Do theoretical physicists care about the protein-folding problem?

The prediction of the biologically active native conformation of a protein is one of the fundamental challenges of structural biology. This problem remains yet unsolved mainly due to three factors: the partial knowledge of the effective free energy function that governs the folding process, the enormous size of the conformational space of a protein and, finally, the relatively small differences of energy between conformations, in particular, between the native one and the ones that make up the unfolded state. Herein, we recall the importance of taking into account, in a detailed manner, the many interactions involved in the protein folding problem (such as steric volume exclusion, Ramachandran forces, hydrogen bonds, weakly polar interactions, coulombic energy or hydrophobic attraction) and we propose a strategy to effectively construct a free energy function that, including the effects of the solvent, could be numerically tractable. It must be pointed out that, since the internal free energy function that is mainly described does not include the constraints of the native conformation, it could only help to reach the 'molten globule' state. We also discuss about the limits and the lacks from which suffer the simple models that we, physicists, love so much.Comment: 27 pages, 4 figures, LaTeX file, aipproc package. To be published in the book: "Meeting on Fundamental Physics 'Alberto Galindo'", Alvarez-Estrada R. F. et al. (Ed.), Madrid: Aula Documental, 200

JANUS: an FPGA-based System for High Performance Scientific Computing

This paper describes JANUS, a modular massively parallel and reconfigurable FPGA-based computing system. Each JANUS module has a computational core and a host. The computational core is a 4x4 array of FPGA-based processing elements with nearest-neighbor data links. Processors are also directly connected to an I/O node attached to the JANUS host, a conventional PC. JANUS is tailored for, but not limited to, the requirements of a class of hard scientific applications characterized by regular code structure, unconventional data manipulation instructions and not too large data-base size. We discuss the architecture of this configurable machine, and focus on its use on Monte Carlo simulations of statistical mechanics. On this class of application JANUS achieves impressive performances: in some cases one JANUS processing element outperfoms high-end PCs by a factor ~ 1000. We also discuss the role of JANUS on other classes of scientific applications.Comment: 11 pages, 6 figures. Improved version, largely rewritten, submitted to Computing in Science & Engineerin

Quantifying memory in spin glasses

10 pages, 8 figuresRejuvenation and memory, long considered the distinguishing features of spin glasses, have recently been proven to result from the growth of multiple length scales. This insight, enabled by simulations on the Janus~II supercomputer, has opened the door to a quantitative analysis. We combine numerical simulations with comparable experiments to introduce two coefficients that quantify memory. A third coefficient has been recently presented by Freedberg et al. We show that these coefficients are physically equivalent by studying their temperature and waiting-time dependence

Superposition principle and nonlinear response in spin glasses

International audienceThe extended principle of superposition has been a touchstone of spin-glass dynamics for almost 30 years. The Uppsala group has demonstrated its validity for the metallic spin glass, CuMn, for magnetic fields H up to 10 Oe at the reduced temperature Tr=T/Tg=0.95, where Tg is the spin-glass condensation temperature. For H>10 Oe, they observe a departure from linear response which they ascribe to the development of nonlinear dynamics. The thrust of this paper is to develop a microscopic origin for this behavior by focusing on the time development of the spin-glass correlation length, ξ(t,tw;H). Here, t is the time after H changes, and tw is the time from the quench for T>Tg to the working temperature T until H changes. We connect the growth of ξ(t,tw;H) to the barrier heights Δ(tw) that set the dynamics. The effect of H on the magnitude of Δ(tw) is responsible for affecting differently the two dynamical protocols associated with turning H off (TRM, or thermoremanent magnetization) or on (ZFC, or zero-field-cooled magnetization). This difference is a consequence of nonlinearity based on the effect of H on Δ(tw). Superposition is preserved if Δ(tw) is linear in the Hamming distance Hd (proportional to the difference between the self-overlap qEA and the overlap q[Δ(tw)]). However, superposition is violated if Δ(tw) increases faster than linear in Hd. We have previously shown, through experiment and simulation, that the barriers Δ(tw) do increase more rapidly than linearly with Hd through the observation that the growth of ξ(t,tw;H) slows down as ξ(t,tw;H) increases. In this paper, we display the difference between the zero-field-cooled ξZFC(t,tw;H) and the thermoremanent magnetization ξTRM(t,tw;H) correlation lengths as H increases, both experimentally and through numerical simulations, corresponding to the violation of the extended principle of superposition in line with the finding of the Uppsala Group