E-BioFlow: Different Perspectives on Scientific Workflows

We introduce a new type of workflow design system called\ud e-BioFlow and illustrate it by means of a simple sequence alignment workflow. E-BioFlow, intended to model advanced scientific workflows, enables the user to model a workflow from three different but strongly coupled perspectives: the control flow perspective, the data flow perspective, and the resource perspective. All three perspectives are of\ud equal importance, but workflow designers from different domains prefer different perspectives as entry points for their design, and a single workflow designer may prefer different perspectives in different stages of workflow design. Each perspective provides its own type of information, visualisation and support for validation. Combining these three perspectives in a single application provides a new and flexible way of modelling workflows

A new method of quantization of classical solutions

Using stochastic quantization method we derive equations for correlators of quantum fluctuations around the classical solution in the massless phi^4 theory. The obtained equations are then solved in the lowest orders of perturbation theory, and the first correction to the free propagator of a quantum fluctuation is calculated.Comment: 8 page

Induced two-photon decay of the 2s level and the rate of cosmological hydrogen recombination

Induced emission due to the presence of soft CMB photons slightly increases the two-photon decay rate of the 2s level of hydrogen defining the rate of cosmological recombination. This correspondingly changes the degree of ionization, the visibility function and the resulting primordial temperature anisotropies and polarization of the CMB on the percent level. These changes exceed the precision of the widely used CMBFAST and CAMB codes by more than one order of magnitude and can be easily taken into account.Comment: 5 pages, 5 figure, accepted by Astronomy and Astrophysic

How to study basement membrane stiffness as a biophysical trigger in prostate cancer and other age-related pathologies or metabolic diseases

Here we describe a protocol that can be used to study the biophysical microenvironment related to increased thickness and stiffness of the basement membrane (BM) during age-related pathologies and metabolic disorders (e.g. cancer, diabetes, microvascular disease, retinopathy, nephropathy and neuropathy). The premise of the model is non-enzymatic crosslinking of reconstituted BM (rBM) matrix by treatment with glycolaldehyde (GLA) to promote advanced glycation endproduct (AGE) generation via the Maillard reaction. Examples of laboratory techniques that can be used to confirm AGE generation, non-enzymatic crosslinking and increased stiffness in GLA treated rBM are outlined. These include preparation of native rBM (treated with phosphate-buffered saline, PBS) and stiff rBM (treated with GLA) for determination of: its AGE content by photometric analysis and immunofluorescent microscopy, its non-enzymatic crosslinking by ((sodium dodecyl sulfate polyacrylamide gel electrophoresis)) (SDS PAGE) as well as confocal microscopy, and its increased stiffness using rheometry. The procedure described here can be used to increase the rigidity (elastic moduli, E) of rBM up to 3.2-fold, consistent with measurements made in healthy versus diseased human prostate tissue. To recreate the biophysical microenvironment associated with the aging and diseased prostate gland three prostate cell types were introduced on to native rBM and stiff rBM: RWPE-1, prostate epithelial cells (PECs) derived from a normal prostate gland; BPH-1, PECs derived from a prostate gland affected by benign prostatic hyperplasia (BPH); and PC3, metastatic cells derived from a secondary bone tumor originating from prostate cancer. Multiple parameters can be measured, including the size, shape and invasive characteristics of the 3D glandular acini formed by RWPE-1 and BPH-1 on native versus stiff rBM, and average cell length, migratory velocity and persistence of cell movement of 3D spheroids formed by PC3 cells under the same conditions. Cell signaling pathways and the subcellular localization of proteins can also be assessed

One- and two-proton transfer reactions with vibrational Nuclei

We extend a semiclassical model of transfer reactions to the case in which one of the collision partners is a vibrational nucleus. The model is applied to one- and two-proton stripping reactions in the 37Cl + 98Mo system, for which a rapid transition from normal to anomalous slope in the two proton transfer reaction at energies around the Coulomb barrier is experimentally observed. This behavior is satisfactorily reproduced by the present extension of the model.Comment: LaTeX, 10 pages, 1 figure (PostScript

Correlated many-body treatment of Breit interaction with application to cesium atomic properties and parity violation

Corrections from Breit interaction to basic properties of atomic 133Cs are determined in the framework of third-order relativistic many-body perturbation theory. The corrections to energies, hyperfine-structure constants, off-diagonal hyperfine 6S-7S amplitude, and electric-dipole matrix elements are tabulated. It is demonstrated that the Breit corrections to correlations are comparable to the Breit corrections at the Dirac-Hartree-Fock level. Modification of the parity-nonconserving (PNC) 6S-7S amplitude due to Breit interaction is also evaluated; the resulting weak charge of $^{133}$Cs shows no significant deviation from the prediction of the standard model of elementary particles. The neutron skin correction to the PNC amplitude is also estimated to be -0.2% with an error bound of 30% based on the analysis of recent experiments with antiprotonic atoms. The present work supplements publication [A. Derevianko, Phys. Rev. Lett. 85, 1618 (2000)] with a discussion of the formalism and provides additional numerical results and updated discussion of parity violation.Comment: 16 pages; 5 figs; submitted to Phys. Rev.

Role of Present and Future Atomic Parity Violation Experiments in Precision Electroweak Tests

Recent reanalyses of the atomic physics effects on the weak charge in cesium have led to a value in much closer agreement with predictions of the Standard Model. We review precision electroweak tests, their implications for upper bounds on the mass of the Higgs boson, possible ways in which these bounds may be circumvented, and the requirements placed upon accuracy of future atomic parity violation experiments by these considerations.Comment: 10 pages, LaTeX, 1 figure, to be submitted to Physical Review D, new data on neutrino deep inelastic scattering include

Evaluation of the self-energy correction to the g-factor of S states in H-like ions

A detailed description of the numerical procedure is presented for the evaluation of the one-loop self-energy correction to the $g$-factor of an electron in the $1s$ and $2s$ states in H-like ions to all orders in $Z\alpha$.Comment: Final version, December 30, 200

On the Detectability of the Hydrogen 3-cm Fine Structure Line from the EoR

A soft ultraviolet radiation field, 10.2 eV < E <13.6 eV, that permeates neutral intergalactic gas during the Epoch of Reionization (EoR) excites the 2p (directly) and 2s (indirectly) states of atomic hydrogen. Because the 2s state is metastable, the lifetime of atoms in this level is relatively long, which may cause the 2s state to be overpopulated relative to the 2p state. It has recently been proposed that for this reason, neutral intergalactic atomic hydrogen gas may be detected in absorption in its 3-cm fine-structure line (2s_1/2 -> 2p_3/2) against the Cosmic Microwave Background out to very high redshifts. In particular, the optical depth in the fine-structure line through neutral intergalactic gas surrounding bright quasars during the EoR may reach tau~1e-5. The resulting surface brightness temperature of tens of micro K (in absorption) may be detectable with existing radio telescopes. Motivated by this exciting proposal, we perform a detailed analysis of the transfer of Lyman beta,gamma,delta,... radiation, and re-analyze the detectability of the fine-structure line in neutral intergalactic gas surrounding high-redshift quasars. We find that proper radiative transfer modeling causes the fine-structure absorption signature to be reduced tremendously to tau< 1e-10. We therefore conclude that neutral intergalactic gas during the EoR cannot reveal its presence in the 3-cm fine-structure line to existing radio telescopes.Comment: 7 pages, 4 figures, MNRAS in press; v2. some typos fixe

Dephasing and Measurement Efficiency via a Quantum Dot Detector

We study charge detection and controlled dephasing of a mesoscopic system via a quantum dot detector (QDD), where the mesoscopic system and the QDD are capacitively coupled. The QDD is considered to have coherent resonant tunnelling via a single level. It is found that the dephasing rate is proportional to the square of the conductance of the QDD for the Breit-Wigner model, showing that the dephasing is completely different from the shot noise of the detector. The measurement rate, on the other hand, shows a dip near the resonance. Our findings are peculiar especially for a symmetric detector in the following aspect: The dephasing rate is maximum at resonance of the QDD where the detector conductance is insensitive to the charge state of the mesoscopic system. As a result, the efficiency of the detector shows a dip and vanishes at resonance, in contrast to the single-channel symmetric non-resonant detector that has always a maximum efficiency. We find that this difference originates from a very general property of the scattering matrix: The abrupt phase change exists in the scattering amplitudes in the presence of the symmetry, which is insensitive to the detector current but {\em stores} the information of the quantum state of the mesoscopic system.Comment: 7 pages, 3 figure