Growth curves with time-dependent explanatory variables

A class of growth models incorporating time-dependent factors and stochastic perturbations are introduced. The proposed model includes the existing growth models used in fisheries as special cases. Particular attention is given to growth of a population (in average weight or length) from which observations are taken randomly each time and the analysis of tag-recapture data. Two real data sets are used for illustration: (a) to estimate the seasonal effect and population density effect on growth of farmed prawn (Penaeus monodon) from weight data and (b) to assess the effect of tagging on growth of barramundi (Lates calcarifer)

Small-amplitude cyclic voltammetry: Part I. A simple fourier synthesis approach

Current-potential relationships are derived for small-amplitude periodic inputs for linear electrochemical systems using a Fourier synthesis procedure. Specific results have been obtained for a triangular potential waveform for two simple model systems.

Elastic analysis of pin joints in plates under some combined pin and plate loads

Joints are primary sources of weakness in structures. Pin joints are very common and are used where periodic disassembly of components is needed. A circular pin in a circular hole in an infinitely large plate is an abstraction of such a pin joint. A two-dimensional plane-stress analysis of such a configuration is carried out, here, subjected to pin-bearing and/or biaxial-plate loading. The pin is assumed to be rigid compared to the plate material. For pin load the reactive stresses at the edges of the infinite plate tend to zero though their integral over the external boundary equals to the pin load. The pin-hole interface is unbonded and so beyond some load levels the plate separates from the pin and the extent of separation is a non-linear function of load level. The problem is solved by inverse technique where the extent of contact is specified and the causative loads are evaluated directly. In the situations where combined load is acting the separation-contact zone specification generally needs two parameters (angles) to be specified. The present report deals with analysing such a situation in metallic (or isotropic) plates. Numerical results are provided for parametric representation and the methodology is demonstrated.

Systematic stability analysis of the renormalization group flow for the normal-superconductor-normal junction of Luttinger liquid wires

We study the renormalization group flows of the two terminal conductance of a superconducting junction of two Luttinger liquid wires. We compute the power laws associated with the renormalization group flow around the various fixed points of this system using the generators of the SU(4) group to generate the appropriate parametrization of an matrix representing small deviations from a given fixed point matrix [obtained earlier in S. Das, S. Rao, and A. Saha, Phys. Rev. B 77, 155418 (2008)], and we then perform a comprehensive stability analysis. In particular, for the nontrivial fixed point which has intermediate values of transmission, reflection, Andreev reflection, and crossed Andreev reflection, we show that there are eleven independent directions in which the system can be perturbed, which are relevant or irrelevant, and five directions which are marginal. We obtain power laws associated with these relevant and irrelevant perturbations. Unlike the case of the two-wire charge-conserving junction, here we show that there are power laws which are nonlinear functions of V(0) and V(2kF) [where V(k) represents the Fourier transform of the interelectron interaction potential at momentum k]. We also obtain the power law dependence of linear response conductance on voltage bias or temperature around this fixed point.

Conformational Dynamics in Alkyl Chains of an Anchored Bilayer: A Molecular Dynamics Study

Molecular dynamics (MD) simulations are reported for an anchored bilayer formed by the intercalation of cetyl trimethyl ammonium (CTA) and CH3(CH2)15N+(CH3) ions in a layered solid, CdPS3. The intercalated CTA ions are organized with the cationic headgroups tethered to the inorganic sheet and the hydrocarbon tails arranged as bilayers. Simulations were performed at three temperatures, 65, 180, and 298 K, using an isothermal−isobaric ensemble that was subsequently switched once macroscopic parameters had converged to a canonical isothermal−isochoric ensemble. The simulations are able to reproduce the experimental features of this system, including the formation of the bilayer and layer-to-layer separation distance. An analysis of the conformation of the chains showed that at all three temperatures a fraction of the alkyl chains retained a planar all-trans conformation, and that gauche bonds occurred as part of a “kink” (gauche+−trans−gauche−) sequence and not as isolated gauche bonds. Trans−gauche isomerization rates for the alkyl chains in the anchored bilayer are slower than those in lipid bilayers at the same temperature and show a progressive increase as the torsion numbers approach the tail. A two-dimensional periodic Voronoi tessellation analysis was performed to obtain the single-molecular area of an alkyl chain in the bilayer. The single-molecular area relaxation times are an order of magnitude longer than the trans−gauche isomerization times. The results indicate that the trans−gauche isomerization is associated with the creation and annihilation of a kink defect sequence. The results of the present MD simulation explain the apparent conflicting estimates of the gauche disorder in this system as obtained from infrared and 13C nuclear magnetic resonance measurements.

The influence of the motion of a rotor grid on a stator grid

In this paper we have used the method of characteristics developed for two dimensional unsteady flow problems to study a simplified axial turbine problem. The system consists of two sets of blades —the guiding vanes which are fixed and the rotor blades which move perpendicular to these vanes. The initial undisturbed constant flow in the system is perturbed by introducing a small velocity normal to the rotor blades to simulate a slight constant inclination. The resulting perturbed flow is periodic after the first three cycles. We have studied the perturbed density distribution throughout the system during a period.

Photodimerization of coumarin in aqueous and micellar media

The photochemical and photophysical processes of many organic compounds are a function of the environment in which they are present. In this connection we have chosen to investigate the environmental perturbations on the photodimerization of coumarin,l and the results of our study in aqueous and micellar media are presented in this paper. Coumarin has historically been the subject of intense photochemical and spectroscopic interest, mainly as a consequence of its importance in biological systems. Coumarin has been chosen for our investigation as its fascinating photochemical behavior has been fairly well explored,2 and therefore the environmental influence, which is the subject of our concern, would be easily understandable.

M. bovis BCG induced expression of COX-2 involves nitric oxide-dependent and -independent signaling pathways

In a multifaceted immunity to mycobacterial infection, induced expression of cyclooxygenase-2 (COX-2) by Mycobacterium bovis bacillus Calmette-Guerin (BCG) may act as an important influencing factor for the effective host immunity. We here demonstrate that M. bovis BCG-triggered TLR2-dependent signaling leads to COX-2 and PGE2 expression in vitro in macrophages and in vivo in mice. Further, the presence of PGE2 could be demonstrated in sera or cerebrospinal fluid of tuberculosis patients. The induced COX-2 expression in macrophages is dependent on NF-kappa B activation, which is mediated by inducible NO synthase (iNOS)/NO-dependent participation of the members of Notch1-PI-3K signaling cascades as well as iNOS-independent activation of ERK1/2 and p38 MAPKs. Inhibition of iNOS activity abrogated the M. bovis BCG ability to trigger the generation of Notch1 intracellular domain (NICD), a marker for Notch1 signaling activation, as well as activation of the PI-3K signaling cascade. On the contrary, treatment of macrophages with 3-morpholinosydnonimine, a NO donor, resulted in a rapid increase in generation of NICD, activation of PI-3K pathway, as well as the expression of COX-2. Stable expression of NICD in RAW 264.7 macrophages resulted in augmented expression of COX-2. Further, signaling perturbations suggested the involvement of the cross-talk of Notch1 with members with the PI-3K signaling cascade. These results implicate the dichotomous nature of TLR2 signaling during M. bovis BCG-triggered expression of COX-2. In this perspective, we propose the involvement of iNOS/NO as one of the obligatory, early, proximal signaling events during M. bovis BCG-induced COX-2 expression in macrophages.

Strong-coupling expansion for the momentum distribution of the Bose-Hubbard model with benchmarking against exact numerical results

A strong-coupling expansion for the Green's functions, self-energies, and correlation functions of the Bose-Hubbard model is developed. We illustrate the general formalism, which includes all possible (normal-phase) inhomogeneous effects in the formalism, such as disorder or a trap potential, as well as effects of thermal excitations. The expansion is then employed to calculate the momentum distribution of the bosons in the Mott phase for an infinite homogeneous periodic system at zero temperature through third order in the hopping. By using scaling theory for the critical behavior at zero momentum and at the critical value of the hopping for the Mott insulator–to–superfluid transition along with a generalization of the random-phase-approximation-like form for the momentum distribution, we are able to extrapolate the series to infinite order and produce very accurate quantitative results for the momentum distribution in a simple functional form for one, two, and three dimensions. The accuracy is better in higher dimensions and is on the order of a few percent relative error everywhere except close to the critical value of the hopping divided by the on-site repulsion. In addition, we find simple phenomenological expressions for the Mott-phase lobes in two and three dimensions which are much more accurate than the truncated strong-coupling expansions and any other analytic approximation we are aware of. The strong-coupling expansions and scaling-theory results are benchmarked against numerically exact quantum Monte Carlo simulations in two and three dimensions and against density-matrix renormalization-group calculations in one dimension. These analytic expressions will be useful for quick comparison of experimental results to theory and in many cases can bypass the need for expensive numerical simulations.

Flux balance analysis of biological systems: applications and challenges

Systems level modelling and simulations of biological processes are proving to be invaluable in obtaining a quantitative and dynamic perspective of various aspects of cellular function. In particular, constraint-based analyses of metabolic networks have gained considerable popularity for simulating cellular metabolism, of which flux balance analysis (FBA), is most widely used. Unlike mechanistic simulations that depend on accurate kinetic data, which are scarcely available, FBA is based on the principle of conservation of mass in a network, which utilizes the stoichiometric matrix and a biologically relevant objective function to identify optimal reaction flux distributions. FBA has been used to analyse genome-scale reconstructions of several organisms; it has also been used to analyse the effect of perturbations, such as gene deletions or drug inhibitions in silico. This article reviews the usefulness of FBA as a tool for gaining biological insights, advances in methodology enabling integration of regulatory information and thermodynamic constraints, and finally addresses the challenges that lie ahead. Various use scenarios and biological insights obtained from FBA, and applications in fields such metabolic engineering and drug target identification, are also discussed. Genome-scale constraint-based models have an immense potential for building and testing hypotheses, as well as to guide experimentation.

Normal-mode sound propagation in an ocean with sinusoidal surface waves

The normal-mode solution to the problem of acoustic wave propagation in an isovelocity ocean with a wavy surface is considered. The surface wave amplitude is assumed to be small compared to the acoustic wavelength, and the method of multiple scales is employed to study the interaction between normal-mode acoustic waves and the surface waves. A nonresonant interaction causes small fluctuations of the amplitude and phase of the acoustic wave at a rate dependent on the frequency of the surface wave. Backscatter occurs if the wavenumber of the surface wave is larger than that of the acoustic wave. The interaction becomes resonant if appropriate phase-matching conditions are satisfied. In this case, two acoustic normal modes get coupled, resulting in a large-scale periodic exchange of energy from one mode to another.

The Eligibility Definition Used in the Social Security Administration’s Disability Programs Needs to be Changed

In its October 2003 report on the definition of disability used by the Social Security Administration’s (SSA’s) disability programs [i.e., Social Security Disability Insurance (SSDI) and Supplemental Security Income (SSI) for people with disabilities], the Social Security Advisory Board raises the issue of whether this definition is at odds with the concept of disability embodied in the Americans with Disabilities Act (ADA) and, more importantly, with the aspirations of people with disabilities to be full participants in mainstream social activities and lead fulfilling, productive lives. The Board declares that “the Nation must face up to the contradictions created by the existing definition of disability.” I wholeheartedly agree. Further, I have concluded that we have to make fundamental, conceptual changes to both how we define eligibility for economic security benefits, and how we provide those benefits, if we are ever to fulfill the promise of the ADA. To convince you of that proposition, I will begin by relating a number of facts that paint a very bleak picture – a picture of deterioration in the economic security of the population that the disability programs are intended to serve; a picture of programs that purport to provide economic security, but are themselves financially insecure and subject to cycles of expansion and cuts that undermine their purpose; a picture of programs that are facing their biggest expenditure crisis ever; and a picture of an eligibility determination process that is inefficient and inequitable -- one that rations benefits by imposing high application costs on applicants in an arbitrary fashion. I will then argue that the fundamental reason for this bleak picture is the conceptual definition of eligibility that these programs use – one rooted in a disability paradigm that social scientists, people with disabilities, and, to a substantial extent, the public have rejected as being flawed, most emphatically through the passage of the ADA. Current law requires eligibility rules to be based on the premise that disability is medically determinable. That’s wrong because, as the ADA recognizes, a person’s environment matters. I will further argue that programs relying on this eligibility definition must inevitably: reward people if they do not try to help themselves, but not if they do; push the people they serve out of society’s mainstream, fostering a culture of isolation and dependency; relegate many to a lifetime of poverty; and undermine their promise of economic security because of the periodic “reforms” that are necessary to maintain taxpayer support. I conclude by pointing out that to change the conceptual definition for program eligibility, we also must change our whole approach to providing for the economic security of people with disabilities. We need to replace our current “caretaker” approach with one that emphasizes helping people with disabilities help themselves. I will briefly describe features that such a program might require, and point out the most significant challenges we would face in making the transition.

Vacancy ordered phases and one-dimensional quasiperiodicity

The metastable vacancy ordered phases observed in aluminium transition metal alloys on rapid solidification or vapour deposition can be considered as a periodic arrangement of a truncated quasiperiodic string based on the Fibonacci sequence along the left angle bracket111right-pointing angle bracket stacking direction of the original CsCl cell. Using the projection formalism developed in the context of quasicrystals, the diffraction patterns of the vacancy ordered phases are calculated for both commensurate and incommensurate projection from a periodic cubic cell in four dimensions. These are compared with experimentally observed patterns. It is shown that at increasingly longer periodicity the patterns from commensurate crystals become indistinguishable from the truly quasiperiodic one. It is suggested that there is a strong link between vacancy ordered phases and quasicrystals.

Weed eradication - an economic perspective

There has been recent interest in determining the upper limits to the feasibility of weed eradication. Although a number of disparate factors determine the success of an eradication program, ultimately eradication feasibility must be viewed in the context of the amount of investment that can be made. The latter should reflect the hazard posed by an invasion, with greater investment justified by greater threats. In simplest terms, the effort (and hence investment) to achieve weed eradication comprises the detection effort required to delimit an invasion plus the search and control effort required to prevent reproduction until extirpation occurs over the entire infested area. The difficulty of estimating the required investment at the commencement of a weed eradication program (as well as during periodic reviews) is a serious problem. Bioeconomics show promise in determining the optimal approach to managing weed invasions, notwithstanding ongoing difficulties in estimating the costs and benefits of eradication and alternative invasion management strategies. A flexible approach to the management of weed invasions is needed, allowing for the adoption of another strategy when it becomes clear that the probability of eradication is low, owing to resourcing or intractable technical issues. Whether the considerable progress that has been achieved towards eradication of the once massive witchweed invasion can be duplicated for other weeds of agricultural systems will depend to a large extent upon investment (. $250 million over 50 yr in this instance). Weeds of natural ecosystems seem destined to remain more difficult eradication targets for a variety of reasons, including higher impedance to eradication, more difficulty in valuing the benefits arising from eradication, and possibly less willingness to pay from society at large.

The Alpha-Method Direct Transcription In Path Constrained Dynamic Optimization

Numerically discretized dynamic optimization problems having active inequality and equality path constraints that along with the dynamics induce locally high index differential algebraic equations often cause the optimizer to fail in convergence or to produce degraded control solutions. In many applications, regularization of the numerically discretized problem in direct transcription schemes by perturbing the high index path constraints helps the optimizer to converge to usefulm control solutions. For complex engineering problems with many constraints it is often difficult to find effective nondegenerat perturbations that produce useful solutions in some neighborhood of the correct solution. In this paper we describe a numerical discretization that regularizes the numerically consistent discretized dynamics and does not perturb the path constraints. For all values of the regularization parameter the discretization remains numerically consistent with the dynamics and the path constraints specified in the, original problem. The regularization is quanti. able in terms of time step size in the mesh and the regularization parameter. For full regularized systems the scheme converges linearly in time step size.The method is illustrated with examples.