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

Spontaneous flow states in active nematics: a unified picture

Continuum hydrodynamic models of active liquid crystals have been used to describe dynamic self-organising systems such as bacterial swarms and cytoskeletal gels. A key prediction of such models is the existence of self-stabilising kink states that spontaneously generate fluid flow in quasi-one dimensional channels. Using simple stability arguments and numerical calculations we extend previous studies to give a complete characterisation of the phase space for both contractile and extensile particles (ie pullers and pushers) moving in a narrow channel as a function of their flow alignment properties and initial orientation. This gives a framework for unifying many of the results in the literature. We describe the response of the kink states to an imposed shear, and investigate how allowing the system to be polar modifies its dynamical behaviour.Comment: 6 pages, 6 figures; submitted to Europhysics Letter

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

Elasticity-mediated self-organization and colloidal interactions of solid spheres with tangential anchoring in a nematic liquid crystal

Using laser tweezers and fluorescence confocal polarizing microscopy, we study colloidal interactions of solid microspheres in the nematic bulk caused by elastic distortions around the particles with strong tangential surface anchoring. The particles aggregate into chains directed at about 30 degrees to the far field director and, at higher concentrations, form complex kinetically trapped structures. We characterize the distance and angular dependencies of the colloidal interaction forces.Comment: 6 pages, 5 figure

Phytochrome regulation of nitrate reductase in wheat

In excised wheat leaves, the activity of nitrate reductase was enhanced by a brief pulse of red light and this increase was reversed by far-red light irradiation. Even under continuous far-red light, nitrate reductase activity increased by 258% after 18 h. When leaves were kept in distilled water during exposure to red light and then transferred to potassium nitrate, there was no difference in endogenous nitrate concentration. The nitrate reductase activity was the same whether leaves were floated in potassium nitrate or in distilled water during irradiation. Partial to complete inhibition of enzyme activity was observed when leaves were incubated in actinomycin-D and cycloheximide respectively, following 4 h of red light irradiation.In vitro irradiation of extract had no significant effect on nitrate reductase activity

Mesh update techniques for free-surface flow solvers using spectral element method

This paper presents a novel mesh-update technique for unsteady free-surface Newtonian flows using spectral element method and relying on the arbitrary Lagrangian--Eulerian kinematic description for moving the grid. Selected results showing compatibility of this mesh-update technique with spectral element method are given

Active Membrane Fluctuations Studied by Micropipet Aspiration

We present a detailed analysis of the micropipet experiments recently reported in J-B. Manneville et al., Phys. Rev. Lett. 82, 4356--4359 (1999), including a derivation of the expected behaviour of the membrane tension as a function of the areal strain in the case of an active membrane, i.e., containing a nonequilibrium noise source. We give a general expression, which takes into account the effect of active centers both directly on the membrane, and on the embedding fluid dynamics, keeping track of the coupling between the density of active centers and the membrane curvature. The data of the micropipet experiments are well reproduced by the new expressions. In particular, we show that a natural choice of the parameters quantifying the strength of the active noise explains both the large amplitude of the observed effects and its remarkable insensitivity to the active-center density in the investigated range. [Submitted to Phys Rev E, 22 March 2001]Comment: 14 pages, 5 encapsulated Postscript figure

A hiatus in the stratosphere?

Rapid CommunicationCopyright © 2015 Nature Publishing GroupTo the Editor — Since the turn of the twenty-first century there has been a hiatus in the cooling of the lower stratosphere (Fig. 1a). This 'stratospheric hiatus' is happening at the same time as the well-documented hiatus in global surface warming1, during a time of increasing CO2 concentrations ('Surface' line in Fig. 1a). Although CO2 acts to warm the surface and troposphere by decreasing outgoing radiative flux at the tropopause, it cools the stratosphere by increasing net infrared emission, so we might expect the continued increase in CO2 concentrations to have produced lower-stratospheric cooling, as observed through much of the depth of the stratosphere2. Why, then, do we observe a hiatus in the lower stratosphere?NER

Forces between elongated particles in a nematic colloid

Using molecular dynamics simulations we study the interactions between elongated colloidal particles (length to breath ratio ≫1) in a nematic host. The simulation results are compared to the results of a Landau–de Gennes elastic free energy. We find that depletion forces dominate for the sizes of the colloidal particles studied. The tangential component of the force, however, allows us to resolve the elastic contribution to the total interaction. We find that this contribution differs from the quadrupolar interaction predicted at large separations. The difference is due to the presence of nonlinear effects, namely, the change in the positions and structure of the defects and their annihilation at small separations

Effective interactions of colloids on nematic films

The elastic and capillary interactions between a pair of colloidal particles trapped on top of a nematic film are studied theoretically for large separations $d$. The elastic interaction is repulsive and of quadrupolar type, varying as $d^{-5}$. For macroscopically thick films, the capillary interaction is likewise repulsive and proportional to $d^{-5}$ as a consequence of mechanical isolation of the system comprised of the colloids and the interface. A finite film thickness introduces a nonvanishing force on the system (exerted by the substrate supporting the film) leading to logarithmically varying capillary attractions. However, their strength turns out to be too small to be of importance for the recently observed pattern formation of colloidal droplets on nematic films.Comment: 13 pages, accepted by EPJ