Two unlinked double-strand breaks can induce reciprocal exchanges in plant genomes via homologous recombination and non-homologous end-joining

Using the rare-cutting endonuclease I-SceI we were able to demonstrate before that the repair of a single double-strand break (DSB) in a plant genome can be mutagenic due to insertions and deletions. However, during replication or due to irradiation several breaks might be induced simultaneously. To analyze the mutagenic potential of such a situation we established an experimental system in tobacco harboring two unlinked transgenes, each carrying an I-SceI site. After transient expression of I-SceI a kanamycin-resistance marker could be restored by joining two previously unlinked broken ends, either by homologous recombination (HR) or by nonhomologous end joining (NHEJ). Indeed, we were able to recover HR and NHEJ events with similar frequencies. Despite the fact that no selection was applied for joining the two other ends, the respective linkage could be detected in most cases tested, demonstrating that the respective exchanges were reciprocal. The frequencies obtained indicate that DSB-induced translocation is up to two orders of magnitude more frequent in somatic cells than ectopic gene conversion. Thus, DSB-induced reciprocal exchanges might play a significant role in plant genome evolution. The technique applied in this study may also be useful for the controlled exchange of unlinked sequences in plant genomes

Rigorous derivation of coherent resonant tunneling time and velocity in finite periodic systems

The velocity $v_{res}$ of resonant tunneling electrons in finite periodic structures is analytically calculated in two ways. The first method is based on the fact that a transmission of unity leads to a coincidence of all still competing tunneling time definitions. Thus, having an indisputable resonant tunneling time $\tau_{res},$ we apply the natural definition $v_{res}=L/\tau_{res}$ to calculate the velocity. For the second method we combine Bloch's theorem with the transfer matrix approach to decompose the wave function into two Bloch waves. Then the expectation value of the velocity is calculated. Both different approaches lead to the same result, showing their physical equivalence. The obtained resonant tunneling velocity $v_{res}$ is smaller or equal to the group velocity times the magnitude of the complex transmission amplitude of the unit cell. Only at energies where the unit cell of the periodic structure has a transmission of unity $v_{res}$ equals the group velocity. Numerical calculations for a GaAs/AlGaAs superlattice are performed. For typical parameters the resonant velocity is below one third of the group velocity.Comment: 12 pages, 3 figures, LaTe

ELM triggering conditions for the integrated modeling of H-mode plasmas

Recent advances in the integrated modeling of ELMy H-mode plasmas are presented. A model for the H-mode pedestal and for the triggering of ELMs predicts the height, width, and shape of the H-mode pedestal and the frequency and width of ELMs. Formation of the pedestal and the L-H transition is the direct result of ExB flow shear suppression of anomalous transport. The periodic ELM crashes are triggered by either the ballooning or peeling MHD instabilities. The BALOO, DCON, and ELITE ideal MHD stability codes are used to derive a new parametric expression for the peeling-ballooning threshold. The new dependence for the peeling-ballooning threshold is implemented in the ASTRA transport code. Results of integrated modeling of DIII-D like discharges are presented and compared with experimental observations. The results from the ideal MHD stability codes are compared with results from the resistive MHD stability code NIMROD.Comment: 12th International Congress on Plasma Physics, 25-29 October 2004, Nice (France

Attacks on quantum key distribution protocols that employ non-ITS authentication

We demonstrate how adversaries with unbounded computing resources can break Quantum Key Distribution (QKD) protocols which employ a particular message authentication code suggested previously. This authentication code, featuring low key consumption, is not Information-Theoretically Secure (ITS) since for each message the eavesdropper has intercepted she is able to send a different message from a set of messages that she can calculate by finding collisions of a cryptographic hash function. However, when this authentication code was introduced it was shown to prevent straightforward Man-In-The-Middle (MITM) attacks against QKD protocols. In this paper, we prove that the set of messages that collide with any given message under this authentication code contains with high probability a message that has small Hamming distance to any other given message. Based on this fact we present extended MITM attacks against different versions of BB84 QKD protocols using the addressed authentication code; for three protocols we describe every single action taken by the adversary. For all protocols the adversary can obtain complete knowledge of the key, and for most protocols her success probability in doing so approaches unity. Since the attacks work against all authentication methods which allow to calculate colliding messages, the underlying building blocks of the presented attacks expose the potential pitfalls arising as a consequence of non-ITS authentication in QKD-postprocessing. We propose countermeasures, increasing the eavesdroppers demand for computational power, and also prove necessary and sufficient conditions for upgrading the discussed authentication code to the ITS level.Comment: 34 page

Cosmological particle production, causal thermodynamics, and inflationary expansion

Combining the equivalence between cosmological particle creation and an effective viscous fluid pressure with the fact that the latter represents a dynamical degree of freedom within the second-order Israel-Stewart theory for imperfect fluids, we reconsider the possibility of accelerated expansion in fluid cosmology. We find an inherent self-limitation for the magnitude of an effective bulk pressure which is due to adiabatic (isentropic) particle production. For a production rate which depends quadratically on the Hubble rate we confirm the existence of solutions which describe a smooth transition from inflationary to noninflationary behavior and discuss their interpretation within the model of a decaying vacuum energy density. An alternative formulation of the effective imperfect fluid dynamics in terms of a minimally coupled scalar field is given. The corresponding potential is discussed and an entropy equivalent for the scalar field is found.Comment: 16 pages, revtex file, submitted to Phys. Rev.

Interacting spinor and scalar fields in Bianchi type-I Universe filled with viscous fluid: exact and numerical solutions

We consider a self-consistent system of spinor and scalar fields within the framework of a Bianchi type I gravitational field filled with viscous fluid in presence of a $\Lambda$ term. Exact self-consistent solutions to the corresponding spinor, scalar and BI gravitational field equations are obtained in terms of $\tau$, where $\tau$ is the volume scale of BI universe. System of equations for $\tau$ and \ve, where \ve is the energy of the viscous fluid, is deduced. Some special cases allowing exact solutions are thoroughly studied.Comment: 18 pages, 6 figure

Electron transmission and phase time in semiconductor superlattices

We discuss the time spent by an electron propagating through a finite periodic system such as a semiconductor superlattice. The relation between dwell-time and phase-time is outlined. The envelopes of phase-time at maximum and minimum transmission are derived, and it is shown that the peaks and valleys of phase-time can be well described by parameters fitted at the extrema. For a many-period system this covers most of the allowed band. Comparison is made to direct numerical solutions of the time-dependent Schr\"odinger equation by Veenstra et al. [cond-mat/0411118] who compared systems with and without addition of an anti-reflection coating (ARC). With an ARC, the time delay is consistent with propagation at the Bloch velocity of the periodic system, which significantly reduces the time delay, in addition to increasing the transmissivity.Comment: 8 pages, 10 figures, based on a talk at Theory-Canada 3 in Edmonton AB, June 200

A multiscale hybrid model for pro-angiogenic calcium signals in a vascular endothelial cell

Cytosolic calcium machinery is one of the principal signaling mechanisms by which endothelial cells (ECs) respond to external stimuli during several biological processes, including vascular progression in both physiological and pathological conditions. Low concentrations of angiogenic factors (such as VEGF) activate in fact complex pathways involving, among others, second messengers arachidonic acid (AA) and nitric oxide (NO), which in turn control the activity of plasma membrane calcium channels. The subsequent increase in the intracellular level of the ion regulates fundamental biophysical properties of ECs (such as elasticity, intrinsic motility, and chemical strength), enhancing their migratory capacity. Previously, a number of continuous models have represented cytosolic calcium dynamics, while EC migration in angiogenesis has been separately approached with discrete, lattice-based techniques. These two components are here integrated and interfaced to provide a multiscale and hybrid Cellular Potts Model (CPM), where the phenomenology of a motile EC is realistically mediated by its calcium-dependent subcellular events. The model, based on a realistic 3-D cell morphology with a nuclear and a cytosolic region, is set with known biochemical and electrophysiological data. In particular, the resulting simulations are able to reproduce and describe the polarization process, typical of stimulated vascular cells, in various experimental conditions.Moreover, by analyzing the mutual interactions between multilevel biochemical and biomechanical aspects, our study investigates ways to inhibit cell migration: such strategies have in fact the potential to result in pharmacological interventions useful to disrupt malignant vascular progressio