct in situ measurement is possible, using the mirror reaction D+3He→α+p. Designs for a proof-of-principle exp ITER plasma have projected negligible wall recycling in a high power reactor. In addition, a combination of advances in three areas—polarized material technologies developed for nuclear and particle physics as well as medical imaging, polymer pellets developed for Inertial Confinement, and cryogenic injection guns developed for fueling tokamaks—have matured to the point where a direct in situ measurement is possible, using the mirror reaction D+3He→α+p. Designs for a proof-of-principle experiment at a research tokamak, such as the DIII-D facility in San Diego, are discussed