Phase transition in the computational complexity of the shortest common superstring and genome assembly.

Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle formulation. That is, the computing time is believed to grow exponentially with the problem size in the worst case. Despite this fact, high-throughput technologies and modern algorithms currently allow bioinformaticians to handle datasets of billions of reads. Using methods from statistical mechanics, we address this conundrum by demonstrating the existence of a phase transition in the computational complexity of the problem and showing that practical instances always fall in the "easy" phase (solvable by polynomial-time algorithms). In addition, we propose a Markov-chain Monte Carlo method that outperforms common deterministic algorithms in the hard regime.

Scaling Law Describes the Spin-Glass Response in Theory, Experiments, and Simulations.

The correlation length ξ, a key quantity in glassy dynamics, can now be precisely measured for spin glasses both in experiments and in simulations. However, known analysis methods lead to discrepancies either for large external fields or close to the glass temperature. We solve this problem by introducing a scaling law that takes into account both the magnetic field and the time-dependent spin-glass correlation length. The scaling law is successfully tested against experimental measurements in a CuMn single crystal and against large-scale simulations on the Janus II dedicated computer.

Folding pathways to crumpling in thermalized elastic frames.

The mechanical properties of thermally excited two-dimensional crystalline membranes can depend dramatically on their geometry and topology. A particularly relevant example is the effect on the crumpling transition of holes in the membrane. Here we use molecular dynamics simulations to study the case of elastic frames (sheets with a single large hole in the center) and find that the system approaches the crumpled phase through a sequence of origami-like folds at decreasing length scales when temperature is increased. We use normal-normal correlation functions to quantify the temperature-dependent number of folds.

Aging Rate of Spin Glasses from Simulations Matches Experiments.

Experiments on spin glasses can now make precise measurements of the exponent z(T) governing the growth of glassy domains, while our computational capabilities allow us to make quantitative predictions for experimental scales. However, experimental and numerical values for z(T) have differed. We use new simulations on the Janus II computer to resolve this discrepancy, finding a time-dependent z(T,t_{w}), which leads to the experimental value through mild extrapolations. Furthermore, theoretical insight is gained by studying a crossover between the T=T_{c} and T=0 fixed points.

Matching Microscopic and Macroscopic Responses in Glasses.

We first reproduce on the Janus and Janus II computers a milestone experiment that measures the spin-glass coherence length through the lowering of free-energy barriers induced by the Zeeman effect. Secondly, we determine the scaling behavior that allows a quantitative analysis of a new experiment reported in the companion Letter [S. Guchhait and R. Orbach, Phys. Rev. Lett. 118, 157203 (2017)].PRLTAO0031-900710.1103/PhysRevLett.118.157203 The value of the coherence length estimated through the analysis of microscopic correlation functions turns out to be quantitatively consistent with its measurement through macroscopic response functions. Further, nonlinear susceptibilities, recently measured in glass-forming liquids, scale as powers of the same microscopic length.

Dynamical transition in the D=3 Edwards-Anderson spin glass in an external magnetic field.

We study the off-equilibrium dynamics of the three-dimensional Ising spin glass in the presence of an external magnetic field. We have performed simulations both at fixed temperature and with an annealing protocol. Thanks to the Janus special-purpose computer, based on field-programmable gate array (FPGAs), we have been able to reach times equivalent to 0.01 s in experiments. We have studied the system relaxation both for high and for low temperatures, clearly identifying a dynamical transition point. This dynamical temperature is strictly positive and depends on the external applied magnetic field. We discuss different possibilities for the underlying physics, which include a thermodynamical spin-glass transition, a mode-coupling crossover, or an interpretation reminiscent of the random first-order picture of structural glasses.

Static versus dynamic heterogeneities in the D = 3 Edwards-Anderson-Ising spin glass.

We numerically study the aging properties of the dynamical heterogeneities in the Ising spin glass. We find that a phase transition takes place during the aging process. Statics-dynamics correspondence implies that systems of finite size in equilibrium have static heterogeneities that obey finite-size scaling, thus signaling an analogous phase transition in the thermodynamical limit. We compute the critical exponents and the transition point in the equilibrium setting, and use them to show that aging in dynamic heterogeneities can be described by a finite-time scaling ansatz, with potential implications for experimental work.

Cluster Monte Carlo algorithm with a conserved order parameter.

We propose a cluster simulation algorithm for statistical ensembles with fixed order parameter. We use the tethered ensemble, which features Helmholtz's effective potential rather than Gibbs's free energy and in which canonical averages are recovered with arbitrary accuracy. For the D=2,3 Ising model our method's critical slowing down is comparable to that of canonical cluster algorithms. Yet, we can do more than merely reproduce canonical values. As an example, we obtain a competitive value for the 3D Ising anomalous dimension from the maxima of the effective potential.

Nonequilibrium spin-glass dynamics from picoseconds to a tenth of a second.

We study numerically the nonequilibrium dynamics of the Ising spin glass, for a time spanning 11 orders of magnitude, thus approaching the experimentally relevant scale (i.e., seconds). We introduce novel analysis techniques to compute the coherence length in a model-independent way. We present strong evidence for a replicon correlator and for overlap equivalence. The emerging picture is compatible with noncoarsening behavior.

[Anatomical basis of sleep]. / Bases anatómicas del sueño.

Sleep is an active and periodic biological state composed of NREM and REM phases, which alternate during the night. Both biological clocks and specific neurotransmitters are involved in the modulation of this system. It is a complex neuronal network in which several areas of the central nervous system are involved. The oneiric processes are also controlled neurally. This work summarises the history of the investigations on this topic from the 19th century to date. It is worth mentioning the recent findings of Lugaresi and colleages who described fatal familial insomnia, a disease that helped to show the importance of the mediodorsal thalamic nucleus in the genesis of slow-wave sleep. Reinoso s group found out that the paramedian ventral area of the oral pontine reticular nucleus is the conductor in the establishment of REM sleep.

Bases anatómicas del sueño / Anatomical basis of sleep

El sueño es un estado biológico activo, periódico, en el que se distinguen las etapas NREM y REM, que se alternan sucesivamente durante la noche. Intervienen los relojes biológicos en la modulación del sistema, así como neurotransmisores específicos. Se trata de una red neuronal compleja, en la que intervienen diversas zonas del sistema nervioso central. Los procesos oníricos están controlados además de forma neural. Se resume la historia de las investigaciones sobre el tema, desde el siglo XIX hasta nuestra época. Hay que destacar los recientes descubrimientos de Lugaresi y su equipo, que, al describir el insomnio familiar grave, dieron importancia al núcleo dorsomedial del tálamo en la instauración de la fase de sueño profundo. Al grupo de Reinoso se debe el hallazgo de que el “director de orquesta” en la instauración del sueño REM es la zona ventral paramediana del núcleo reticular pontino oral

Sleep is an active and periodic biological state composed of NREM and REM phases, which alternate during the night. Both biological clocks and specific neurotransmitters are involved in the modulation of this system. It is a complex neuronal network in which several areas of the central nervous system are involved. The oneiric processes are also controlled neurally. This work summarises the history of the investigations on this topic from the 19th century to date. It is worth mentioning the recent findings of Lugaresi and colleages who described fatal familial insomnia, a disease that helped to show the importance of the mediodorsal thalamic nucleus in the genesis of slow-wave sleep. Reinoso´s group found out that the paramedian ventral area of the oral pontine reticular nucleus is the conductor in the establishment of REM sleep