152 research outputs found
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 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 -capture
in stable nuclei with mass numbers of about A=140-180 or A=40-60, where the
or neutron shell model state reaches zero binding energy.
These halo nuclei can be produced for the first time with new -beams of
high intensity and small band width ( 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 -decay back to the ground state in the 100
ps-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, -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 -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
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