Bio-logic: gene expression and the laws of combinatorial logic

Original article can be found at: http://www.mitpressjournals.org/ Copyright MIT Press DOI: 10.1162/artl.2008.14.1.121At the heart of the development of fertilized eggs into fully formed organisms and the adaptation of cells to changed conditions are genetic regulatory networks (GRNs). In higher multi-cellular organisms, signal selection and multiplexing is performed at the cis-regulatory domains of genes, where combinations of transcription factors (TFs) regulate the rates at which the genes are transcribed into mRNA. To be able to act as activators or repressors of gene transcription, TFs must first bind to target sequences on the regulatory domains. Two TFs that act in concert may bind entirely independently of each other, but more often binding of the first one will alter the affinity of the other for its binding site. This paper presents a systematic investigation into the effect of TF binding dependencies on the predicted regulatory function of this “bio-logic”. Four extreme scenarios, commonly used to classify enzyme activation and inhibition patterns, for the binding of two TFs were explored: independent (the TFs bind without affecting each other’s affinities), competitive (the TFs compete for the same binding site), ordered (the TFs bind in a compulsory order), and joint binding (the TFs either bind as a preformed complex, or binding of one is virtually impossible in the absence of the other). The conclusions are: 1) the laws of combinatorial logic hold only for systems with independently binding TFs; 2) systems formed according to the other scenarios can mimic the functions of their Boolean logical counterparts, but cannot be combined or decomposed in the same way; and 3) the continuously scaled output of systems consisting of competitively binding activators and repressors can be more robustly controlled than that of single TF or (quasi-) logical multi-TF systems. Keywords: Transcription regulation, Genetic regulatory networks, Enzyme kinetics, Combinatorial logic, Non-Boolean continuous logic, Modelling.Peer reviewe

Low temperature characterization of modulation doped SiGe grown on bonded silicon-on-insulator

Modulation doped pseudomorphic Si0.87Ge0.13 strained quantum wells were grown on bonded silicon-on-insulator (SOI) substrates. Comparison with similar structures grown on bulk Si(100) wafers shows that the SOI material has higher mobility at low temperatures with a maximum value of 16 810 cm 2/V s for 2.05 × 1011 cm – 2 carries at 298 mK. Effective masses obtained from the temperature dependence of Shubnikov–de Haas oscillations have a value of (0.27 ± 0.02) m0 compared to (0.23 ± 0.02) m0 for quantum wells on Si(100) while the cyclotron resonance effective masses obtained at higher magnetic fields without consideration for nonparabolicity effects have values between 0.25 and 0.29 m0. Ratios of the transport and quantum lifetimes, tau/tau q=2.13 ± 0.10, were obtained for the SOI material that are, we believe, the highest reported for any pseudomorphic SiGe modulation doped structure and demonstrates that there is less interface roughness or charge scattering in the SOI material than in metal–oxide–semiconductor field effect transistors or other pseudomorphic SiGe modulation doped quantum wells

A perturbative re-analysis of N=4 supersymmetric Yang--Mills theory

The finiteness properties of the N=4 supersymmetric Yang-Mills theory are reanalyzed both in the component formulation and using N=1 superfields, in order to discuss some subtleties that emerge in the computation of gauge dependent quantities. The one-loop corrections to various Green functions of elementary fields are calculated. In the component formulation it is shown that the choice of the Wess-Zumino gauge, that is standard in supersymmetric gauge theories, introduces ultraviolet divergences in the propagators at the one-loop level. Such divergences are exactly cancelled when the contributions of the fields that are put to zero in the Wess-Zumino gauge are taken into account. In the description in terms of N=1 superfields infrared divergences are found for every choice of gauge different from the supersymmetric generalization of the Fermi-Feynman gauge. Two-, three- and four-point functions of N=1 superfields are computed and some general features of the infrared problem are discussed. We also examine the effect of the introduction of mass terms for the (anti) chiral superfields in the theory, which break supersymmetry from N=4 to N=1. It is shown that in the mass deformed model no ultraviolet divergences appear in two-point functions. It argued that this result can be generalized to n-point functions, supporting the proposal of a possible of use of this modified model as a supersymmetry-preserving regularization scheme for N=1 theories.Comment: 41 pages, LaTeX2e, uses feynMP package to draw Feynman diagram

A Manifestly Gauge Invariant and Universal Calculus for SU(N) Yang-Mills

Within the framework of the Exact Renormalization Group, a manifestly gauge invariant calculus is constructed for SU(N) Yang-Mills. The methodology is comprehensively illustrated with a proof, to all orders in perturbation theory, that the beta function has no explicit dependence on either the seed action or details of the covariantization of the cutoff. The cancellation of these non-universal contributions is done in an entirely diagrammatic fashion.Comment: 128 pages, 89 figures; v2: published in ijmpa - intro extended, refs added, refinements and minor corrections made; v3 small corrections made compared to published versio

N=1* model and glueball superpotential from Renormalization-Group-improved perturbation theory

A method for computing the low-energy non-perturbative properties of SUSY GFT, starting from the microscopic lagrangian model, is presented. The method relies on covariant SUSY Feynman graph techniques, adapted to low energy, and Renormalization-Group-improved perturbation theory. We apply the method to calculate the glueball superpotential in N=1 SU(2) SYM and obtain a potential of the Veneziano-Yankielowicz type.Comment: 19 pages, no figures; added references; note added at the end of the paper; version to appear in JHE

The superfield quantisation of a superparticle action with an extended line element

A massive superparticle action based on the generalised line element in N = 1 global superspace is quantised canonically. A previous method of quantising this action, based on a Fock space analysis, showed that states existed in three supersymmetric multiplets, each of a different mass. The quantisation procedure presented uses the single first class constraint as an operator condition on a general N = 1 superwavefunction. The constraint produces coupled equations of motion for the component wavefunctions. Transformations of the component wavefunctions are derived that decouple the equations of motion and partition the resulting wavefunctions into three separate supermultiplets. Unlike previous quantisations of superparticle actions in N = 1 global superspace, the spinor wavefunctions satisfy the Dirac equation and the vector wavefunctions satisfy the Proca equation. The off-shell closure of the commutators of the supersymmetry transformations, that include mass parameters, are derived by the introduction of auxiliary wavefunctions. To avoid the ghosts arising in a previous Fock space quantisation an alternative conjugation is used in the definition of the current, based on a Krein space approach

Flow Equation for Supersymmetric Quantum Mechanics

We study supersymmetric quantum mechanics with the functional RG formulated in terms of an exact and manifestly off-shell supersymmetric flow equation for the effective action. We solve the flow equation nonperturbatively in a systematic super-covariant derivative expansion and concentrate on systems with unbroken supersymmetry. Already at next-to-leading order, the energy of the first excited state for convex potentials is accurately determined within a 1% error for a wide range of couplings including deeply nonperturbative regimes.Comment: 24 pages, 8 figures, references added, typos correcte

On the Renormalization of Theories of a Scalar Chiral Superfield

An exact renormalization group for theories of a scalar chiral superfield is formulated, directly in four dimensional Euclidean space. By constructing a projector which isolates the superpotential from the full Wilsonian effective action, it is shown that the nonperturbative nonrenormalization theorem follows, quite simply, from the flow equation. Next, it is argued that there do not exist any physically acceptable non-trivial fixed points. Finally, the Wess-Zumino model is considered, as a low energy effective theory. Following an evaluation of the one and two loop beta-function coefficients, to illustrate the ease of use of the formalism, it is shown that the beta-function in the massless case does not receive any nonperturbative power corrections.Comment: 52 pages, 4 figures; v2: 57 pages - refs added and some minor corrections/clarifications made; v3: published in JHEP - some further clarifications mad

Shoes and Insoles: The Influence on Motor Tasks Related to Walking Gait Variability and Stability

The rhythmic control of the lower limb muscles influences the cycle-to-cycle variability during a walking task. The benefits of insoles, commonly used to improve the walking gait, have been little studied. Therefore, the aim of this study was to assess the walking gait variability and stability on different walking conditions (without shoes, WTS, with shoes, WS, with shoes and insoles, WSI) related to brain activity. Twelve participants randomly (WTS/WS/WSI) walked on a treadmill at 4 km/h for 10 min. Kinematic analysis (i.e., footstep and gait variability), brain activation (beta wave signal), rating of perceived exertion (RPE, CR-10 scale), and time domain measures of walking variability were assessed. The maximum Lyapunov exponent (LyE) on the stride cycle period\u2019s datasets was also calculated. Stride length and cycle calculated for all walking conditions were 61.59 \ub1 2.53/63.38 \ub1 1.43/64.09 \ub1 2.40 cm and 1.11 \ub1 0.03/1.14 \ub1 0.03/1.15 \ub1 0.04 s (F1,10 = 4.941/p = 0.01, F1,10 = 4.938/p = 0.012) for WTS, WS, WSI, respectively. Beta wave (F1,10 = 564.201/p = 0.0001) was higher in WTS compared to WS and WSI. Analysis of variance\u2019s (ANOVA) LyE showed a F1,10 = 3.209/p = 0.056, while post hoc analysis showed a significant effect between WS and WSI with p = 0.023, and nonsignificant effects between WTS and WS/WSI (p = 0.070/0.607), respectively. Small perturbations of the foot can influence the control of gait rhythmicity by increasing the variability in a dissipative deterministic regimen