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.

New insights on surface-enhanced Raman scattering based on controlled aggregation and spectroscopic studies, DFT calculations and symmetry analysis for 3,6-bi-2-pyridyl-1,2,4,5-tetrazine adsorbed onto citrate-stabilized gold nanoparticles

Asystematic study on the surface-enhanced Raman scattering (SERS) for 3,6-bi-2-pyridyl-1,2,4,5-tetrazine (bptz) adsorbed onto citrate-modified gold nanoparticles (cit-AuNps) was carried out based on electronic and vibrational spectroscopy and density functional methods. The citrate/bptz exchange was carefully controlled by the stepwise addition of bptz to the cit-AuNps, inducing flocculation and leading to the rise of a characteristic plasmon coupling band in the visible region. Such stepwise procedure led to a uniform decrease of the citrate SERS signals and to the rise of characteristic peaks of bptz, consistent with surface binding via the N heterocyclic atoms. In contrast, single addition of a large amount of bptz promoted complete aggregation of the nanoparticles, leading to a strong enhancement of the SERS signals. In this case, from the distinct Raman profiles involved, the formation of a new SERS environment became apparent, conjugating the influence of the local hot spots and charge-transfer (CT) effects. The most strongly enhanced vibrations belong to a(1) and b(2) representations, and were interpreted in terms of the electromagnetic and the CT mechanisms: the latter involving significant contribution of vibronic coupling in the system. Copyright (C) 2010 John Wiley & Sons, Ltd.

Hamiltonian constraint analysis of vector field theories with spontaneous Lorentz symmetry breaking

Recent investigations of various quantum-gravity theories have revealed a variety of possible mechanisms that lead to Lorentz violation. One of the more elegant of these mechanisms is known as Spontaneous Lorentz Symmetry Breaking (SLSB), where a vector or tensor field acquires a nonzero vacuum expectation value. As a consequence of this symmetry breaking, massless Nambu-Goldstone modes appear with properties similar to the photon in Electromagnetism. This thesis considers the most general class of vector field theories that exhibit spontaneous Lorentz violation-known as bumblebee models-and examines their candidacy as potential alternative explanations of E&M, offering the possibility that Einstein-Maxwell theory could emerge as a result of SLSB rather than of local U(1) gauge invariance. With this aim we employ Dirac's Hamiltonian Constraint Analysis procedure to examine the constraint structures and degrees of freedom inherent in three candidate bumblebee models, each with a different potential function, and compare these results to those of Electromagnetism. We find that none of these models share similar constraint structures to that of E&M, and that the number of degrees of freedom for each model exceeds that of Electromagnetism by at least two, pointing to the potential existence of massive modes or propagating ghost modes in the bumblebee theories.

Parallel matrix inversion techniques

In this paper, we present techniques for inverting sparse, symmetric and positive definite matrices on parallel and distributed computers. We propose two algorithms, one for SIMD implementation and the other for MIMD implementation. These algorithms are modified versions of Gaussian elimination and they take into account the sparseness of the matrix. Our algorithms perform better than the general parallel Gaussian elimination algorithm. In order to demonstrate the usefulness of our technique, we implemented the snake problem using our sparse matrix algorithm. Our studies reveal that the proposed sparse matrix inversion algorithm significantly reduces the time taken for obtaining the solution of the snake problem. In this paper, we present the results of our experimental work.

High volume versus low volume balance training on postural sway in adults with previous ankle inversion injury

Balance training is commonly used in the rehabilitation process of ankle injuries; however, the exercise prescription guidelines for prescribing balance training are poorly understood. The aim of the present study was to determine if high or low volume balance training is more effective in improving postural sway after an 8 week balance training program utilising the same exercises. Seventeen subjects (14 male, 3 female) with a mean age of 24.06 ± 5.6 years were randomly allocated into a control group (CG), low volume training (LVT) or high volume training (HVT). All subjects had sustained at least two inversion ankle injuries within the last 18 months. Subjects completed 8 weeks of balance training of up to 30 mins duration, 3 times per week. LVT consisted of 40 repetitions for week 1, progressing to 90 repetitions by week 8. HVT consisted of 60 repetitions for week 1, progressing to 130 repetitions by week 8. The maximum centre of pressure (COP) excursion was obtained from the porce plate in the medial-lateral (ML) direction and subsequently used for pre-test and post-test analysis. After the 8 week training intervention, there was a significant (P<0.001) difference in postural sway between pre and post testing for both the LVT (pre = 88.69mm ± 25.08mm, post = 72.17mm ± 27.53mm) and HVT (pre = 77.47mm ±10.57mm, post = 58.54mm ± 7.01mm) groups. There was no significant (P>0.01) difference detected for improvements between the LVT and HVT, however reported effect sizes (ES) showed large effect size chances in the high volume training (ES = 1.7) whereas low volume training showed medium effect sizes changes (ES = 0.6). This preliminary study demonstrates the importance of training volume in the rehabilitation of ankle injuries, with the HVT being superior to LVT.

Applications of symbolic computing for symmetry analysis of differential equations

 This thesis presents a number of applications of symbolic computing to the study of differential equations. In particular, three packages have been produced for the computer algebra system MAPLE and used to find a variety of symmetries (and corresponding invariant solutions) for a range of differential systems.