On the discrete Peyrard-Bishop model of DNA: stationary solutions and stability

As a first step in the search of an analytical study of mechanical denaturation of DNA in terms of the sequence, we study stable, stationary solutions in the discrete, finite and homogeneous Peyrard-Bishop DNA model. We find and classify all the stationary solutions of the model, as well as analytic approximations of them, both in the continuum and in the discrete limits. Our results explain the structure of the solutions reported by Theodorakopoulos {\em et al.} [Phys. Rev. Lett. {\bf 93}, 258101 (2004)] and provide a way to proceed to the analysis of the generalized version of the model incorporating the genetic information.Comment: 15 pages, 12 figure

Teaching Theoretical Physics: the cases of Enrico Fermi and Ettore Majorana

We report on theoretical courses by Fermi and Majorana, giving evidence of the first appearance and further development of Quantum Mechanics teaching in Italy. On the basis of original documents, we make a comparison between Fermi's and Majorana's approaches. A detailed analysis is carried out of Fermi's course on Theoretical Physics attended by Majorana in 1927-28. Three (previously unknown) programs on advanced Physics courses submitted by Majorana to the University of Rome between 1933 and 1936 and the course he held in Naples in 1938 complete our analysis: Fermi's phenomenological approach resounded in Majorana, who however combined it with a deeper theoretical approach, closer to the modern way of presenting Quantum Mechanics.Comment: latex, 21 pages; a contribution in the centenary of the birth of Ettore Majoran

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

The effect of atomic electrons on nuclear fission

We calculate correction to the nuclear fission barrier produced by the atomic electrons. The result presented in analytical form is convenient to use in future nuclear calculations. The atomic electrons have a small stabilizing effect on nuclei, increasing lifetime in nuclear fission channel. This effect gives a new instrument to study the fission process.Comment: 4 pages, 1 figur

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.

Banking union in historical perspective: the initiative of the European Commission in the 1960s-1970s

This article shows that planning for the organization of EU banking regulation and supervision did not just appear on the agenda in recent years with discussions over the creation of the eurozone banking union. It unveils a hitherto neglected initiative of the European Commission in the 1960s and early 1970s. Drawing on extensive archival work, this article explains that this initiative, however, rested on a number of different assumptions, and emerged in a much different context. It first explains that the Commission's initial project was not crisis-driven; that it articulated the link between monetary integration and banking regulation; and finally that it did not set out to move the supervisory framework to the supranational level, unlike present-day developments

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

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

The stochastic Gross-Pitaevskii equation II

We provide a derivation of a more accurate version of the stochastic Gross-Pitaevskii equation, as introduced by Gardiner et al. (J. Phys. B 35,1555,(2002). The derivation does not rely on the concept of local energy and momentum conservation, and is based on a quasi-classical Wigner function representation of a "high temperature" master equation for a Bose gas, which includes only modes below an energy cutoff E_R that are sufficiently highly occupied (the condensate band). The modes above this cutoff (the non-condensate band) are treated as being essentially thermalized. The interaction between these two bands, known as growth and scattering processes, provide noise and damping terms in the equation of motion for the condensate band, which we call the stochastic Gross-Pitaevskii equation. This approach is distinguished by the control of the approximations made in its derivation, and by the feasibility of its numerical implementation.Comment: 24 pages of LaTeX, one figur

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