Systems Biology Graphical Notation: Process Description language Level 1

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps

Self-Organization, Coherence and Turbulence in Laser Optics

In the last decades, rapid progress in modern nonlinear science was marked by the development of the concept of dissipative soliton (DS). This concept is highly useful in many different fields of science ranging from field theory, optics, and condensed matter physics to biology, medicine, and even sociology. This chapter aims to present a DS appearance from random fluctuations, development, and growth, the formation of the nontrivial internal structure of mature DS and its breakup, in other words, a full life cycle of DS as a self-organized object. Our extensive numerical simulations of the generalized cubic-quintic nonlinear Ginzburg-Landau equation, which models, in particular, dynamics of mode-locked fiber lasers, demonstrate a close analogy between the properties of DS and the general properties of turbulent and chaotic systems. In particular, we show a disintegration of DS into a noncoherent (or partially coherent) multisoliton complex. Thus, a DS can be interpreted as a complex of nonlinearly coupled coherent “internal modes” that allows developing the kinetic and thermodynamic theory of the nonequilibrious dissipative phenomena. Also, we demonstrate an improvement of DS integrity and, as a result, its disintegration suppression due to noninstantaneous nonlinearity caused by the stimulated Raman scattering. This effect leads to an appearance of a new coherent structure, namely, a dissipative Raman soliton

X-radiation of the moon and Roentgen cosmic background according to data of AMS ''Luna-12''

Satellite measurements of lunar soft X radiation, and Roentgen cosmic backgroun

Constructing the Cubic Interaction Vertex of Higher Spin Gauge Fields

We propose a method of construction of a cubic interaction in massless Higher Spin gauge theory both in flat and in AdS space-times of arbitrary dimensions. We consider a triplet formulation of the Higher Spin gauge theory and generalize the Higher Spin symmetry algebra of the free model to the corresponding algebra for the case of cubic interaction. The generators of this new algebra carry indexes which label the three Higher Spin fields involved into the cubic interaction. The method is based on the use of oscillator formalism and on the Becchi-Rouet-Stora-Tyutin (BRST) technique. We derive general conditions on the form of cubic interaction vertex and discuss the ambiguities of the vertex which result from field redefinitions. This method can in principle be applied for constructing the Higher Spin interaction vertex at any order. Our results are a first step towards the construction of a Lagrangian for interacting Higher Spin gauge fields that can be holographically studied.Comment: Published Version; comments added in introduction; minor typos and references correcte