Stability of adhesion clusters under constant force

We solve the stochastic equations for a cluster of parallel bonds with shared constant loading, rebinding and the completely dissociated state as an absorbing boundary. In the small force regime, cluster lifetime grows only logarithmically with bond number for weak rebinding, but exponentially for strong rebinding. Therefore rebinding is essential to ensure physiological lifetimes. The number of bonds decays exponentially with time for most cases, but in the intermediate force regime, a small increase in loading can lead to much faster decay. This effect might be used by cell-matrix adhesions to induce signaling events through cytoskeletal loading.Comment: Revtex, 4 pages, 4 Postscript files include

Charge Oscillations in Debye-Hueckel Theory

The recent generalized Debye-Hueckel (GDH) theory is applied to the calculation of the charge-charge correlation function G_{ZZ}(r). The resulting expression satisfies both (i) the charge neutrality condition and (ii) the Stillinger-Lovett second-moment condition for all T and rho_N, the overall ion density, and (iii) exhibits charge oscillations for densities above a "Kirkwood line" in the (rho_N,T) plane. This corrects the normally assumed DH correlations, and, when combined with the GDH analysis of the density correlations, leaves the GDH theory as the only complete description of ionic correlation functions, as judged by (i)-(iii), (iv) exact low-density (rho_N,T) variation, and (v) reasonable behavior near criticality.Comment: 6 pages, EuroPhys.sty (now available on archive), 1 eps figur

Kinetic theory of age-structured stochastic birth-death processes

Classical age-structured mass-action models such as the McKendrick-von Foerster equation have been extensively studied but are unable to describe stochastic fluctuations or population-size-dependent birth and death rates. Stochastic theories that treat semi-Markov age-dependent processes using, e.g., the Bellman-Harris equation do not resolve a population's age structure and are unable to quantify population-size dependencies. Conversely, current theories that include size-dependent population dynamics (e.g., mathematical models that include carrying capacity such as the logistic equation) cannot be easily extended to take into account age-dependent birth and death rates. In this paper, we present a systematic derivation of a new, fully stochastic kinetic theory for interacting age-structured populations. By defining multiparticle probability density functions, we derive a hierarchy of kinetic equations for the stochastic evolution of an aging population undergoing birth and death. We show that the fully stochastic age-dependent birth-death process precludes factorization of the corresponding probability densities, which then must be solved by using a Bogoliubov-–Born–-Green–-Kirkwood-–Yvon-like hierarchy. Explicit solutions are derived in three limits: no birth, no death, and steady state. These are then compared with their corresponding mean-field results. Our results generalize both deterministic models and existing master equation approaches by providing an intuitive and efficient way to simultaneously model age- and population-dependent stochastic dynamics applicable to the study of demography, stem cell dynamics, and disease evolution

Economic analysis of condition monitoring systems for offshore wind turbine sub-systems

The use of condition monitoring systems on wind turbines has increased dramatically in recent times. However, their use is mostly restricted to vibration based monitoring systems for the gearbox, generator and drive train. There are many forms and types of condition monitoring systems now available for wind turbines. A survey of commercially available condition monitoring systems and their associated costs has been undertaken for the blades, drive train and tower. This paper considers what value can be obtained from these systems if they are used correctly. This is achieved by running simulations on an operations and maintenance model for a 20 year life cycle wind farm. The model uses Hidden Markov Models to represent both the actual system state and the observed state. The costs for system failures are derived, as are possible reductions in these costs due to early detection. Various scenarios are simulated including the addition of condition monitoring systems to the drive train and blade and tower monitoring. Finally, the efficacy of these systems is examined and its effect on operation costs

CRISPR antiphage defence mediated by the cyclic nucleotide-binding membrane protein Csx23

Biotechnology and Biological Sciences Research Council [BB/T004789/1 to M.F.W., T.M.G.]; European Research Council Advanced Grant [101018608 to M.F.W.]; Engineering and Physical Sciences Research Council [EP/X016455/1 to K.A., B.E.B., M.F.W.]; BBSRC equipment grants [BB/R013780/1, BB/T017740/1 to B.E.B.]. Funding for open access charge: University of St Andrews block grant.CRISPR-Cas provides adaptive immunity in prokaryotes. Type III CRISPR systems detect invading RNA and activate the catalytic Cas10 subunit, which generates a range of nucleotide second messengers to signal infection. These molecules bind and activate a diverse range of effector proteins that provide immunity by degrading viral components and/or by disturbing key aspects of cellular metabolism to slow down viral replication. Here, we focus on the uncharacterised effector Csx23, which is widespread in Vibrio cholerae. Csx23 provides immunity against plasmids and phage when expressed in Escherichia coli along with its cognate type III CRISPR system. The Csx23 protein localises in the membrane using an N-terminal transmembrane α-helical domain and has a cytoplasmic C-terminal domain that binds cyclic tetra-adenylate (cA4), activating its defence function. Structural studies reveal a tetrameric structure with a novel fold that binds cA4 specifically. Using pulse EPR, we demonstrate that cA4 binding to the cytoplasmic domain of Csx23 results in a major perturbation of the transmembrane domain, consistent with the opening of a pore and/or disruption of membrane integrity. This work reveals a new class of cyclic nucleotide binding protein and provides key mechanistic detail on a membrane-associated CRISPR effector.Many anti-viral defence systems generate a cyclic nucleotide signal that activates cellular defences in response to infection. Type III CRISPR systems use a specialised polymerase to make cyclic oligoadenylate (cOA) molecules from ATP. These can bind and activate a range of effector proteins that slow down viral replication. In this study, we focussed on the Csx23 effector from the human pathogen Vibrio cholerae – a trans-membrane protein that binds a cOA molecule, leading to anti-viral immunity. Structural studies revealed a new class of nucleotide recognition domain, where cOA binding is transmitted to changes in the trans-membrane domain, most likely resulting in membrane depolarisation. This study highlights the diversity of mechanisms for anti-viral defence via nucleotide signalling.Peer reviewe

Inductive Construction of 2-Connected Graphs for Calculating the Virial Coefficients

In this paper we give a method for constructing systematically all simple 2-connected graphs with n vertices from the set of simple 2-connected graphs with n-1 vertices, by means of two operations: subdivision of an edge and addition of a vertex. The motivation of our study comes from the theory of non-ideal gases and, more specifically, from the virial equation of state. It is a known result of Statistical Mechanics that the coefficients in the virial equation of state are sums over labelled 2-connected graphs. These graphs correspond to clusters of particles. Thus, theoretically, the virial coefficients of any order can be calculated by means of 2-connected graphs used in the virial coefficient of the previous order. Our main result gives a method for constructing inductively all simple 2-connected graphs, by induction on the number of vertices. Moreover, the two operations we are using maintain the correspondence between graphs and clusters of particles.Comment: 23 pages, 5 figures, 3 table

Mixed Weyl Symbol Calculus and Spectral Line Shape Theory

A new and computationally viable full quantum version of line shape theory is obtained in terms of a mixed Weyl symbol calculus. The basic ingredient in the collision--broadened line shape theory is the time dependent dipole autocorrelation function of the radiator-perturber system. The observed spectral intensity is the Fourier transform of this correlation function. A modified form of the Wigner--Weyl isomorphism between quantum operators and phase space functions (Weyl symbols) is introduced in order to describe the quantum structure of this system. This modification uses a partial Wigner transform in which the radiator-perturber relative motion degrees of freedom are transformed into a phase space dependence, while operators associated with the internal molecular degrees of freedom are kept in their original Hilbert space form. The result of this partial Wigner transform is called a mixed Weyl symbol. The star product, Moyal bracket and asymptotic expansions native to the mixed Weyl symbol calculus are determined. The correlation function is represented as the phase space integral of the product of two mixed symbols: one corresponding to the initial configuration of the system, the other being its time evolving dynamical value. There are, in this approach, two semiclassical expansions -- one associated with the perturber scattering process, the other with the mixed symbol star product. These approximations are used in combination to obtain representations of the autocorrelation that are sufficiently simple to allow numerical calculation. The leading O(\hbar^0) approximation recovers the standard classical path approximation for line shapes. The higher order O(\hbar^1) corrections arise from the noncommutative nature of the star product.Comment: 26 pages, LaTeX 2.09, 1 eps figure, submitted to 'J. Phys. B.

Dimensional crossover of a boson gas in multilayers

We obtain the thermodynamic properties for a non-interacting Bose gas constrained on multilayers modeled by a periodic Kronig-Penney delta potential in one direction and allowed to be free in the other two directions. We report Bose-Einstein condensation (BEC) critical temperatures, chemical potential, internal energy, specific heat, and entropy for different values of a dimensionless impenetrability $P\geqslant 0$ between layers. The BEC critical temperature $T_{c}$ coincides with the ideal gas BEC critical temperature $T_{0}$ when $P=0$ and rapidly goes to zero as $P$ increases to infinity for any finite interlayer separation. The specific heat $C_{V}$ \textit{vs} $T$ for finite $P$ and plane separation $a$ exhibits one minimum and one or two maxima in addition to the BEC, for temperatures larger than $T_{c}$ which highlights the effects due to particle confinement. Then we discuss a distinctive dimensional crossover of the system through the specific heat behavior driven by the magnitude of $P$. For $T<T_{c}$ the crossover is revealed by the change in the slope of $\log C_{V}(T)$ and when $T>T_{c}$, it is evidenced by a broad minimum in $C_{V}(T)$.Comment: Ten pages, nine figure

Asymmetric Primitive-Model Electrolytes: Debye-Huckel Theory, Criticality and Energy Bounds

Debye-Huckel (DH) theory is extended to treat two-component size- and charge-asymmetric primitive models, focussing primarily on the 1:1 additive hard-sphere electrolyte with, say, negative ion diameters, a--, larger than the positive ion diameters, a++. The treatment highlights the crucial importance of the charge-unbalanced ``border zones'' around each ion into which other ions of only one species may penetrate. Extensions of the DH approach which describe the border zones in a physically reasonable way are exact at high $T$ and low density, $\rho$, and, furthermore, are also in substantial agreement with recent simulation predictions for \emph{trends} in the critical parameters, $T_c$ and $\rho_c$, with increasing size asymmetry. Conversely, the simplest linear asymmetric DH description, which fails to account for physically expected behavior in the border zones at low $T$, can violate a new lower bound on the energy (which applies generally to models asymmetric in both charge and size). Other recent theories, including those based on the mean spherical approximation, have predicted trends in the critical parameters quite opposite to those established by the simulations.Comment: to appear in Physical Review

Dynamic of a non homogeneously coarse grained system

To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been developed. In this letter, we present an approach that leads to a dynamics for such coarse-grained models. This allows us to obtain temperature-dependent and transport properties. Renormalization group theory is used to create new local potentials model between nodes, within the approximation of local thermodynamical equilibrium. Assuming that these potentials give an averaged description of node dynamics, we calculate thermal and mechanical properties. If this method can be sufficiently generalized it may form the basis of a Molecular Dynamics method with time and spatial coarse-graining.Comment: 4 pages, 4 figure