Electro-optic bunch diagnostics on ALICE

An electro-optic longitudinal bunch profile monitor has been implemented on ALICE (Accelerators and Lasers in Combined Experiments) at the Daresbury Laboratories and will be used both to characterise the electron bunch and to provide a testbed for electro-optic techniques. The electro-optic station is located immediately after the bunch compressor, within the FEL cavity; its location allows nearby OTR, beam profile monitors and Coherent Synchrontron Radiation (CSR) diagnostics to be used for calibration and benchmarking. We discuss the implementation and the planned studies on electro-optic diagnostics using this diagnostic station

Upconversion of a relativistic Coulomb field terahertz pulse to the near infrared

We demonstrate the spectral upconversion of a unipolar subpicosecond terahertz (THz) pulse, where the THz pulse is the Coulomb field of a single relativistic electron bunch. The upconversion to the optical allows remotely located detection of long wavelength and nonpropagating components of the THz spectrum, as required for ultrafast electron bunch diagnostics. The upconversion of quasimonochromatic THz radiation has also been demonstrated, allowing the observation of distinct sum- and difference-frequency mixing components in the spectrum. Polarization dependence of first and second order sidebands at ωopt±ωTHz, and ωopt±2ωTHz, respectively, confirms the χ(2) frequency mixing mechanism

A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics

We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic framework. The technique correctly accounts for stochastic noise at significantly reduced computational cost, requires the definition of only three model-independent parameters and is particularly well-suited for simulating systems containing widely disparate species populations. We present the theoretical foundations of partitioned leaping, discuss various options for its practical implementation and demonstrate the utility of the method via illustrative examples.Comment: v4: 12 pages, 5 figures, final accepted version. Error found and fixed in Appendi

Chk1 requirement for high global rates of replication fork progression during normal vertebrate S phase

Chk1 protein kinase maintains replication fork stability in metazoan cells in response to DNA damage and DNA replication inhibitors. Here, we have employed DNA fiber labeling to quantify, for the first time, the extent to which Chk1 maintains global replication fork rates during normal vertebrate S phase. We report that replication fork rates in Chk1¿/¿ chicken DT40 cells are on average half of those observed with wild-type cells. Similar results were observed if Chk1 was inhibited or depleted in wild-type DT40 cells or HeLa cells by incubation with Chk1 inhibitor or small interfering RNA. In addition, reduced rates of fork extension were observed with permeabilized Chk1¿/¿ cells in vitro. The requirement for Chk1 for high fork rates during normal S phase was not to suppress promiscuous homologous recombination at replication forks, because inhibition of Chk1 similarly slowed fork progression in XRCC3¿/¿ DT40 cells. Rather, we observed an increased number of replication fibers in Chk1¿/¿ cells in which the nascent strand is single-stranded, supporting the idea that slow global fork rates in unperturbed Chk1¿/¿ cells are associated with the accumulation of aberrant replication fork structure

Enhancement of the stability of genetic switches by overlapping upstream regulatory domains

We study genetic switches formed from pairs of mutually repressing operons. The switch stability is characterised by a well defined lifetime which grows sub-exponentially with the number of copies of the most-expressed transcription factor, in the regime accessible by our numerical simulations. The stability can be markedly enhanced by a suitable choice of overlap between the upstream regulatory domains. Our results suggest that robustness against biochemical noise can provide a selection pressure that drives operons, that regulate each other, together in the course of evolution.Comment: 4 pages, 5 figures, RevTeX

Longtitudinal electron beam diagnostics via upconversion of THz to visible radiation

Longitudinal electro-optic electron bunch diagnostics has been successfully applied at several accelerators. The electro-optic effect can be seen as an upconversion of the Coulomb field of the relativistic electron bunch (THz radiation) to the visible spectral range, where a variety of standard diagnostic tools are available. Standard techniques to characterise femtosecond optical laser pulses (auto- and cross-correlators) have led to the schemes that can measure electron bunch profiles with femtosecond resolution. These techniques require, however, well synchronized femtosecond laser pulses, in order to obtain the desired temporal resolution. Currently, we are exploring other electro-optic variants which require less advanced laser systems and will be more amenable to beam based longitudinal feedback applications. The first results of one such new scheme will be presented in this paper

Reconstruction and architecture of medullosan pteridosperms (Pennsylvanian)

A new reconstruction of the architecture of medullosan pteridosperms is proposed on the basis of three stems preserved as compression-impression fossils: one from the Southern Anthracite Coal Field of Pennsylvania (lower part of Llewellyn Formation, Pennsylvania, Westphalian D) probably belonging to Alethopteris foliage; a second stem from the roof shale of the Eagle coal bed (Kanawha Formation, Middle Pennsylvanian, Westphalian B) of West Virginia, associated with Neuropteris foliage; and a third reported from the Stephanian of Commentry, France, in connection with Odontopteris foliage. The diameters of the Llewellyn, Eagle, and Commentry stems are 17 cm, 13 cm, and 6.5 cm, respectively. All three stems bear remnants of petioles up to several centimeters in length. The petolar remnants indicate that the living leaves grew upward at an angle of 30 - 60 degrees from the vertical, a growth habit that is common in present day tropical plants with similar overall architecture. Leaves drooped only when they were dying. After decay they broke off and left short petiolar remnants bent downward. The Llewellyn and Eagle stems represent plants with thick, straight stems, whereas the Commentry specimen shows a thin and slightly curved stem

On-the-fly Uniformization of Time-Inhomogeneous Infinite Markov Population Models

This paper presents an on-the-fly uniformization technique for the analysis of time-inhomogeneous Markov population models. This technique is applicable to models with infinite state spaces and unbounded rates, which are, for instance, encountered in the realm of biochemical reaction networks. To deal with the infinite state space, we dynamically maintain a finite subset of the states where most of the probability mass is located. This approach yields an underapproximation of the original, infinite system. We present experimental results to show the applicability of our technique