Prolonging assembly through dissociation:A self assembly paradigm in microtubules

We study a one-dimensional model of microtubule assembly/disassembly in which GTP bound to tubulins within the microtubule undergoes stochastic hydrolysis. In contrast to models that only consider a cap of GTP-bound tubulin, stochastic hydrolysis allows GTP-bound tubulin remnants to exist within the microtubule. We find that these buried GTP remnants enable an alternative mechanism of recovery from shrinkage, and enhances fluctuations of filament lengths. Under conditions for which this alternative mechanism dominates, an increasing depolymerization rate leads to a decrease in dissociation rate and thus a net increase in assembly.Comment: accepted for publication in Physical Review

Entropy and Temperature of a Static Granular Assembly

Granular matter is comprised of a large number of particles whose collective behavior determines macroscopic properties such as flow and mechanical strength. A comprehensive theory of the properties of granular matter, therefore, requires a statistical framework. In molecular matter, equilibrium statistical mechanics, which is founded on the principle of conservation of energy, provides this framework. Grains, however, are small but macroscopic objects whose interactions are dissipative since energy can be lost through excitations of the internal degrees of freedom. In this work, we construct a statistical framework for static, mechanically stable packings of grains, which parallels that of equilibrium statistical mechanics but with conservation of energy replaced by the conservation of a function related to the mechanical stress tensor. Our analysis demonstrates the existence of a state function that has all the attributes of entropy. In particular, maximizing this state function leads to a well-defined granular temperature for these systems. Predictions of the ensemble are verified against simulated packings of frictionless, deformable disks. Our demonstration that a statistical ensemble can be constructed through the identification of conserved quantities other than energy is a new approach that is expected to open up avenues for statistical descriptions of other non-equilibrium systems.Comment: 5 pages, 4 figure

A linear programming-based method for job shop scheduling

We present a decomposition heuristic for a large class of job shop scheduling problems. This heuristic utilizes information from the linear programming formulation of the associated optimal timing problem to solve subproblems, can be used for any objective function whose associated optimal timing problem can be expressed as a linear program (LP), and is particularly effective for objectives that include a component that is a function of individual operation completion times. Using the proposed heuristic framework, we address job shop scheduling problems with a variety of objectives where intermediate holding costs need to be explicitly considered. In computational testing, we demonstrate the performance of our proposed solution approach

Microscopic Modeling of the Growth of Order in an Alloy: Nucleated and Continuous Ordering

We study the early-stages of ordering in $Cu_3 Au$ using a model Hamiltonian derived from the effective medium theory of cohesion in metals: an approach providing a microscopic description of interatomic interactions in alloys. Our simulations show a crossover from a nucleated growth regime to a region where the ordering does not follow any simple growth laws. This mirrors the experimental observations in $Cu_3 Au$. The kinetics of growth, obtained from the simulations, is in semi-quantitative agreement with experiments. The real-space structures observed in our simulations offer some insight into the nature of early-stage kineticsComment: 13 pages, Revtex, 3 postscript figures in a second file

Jamming in Systems Composed of Frictionless Ellipse-Shaped Particles

We study the structural and mechanical properties of jammed ellipse packings, and find that the nature of the jamming transition in these systems is fundamentally different from that for spherical particles. Ellipse packings are generically hypostatic with more degrees of freedom than constraints. The spectra of low energy excitations possess two gaps and three distinct branches over a range of aspect ratios. In the zero compression limit, the energy of the modes in the lowest branch increases {\it quartically} with deformation amplitude, and the density of states possesses a $\delta$-function at zero frequency. We identify scaling relations that collapse the low-frequency part of the spectra for different aspect ratios. Finally, we find that the degree of hypostaticity is determined by the number of quartic modes of the packing.Comment: 4 pages, 4 figure

Tulathromycin disturbs blood oxidative and coagulation status

The aim of this study was to determine the effect of tulathromycin on serum oxidative status and coagulation factors in rabbits. Tulathromycin was administered to eight rabbits, and blood samples were obtained 0, 1, 5, 10 and 15 days after treatment. Indicators of serum oxidative status (malondialdehyde, nitric oxide, superoxide dismutase, retinol and -carotene) and coagulation values (antithrombin III, fibrinogen) were measured after tulathromycin treatment. In addition, routine serum biochemical values (creatine kinase-MB, lactate dehydrogenase, alkaline phosphatase, alanine aminotransferase, aspartate aminotransferase, gamma glutamyl transferase, creatinine, blood urea nitrogen, cholesterol, triglyceride, high density lipoprotein, amylase, total protein, albumin, glucose and calcium), haemacell counts (white and red blood cells) and arterial blood gas parameters (packed cell volume, hemoglobin, pH, partial pressure of carbon dioxide, partial pressure of oxygen, actual bicarbonate, standard bicarbonate, total carbon dioxide, base excess in vivo, base excess in vitro, oxygen saturation, sodium and potassium) were also determined. Tulathromycin increased (P < 0.05) the levels of malondialdehyde, nitric oxide and superoxide dismutase activity, and decreased (P < 0.05) the level of antithrombin III. In conclusion, tulathromycin may cause oxidative damage and coagulation disorders during the treatment period.Key words: Tulathromycin, oxidative damage, coagulation disorder

Constraints and vibrations in static packings of ellipsoidal particles

We numerically investigate the mechanical properties of static packings of ellipsoidal particles in 2D and 3D over a range of aspect ratio and compression $\Delta \phi$. While amorphous packings of spherical particles at jamming onset ($\Delta \phi=0$) are isostatic and possess the minimum contact number $z_{\rm iso}$ required for them to be collectively jammed, amorphous packings of ellipsoidal particles generally possess fewer contacts than expected for collective jamming ($z < z_{\rm iso}$) from naive counting arguments, which assume that all contacts give rise to linearly independent constraints on interparticle separations. To understand this behavior, we decompose the dynamical matrix $M=H-S$ for static packings of ellipsoidal particles into two important components: the stiffness $H$ and stress $S$ matrices. We find that the stiffness matrix possesses $N(z_{\rm iso} - z)$ eigenmodes ${\hat e}_0$ with zero eigenvalues even at finite compression, where $N$ is the number of particles. In addition, these modes ${\hat e}_0$ are nearly eigenvectors of the dynamical matrix with eigenvalues that scale as $\Delta \phi$, and thus finite compression stabilizes packings of ellipsoidal particles. At jamming onset, the harmonic response of static packings of ellipsoidal particles vanishes, and the total potential energy scales as $\delta^4$ for perturbations by amplitude $\delta$ along these `quartic' modes, ${\hat e}_0$. These findings illustrate the significant differences between static packings of spherical and ellipsoidal particles.Comment: 18 pages, 21 figure

Dynamics of Ordering in Alloys with Modulated Phases

This paper presents a theoretical model for studying the dynamics of ordering in alloys which exhibit modulated phases. The model is different from the standard time-dependent Ginzburg-Landau description of the evolution of a non-conserved order parameter and resembles the Swift-Hohenberg model. The early-stage growth kinetics is analyzed and compared to the Cahn-Hilliard theory of continuous ordering. The effects of non-linearities on the growth kinetics are discussed qualitatively and it is shown that the presence of an underlying elastic lattice introduces qualitatively new effects. A lattice Hamiltonian capable of describing these effects and suitable for carrying out simulations of the growth kinetics is also constructed.Comment: 18 pages, 3 figures (postscript files appended), Brandeis-BC9