The Inherent Structure Landscape Connection Between Liquids, Granular materials and the Jamming Phase Diagram

We provide a comprehensive picture of the jamming phase diagram by connecting the athermal, granular ensemble of jammed states and the equilibrium fluid through the inherent structure paradigm for a system hard discs confined to a narrow channel. The J-line is shown to be divided into packings that are thermodynamically accessible from the equilibrium fluid and inaccessible packings. The J-point is found to occur at the transition between these two sets of packings and is located at the maximum the inherent structure distribution. A general thermodynamic argument suggests that the density of the states at the configurational entropy maximum represents a lower bound on the J-point density in hard sphere systems. Finally, we find that the granular and fluid systems only occupy the same set of inherent structures, under the same thermodynamic conditions, at two points, corresponding to zero and infinite pressures, where they sample the J-point states and the most dense packing respectively.Comment: 5 pages, 3 Figure

Characterization and In Silico Analysis of Pregnancy-Associated Glycoprotein-1 Gene of Buffalo (Bubalus bubalis)

Pregnancy-Associated Glycoproteins (PAGs) are trophoblastic proteins belonging to the Aspartic proteinase family secreted by different placental cells of many mammalian species. They play a pivotal role in placentogenesis, foetomaternal unit remodeling, and implantation. The identification of the genes encoding those proteins will be helpful to unravel the intricate embryogenomic functions during pregnancy establishment. Considering importance of these proteins, the present study was undertaken to characterize the pregnancy associated glycoprotein-1 gene of buffalo. An 1181 base pairs buffalo Pregnancy-Associated Glycoprotein PAG-1 gene was PCR amplified from the RNA obtained from the fetal cotyledons. BLAST analysis of the buffalo PAG-1 sequence retrieved a total of 20 cattle, 5 goat, and 4 sheep PAG sequences, exhibiting more than 80% similarity. Buffalo PAG-1 gene contained an uninterrupted open reading frame of 1140 base pairs encoding 380 amino acids that possess a 15 amino acid signal peptide and mature peptide of 365 amino acids. The phylogenetic study of the buffalo PAG-1 gene revealed buffalo PAG-1 is more related to cattle, goat, and sheep PAG-1 sequences. By this study characterization of buffalo PAG-1 gene and its evolutionary relationship was deduced for the first time

Plankton lattices and the role of chaos in plankton patchiness

Spatiotemporal and interspecies irregularities in planktonic populations have been widely observed. Much research into the drivers of such plankton patches has been initiated over the past few decades but only recently have the dynamics of the interacting patches themselves been considered. We take a coupled lattice approach to model continuous-in-time plankton patch dynamics, as opposed to the more common continuum type reaction-diffusion-advection model, because it potentially offers a broader scope of application and numerical study with relative ease. We show that nonsynchronous plankton patch dynamics (the discrete analog of spatiotemporal irregularity) arise quite naturally for patches whose underlying dynamics are chaotic. However, we also observe that for parameters in a neighborhood of the chaotic regime, smooth generalized synchronization of nonidentical patches is more readily supported which reduces the incidence of distinct patchiness. We demonstrate that simply associating the coupling strength with measurements of (effective) turbulent diffusivity results in a realistic critical length of the order of 100 km, above which one would expect to observe unsynchronized behavior. It is likely that this estimate of critical length may be reduced by a more exact interpretation of coupling in turbulent flows

A new approach to partial synchronization in globally coupled rotators

We develop a formalism to analyze the behaviour of pulse--coupled identical phase oscillators with a specific attention devoted to the onset of partial synchronization. The method, which allows describing the dynamics both at the microscopic and macroscopic level, is introduced in a general context, but then the application to the dynamics of leaky integrate-and-fire (LIF) neurons is analysed. As a result, we derive a set of delayed equations describing exactly the LIF behaviour in the thermodynamic limit. We also investigate the weak coupling regime by means of a perturbative analysis, which reveals that the evolution rule reduces to a set of ordinary differential equations. Robustness and generality of the partial synchronization regime is finally tested both by adding noise and considering different force fields.Comment: 5 pages, 3 eps figure

Improving Assessment of Drug Safety Through Proteomics: Early Detection and Mechanistic Characterization of the Unforeseen Harmful Effects of Torcetrapib.

BackgroundEarly detection of adverse effects of novel therapies and understanding of their mechanisms could improve the safety and efficiency of drug development. We have retrospectively applied large-scale proteomics to blood samples from ILLUMINATE (Investigation of Lipid Level Management to Understand its Impact in Atherosclerotic Events), a trial of torcetrapib (a cholesterol ester transfer protein inhibitor), that involved 15 067 participants at high cardiovascular risk. ILLUMINATE was terminated at a median of 550 days because of significant absolute increases of 1.2% in cardiovascular events and 0.4% in mortality with torcetrapib. The aims of our analysis were to determine whether a proteomic analysis might reveal biological mechanisms responsible for these harmful effects and whether harmful effects of torcetrapib could have been detected early in the ILLUMINATE trial with proteomics.MethodsA nested case-control analysis of paired plasma samples at baseline and at 3 months was performed in 249 participants assigned to torcetrapib plus atorvastatin and 223 participants assigned to atorvastatin only. Within each treatment arm, cases with events were matched to controls 1:1. Main outcomes were a survey of 1129 proteins for discovery of biological pathways altered by torcetrapib and a 9-protein risk score validated to predict myocardial infarction, stroke, heart failure, or death.ResultsPlasma concentrations of 200 proteins changed significantly with torcetrapib. Their pathway analysis revealed unexpected and widespread changes in immune and inflammatory functions, as well as changes in endocrine systems, including in aldosterone function and glycemic control. At baseline, 9-protein risk scores were similar in the 2 treatment arms and higher in participants with subsequent events. At 3 months, the absolute 9-protein derived risk increased in the torcetrapib plus atorvastatin arm compared with the atorvastatin-only arm by 1.08% (P=0.0004). Thirty-seven proteins changed in the direction of increased risk of 49 proteins previously associated with cardiovascular and mortality risk.ConclusionsHeretofore unknown effects of torcetrapib were revealed in immune and inflammatory functions. A protein-based risk score predicted harm from torcetrapib within just 3 months. A protein-based risk assessment embedded within a large proteomic survey may prove to be useful in the evaluation of therapies to prevent harm to patients.Clinical trial registrationURL: https://www.clinicaltrials.gov. Unique identifier: NCT00134264

Encoding via conjugate symmetries of slow oscillations for globally coupled oscillators

Peter Ashwin and Jon Borresen, Physical Review E, Vol. 70, p. 026203 (2004). "Copyright © 2004 by the American Physical Society."We study properties of the dynamics underlying slow cluster oscillations in two systems of five globally coupled oscillators. These slow oscillations are due to the appearance of structurally stable heteroclinic connections between cluster states in the noise-free dynamics. In the presence of low levels of noise they give rise to long periods of residence near cluster states interspersed with sudden transitions between them. Moreover, these transitions may occur between cluster states of the same symmetry, or between cluster states with conjugate symmetries given by some rearrangement of the oscillators. We consider the system of coupled phase oscillators studied by Hansel et al. [Phys. Rev. E 48, 3470 (1993)] in which one can observe slow, noise-driven oscillations that occur between two families of two cluster periodic states; in the noise-free case there is a robust attracting heteroclinic cycle connecting these families. The two families consist of symmetric images of two inequivalent periodic orbits that have the same symmetry. For N=5 oscillators, one of the periodic orbits has one unstable direction and the other has two unstable directions. Examining the behavior on the unstable manifold for the two unstable directions, we observe that the dimensionality of the manifold can give rise to switching between conjugate symmetry orbits. By applying small perturbations to the system we can easily steer it between a number of different marginally stable attractors. Finally, we show that similar behavior occurs in a system of phase-energy oscillators that are a natural extension of the phase model to two dimensional oscillators. We suggest that switching between conjugate symmetries is a very efficient method of encoding information into a globally coupled system of oscillators and may therefore be a good and simple model for the neural encoding of information

The Glass Transition and Liquid-Gas Spinodal Boundaries of Metastable Liquids

A liquid can exist under conditions of thermodynamic stability or metastability within boundaries defined by the liquid-gas spinodal and the glass transition line. The relationship between these boundaries has been investigated previously using computer simulations, the energy landscape formalism, and simplified model calculations. We calculate these stability boundaries semi-analytically for a model glass forming liquid, employing accurate liquid state theory and a first-principles approach to the glass transition. These boundaries intersect at a finite temperature, consistent with previous simulation-based studies.Comment: Minor text revisions. Fig.s 4, 5 update