10,279 research outputs found

### An in-depth view of the microscopic dynamics of Ising spin glasses at fixed temperature

Using the dedicated computer Janus, we follow the nonequilibrium dynamics of
the Ising spin glass in three dimensions for eleven orders of magnitude. The
use of integral estimators for the coherence and correlation lengths allows us
to study dynamic heterogeneities and the presence of a replicon mode and to
obtain safe bounds on the Edwards-Anderson order parameter below the critical
temperature. We obtain good agreement with experimental determinations of the
temperature-dependent decay exponents for the thermoremanent magnetization.
This magnitude is observed to scale with the much harder to measure coherence
length, a potentially useful result for experimentalists. The exponents for
energy relaxation display a linear dependence on temperature and reasonable
extrapolations to the critical point. We conclude examining the time growth of
the coherence length, with a comparison of critical and activated dynamics.Comment: 38 pages, 26 figure

### Functional and genomic analyses of Î±-solenoid proteins

{alpha}-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some {alpha}-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of {alpha}-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of {alpha}-solenoids. Unexpectedly, we identified occurrences of {alpha}-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known {alpha}-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that {alpha}-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of {alpha}-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that {alpha}-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of {alpha}-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/

### The Spin Glass Phase in the Four-State, Three-Dimensional Potts Model

We perform numerical simulations, including parallel tempering, on the Potts
glass model with binary random quenched couplings using the JANUS
application-oriented computer. We find and characterize a glassy transition,
estimating the location of the transition and the value of the critical
exponents. We show that there is no ferromagnetic transition in a large
temperature range around the glassy critical temperature. We also compare our
results with those obtained recently on the "random permutation" Potts glass.Comment: 7 pages and 3 figures. Corrected minor typo

### Ianus: an Adpative FPGA Computer

Dedicated machines designed for specific computational algorithms can
outperform conventional computers by several orders of magnitude. In this note
we describe {\it Ianus}, a new generation FPGA based machine and its basic
features: hardware integration and wide reprogrammability. Our goal is to build
a machine that can fully exploit the performance potential of new generation
FPGA devices. We also plan a software platform which simplifies its
programming, in order to extend its intended range of application to a wide
class of interesting and computationally demanding problems. The decision to
develop a dedicated processor is a complex one, involving careful assessment of
its performance lead, during its expected lifetime, over traditional computers,
taking into account their performance increase, as predicted by Moore's law. We
discuss this point in detail

### 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)]. 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, non-linear susceptibilities, recently measured in glass-forming
liquids, scale as powers of the same microscopic length.Comment: 6 pages, 4 figure

### The Mpemba effect in spin glasses is a persistent memory effect

The Mpemba effect occurs when a hot system cools faster than an initially
colder one, when both are refrigerated in the same thermal reservoir. Using the
custom built supercomputer Janus II, we study the Mpemba effect in spin glasses
and show that it is a non-equilibrium process, governed by the coherence length
\xi of the system. The effect occurs when the bath temperature lies in the
glassy phase, but it is not necessary for the thermal protocol to cross the
critical temperature. In fact, the Mpemba effect follows from a strong
relationship between the internal energy and \xi that turns out to be a
sure-tell sign of being in the glassy phase. Thus, the Mpemba effect presents
itself as an intriguing new avenue for the experimental study of the coherence
length in supercooled liquids and other glass formers.Comment: Version accepted for publication in PNAS. 6 pages, 7 figure

### Critical Behavior of Three-Dimensional Disordered Potts Models with Many States

We study the 3D Disordered Potts Model with p=5 and p=6. Our numerical
simulations (that severely slow down for increasing p) detect a very clear spin
glass phase transition. We evaluate the critical exponents and the critical
value of the temperature, and we use known results at lower $p$ values to
discuss how they evolve for increasing p. We do not find any sign of the
presence of a transition to a ferromagnetic regime.Comment: 9 pages and 9 Postscript figures. Final version published in J. Stat.
Mec

### The three dimensional Ising spin glass in an external magnetic field: the role of the silent majority

We perform equilibrium parallel-tempering simulations of the 3D Ising
Edwards-Anderson spin glass in a field. A traditional analysis shows no signs
of a phase transition. Yet, we encounter dramatic fluctuations in the behaviour
of the model: Averages over all the data only describe the behaviour of a small
fraction of it. Therefore we develop a new approach to study the equilibrium
behaviour of the system, by classifying the measurements as a function of a
conditioning variate. We propose a finite-size scaling analysis based on the
probability distribution function of the conditioning variate, which may
accelerate the convergence to the thermodynamic limit. In this way, we find a
non-trivial spectrum of behaviours, where a part of the measurements behaves as
the average, while the majority of them shows signs of scale invariance. As a
result, we can estimate the temperature interval where the phase transition in
a field ought to lie, if it exists. Although this would-be critical regime is
unreachable with present resources, the numerical challenge is finally well
posed.Comment: 42 pages, 19 figures. Minor changes and added figure (results
unchanged

### Nature of the spin-glass phase at experimental length scales

We present a massive equilibrium simulation of the three-dimensional Ising
spin glass at low temperatures. The Janus special-purpose computer has allowed
us to equilibrate, using parallel tempering, L=32 lattices down to T=0.64 Tc.
We demonstrate the relevance of equilibrium finite-size simulations to
understand experimental non-equilibrium spin glasses in the thermodynamical
limit by establishing a time-length dictionary. We conclude that
non-equilibrium experiments performed on a time scale of one hour can be
matched with equilibrium results on L=110 lattices. A detailed investigation of
the probability distribution functions of the spin and link overlap, as well as
of their correlation functions, shows that Replica Symmetry Breaking is the
appropriate theoretical framework for the physically relevant length scales.
Besides, we improve over existing methodologies to ensure equilibration in
parallel tempering simulations.Comment: 48 pages, 19 postscript figures, 9 tables. Version accepted for
publication in the Journal of Statistical Mechanic

### Critical parameters of the three-dimensional Ising spin glass

We report a high-precision finite-size scaling study of the critical behavior
of the three-dimensional Ising Edwards-Anderson model (the Ising spin glass).
We have thermalized lattices up to L=40 using the Janus dedicated computer. Our
analysis takes into account leading-order corrections to scaling. We obtain Tc
= 1.1019(29) for the critical temperature, \nu = 2.562(42) for the thermal
exponent, \eta = -0.3900(36) for the anomalous dimension and \omega = 1.12(10)
for the exponent of the leading corrections to scaling. Standard (hyper)scaling
relations yield \alpha = -5.69(13), \beta = 0.782(10) and \gamma = 6.13(11). We
also compute several universal quantities at Tc.Comment: 9 pages, 5 figure

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