Convergence of Logic of Cellular Regulation in Different Premalignant Cells by an Information Theoretic Approach

Abstract Background Surprisal analysis is a thermodynamic-like molecular level approach that identifies biological constraints that prevents the entropy from reaching its maximum. To examine the significance of altered gene expression levels in tumorigenesis we apply surprisal analysis to the WI-38 model through its precancerous states. The constraints identified by the analysis are transcription patterns underlying the process of transformation. Each pattern highlights the role of a group of genes that act coherently to define a transformed phenotype. Results We identify a major transcription pattern that represents a contraction of signaling networks accompanied by induction of cellular proliferation and protein metabolism, which is essential for full transformation. In addition, a more minor, "tumor signature" transcription pattern completes the transformation process. The variation with time of the importance of each transcription pattern is determined. Midway through the transformation, at the stage when cells switch from slow to fast growth rate, the major transcription pattern undergoes a total inversion of its weight while the more minor pattern does not contribute before that stage. Conclusions A similar network reorganization occurs in two very different cellular transformation models: WI-38 and the cervical cancer HF1 models. Our results suggest that despite differences in a list of transcripts expressed in different cancer models the rationale of the network reorganization remains essentially the same

Timing interactions in social simulations: The voter model

The recent availability of huge high resolution datasets on human activities has revealed the heavy-tailed nature of the interevent time distributions. In social simulations of interacting agents the standard approach has been to use Poisson processes to update the state of the agents, which gives rise to very homogeneous activity patterns with a well defined characteristic interevent time. As a paradigmatic opinion model we investigate the voter model and review the standard update rules and propose two new update rules which are able to account for heterogeneous activity patterns. For the new update rules each node gets updated with a probability that depends on the time since the last event of the node, where an event can be an update attempt (exogenous update) or a change of state (endogenous update). We find that both update rules can give rise to power law interevent time distributions, although the endogenous one more robustly. Apart from that for the exogenous update rule and the standard update rules the voter model does not reach consensus in the infinite size limit, while for the endogenous update there exist a coarsening process that drives the system toward consensus configurations.Comment: Book Chapter, 23 pages, 9 figures, 5 table

Bounds for State Degeneracies in 2D Conformal Field Theory

In this note we explore the application of modular invariance in 2-dimensional CFT to derive universal bounds for quantities describing certain state degeneracies, such as the thermodynamic entropy, or the number of marginal operators. We show that the entropy at inverse temperature 2 pi satisfies a universal lower bound, and we enumerate the principal obstacles to deriving upper bounds on entropies or quantum mechanical degeneracies for fully general CFTs. We then restrict our attention to infrared stable CFT with moderately low central charge, in addition to the usual assumptions of modular invariance, unitarity and discrete operator spectrum. For CFT in the range c_left + c_right < 48 with no relevant operators, we are able to prove an upper bound on the thermodynamic entropy at inverse temperature 2 pi. Under the same conditions we also prove that a CFT can have a number of marginal deformations no greater than ((c_left + c_right) / (48 - c_left - c_right)) e^(4 Pi) - 2.Comment: 23 pages, LaTeX, minor change

Supersymmetric Chern-Simons Theories with Vector Matter

In this paper we discuss SU(N) Chern-Simons theories at level k with both fermionic and bosonic vector matter. In particular we present an exact calculation of the free energy of the N=2 supersymmetric model (with one chiral field) for all values of the 't Hooft coupling in the large N limit. This is done by using a generalization of the standard Hubbard-Stratanovich method because the SUSY model contains higher order polynomial interactions.Comment: 46 pages, 24 figures, v2: comments and references added, v3: a footnote in Section 3.5 adde

KK6 from M2 in BLG

We study the possibility that the Kaluza-Klein monopole (KK6) world-volume action may be obtained from the multiple membranes (M2) action which is described by BLG theory. We first point out that the infinite dimensional Lie 3-algebra based on the Nambu-Poisson structure could not only provide three dimensional manifolds to allow M5 from M2, which was studied by previous authors, but also provide five dimensional manifolds to allow KK6 from M2. We next present a possible way that the U(1) field on KK6 world-volume action could be produced form the gauge potential in BLG theory.Comment: Latex, 15 pages. V3: Add theorem 2 to complete proof. V4: Detail physical interpretations and calculations in section

Efimov physics beyond three particles

Efimov physics originally refers to a system of three particles. Here we review recent theoretical progress seeking for manifestations of Efimov physics in systems composed of more than three particles. Clusters of more than three bosons are tied to each Efimov trimer, but no independent Efimov physics exists there beyond three bosons. The case of a few heavy fermions interacting with a lighter atom is also considered, where the mass ratio of the constituent particles plays a significant role. Following Efimov's study of the (2+1) system, the (3+1) system was shown to have its own critical mass ratio to become Efimovian. We show that the (4+1) system becomes Efimovian at a mass ratio which is smaller than its sub-systems thresholds, giving a pure five-body Efimov effect. The (5+1) and (6+1) systems are also discussed, and we show the absence of 6- and 7-body Efimov physics there

The order of the quantum chromodynamics transition predicted by the standard model of particle physics

We determine the nature of the QCD transition using lattice calculations for physical quark masses. Susceptibilities are extrapolated to vanishing lattice spacing for three physical volumes, the smallest and largest of which differ by a factor of five. This ensures that a true transition should result in a dramatic increase of the susceptibilities.No such behaviour is observed: our finite-size scaling analysis shows that the finite-temperature QCD transition in the hot early Universe was not a real phase transition, but an analytic crossover (involving a rapid change, as opposed to a jump, as the temperature varied). As such, it will be difficult to find experimental evidence of this transition from astronomical observations.Comment: 7 pages, 4 figure

Centre symmetric 3d effective actions for thermal SU(N) Yang-Mills from strong coupling series

We derive three-dimensional, Z(N)-symmetric effective actions in terms of Polyakov loops by means of strong coupling expansions, starting from thermal SU(N) Yang-Mills theory in four dimensions on the lattice. An earlier action in the literature, corresponding to the (spatial) strong coupling limit, is thus extended by several higher orders, as well as by additional interaction terms. We provide analytic mappings between the couplings of the effective theory and the parameters $N_\tau,\beta$ of the original thermal lattice theory, which can be systematically improved. We then investigate the deconfinement transition for the cases SU(2) and SU(3) by means of Monte Carlo simulations of the effective theory. Our effective models correctly reproduce second order 3d Ising and first order phase transitions, respectively. Furthermore, we calculate the critical couplings $\beta_c(N_\tau)$ and find agreement with results from simulations of the 4d theory at the few percent level for $N_\tau=4-16$.Comment: 27 pages, 21 figures; final version published in JHEP; attached the corresponding Erratum (ref. JHEP 1107:014,2011, DOI 10.1007/JHEP07(2011)014) for ease of consultatio

Two-color QCD via dimensional reduction

We study the thermodynamics of two-color QCD at high temperature and/or density using a dimensionally reduced superrenormalizable effective theory, formulated in terms of a coarse grained Wilson line. In the absence of quarks, the theory is required to respect the Z(2) center symmetry, while the effects of quarks of arbitrary masses and chemical potentials are introduced via soft Z(2) breaking operators. Perturbative matching of the effective theory parameters to the full theory is carried out explicitly, and it is argued how the new theory can be used to explore the phase diagram of two-color QCD.Comment: 17 pages, 1 eps figure, jheppub style; v2: minor update, references added, published versio

Conformal weights in the Kerr/CFT correspondence

It has been conjectured that a near-extreme Kerr black hole is described by a 2d CFT. Previous work has shown that CFT operators dual to axisymmetric gravitational perturbations have integer conformal weights. In this paper, we study the analogous problem in 5d. We consider the most general near-extreme vacuum black hole with two rotational symmetries. This includes Myers-Perry black holes, black rings and Kaluza-Klein black holes. We find that operators dual to gravitational (or electromagnetic or massless scalar field) perturbations preserving both rotational symmetries have integer conformal weights, the same for all black holes considered.Comment: 19 page