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

Recursiveness, Switching, and Fluctuations in a Replicating Catalytic Network

A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers of molecules and species, three phases are found: fast switching state without recursive production, recursive production, and itinerancy between the above two states. The number distributions of the molecules in the recursive states are shown to be log-normal except for those species that form a core hypercycle, and are explained with the help of a heuristic argument.Comment: 4 pages (with 7 figures (6 color)), submitted to PR

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

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 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

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

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

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

Simulation study of Non-ergodicity Transitions: Gelation in Colloidal Systems with Short Range Attractions

Computer simulations were used to study the gel transition occurring in colloidal systems with short range attractions. A colloid-polymer mixture was modelled and the results were compared with mode coupling theory expectations and with the results for other systems (hard spheres and Lennard Jones). The self-intermediate scattering function and the mean squared displacement were used as the main dynamical quantities. Two different colloid packing fractions have been studied. For the lower packing fraction, $\alpha$-scaling holds and the wave-vector analysis of the correlation function shows that gelation is a regular non-ergodicity transition within MCT. The leading mechanism for this novel non-ergodicity transition is identified as bond formation caused by the short range attraction. The time scale and diffusion coefficient also show qualitatively the expected behaviour, although different exponents are found for the power-law divergences of these two quantities. The non-Gaussian parameter was also studied and very large correction to Gaussian behaviour found. The system with higher colloid packing fraction shows indications of a nearby high-order singularity, causing $\alpha$-scaling to fail, but the general expectations for non-ergodicity transitions still hold.Comment: 13 pages, 15 figure

The compositional and evolutionary logic of metabolism

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Comment: 56 pages, 28 figure