Large phenotype jumps in biomolecular evolution

By defining the phenotype of a biopolymer by its active three-dimensional shape, and its genotype by its primary sequence, we propose a model that predicts and characterizes the statistical distribution of a population of biopolymers with a specific phenotype, that originated from a given genotypic sequence by a single mutational event. Depending on the ratio g0 that characterizes the spread of potential energies of the mutated population with respect to temperature, three different statistical regimes have been identified. We suggest that biopolymers found in nature are in a critical regime with g0 in the range 1-6, corresponding to a broad, but not too broad, phenotypic distribution resembling a truncated Levy flight. Thus the biopolymer phenotype can be considerably modified in just a few mutations. The proposed model is in good agreement with the experimental distribution of activities determined for a population of single mutants of a group I ribozyme.Comment: to appear in Phys. Rev. E; 7 pages, 6 figures; longer discussion in VII, new fig.

Phase transition in inelastic disks

This letter investigates the molecular dynamics of inelastic disks without external forcing. By introducing a new observation frame with a rescaled time, we observe the virtual steady states converted from asymptotic energy dissipation processes. System behavior in the thermodynamic limit is carefully investigated. It is found that a phase transition with symmetry breaking occurs when the magnitude of dissipation is greater than a critical value.Comment: 9 pages, 6 figure

A Model for Force Fluctuations in Bead Packs

We study theoretically the complex network of forces that is responsible for the static structure and properties of granular materials. We present detailed calculations for a model in which the fluctuations in the force distribution arise because of variations in the contact angles and the constraints imposed by the force balance on each bead of the pile. We compare our results for force distribution function for this model, including exact results for certain contact angle probability distributions, with numerical simulations of force distributions in random sphere packings. This model reproduces many aspects of the force distribution observed both in experiment and in numerical simulations of sphere packings

Suppression of mitochondrial respiration through recruitment of p160 myb binding protein to PGC-1α : modulation by p38 MAPK

The transcriptional coactivator PPAR gamma coactivator 1 α (PGC-1α) is a key regulator of metabolic processes such as mitochondrial biogenesis and respiration in muscle and gluconeogenesis in liver. Reduced levels of PGC-1α in humans have been associated with type II diabetes. PGC-1α contains a negative regulatory domain that attenuates its transcriptional activity. This negative regulation is removed by phosphorylation of PGC-1α by p38 MAPK, an important kinase downstream of cytokine signaling in muscle and β-adrenergic signaling in brown fat. We describe here the identification of p160 myb binding protein (p160MBP) as a repressor of PGC-1α. The binding and repression of PGC-1α by p160MBP is disrupted by p38 MAPK phosphorylation of PGC-1α. Adenoviral expression of p160MBP in myoblasts strongly reduces PGC-1α's ability to stimulate mitochondrial respiration and the expression of the genes of the electron transport system. This repression does not require removal of PGC-1α from chromatin, suggesting that p160MBP is or recruits a direct transcriptional suppressor. Overall, these data indicate that p160MBP is a powerful negative regulator of PGC-1α function and provide a molecular mechanism for the activation of PGC-1α by p38 MAPK. The discovery of p160MBP as a PGC-1α regulator has important implications for the understanding of energy balance and diabetes

Breakdown of self-organized criticality

We introduce two sandpile models which show the same behavior of real sandpiles, that is, an almost self-organized critical behavior for small systems and the dominance of large avalanches as the system size increases. The systems become fully self-organized critical, with the critical exponents of the Bak, Tang and Wiesenfeld model, as the system parameters are changed, showing that these systems can make a bridge between the well known theoretical and numerical results and what is observed in real experiments. We find that a simple mechanism determines the boundary where self-organized can or cannot exist, which is the presence of local chaos.Comment: 3 pages, 4 figure

Slowly driven sandpile formation with granular mixtures

We introduce a one-dimensional sandpile model with $N$ different particle types and an infinitesimal driving rate. The parameters for the model are the N^2 critical slopes for one type of particle on top of another. The model is trivial when N=1, but for N=2 we observe four broad classes of sandpile structure in different regions of the parameter space. We describe and explain the behaviour of each of these classes, giving quantitative analysis wherever possible. The behaviour of sandpiles with N>2 essentially consists of combinations of these four classes. We investigate the model's robustness and highlight the key areas that any experiment designed to reproduce these results should focus on

Inelastic Collapse of Three Particles

A system of three particles undergoing inelastic collisions in arbitrary spatial dimensions is studied with the aim of establishing the domain of ``inelastic collapse''---an infinite number of collisions which take place in a finite time. Analytic and simulation results show that for a sufficiently small restitution coefficient, $0\leq r<7-4\sqrt{3}\approx 0.072$, collapse can occur. In one dimension, such a collapse is stable against small perturbations within this entire range. In higher dimensions, the collapse can be stable against small variations of initial conditions, within a smaller $r$ range, $0\leq r<9-4\sqrt{5}\approx 0.056$.Comment: 6 pages, figures on request, accepted by PR

Demonstration of the Complementarity of One- and Two-Photon Interference

The visibilities of second-order (single-photon) and fourth-order (two-photon) interference have been observed in a Young's double-slit experiment using light generated by spontaneous parametric down-conversion and a photon-counting intensified CCD camera. Coherence and entanglement underlie one-and two-photon interference, respectively. As the effective source size is increased, coherence is diminished while entanglement is enhanced, so that the visibility of single-photon interference decreases while that of two-photon interference increases. This is the first experimental demonstration of the complementarity between single- and two-photon interference (coherence and entanglement) in the spatial domain.Comment: 21 pages, 7 figure

Silicates in D-type symbiotic stars: an ISO overview

We investigate the IR spectral features of a sample of D-type symbiotic stars. Analyzing unexploited ISO-SWS data, deriving the basic observational parameters of dust bands and comparing them with respect to those observed in other astronomical sources, we try to highlight the effect of environment on grain chemistry and physic. We find strong amorphous silicate emission bands at 10 micron and 18 micron in a large fraction of the sample. The analysis of the 10 micron band, along with a direct comparison with several astronomical sources, reveals that silicate dust in symbiotic stars shows features between the characteristic circumstellar environments and the interstellar medium. This indicates an increasing reprocessing of grains in relation to specific symbiotic behavior of the objects. A correlation between the central wavelength of the 10 and 18 micron dust bands is found. By the modeling of IR spectral lines we investigate also dust grains conditions within the shocked nebulae. Both the unusual depletion values and the high sputtering efficiency might be explained by the formation of SiO moleculae, which are known to be a very reliable shock tracer. We conclude that the signature of dust chemical disturbance due to symbiotic activity should be looked for in the outer, circumbinary, expanding shells where the environmental conditions for grain processing might be achieved. Symbiotic stars are thus attractive targets for new mid-infrared and mm observations.Comment: 24 pages, 6 figures, 5 tables - to be published in A