The role of tank-treading motions in the transverse migration of a spheroidal vesicle in a shear flow

The behavior of a spheroidal vesicle, in a plane shear flow bounded from one side by a wall, is analysed when the distance from the wall is much larger than the spheroid radius. It is found that tank treading motions produce a transverse drift away from the wall, proportional to the spheroid eccentricity and the inverse square of the distance from the wall. This drift is independent of inertia, and is completely determined by the characteristics of the vesicle membrane. The relative strength of the contribution to drift from tank-treading motions and from the presence of inertial corrections, is discussed.Comment: 16 pages, 1 figure, Latex. To appear on J. Phys. A (Math. Gen.

Skeleton and fractal scaling in complex networks

We find that the fractal scaling in a class of scale-free networks originates from the underlying tree structure called skeleton, a special type of spanning tree based on the edge betweenness centrality. The fractal skeleton has the property of the critical branching tree. The original fractal networks are viewed as a fractal skeleton dressed with local shortcuts. An in-silico model with both the fractal scaling and the scale-invariance properties is also constructed. The framework of fractal networks is useful in understanding the utility and the redundancy in networked systems.Comment: 4 pages, 2 figures, final version published in PR

Transition to turbulence in particulate pipe flow

We investigate experimentally the influence of suspended particles on the transition to turbulence. The particles are monodisperse and neutrally-buoyant with the liquid. The role of the particles on the transition depends both upon the pipe to particle diameter ratios and the concentration. For large pipe-to-particle diameter ratios the transition is delayed while it is lowered for small ratios. A scaling is proposed to collapse the departure from the critical Reynolds number for pure fluid as a function of concentration into a single master curve.Comment: 4 pages, 4 figure

Unifying CP violations of quark and lepton sectors

A preliminary determination of the Dirac phase in the PMNS matrix is \dell\approx -\frac{\pi}{2}. A rather accurately determined Jarlskog invariant $J$ in the CKM matrix is close to the maximum. Since the phases in the CKM and PMNS matrices will be accurately determined in the future, it is an interesting problem to relate these two phases. This can be achieved in a families-unified grand unification if the weak CP violation is introduced spontaneously {\it \`a la} Froggatt and Nielsen at a high energy scale, where only one meaningful Dirac CP phase appears.Comment: 10 pages with 3 figure

The Algorithmic Origins of Life

Although it has been notoriously difficult to pin down precisely what it is that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique informational narrative of living systems suggests that life may be characterized by context-dependent causal influences, and in particular, that top-down (or downward) causation -- where higher-levels influence and constrain the dynamics of lower-levels in organizational hierarchies -- may be a major contributor to the hierarchal structure of living systems. Here we propose that the origin of life may correspond to a physical transition associated with a shift in causal structure, where information gains direct, and context-dependent causal efficacy over the matter it is instantiated in. Such a transition may be akin to more traditional physical transitions (e.g. thermodynamic phase transitions), with the crucial distinction that determining which phase (non-life or life) a given system is in requires dynamical information and therefore can only be inferred by identifying causal architecture. We discuss some potential novel research directions based on this hypothesis, including potential measures of such a transition that may be amenable to laboratory study, and how the proposed mechanism corresponds to the onset of the unique mode of (algorithmic) information processing characteristic of living systems.Comment: 13 pages, 1 tabl

Anomalous Pressure in Fluctuating Shear Flow

We investigate how the pressure in fluctuating shear flow depends on the shear rate $S$ and on the system size $L$ by studying fluctuating hydrodynamics under shear conditions. We derive anomalous forms of the pressure for two limiting values of the dimensionless parameter $\lambda=SL^2/\nu$, where $\nu$ is the kinematic viscosity. In the case $\lambda \ll 1$, the pressure is not an intensive quantity because of the influence of the long-range spatial correlations of momentum fluctuations. In the other limit $\lambda \gg 1$, the long-range correlations are suppressed at large distances, and the pressure is intensive. In this case, however, there is the interesting effect that the non-equilibrium correction to the pressure is proportional to $S^{3/2}$, which was previously obtained with the projection operator method [K. Kawasaki and J. D. Gunton, Phys. Rev. {\bf A 8}, 2048, (1973)].Comment: Breakdown of the intensivity of pressure is emphasized. Fig.1 and references added; accepted for publication as a Rapid Communication in Phys. Rev.

Neutron Halo Isomers in Stable Nuclei and their Possible Application for the Production of Low Energy, Pulsed, Polarized Neutron Beams of High Intensity and High Brilliance

We propose to search for neutron halo isomers populated via $\gamma$-capture in stable nuclei with mass numbers of about A=140-180 or A=40-60, where the $4s_{1/2}$ or $3s_{1/2}$ neutron shell model state reaches zero binding energy. These halo nuclei can be produced for the first time with new $\gamma$-beams of high intensity and small band width ($\le$ 0.1%) achievable via Compton back-scattering off brilliant electron beams thus offering a promising perspective to selectively populate these isomers with small separation energies of 1 eV to a few keV. Similar to single-neutron halo states for very light, extremely neutron-rich, radioactive nuclei \cite{hansen95,tanihata96,aumann00}, the low neutron separation energy and short-range nuclear force allows the neutron to tunnel far out into free space much beyond the nuclear core radius. This results in prolonged half lives of the isomers for the $\gamma$-decay back to the ground state in the 100 ps-$\mu$s range. Similar to the treatment of photodisintegration of the deuteron, the neutron release from the neutron halo isomer via a second, low-energy, intense photon beam has a known much larger cross section with a typical energy threshold behavior. In the second step, the neutrons can be released as a low-energy, pulsed, polarized neutron beam of high intensity and high brilliance, possibly being much superior to presently existing beams from reactors or spallation neutron sources.Comment: accepted for publication in Applied Physics

The origin of large molecules in primordial autocatalytic reaction networks

Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we know that can accomplish this task consist of large molecules. Thus the origin of large molecules is a chicken and egg problem in chemistry. Here we present a mechanism, based on autocatalytic sets (ACSs), that is a possible solution to this problem. We discuss a mathematical model describing the population dynamics of molecules in a stylized but prebiotically plausible chemistry. Large molecules can be produced in this chemistry by the coalescing of smaller ones, with the smallest molecules, the `food set', being buffered. Some of the reactions can be catalyzed by molecules within the chemistry with varying catalytic strengths. Normally the concentrations of large molecules in such a scenario are very small, diminishing exponentially with their size. ACSs, if present in the catalytic network, can focus the resources of the system into a sparse set of molecules. ACSs can produce a bistability in the population dynamics and, in particular, steady states wherein the ACS molecules dominate the population. However to reach these steady states from initial conditions that contain only the food set typically requires very large catalytic strengths, growing exponentially with the size of the catalyst molecule. We present a solution to this problem by studying `nested ACSs', a structure in which a small ACS is connected to a larger one and reinforces it. We show that when the network contains a cascade of nested ACSs with the catalytic strengths of molecules increasing gradually with their size (e.g., as a power law), a sparse subset of molecules including some very large molecules can come to dominate the system.Comment: 49 pages, 17 figures including supporting informatio

Photoproduction off Nuclei and Point-like Photon Interactions Part I: Cross Sections and Nuclear Shadowing

High energy photoproduction off nuclear targets is studied within the Glauber-Gribov approximation. The photon is assumed to interact as a $q\bar{q}$-system according to the Generalized Vector Dominance Model and as a ``bare photon'' in direct scattering processes with target nucleons. We calculate total cross sections for interactions of photons with nuclei taking into account coherence length effects and point-like interactions of the photon. Results are compared to data on photon-nucleus cross sections, nuclear shadowing, and quasi- elastic $\rho$-production. Extrapolations of cross sections and of the shadowing behaviour to high energies are given.Comment: 15 pages, 12 figure

Partial inhibition and bilevel optimization in flux balance analysis

Motivation: Within Flux Balance Analysis, the investigation of complex subtasks, such as finding the optimal perturbation of the network or finding an optimal combination of drugs, often requires to set up a bilevel optimization problem. In order to keep the linearity and convexity of these nested optimization problems, an ON/OFF description of the effect of the perturbation (i.e. Boolean variable) is normally used. This restriction may not be realistic when one wants, for instance, to describe the partial inhibition of a reaction induced by a drug.Results: In this paper we present a formulation of the bilevel optimization which overcomes the oversimplified ON/OFF modeling while preserving the linear nature of the problem. A case study is considered: the search of the best multi-drug treatment which modulates an objective reaction and has the minimal perturbation on the whole network. The drug inhibition is described and modulated through a convex combination of a fixed number of Boolean variables. The results obtained from the application of the algorithm to the core metabolism of E.coli highlight the possibility of finding a broader spectrum of drug combinations compared to a simple ON/OFF modeling.Conclusions: The method we have presented is capable of treating partial inhibition inside a bilevel optimization, without loosing the linearity property, and with reasonable computational performances also on large metabolic networks. The more fine-graded representation of the perturbation allows to enlarge the repertoire of synergistic combination of drugs for tasks such as selective perturbation of cellular metabolism. This may encourage the use of the approach also for other cases in which a more realistic modeling is required. \ua9 2013 Facchetti and Altafini; licensee BioMed Central Ltd