Proton translocation in proteins

The active transport of protons across the low dielectric barrier imposed by biological membranes is accomplished by a plethora of proteins that span the ca. 40 Å of the phospholipid bilayer. The free energy derived from the proton electrochemical potential established by the translocation of these protons can subsequently be used to drive vital chemical reactions of the cell, such as ATP synthesis and cell locomotion. Membrane-bound proton translocating proteins have now been found for a variety of organisms and tissues (1). The driving force for proton pumping in these proteins is supplied by numerous mechanisms, including light absorption (e.g. bacteriorhodopsin) (2a,b), ligand binding (e.g. ATPase) (3), and electrochemistry (e.g. electron transfer through cytochrome c oxidase) (4). Thus nature has devised a variety of methods for supplying the energy required for proton pumping by these proteins. Such diversity notwithstanding, the proteins most likely share some common elements of structure and mechanism that allow them to function as proton pumps. A number of theoretical mechanisms have been put forth for both general proton translocation (5-7) and for energy coupling in specific proton pumps. However, despite almost three decades of intensive research, the details of the mechanism(s) and structural requirements for proton pumping remain largely unresolved. To some extent this is the result of the paucity of structural information available for integral membrane proteins. This situation may soon improve as a result of advances in protein methodologies that have allowed several integral membrane proteins to be successfully crystalized (8), and the increased use of genetic engineering to obtain recombinant proton translocating proteins that will offer an opportunity to assess the importance of specific amino acids for the proton translocation process (9)

The Inconceivable Popularity of Conceivability Arguments

Famous examples of conceivability arguments include (i) Descartes’ argument for mind-body dualism, (ii) Kripke's ‘modal argument’ against psychophysical identity theory, (iii) Chalmers’ ‘zombie argument’ against materialism, and (iv) modal versions of the ontological argument for theism. In this paper, we show that for any such conceivability argument, C, there is a corresponding ‘mirror argument’, M. M is deductively valid and has a conclusion that contradicts C's conclusion. Hence, a proponent of C—henceforth, a ‘conceivabilist’—can be warranted in holding that C's premises are conjointly true only if she can find fault with one of M's premises. But M's premises are modelled on a pair of C's premises. The same reasoning that supports the latter supports the former. For this reason, a conceivabilist can repudiate M's premises only on pain of severely undermining C's premises. We conclude on this basis that all conceivability arguments, including each of (i)–(iv), are fallacious

Optimal solution error covariance in highly nonlinear problems of variational data assimilation

The problem of variational data assimilation for a nonlinear evolution model is formulated as an optimal control problem (see, e.g.[1]) to find the initial condition, boundary conditions or model parameters. The input data contain observation and background errors, hence there is an error in the optimal solution. For mildly nonlinear dynamics, the covariance matrix of the optimal solution error can be approximated by the inverse Hessian of the cost functional of an auxiliary data assimilation problem ([2], [3]). The relationship between the optimal solution error covariance matrix and the Hessian of the auxiliary control problem is discussed for different degrees of validity of the tangent linear hypothesis. For problems with strongly nonlinear dynamics a new statistical method based on computation of a sample of inverse Hessians is suggested. This method relies on the efficient computation of the inverse Hessian by means of iterative methods (Lanczos and quasi-Newton BFGS) with preconditioning. The method allows us to get a sensible approximation of the posterior covariance matrix with a small sample size. Numerical examples are presented for the model governed by Burgers equation with a nonlinear viscous term. The first author acknowledges the funding through the project 09-01-00284 of the Russian Foundation for Basic Research, and the FCP program "Kadry"

Some stationary properties of a QQ-ball in arbitrary space dimensions

Introducing new physically motivated ans\"{a}tze, we explore both analytically and numerically the classical and absolute stabilities of a single $Q$-ball in an arbitrary number of spatial dimensions $D$, working in both the thin and thick wall limits.Comment: 35 pages, 32 figures; added references, corrected typo

Cayratia clematidea (F.Muell.) Domin

https://thekeep.eiu.edu/herbarium_specimens_byname/19435/thumbnail.jp

On the reliability of inflaton potential reconstruction

If primordial scalar and tensor perturbation spectra can be inferred from observations of the cosmic background radiation and large-scale structure, then one might hope to reconstruct a unique single-field inflaton potential capable of generating the observed spectra. In this paper we examine conditions under which such a potential can be reliably reconstructed. For it to be possible at all, the spectra must be well fit by a Taylor series expansion. A complete reconstruction requires a statistically-significant tensor mode to be measured in the microwave background. We find that the observational uncertainties dominate the theoretical error from use of the slow-roll approximation, and conclude that the reconstruction procedure will never insidiously lead to an irrelevant potential.Comment: 16 page LaTeX file with eight postscript figures embedded with epsf; no special macros neede

Universality and Critical Phenomena in String Defect Statistics

The idea of biased symmetries to avoid or alleviate cosmological problems caused by the appearance of some topological defects is familiar in the context of domain walls, where the defect statistics lend themselves naturally to a percolation theory description, and for cosmic strings, where the proportion of infinite strings can be varied or disappear entirely depending on the bias in the symmetry. In this paper we measure the initial configurational statistics of a network of string defects after a symmetry-breaking phase transition with initial bias in the symmetry of the ground state. Using an improved algorithm, which is useful for a more general class of self-interacting walks on an infinite lattice, we extend the work in \cite{MHKS} to better statistics and a different ground state manifold, namely $\R P^2$, and explore various different discretisations. Within the statistical errors, the critical exponents of the Hagedorn transition are found to be quite possibly universal and identical to the critical exponents of three-dimensional bond or site percolation. This improves our understanding of the percolation theory description of defect statistics after a biased phase transition, as proposed in \cite{MHKS}. We also find strong evidence that the existence of infinite strings in the Vachaspati Vilenkin algorithm is generic to all (string-bearing) vacuum manifolds, all discretisations thereof, and all regular three-dimensional lattices.Comment: 62 pages, plain LaTeX, macro mathsymb.sty included, figures included. also available on http://starsky.pcss.maps.susx.ac.uk/groups/pt/preprints/96/96011.ps.g

Long Lived Large Type II Strings: decay within compactification

Motivated also by recent revival of interest about metastable string states (as cosmic strings or in accelerator physics), we study the decay, in presence of dimensional compactification, of a particular superstring state, which was proven to be remarkably long-lived in the flat uncompactified scenario. We compute the decay rate by an exact numerical evaluation of the imaginary part of the one-loop propagator. For large radii of compactification, the result tends to the fully uncompactified one (lifetime T = const M^5/g^2), as expected, the string mainly decaying by massless radiation. For small radii, the features of the decay (emitted states, initial mass dependence,....) change, depending on how the string wraps on the compact dimensions.Comment: 32 pages, 24 text plus appendices, 4 figure

A new view of k-essence

K-essence models, relying on scalar fields with non-canonical kinetic terms, have been proposed as an alternative to quintessence in explaining the observed acceleration of the Universe. We consider the use of field redefinitions to cast k-essence in a more familiar form. While k-essence models cannot in general be rewritten in the form of quintessence models, we show that in certain dynamical regimes an equivalence can be made, which in particular can shed light on the tracking behaviour of k-essence. In several cases, k-essence cannot be observationally distinguished from quintessence using the homogeneous evolution, though there may be small effects on the perturbation spectrum. We make a detailed analysis of two k-essence models from the literature and comment on the nature of the fine tuning arising in the models.Comment: 7 pages RevTeX4 file with four figures incorporate