Genetic Analysis of Yeast Sec24p Mutants Suggests Cargo Binding Is Not Co-operative during ER Export

Many eukaryotic secretory proteins are selected forexport from the endoplasmic reticulum (ER) through theirinteraction with the Sec24p subunit of the coat protein II(COPII) coat. Three distinct cargo-binding sites on yeastSec24p have been described by biochemical, genetic andstructural studies. Each site recognizes a limited set ofpeptide motifs or a folded structural domain, however,the breadth of cargo recognized by a given site and thedynamics of cargo engagement remain poorly under-stood. We aimed to gain further insight into the broadermolecular function of one of these cargo-binding sitesusing a non-biased genetic approach. We exploited thein vivolethality associated with mutation of the Sec24pB-site to identify genes that suppress this phenotypewhen overexpressed. We identifiedSMY2as a gen-eral suppressor that rescued multiple defects in Sec24p,andSEC22as a specific suppressor of two adjacentcargo-binding sites, raising the possibility of allostericregulation of these domains. We generated a novel setof mutations in Sec24p thatdistinguish these two sitesand examined the ability of Sec22p to rescue these muta-tions. Our findings suggest that co-operativity does notinfluence cargo capture at these sites, and that Sec22prescue occurs via its function as a retrograde SNARE

Muon Spectra of Quasi-Elastic and 1-Pion Production Events in LBL Neutrino Oscillation Experiments

The muon energy spectra of the quasi-elastic and 1-pion production events in a LBL experiment, like K2K, are predicted to follow closely the neutrino energy spectrum, with downward shifts of the energy scale by $/2 M$ and $( + M_\Delta^2 - M^2)/2 M$ respectively. These predictions seem to agree with the observed muon spectra in the K2K nearby detector. The corresponding muon spectra in the far-away (SK) detector are predicted to show characteristic spectral distortions induced by $\nu_\mu$ oscillation. Comparison of the predicted spectral distortions with the observed muon spectra of the 1-Ring and 2-Ring muon events in the SK detector will help to determine the oscillation parameters. The results will be applicable to other LBL experiments as well.Comment: 13 pages. One figure and a few comments added, final version to appear in P

Application of B-splines to determining eigen-spectrum of Feshbach molecules

The B-spline basis set method is applied to determining the rovibrational eigen-spectrum of diatomic molecules. A particular attention is paid to a challenging numerical task of an accurate and efficient description of the vibrational levels near the dissociation limit (halo-state and Feshbach molecules). Advantages of using B-splines are highlighted by comparing the performance of the method with that of the commonly-used discrete variable representation (DVR) approach. Several model cases, including the Morse potential and realistic potentials with 1/R^3 and 1/R^6 long-range dependence of the internuclear separation are studied. We find that the B-spline method is superior to the DVR approach and it is robust enough to properly describe the Feshbach molecules. The developed numerical method is applied to studying the universal relation of the energy of the last bound state to the scattering length. We numerically illustrate the validity of the quantum-defect-theoretic formulation of such a relation for a 1/R^6 potential.Comment: submitted to can j phys: Walter Johnson symposu

The influence of gene expression time delays on Gierer-Meinhardt pattern formation systems

There are numerous examples of morphogen gradients controlling long range signalling in developmental and cellular systems. The prospect of two such interacting morphogens instigating long range self-organisation in biological systems via a Turing bifurcation has been explored, postulated, or implicated in the context of numerous developmental processes. However, modelling investigations of cellular systems typically neglect the influence of gene expression on such dynamics, even though transcription and translation are observed to be important in morphogenetic systems. In particular, the influence of gene expression on a large class of Turing bifurcation models, namely those with pure kinetics such as the Gierer–Meinhardt system, is unexplored. Our investigations demonstrate that the behaviour of the Gierer–Meinhardt model profoundly changes on the inclusion of gene expression dynamics and is sensitive to the sub-cellular details of gene expression. Features such as concentration blow up, morphogen oscillations and radical sensitivities to the duration of gene expression are observed and, at best, severely restrict the possible parameter spaces for feasible biological behaviour. These results also indicate that the behaviour of Turing pattern formation systems on the inclusion of gene expression time delays may provide a means of distinguishing between possible forms of interaction kinetics. Finally, this study also emphasises that sub-cellular and gene expression dynamics should not be simply neglected in models of long range biological pattern formation via morphogens

Magnetized cosmological perturbations

A large-scale cosmic magnetic field affects not only the growth of density perturbations, but also rotational instabilities and anisotropic deformation in the density distribution. We give a fully relativistic treatment of all these effects, incorporating the magneto-curvature coupling that arises in a relativistic approach. We show that this coupling produces a small enhancement of the growing mode on superhorizon scales. The magnetic field generates new nonadiabatic constant and decaying modes, as well as nonadiabatic corrections to the standard growing and decaying modes. Magnetized isocurvature perturbations are purely decaying on superhorizon scales. On subhorizon scales before recombination, magnetized density perturbations propagate as magneto-sonic waves, leading to a small decrease in the spacing of acoustic peaks. Fluctuations in the field direction induce scale-dependent vorticity, and generate precession in the rotational vector. On small scales, magnetized density vortices propagate as Alfv\'{e}n waves during the radiation era. After recombination, they decay slower than non-magnetized vortices. Magnetic fluctuations are also an active source of anisotropic distortion in the density distribution. We derive the evolution equations for this distortion, and find a particular growing solution.Comment: Revised version, typos corrected, to appear in Phys. Rev.

Aberrant behaviours of reaction diffusion self-organisation models on growing domains in the presence of gene expression time delays

Turing’s pattern formation mechanism exhibits sensitivity to the details of the initial conditions suggesting that, in isolation, it cannot robustly generate pattern within noisy biological environments. Nonetheless, secondary aspects of developmental self-organisation, such as a growing domain, have been shown to ameliorate this aberrant model behaviour. Furthermore, while in-situ hybridisation reveals the presence of gene expression in developmental processes, the influence of such dynamics on Turing’s model has received limited attention. Here, we novelly focus on the Gierer–Meinhardt reaction diffusion system considering delays due the time taken for gene expression, while incorporating a number of different domain growth profiles to further explore the influence and interplay of domain growth and gene expression on Turing’s mechanism. We find extensive pathological model behaviour, exhibiting one or more of the following: temporal oscillations with no spatial structure, a failure of the Turing instability and an extreme sensitivity to the initial conditions, the growth profile and the duration of gene expression. This deviant behaviour is even more severe than observed in previous studies of Schnakenberg kinetics on exponentially growing domains in the presence of gene expression (Gaffney and Monk in Bull. Math. Biol. 68:99–130, 2006). Our results emphasise that gene expression dynamics induce unrealistic behaviour in Turing’s model for multiple choices of kinetics and thus such aberrant modelling predictions are likely to be generic. They also highlight that domain growth can no longer ameliorate the excessive sensitivity of Turing’s mechanism in the presence of gene expression time delays. The above, extensive, pathologies suggest that, in the presence of gene expression, Turing’s mechanism would generally require a novel and extensive secondary mechanism to control reaction diffusion patterning

Coherent states for exactly solvable potentials

A general algebraic procedure for constructing coherent states of a wide class of exactly solvable potentials e.g., Morse and P{\"o}schl-Teller, is given. The method, {\it a priori}, is potential independent and connects with earlier developed ones, including the oscillator based approaches for coherent states and their generalizations. This approach can be straightforwardly extended to construct more general coherent states for the quantum mechanical potential problems, like the nonlinear coherent states for the oscillators. The time evolution properties of some of these coherent states, show revival and fractional revival, as manifested in the autocorrelation functions, as well as, in the quantum carpet structures.Comment: 11 pages, 4 eps figures, uses graphicx packag

ThermoElectric Transport Properties of a Chain of Quantum Dots with Self-Consistent Reservoirs

We introduce a model for charge and heat transport based on the Landauer-Buttiker scattering approach. The system consists of a chain of $N$ quantum dots, each of them being coupled to a particle reservoir. Additionally, the left and right ends of the chain are coupled to two particle reservoirs. All these reservoirs are independent and can be described by any of the standard physical distributions: Maxwell-Boltzmann, Fermi-Dirac and Bose-Einstein. In the linear response regime, and under some assumptions, we first describe the general transport properties of the system. Then we impose the self-consistency condition, i.e. we fix the boundary values (T_L,\mu_L) and (T_R,mu_R), and adjust the parameters (T_i,mu_i), for i = 1,...,N, so that the net average electric and heat currents into all the intermediate reservoirs vanish. This condition leads to expressions for the temperature and chemical potential profiles along the system, which turn out to be independent of the distribution describing the reservoirs. We also determine the average electric and heat currents flowing through the system and present some numerical results, using random matrix theory, showing that these currents are typically governed by Ohm and Fourier laws.Comment: Minor changes (45 pages

SD-brane gravity fields and rolling tachyons

S(pacelike)D-branes are objects arising naturally in string theory when Dirichlet boundary conditions are imposed on the time direction. SD-brane physics is inherently time-dependent. Previous investigations of gravity fields of SD-branes have yielded undesirable naked spacelike singularities. We set up the problem of coupling the most relevant open-string tachyonic mode to massless closed-string modes in the bulk, with backreaction and Ramond-Ramond fields included. We find solutions numerically in a self-consistent approximation; our solutions are naturally asymptotically flat and time-reversal asymmetric. We find completely nonsingular evolution; in particular, the dilaton and curvature are well-behaved for all time. The essential mechanism for spacetime singularity resolution is the inclusion of full backreaction between the bulk fields and the rolling tachyon. Our analysis is not the final word on the story, because we have to make some significant approximations, most notably homogeneity of the tachyon on the unstable branes. Nonetheless, we provide significant progress in plugging a gaping hole in prior understanding of the gravity fields of SD-branes.Comment: References added. Analysis for much broader range of solutions presented. Conclusions unchanged. Time-reversal symmetric examples ruled out, new examples are provide

Energy and decay width of the pi-K atom

The energy and decay width of the pi-K atom are evaluated in the framework of the quasipotential-constraint theory approach. The main electromagnetic and isospin symmetry breaking corrections to the lowest-order formulas for the energy shift from the Coulomb binding energy and for the decay width are calculated. They are estimated to be of the order of a few per cent. We display formulas to extract the strong interaction S-wave pi-K scattering lengths from future experimental data concerning the pi-K atom.Comment: 37 pages, 5 figures, uses Axodra