Symmetry in biology: from genetic code to stochastic gene regulation

Mathematical models, as instruments for understanding the workings of nature, are a traditional tool of physics, but they also play an ever increasing role in biology - in the description of fundamental processes as well as that of complex systems. In this review, the authors discuss two examples of the application of group theoretical methods, which constitute the mathematical discipline for a quantitative description of the idea of symmetry, to genetics. The first one appears, in the form of a pseudo-orthogonal (Lorentz like) symmetry, in the stochastic modelling of what may be regarded as the simplest possible example of a genetic network and, hopefully, a building block for more complicated ones: a single self-interacting or externally regulated gene with only two possible states: ` on` and ` off`. The second is the algebraic approach to the evolution of the genetic code, according to which the current code results from a dynamical symmetry breaking process, starting out from an initial state of complete symmetry and ending in the presently observed final state of low symmetry. In both cases, symmetry plays a decisive role: in the first, it is a characteristic feature of the dynamics of the gene switch and its decay to equilibrium, whereas in the second, it provides the guidelines for the evolution of the coding rules.

Calculable lepton masses, seesaw relations, and four neutrino mixings in a 3-3-1 model with an extra U(1) symmetry

We propose a scheme in which the masses of the heavier leptons obey seesaw type relations. The light lepton masses, except the electron and the electron neutrino ones, are generated by one loop level radiative corrections. We work in a version of the 3-3-1 electroweak model that predicts singlets (charged and neutral) of heavy leptons beyond the known ones. An extra U(1)(Omega) symmetry is introduced in order to avoid the light leptons getting masses at the tree level. The electron mass induces an explicit symmetry breaking at U(1)(Omega). We discuss also the mixing matrix among four neutrinos. The new energy scale required is not higher than a few TeV.

Chiral symmetry, massive gluons and confinement

It is quite difficult to obtain non-trivial chiral symmetry breaking solutions for the quark gap equation in the presence of dynamically generated gluon masses. An effective confining propagator has recently been proposed by Cornwall in order to solve this problem. We study phenomenological consequences of this approach, showing its compatibility with the experimental data. We argue that this confining propagator should be restricted to a small region of momenta, leading to effective four-fermion interactions at low energy. © 2013 American Institute of Physics.

QCD chiral symmetry restoration with a large number of quarks in a model with a confining propagator and dynamically massive gluons

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Entropic information for travelling solitons in Lorentz and CPT breaking systems

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

SU(3) breaking and annihilation effects in the η and η′ masses

The mass splitting of the pseudoscalar mesons η and η′ is approached by taking into account the SU(3)-flavor symmetry breaking and annihilation effects. An extended version of the Schwinger sum rule and a mixing angle equal to -19.51° are obtained.

Dynamical (super)symmetry vacuum properties of the supersymmetric Chern-Simons-matter model

By computing the two-loop effective potential of the D=3 N=1 supersymmetric Chern-Simons model minimally coupled to a massless self-interacting matter superfield, it is shown that supersymmetry is preserved, while the internal U(1) and the scale symmetries are broken at two-loop order, dynamically generating masses both for the gauge superfield and for the real component of the matter superfield.

Measuring complexity through average symmetry

This work introduces a complexity measure which addresses some conflicting issues between existing ones by using a new principle - measuring the average amount of symmetry broken by an object. It attributes low (although different) complexity to either deterministic or random homogeneous densities and higher complexity to the intermediate cases. This new measure is easily computable, breaks the coarse graining paradigm and can be straightforwardly generalized, including to continuous cases and general networks. By applying this measure to a series of objects, it is shown that it can be consistently used for both small scale structures with exact symmetry breaking and large scale patterns, for which, differently from similar measures, it consistently discriminates between repetitive patterns, random configurations and self-similar structures

Calculable lepton masses, seesaw relations, and four neutrino mixings in a 3-3-1 model with an extra U(1) symmetry

We propose a scheme in which the masses of the heavier leptons obey seesaw type relations. The light lepton masses, except the electron and the electron neutrino ones, are generated by one loop level radiative corrections. We work in a version of the 3-3-1 electroweak model that predicts singlets (charged and neutral) of heavy leptons beyond the known ones. An extra U(1)(Omega) symmetry is introduced in order to avoid the light leptons getting masses at the tree level. The electron mass induces an explicit symmetry breaking at U(1)(Omega). We discuss also the mixing matrix among four neutrinos. The new energy scale required is not higher than a few TeV.

The influence of instructions and body-scaling as constraints on decision-making processes in team sports

Team games conceptualized as dynamical systems engender a view of emergent decision-making behaviour under constraints, although specific effects of instructional and body-scaling constraints have yet to be verified empirically. For this purpose, we studied the effects of task and individual constraints on decision-making processes in basketball. Eleven experienced female players performed 350 trials in 1 vs. 1 sub-phases of basketball in which an attacker tried to perturb the stable state of a dyad formed with a defender (i.e. break the symmetry). In Experiment 1, specific instructions (neutral, risk taking or conservative) were manipulated to observe effects on emergent behaviour of the dyadic system. When attacking players were given conservative instructions, time to cross court mid-line and variability of the attacker's trajectory were significantly greater. In Experiment 2, body-scaling of participants was manipulated by creating dyads with different height relations. When attackers were considerably taller than defenders, there were fewer occurrences of symmetry-breaking. When attackers were considerably shorter than defenders, time to cross court mid-line was significantly shorter than when dyads were composed of athletes of similar height or when attackers were considerably taller than defenders. The data exemplify how interacting task and individual constraints can influence emergent decision-making processes in team ball games.

Singularity-free cosmology: A simple model

The nonminimal coupling of a self-interacting complex scalar field with gravity is studied. For a Robertson-Walker open universe the stable solutions of the scalar-field equations are time dependent. As a result of this, a novel spontaneous symmetry breaking occurs which leads to a varying effective gravitational coupling coefficient. It is found that the coupling coefficient changes sign below a critical ‘‘radius’’ of the Universe implying the appearance of repulsive gravity. The occurrence of the repulsive interaction at an early epoch facilitates singularity avoidance. The model also provides a solution to the horizon problem.

Technicolor

In technicolor theories the scalar sector of the Standard Model is replaced by a strongly interacting sector. Although the Standard Model has been exceptionally successful, the scalar sector causes theoretical problems that make these theories seem an attractive alternative. I begin my thesis by considering QCD, which is the known example of strong interactions. The theory exhibits two phenomena: confinement and chiral symmetry breaking. I find the low-energy dynamics to be similar to that of the sigma models. Then I analyze the problems of the Standard Model Higgs sector, mainly the unnaturalness and triviality. Motivated by the example of QCD, I introduce the minimal technicolor model to resolve these problems. I demonstrate the minimal model to be free of anomalies and then deduce the main elements of its low-energy particle spectrum. I find the particle spectrum contains massless or very light technipions, and also technibaryons and techni-vector mesons with a high mass of over 1 TeV. Standard Model fermions remain strictly massless at this stage. Thus I introduce the technicolor companion theory of flavor, called extended technicolor. I show that the Standard Model fermions and technihadrons receive masses, but that they remain too light. I also discuss flavor-changing neutral currents and precision electroweak measurements. I then show that walking technicolor models partly solve these problems. In these models, contrary to QCD, the coupling evolves slowly over a large energy scale. This behavior adds to the masses so that even the light technihadrons are too heavy to be detected at current particle accelerators. Also all observed masses of the Standard Model particles can be generated, except for the bottom and top quarks. Thus it is shown in this thesis that, excluding the masses of third generation quarks, theories based on walking technicolor can in principle produce the observed particle spectrum.

Quantum Interference in Coherent Molecular Conductance

Coherent electronic transport through individual molecules is crucially sensitive to quantum interference. We investigate the zero-bias and zero-temperature conductance through pi-conjugated annulene molecules weakly coupled to two leads for different source-drain configurations, finding an important reduction for certain transmission channels and for particular geometries as a consequence of destructive quantum interference between states with definite momenta. When translational symmetry is broken by an external perturbation we find an abrupt increase of the conductance through those channels. Previous studies concentrated on the effect at the Fermi energy, where this effect is very small. By analyzing the effect of symmetry breaking on the main transmission channels we find a much larger response thus leading to the possibility of a larger switching of the conductance through single molecules.

Quadratic Nonlinearity of One- and Two-Electron Oxidized Metalloporphyrins and Their Switching in Solution

We report the quadratic nonlinearity of one- and two-electron oxidation products of the first series of transition metal complexes of meso-tetraphenylporphyrin (TPP). Among many MTPP complexes, only CuTPP and ZnTPP show reversible oxidation/reduction cycles as seen from cyclic voltammetry experiments. While centrosymmetric neutral metalloporphyrins have zero first hyperpolarizability, β, as expected, the cation radicals and dications of CuTPP and ZnTPP have very high β values. The one- and two-electron oxidation of the MTPPs leads to symmetry-breaking of the metal−porphyrin core, resulting in a large β value that is perhaps aided in part by contributions from the two-photon resonance enhancement. The calculated static first hyperpolarizabilities, β0, which are evaluated in the framework of density functional theory by a coupled perturbed Hartree−Fock method, support the experimental trend. The switching of optical nonlinearity has been achieved between the neutral and the one-electron oxidation products but not between the one- and the two-electron oxidation products since dications that are electrochemically reversible are unstable due to the formation of stable isoporphyrins in the presence of nucleophiles such as halides.