Static cylindrically symmetric spacetimes

We prove existence of static solutions to the cylindrically symmetric Einstein-Vlasov system, and we show that the matter cylinder has finite extension. The same results are also proved for a quite general class of equations of state for perfect fluids coupled to the Einstein equations, extending the class of equations of state considered in \cite{BL}. We also obtain this result for the Vlasov-Poisson system.Comment: Added acknowledgemen

Critical collapse of collisionless matter - a numerical investigation

In recent years the threshold of black hole formation in spherically symmetric gravitational collapse has been studied for a variety of matter models. In this paper the corresponding issue is investigated for a matter model significantly different from those considered so far in this context. We study the transition from dispersion to black hole formation in the collapse of collisionless matter when the initial data is scaled. This is done by means of a numerical code similar to those commonly used in plasma physics. The result is that for the initial data for which the solutions were computed, most of the matter falls into the black hole whenever a black hole is formed. This results in a discontinuity in the mass of the black hole at the onset of black hole formation.Comment: 22 pages, LaTeX, 7 figures (ps-files, automatically included using psfig

Reaction Brownian Dynamics and the effect of spatial fluctuations on the gain of a push-pull network

Brownian Dynamics algorithms are widely used for simulating soft-matter and biochemical systems. In recent times, their application has been extended to the simulation of coarse-grained models of cellular networks in simple organisms. In these models, components move by diffusion, and can react with one another upon contact. However, when reactions are incorporated into a Brownian Dynamics algorithm, attention must be paid to avoid violations of the detailed-balance rule, and therefore introducing systematic errors in the simulation. We present a Brownian Dynamics algorithm for reaction-diffusion systems that rigorously obeys detailed balance for equilibrium reactions. By comparing the simulation results to exact analytical results for a bimolecular reaction, we show that the algorithm correctly reproduces both equilibrium and dynamical quantities. We apply our scheme to a ``push-pull'' network in which two antagonistic enzymes covalently modify a substrate. Our results highlight that the diffusive behaviour of the reacting species can reduce the gain of the response curve of this network.Comment: 25 pages, 7 figures, submitted to Journal of Chemical Physic

Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique