Rigidity and flexibility of biological networks

The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of protein structures, as well as local flexibility measures of proteins and their applications in explaining allostery and thermostability is given. We also briefly discuss the network aspects of cytoskeletal tensegrity. Finally, we show the importance of the balance between functional flexibility and rigidity in protein-protein interaction, metabolic, gene regulatory and neuronal networks. Our summary raises the possibility that the concepts of flexibility and rigidity can be generalized to all networks.Comment: 21 pages, 4 figures, 1 tabl

Real-time lattice boltzmann shallow waters method for breaking wave simulations

We present a new approach for the simulation of surfacebased fluids based in a hybrid formulation of Lattice Boltzmann Method for Shallow Waters and particle systems. The modified LBM can handle arbitrary underlying terrain conditions and arbitrary fluid depth. It also introduces a novel method for tracking dry-wet regions and moving boundaries. Dynamic rigid bodies are also included in our simulations using a two-way coupling. Certain features of the simulation that the LBM can not handle because of its heightfield nature, as breaking waves, are detected and automatically turned into splash particles. Here we use a ballistic particle system, but our hybrid method can handle more complex systems as SPH. Both the LBM and particle systems are implemented in CUDA, although dynamic rigid bodies are simulated in CPU. We show the effectiveness of our method with various examples which achieve real-time on consumer-level hardware.Peer ReviewedPostprint (author's final draft

Technology for large space systems: A special bibliography with indexes (supplement 04)

This bibliography lists 259 reports, articles, and other documents introduced into the NASA scientific and technical information system between July 1, 1980 and December 31, 1980. Its purpose is to provide information to the researcher, manager, and designer in technology development and mission design in the area of the Large Space Systems Technology Program. Subject matter is grouped according to systems, interactive analysis and design. Structural concepts, control systems, electronics, advanced materials, assembly concepts, propulsion, solar power satellite systems, and flight experiments

Cytoskeleton and Cell Motility

The present article is an invited contribution to the Encyclopedia of Complexity and System Science, Robert A. Meyers Ed., Springer New York (2009). It is a review of the biophysical mechanisms that underly cell motility. It mainly focuses on the eukaryotic cytoskeleton and cell-motility mechanisms. Bacterial motility as well as the composition of the prokaryotic cytoskeleton is only briefly mentioned. The article is organized as follows. In Section III, I first present an overview of the diversity of cellular motility mechanisms, which might at first glance be categorized into two different types of behaviors, namely "swimming" and "crawling". Intracellular transport, mitosis - or cell division - as well as other extensions of cell motility that rely on the same essential machinery are briefly sketched. In Section IV, I introduce the molecular machinery that underlies cell motility - the cytoskeleton - as well as its interactions with the external environment of the cell and its main regulatory pathways. Sections IV D to IV F are more detailed in their biochemical presentations; readers primarily interested in the theoretical modeling of cell motility might want to skip these sections in a first reading. I then describe the motility mechanisms that rely essentially on polymerization-depolymerization dynamics of cytoskeleton filaments in Section V, and the ones that rely essentially on the activity of motor proteins in Section VI. Finally, Section VII is devoted to the description of the integrated approaches that have been developed recently to try to understand the cooperative phenomena that underly self-organization of the cell cytoskeleton as a whole.Comment: 31 pages, 16 figures, 295 reference

Diversity, Stability, Recursivity, and Rule Generation in Biological System: Intra-inter Dynamics Approach

Basic problems for the construction of a scenario for the Life are discussed. To study the problems in terms of dynamical systems theory, a scheme of intra-inter dynamics is presented. It consists of internal dynamics of a unit, interaction among the units, and the dynamics to change the dynamics itself, for example by replication (and death) of units according to their internal states. Applying the dynamics to cell differentiation, isologous diversification theory is proposed. According to it, orbital instability leads to diversified cell behaviors first. At the next stage, several cell types are formed, first triggered by clustering of oscillations, and then as attracting states of internal dynamics stabilized by the cell-to-cell interaction. At the third stage, the differentiation is determined as a recursive state by cell division. At the last stage, hierarchical differentiation proceeds, with the emergence of stochastic rule for the differentiation to sub-groups, where regulation of the probability for the differentiation provides the diversity and stability of cell society. Relevance of the theory to cell biology is discussed.Comment: 19 pages, Int.J. Mod. Phes. B (in press