281 research outputs found
Efficient Parallel Statistical Model Checking of Biochemical Networks
We consider the problem of verifying stochastic models of biochemical
networks against behavioral properties expressed in temporal logic terms. Exact
probabilistic verification approaches such as, for example, CSL/PCTL model
checking, are undermined by a huge computational demand which rule them out for
most real case studies. Less demanding approaches, such as statistical model
checking, estimate the likelihood that a property is satisfied by sampling
executions out of the stochastic model. We propose a methodology for
efficiently estimating the likelihood that a LTL property P holds of a
stochastic model of a biochemical network. As with other statistical
verification techniques, the methodology we propose uses a stochastic
simulation algorithm for generating execution samples, however there are three
key aspects that improve the efficiency: first, the sample generation is driven
by on-the-fly verification of P which results in optimal overall simulation
time. Second, the confidence interval estimation for the probability of P to
hold is based on an efficient variant of the Wilson method which ensures a
faster convergence. Third, the whole methodology is designed according to a
parallel fashion and a prototype software tool has been implemented that
performs the sampling/verification process in parallel over an HPC
architecture
Real-time gauge/gravity duality: Prescription, Renormalization and Examples
We present a comprehensive analysis of the prescription we recently put
forward for the computation of real-time correlation functions using
gauge/gravity duality. The prescription is valid for any holographic
supergravity background and it naturally maps initial and final data in the
bulk to initial and final states or density matrices in the field theory. We
show in detail how the technique of holographic renormalization can be applied
in this setting and we provide numerous illustrative examples, including the
computation of time-ordered, Wightman and retarded 2-point functions in
Poincare and global coordinates, thermal correlators and higher-point
functions.Comment: 85 pages, 13 figures; v2: added comments and reference
Massless BTZ black holes in minisuperspace
We study aspects of the propagation of strings on BTZ black holes. After
performing a careful analysis of the global spacetime structure of generic BTZ
black holes, and its relation to the geometry of the SL(2,R) group manifold, we
focus on the simplest case of the massless BTZ black hole. We study the SL(2,R)
Wess-Zumino-Witten model in the worldsheet minisuperspace limit, taking into
account special features associated to the Lorentzian signature of spacetime.
We analyse the two- and three-point functions in the pointparticle limit. To
lay bare the underlying group structure of the correlation functions, we derive
new results on Clebsch-Gordan coefficients for SL(2,R) in a parabolic basis. We
comment on the application of our results to string theory in singular
time-dependent orbifolds, and to a Lorentzian version of the AdS/CFT
correspondence.Comment: 28 pages, v2: reference adde
Non‐uniqueness and symmetry in stratigraphic interpretations:A quantitative approach for determining stratal controls
Different combinations of stratal controls could produce identical sequence architectures. Consequently, interpretations of the stratigraphic record, for example to infer palaeo-climate and eustatic sea-level history, suffer from non-uniqueness. However, variations in the multiple controls can be encapsulated through discovery of all possible solutions to an interpretation. As this paper demonstrates, a single solution can be directly transformed into an alternative solution that leaves the expected geological outcomes unaltered, which can be regarded as the existence of symmetry in the interpretation. Repetitive application of the symmetry method can therefore allow additional solutions to be rapidly derived given an existing solution. The proposed method has been adapted to a stratigraphic forward model for interpreting the Baltimore Canyon (USA) stratigraphy. Modelling results have indicated the ranges of changes in relative sea-level, sediment supply and subaerial erosion from Oligocene to Mid-Miocene. Using these limits, it is possible to determine what appears to be true in the palaeo-history, even when a solution is not unique
Theory of the first-order isostructural valence phase transitions in mixed valence compounds YbIn_{x}Ag_{1-x}Cu_{4}
For describing the first-order isostructural valence phase transition in
mixed valence compounds we develop a new approach based on the lattice Anderson
model. We take into account the Coulomb interaction between localized f and
conduction band electrons and two mechanisms of electron-lattice coupling. One
is related to the volume dependence of the hybridization. The other is related
to local deformations produced by f- shell size fluctuations accompanying
valence fluctuations. The large f -state degeneracy allows us to use the 1/N
expansion method. Within the model we develop a mean-field theory for the
first-order valence phase transition in YbInCu_{4}. It is shown that the
Coulomb interaction enhances the exchange interaction between f and conduction
band electron spins and is the driving force of the phase transition. A
comparison between the theoretical calculations and experimental measurements
of the valence change, susceptibility, specific heat, entropy, elastic
constants and volume change in YbInCu_{4} and YbAgCu_{4} are presented, and a
good quantitative agreement is found. On the basis of the model we describe the
evolution from the first-order valence phase transition to the continuous
transition into the heavy-fermion ground state in the series of compounds
YbIn_{1-x}Ag_{x}Cu_{4}. The effect of pressure on physical properties of
YbInCu_{4} is studied and the H-T phase diagram is found.Comment: 17 pages RevTeX, 9 Postscript figures, to be submitted to Phys.Rev.
The First Magnetic Fields
We review current ideas on the origin of galactic and extragalactic magnetic
fields. We begin by summarizing observations of magnetic fields at cosmological
redshifts and on cosmological scales. These observations translate into
constraints on the strength and scale magnetic fields must have during the
early stages of galaxy formation in order to seed the galactic dynamo. We
examine mechanisms for the generation of magnetic fields that operate prior
during inflation and during subsequent phase transitions such as electroweak
symmetry breaking and the quark-hadron phase transition. The implications of
strong primordial magnetic fields for the reionization epoch as well as the
first generation of stars is discussed in detail. The exotic, early-Universe
mechanisms are contrasted with astrophysical processes that generate fields
after recombination. For example, a Biermann-type battery can operate in a
proto-galaxy during the early stages of structure formation. Moreover, magnetic
fields in either an early generation of stars or active galactic nuclei can be
dispersed into the intergalactic medium.Comment: Accepted for publication in Space Science Reviews. Pdf can be also
downloaded from http://canopus.cnu.ac.kr/ryu/cosmic-mag1.pd
Multiwavelength studies of MHD waves in the solar chromosphere: An overview of recent results
The chromosphere is a thin layer of the solar atmosphere that bridges the
relatively cool photosphere and the intensely heated transition region and
corona. Compressible and incompressible waves propagating through the
chromosphere can supply significant amounts of energy to the interface region
and corona. In recent years an abundance of high-resolution observations from
state-of-the-art facilities have provided new and exciting ways of
disentangling the characteristics of oscillatory phenomena propagating through
the dynamic chromosphere. Coupled with rapid advancements in
magnetohydrodynamic wave theory, we are now in an ideal position to thoroughly
investigate the role waves play in supplying energy to sustain chromospheric
and coronal heating. Here, we review the recent progress made in
characterising, categorising and interpreting oscillations manifesting in the
solar chromosphere, with an impetus placed on their intrinsic energetics.Comment: 48 pages, 25 figures, accepted into Space Science Review
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
Specification of the near-Earth space environment with SHIELDS
Predicting variations in the near-Earth space environment that can lead to spacecraft damage and failure is one example of “space weather” and a big space physics challenge. A project recently funded through the Los Alamos National Laboratory (LANL) Directed Research and Development (LDRD) program aims at developing a new capability to understand, model, and predict Space Hazards Induced near Earth by Large Dynamic Storms, the SHIELDS framework. The project goals are to understand the dynamics of the surface charging environment (SCE), the hot (keV) electrons representing the source and seed populations for the radiation belts, on both macro- and micro-scale. Important physics questions related to particle injection and acceleration associated with magnetospheric storms and substorms, as well as plasma waves, are investigated. These challenging problems are addressed using a team of world-class experts in the fields of space science and computational plasma physics, and state-of-the-art models and computational facilities. A full two-way coupling of physics-based models across multiple scales, including a global MHD (BATS-R-US) embedding a particle-in-cell (iPIC3D) and an inner magnetosphere (RAM-SCB) codes, is achieved. New data assimilation techniques employing in situ satellite data are developed; these provide an order of magnitude improvement in the accuracy in the simulation of the SCE. SHIELDS also includes a post-processing tool designed to calculate the surface charging for specific spacecraft geometry using the Curvilinear Particle-In-Cell (CPIC) code that can be used for reanalysis of satellite failures or for satellite design
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