1,122 research outputs found
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 . The elastic interaction is repulsive and of quadrupolar type,
varying as . For macroscopically thick films, the capillary interaction
is likewise repulsive and proportional to 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
- …