681 research outputs found
Modeling the geometry of the endoplasmic reticulum network
Conference ProceedingFirst International Conference, AlCoB 2014, held in July 2014 in Tarragona, Spain.We have studied the network geometry of the endoplasmic reticulum by means of graph theoretical and integer programming models. The purpose is to represent this structure as close as possible by a class of finite, undirected and connected graphs the nodes of which have to be either of degree three or at most of degree three. We determine plane graphs of minimal total edge length satisfying degree and angle constraints, and we show that the optimal graphs are close to the ER network geometry. Basically, two procedures are formulated to solve the optimization problem: a binary linear program, that iteratively constructs an optimal solution, and a linear program, that iteratively exploits additional cutting planes from different families to accelerate the solution process. All formulations have been implemented and tested on a series of real-life and randomly generated cases. The cutting plane approach turns out to be particularly efficient for the real-life testcases, since it outperforms the pure integer programming approach by a factor of at least 10. © 2014 Springer International Publishing
Discreteness effects in a reacting system of particles with finite interaction radius
An autocatalytic reacting system with particles interacting at a finite
distance is studied. We investigate the effects of the discrete-particle
character of the model on properties like reaction rate, quenching phenomenon
and front propagation, focusing on differences with respect to the continuous
case. We introduce a renormalized reaction rate depending both on the
interaction radius and the particle density, and we relate it to macroscopic
observables (e.g., front speed and front thickness) of the system.Comment: 23 pages, 13 figure
High reflectivity grating waveguide coatings for 1064nm
We propose thin single-layer grating waveguide structures to be used as
high-reflectivity, but low thermal noise, alternative to conventional coatings
for gravitational wave detector test mass mirrors. Grating waveguide (GWG)
coatings can show a reflectivity of up to 100% with an overall thickness of
less than a wavelength. We theoretically investigate GWG coatings for 1064nm
based on tantala (Ta2O5) on a Silica substrate focussing on broad spectral
response and low thickness
Elastic fluctuations as observed in a confocal slice
Recent confocal experiments on colloidal solids motivate a fuller study of
the projection of three-dimensional fluctuations onto a two-dimensional
confocal slice. We show that the effective theory of a projected crystal
displays several exceptional features, such as non-standard exponents in the
dispersion relations. We provide analytic expressions for the effective
two-dimensional elastic properties which allow one to work back from sliced
experimental observations to three-dimensional elastic constants.Comment: 5 pages, 2 figure
Progress towards an accurate determination of the Boltzmann constant by Doppler spectroscopy
In this paper, we present significant progress performed on an experiment
dedicated to the determination of the Boltzmann constant, k, by accurately
measuring the Doppler absorption profile of a line in a gas of ammonia at
thermal equilibrium. This optical method based on the first principles of
statistical mechanics is an alternative to the acoustical method which has led
to the unique determination of k published by the CODATA with a relative
accuracy of 1.7 ppm. We report on the first measurement of the Boltzmann
constant by laser spectroscopy with a statistical uncertainty below 10 ppm,
more specifically 6.4 ppm. This progress results from improvements in the
detection method and in the statistical treatment of the data. In addition, we
have recorded the hyperfine structure of the probed saQ(6,3) rovibrational line
of ammonia by saturation spectroscopy and thus determine very precisely the
induced 4.36 (2) ppm broadening of the absorption linewidth. We also show that,
in our well chosen experimental conditions, saturation effects have a
negligible impact on the linewidth. Finally, we draw the route to future
developments for an absolute determination of with an accuracy of a few ppm.Comment: 22 pages, 11 figure
Non-Newtonian behavior and molecular structure of Cooee bitumen under shear flow:A non-equilibrium molecular dynamics study
The rheology and molecular structure of a model bitumen (Cooee bitumen) under shear are investigated in the non-Newtonian regime using non-equilibrium molecular dynamics simulations. The shear viscosity, normal stress differences, and pressure of the bitumen mixture are computed at different shear rates and different temperatures. The model bitumen is shown to be a shear-thinning fluid at all temperatures. In addition, the Cooee model is able to reproduce experimental results showing the formation of nanoaggregates composed of stacks of flat aromatic molecules in bitumen. These nanoaggregates are immersed in a solvent of saturated hydrocarbon molecules. At a fixed temperature, the shear-shinning behavior is related not only to the inter- and intramolecular alignments of the solvent molecules but also to the decrease of the average size of the nanoaggregates at high shear rates. The variation of the viscosity with temperature at different shear rates is also related to the size and relative composition of the nanoaggregates. The slight anisotropy of the whole sample due to the nanoaggregates is considered and quantified. Finally, the position of bitumen mixtures in the broad literature of complex systems such as colloidal suspensions, polymer solutions, and associating polymer networks is discussed
Fluctuating "Pulled" Fronts: the Origin and the Effects of a Finite Particle Cutoff
Recently it has been shown that when an equation that allows so-called pulled
fronts in the mean-field limit is modelled with a stochastic model with a
finite number of particles per correlation volume, the convergence to the
speed for is extremely slow -- going only as .
In this paper, we study the front propagation in a simple stochastic lattice
model. A detailed analysis of the microscopic picture of the front dynamics
shows that for the description of the far tip of the front, one has to abandon
the idea of a uniformly translating front solution. The lattice and finite
particle effects lead to a ``stop-and-go'' type dynamics at the far tip of the
front, while the average front behind it ``crosses over'' to a uniformly
translating solution. In this formulation, the effect of stochasticity on the
asymptotic front speed is coded in the probability distribution of the times
required for the advancement of the ``foremost bin''. We derive expressions of
these probability distributions by matching the solution of the far tip with
the uniformly translating solution behind. This matching includes various
correlation effects in a mean-field type approximation. Our results for the
probability distributions compare well to the results of stochastic numerical
simulations. This approach also allows us to deal with much smaller values of
than it is required to have the asymptotics to be valid.Comment: 26 pages, 11 figures, to appear in Phys. rev.
Assessment of a novel, capsid-modified adenovirus with an improved vascular gene transfer profile
<p>Background: Cardiovascular disorders, including coronary artery bypass graft failure and in-stent restenosis remain significant opportunities for the advancement of novel therapeutics that target neointimal hyperplasia, a characteristic of both pathologies. Gene therapy may provide a successful approach to improve the clinical outcome of these conditions, but would benefit from the development of more efficient vectors for vascular gene delivery. The aim of this study was to assess whether a novel genetically engineered Adenovirus could be utilised to produce enhanced levels of vascular gene expression.</p>
<p>Methods: Vascular transduction capacity was assessed in primary human saphenous vein smooth muscle and endothelial cells using vectors expressing the LacZ reporter gene. The therapeutic capacity of the vectors was compared by measuring smooth muscle cell metabolic activity and migration following infection with vectors that over-express the candidate therapeutic gene tissue inhibitor of matrix metalloproteinase-3 (TIMP-3).</p>
<p>Results: Compared to Adenovirus serotype 5 (Ad5), the novel vector Ad5T*F35++ demonstrated improved binding and transduction of human vascular cells. Ad5T*F35++ mediated expression of TIMP-3 reduced smooth muscle cell metabolic activity and migration in vitro. We also demonstrated that in human serum samples pre-existing neutralising antibodies to Ad5T*F35++ were less prevalent than Ad5 neutralising antibodies.</p>
<p>Conclusions: We have developed a novel vector with improved vascular transduction and improved resistance to human serum neutralisation. This may provide a novel vector platform for human vascular gene transfer.</p>
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