Constitutive modeling for isotropic materials

The unified constitutive theories for application to typical isotropic cast nickel base supperalloys used for air-cooled turbine blades were evaluated. The specific modeling aspects evaluated were: uniaxial, monotonic, cyclic, creep, relaxation, multiaxial, notch, and thermomechanical behavior. Further development of the constitutive theories to model thermal history effects, refinement of the material test procedures, evaluation of coating effects, and verification of the models in an alternate material will be accomplished in a follow-on for this base program

A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks

We introduce an alternative formulation of the exact stochastic simulation algorithm (SSA) for sampling trajectories of the chemical master equation for a well-stirred system of coupled chemical reactions. Our formulation is based on factored-out, partial reaction propensities. This novel exact SSA, called the partial propensity direct method (PDM), is highly efficient and has a computational cost that scales at most linearly with the number of chemical species, irrespective of the degree of coupling of the reaction network. In addition, we propose a sorting variant, SPDM, which is especially efficient for multiscale reaction networks.Comment: 23 pages, 3 figures, 4 tables; accepted by J. Chem. Phy

Global parameter identification of stochastic reaction networks from single trajectories

We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from live-cell fluorescence microscopy in image-based systems biology. In addition, fluctuation time-courses from, e.g., fluorescence correlation spectroscopy provide additional information about the system dynamics that can be used to more robustly infer parameters than when considering only mean concentrations. Estimating model parameters from a single experimental trajectory enables single-cell measurements and quantification of cell--cell variability. We propose a novel combination of an adaptive Monte Carlo sampler, called Gaussian Adaptation, and efficient exact stochastic simulation algorithms that allows parameter identification from single stochastic trajectories. We benchmark the proposed method on a linear and a non-linear reaction network at steady state and during transient phases. In addition, we demonstrate that the present method also provides an ellipsoidal volume estimate of the viable part of parameter space and is able to estimate the physical volume of the compartment in which the observed reactions take place.Comment: Article in print as a book chapter in Springer's "Advances in Systems Biology

Instabilities and waves in thin films of living fluids

We formulate the thin-film hydrodynamics of a suspension of polar self-driven particles and show that it is prone to several instabilities through the interplay of activity, polarity and the existence of a free surface. Our approach extends, to self-propelling systems, the work of Ben Amar and Cummings [Phys Fluids 13 (2001) 1160] on thin-film nematics. Based on our estimates the instabilities should be seen in bacterial suspensions and the lamellipodium, and are potentially relevant to the morphology of biofilms. We suggest several experimental tests of our theory.Comment: 4 pages, pdflatex, accepted for publication in Phys Rev Let

Power spectrum of mass and activity fluctuations in a sandpile

We consider a directed abelian sandpile on a strip of size $2\times n$, driven by adding a grain randomly at the left boundary after every $T$ time-steps. We establish the exact equivalence of the problem of mass fluctuations in the steady state and the number of zeroes in the ternary-base representation of the position of a random walker on a ring of size $3^n$. We find that while the fluctuations of mass have a power spectrum that varies as $1/f$ for frequencies in the range $3^{-2n} \ll f \ll 1/T$, the activity fluctuations in the same frequency range have a power spectrum that is linear in $f$.Comment: 8 pages, 10 figure

A Dynamic Renormalization Group Study of Active Nematics

We carry out a systematic construction of the coarse-grained dynamical equation of motion for the orientational order parameter for a two-dimensional active nematic, that is a nonequilibrium steady state with uniaxial, apolar orientational order. Using the dynamical renormalization group, we show that the leading nonlinearities in this equation are marginally \textit{irrelevant}. We discover a special limit of parameters in which the equation of motion for the angle field of bears a close relation to the 2d stochastic Burgers equation. We find nevertheless that, unlike for the Burgers problem, the nonlinearity is marginally irrelevant even in this special limit, as a result of of a hidden fluctuation-dissipation relation. 2d active nematics therefore have quasi-long-range order, just like their equilibrium counterpartsComment: 31 pages 6 figure

Approach to equilibrium in adiabatically evolving potentials

For a potential function (in one dimension) which evolves from a specified initial form $V_{i}(x)$ to a different $V_{f}(x)$ asymptotically, we study the evolution, in an overdamped dynamics, of an initial probability density to its final equilibeium.There can be unexpected effects that can arise from the time dependence. We choose a time variation of the form $V(x,t)=V_{f}(x)+(V_{i}-V_{f})e^{-\lambda t}$. For a $V_{f}(x)$, which is double welled and a $V_{i}(x)$ which is simple harmonic, we show that, in particular, if the evolution is adiabatic, the results in a decrease in the Kramers time characteristics of $V_{f}(x)$. Thus the time dependence makes diffusion over a barrier more efficient. There can also be interesting resonance effects when $V_{i}(x)$ and $V_{f}(x)$ are two harmonic potentials displaced with respect to each other that arise from the coincidence of the intrinsic time scale characterising the potential variation and the Kramers time.Comment: This paper contains 5 page

Melting-freezing cycles in a relatively sheared pair of crystalline monolayers

The nonequilibrium dynamical behaviour that arises when two ordered two-dimensional monolayers of particles are sheared over each other is studied in Brownian dynamics simulations. A curious sequence of nonequilibrium states is observed as the driving rate is increased, the most striking of which is a sliding state with irregular alternation between disordered and ordered states. We comment on possible mechanisms underlying these cycles, and experiments that could observe them.Comment: 7 pages, 8 figures, minor changes in text and figures, references adde

Iontophoresis to enhance topical delivery of terbinafine to the nail

The aim of this study was to investigate the application of electric current to enhance the ungual permeation of terbinafine – an antifungal agent that is currently delivered systemically for the treatment of onychomycosis

Small-angle grain boundaries in quasicrystals

The Read-Shockley treatment of small-angle grain boundaries in crystals is generalized to the case of quasicrystals. The dependence of the grain-boundary energy on the angle of mismatch between abutting quasicrystalline grains is calculated. It is found that, even for a symmetric tilt boundary in a quasicrystal, dislocations with at least two types of Burgers vectors are required; these dislocations have to be arranged quasiperiodically along the boundary. The possible clumping of these dislocations to form composites is discussed. Explicit calculations are presented for a pentagonal quasicrystal