2,790 research outputs found
The effects of intrinsic noise on the behaviour of bistable cell regulatory systems under quasi-steady state conditions
We analyse the effect of intrinsic fluctuations on the properties of bistable
stochastic systems with time scale separation operating under1 quasi-steady
state conditions. We first formulate a stochastic generalisation of the
quasi-steady state approximation based on the semi-classical approximation of
the partial differential equation for the generating function associated with
the Chemical Master Equation. Such approximation proceeds by optimising an
action functional whose associated set of Euler-Lagrange (Hamilton) equations
provide the most likely fluctuation path. We show that, under appropriate
conditions granting time scale separation, the Hamiltonian can be re-scaled so
that the set of Hamilton equations splits up into slow and fast variables,
whereby the quasi-steady state approximation can be applied. We analyse two
particular examples of systems whose mean-field limit has been shown to exhibit
bi-stability: an enzyme-catalysed system of two mutually-inhibitory proteins
and a gene regulatory circuit with self-activation. Our theory establishes that
the number of molecules of the conserved species are order parameters whose
variation regulates bistable behaviour in the associated systems beyond the
predictions of the mean-field theory. This prediction is fully confirmed by
direct numerical simulations using the stochastic simulation algorithm. This
result allows us to propose strategies whereby, by varying the number of
molecules of the three conserved chemical species, cell properties associated
to bistable behaviour (phenotype, cell-cycle status, etc.) can be controlled.Comment: 33 pages, 9 figures, accepted for publication in the Journal of
Chemical Physic
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
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
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
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
Thermodynamic glass transition in a spin glass without time-reversal symmetry
Spin glasses are a longstanding model for the sluggish dynamics that appears
at the glass transition. However, spin glasses differ from structural glasses
for a crucial feature: they enjoy a time reversal symmetry. This symmetry can
be broken by applying an external magnetic field, but embarrassingly little is
known about the critical behaviour of a spin glass in a field. In this context,
the space dimension is crucial. Simulations are easier to interpret in a large
number of dimensions, but one must work below the upper critical dimension
(i.e., in d<6) in order for results to have relevance for experiments. Here we
show conclusive evidence for the presence of a phase transition in a
four-dimensional spin glass in a field. Two ingredients were crucial for this
achievement: massive numerical simulations were carried out on the Janus
special-purpose computer, and a new and powerful finite-size scaling method.Comment: 10 pages, 6 figure
Janus II: a new generation application-driven computer for spin-system simulations
This paper describes the architecture, the development and the implementation
of Janus II, a new generation application-driven number cruncher optimized for
Monte Carlo simulations of spin systems (mainly spin glasses). This domain of
computational physics is a recognized grand challenge of high-performance
computing: the resources necessary to study in detail theoretical models that
can make contact with experimental data are by far beyond those available using
commodity computer systems. On the other hand, several specific features of the
associated algorithms suggest that unconventional computer architectures, which
can be implemented with available electronics technologies, may lead to order
of magnitude increases in performance, reducing to acceptable values on human
scales the time needed to carry out simulation campaigns that would take
centuries on commercially available machines. Janus II is one such machine,
recently developed and commissioned, that builds upon and improves on the
successful JANUS machine, which has been used for physics since 2008 and is
still in operation today. This paper describes in detail the motivations behind
the project, the computational requirements, the architecture and the
implementation of this new machine and compares its expected performances with
those of currently available commercial systems.Comment: 28 pages, 6 figure
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