Deterministic and stochastic descriptions of gene expression dynamics

A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or implicitly etc. Here we consider simple systems of unregulated (constitutive) gene expression and compare different mathematical descriptions systematically to obtain insight into the errors that are introduced by various common approximations such as describing cell growth and division by an effective protein degradation term. In particular, we show that the population average of protein content of a cell exhibits a subtle dependence on the dynamics of growth and division, the specific model for volume growth and the age structure of the population. Nevertheless, the error made by models with implicit cell growth and division is quite small. Furthermore, we compare various models that are partially stochastic to investigate the impact of different sources of (intrinsic) noise. This comparison indicates that different sources of noise (protein synthesis, partitioning in cell division) contribute comparable amounts of noise if protein synthesis is not or only weakly bursty. If protein synthesis is very bursty, the burstiness is the dominant noise source, independent of other details of the model. Finally, we discuss two sources of extrinsic noise: cell-to-cell variations in protein content due to cells being at different stages in the division cycles, which we show to be small (for the protein concentration and, surprisingly, also for the protein copy number per cell) and fluctuations in the growth rate, which can have a significant impact.Comment: 23 pages, 5 figures; Journal of Statistical physics (2012

Search for lepton-flavor violation at HERA

A search for lepton-flavor-violating interactions $e p \to \mu X$ and $e p\to \tau X$ has been performed with the ZEUS detector using the entire HERA I data sample, corresponding to an integrated luminosity of 130 pb^{-1}. The data were taken at center-of-mass energies, $\sqrt{s}$, of 300 and 318 GeV. No evidence of lepton-flavor violation was found, and constraints were derived on leptoquarks (LQs) that could mediate such interactions. For LQ masses below $\sqrt{s}$, limits were set on $\lambda_{eq_1} \sqrt{\beta_{\ell q}}$, where $\lambda_{eq_1}$ is the coupling of the LQ to an electron and a first-generation quark $q_1$, and $\beta_{\ell q}$ is the branching ratio of the LQ to the final-state lepton $\ell$ ($\mu$ or $\tau$) and a quark $q$. For LQ masses much larger than $\sqrt{s}$, limits were set on the four-fermion interaction term $\lambda_{e q_\alpha} \lambda_{\ell q_\beta} / M_{\mathrm{LQ}}^2$ for LQs that couple to an electron and a quark $q_\alpha$ and to a lepton $\ell$ and a quark $q_\beta$, where $\alpha$ and $\beta$ are quark generation indices. Some of the limits are also applicable to lepton-flavor-violating processes mediated by squarks in $R$-Parity-violating supersymmetric models. In some cases, especially when a higher-generation quark is involved and for the process $e p\to \tau X$, the ZEUS limits are the most stringent to date.Comment: 37 pages, 10 figures, Accepted by EPJC. References and 1 figure (Fig. 6) adde

Multijet production in neutral current deep inelastic scattering at HERA and determination of alpha_s

Multijet production rates in neutral current deep inelastic scattering have been measured in the range of exchanged boson virtualities 10 < Q2 < 5000 GeV2. The data were taken at the ep collider HERA with centre-of-mass energy sqrt(s) = 318 GeV using the ZEUS detector and correspond to an integrated luminosity of 82.2 pb-1. Jets were identified in the Breit frame using the k_T cluster algorithm in the longitudinally invariant inclusive mode. Measurements of differential dijet and trijet cross sections are presented as functions of jet transverse energy E_{T,B}{jet}, pseudorapidity eta_{LAB}{jet} and Q2 with E_{T,B}{jet} > 5 GeV and -1 < eta_{LAB}{jet} < 2.5. Next-to-leading-order QCD calculations describe the data well. The value of the strong coupling constant alpha_s(M_Z), determined from the ratio of the trijet to dijet cross sections, is alpha_s(M_Z) = 0.1179 pm 0.0013(stat.) {+0.0028}_{-0.0046}(exp.) {+0.0064}_{-0.0046}(th.)Comment: 22 pages, 5 figure

Photoproduction of D∗±D^{*\pm} mesons associated with a leading neutron

The photoproduction of $D^{*\pm} (2010)$ mesons associated with a leading neutron has been observed with the ZEUS detector in $ep$ collisions at HERA using an integrated luminosity of 80 pb$^{-1}$. The neutron carries a large fraction, {$x_L>0.2$}, of the incoming proton beam energy and is detected at very small production angles, {$\theta_n<0.8$ mrad}, an indication of peripheral scattering. The $D^*$ meson is centrally produced with pseudorapidity {$|\eta| 1.9$ GeV}, which is large compared to the average transverse momentum of the neutron of 0.22 GeV. The ratio of neutron-tagged to inclusive $D^*$ production is $8.85\pm 0.93({\rm stat.})^{+0.48}_{-0.61}({\rm syst.})\%$ in the photon-proton center-of-mass energy range {$130 <W<280$ GeV}. The data suggest that the presence of a hard scale enhances the fraction of events with a leading neutron in the final state.Comment: 28 pages, 4 figures, 2 table

Measurement of beauty production in deep inelastic scattering at HERA

The beauty production cross section for deep inelastic scattering events with at least one hard jet in the Breit frame together with a muon has been measured, for photon virtualities Q^2 > 2 GeV^2, with the ZEUS detector at HERA using integrated luminosity of 72 pb^-1. The total visible cross section is sigma_b-bbar (ep -> e jet mu X) = 40.9 +- 5.7 (stat.) +6.0 -4.4 (syst.) pb. The next-to-leading order QCD prediction lies about 2.5 standard deviations below the data. The differential cross sections are in general consistent with the NLO QCD predictions; however at low values of Q^2, Bjorken x, and muon transverse momentum, and high values of jet transverse energy and muon pseudorapidity, the prediction is about two standard deviations below the data.Comment: 18 pages, 4 figure

Measurement of the open-charm contribution to the diffractive proton structure function

Production of D*+/-(2010) mesons in diffractive deep inelastic scattering has been measured with the ZEUS detector at HERA using an integrated luminosity of 82 pb^{-1}. Diffractive events were identified by the presence of a large rapidity gap in the final state. Differential cross sections have been measured in the kinematic region 1.5 < Q^2 < 200 GeV^2, 0.02 < y < 0.7, x_{IP} < 0.035, beta 1.5 GeV and |\eta(D*+/-)| < 1.5. The measured cross sections are compared to theoretical predictions. The results are presented in terms of the open-charm contribution to the diffractive proton structure function. The data demonstrate a strong sensitivity to the diffractive parton densities.Comment: 35 pages, 11 figures, 6 table

Measurement of charm fragmentation ratios and fractions in photoproduction at HERA

The production of D^*+, D^0, D^+, D_s^+ and Lambda_c^+ charm hadrons and their antiparticles in ep scattering at HERA was measured with the ZEUS detector using an integrated luminosity of 79 pb^-1. The measurement has been performed in the photoproduction regime with the exchanged-photon virtuality Q^2 < 1 GeV^2 and for photon-proton centre-of-mass energies in the range 130 < W < 300 GeV. The charm hadrons were reconstructed in the range of transverse momentum p_T(D, Lambda_c) > 3.8 GeV and pseudorapidity |eta(D, Lambda_c)| < 1.6. The production cross sections were used to determine the ratio of neutral and charged D-meson production rates, R_u/d, the strangeness-suppression factor, gamma_s, and the fraction of charged D mesons produced in a vector state, P_v^d. The measured R_u/d and gamma_s values agree with those obtained in deep inelastic scattering and in e^+e^- annihilations. The measured P_v^d value is smaller than, but consistent with, the previous measurements. The fractions of c quarks hadronising as a particular charm hadron, f(c -> D, Lambda_c), were derived in the given kinematic range. The measured open-charm fragmentation fractions are consistent with previous results, although the measured f(c -> D^*+) is smaller and f(c -> Lambda_c^+) is larger than those obtained in e^+e^- annihilations. These results generally support the hypothesis that fragmentation proceeds independently of the hard sub-process.Comment: 29 pages, 5 figures, 6 tables; minor text revision

Observation of isolated high-E_T photons in deep inelastic scattering

First measurements of cross sections for isolated prompt photon production in deep inelastic ep scattering have been made using the ZEUS detector at the HERA electron-proton collider using an integrated luminosity of 121 pb^-1. A signal for isolated photons in the transverse energy and rapidity ranges 5 < E_T^gamma < 10 GeV and -0.7 < eta^gamma < 0.9 was observed for virtualities of the exchanged photon of Q^2 > 35 GeV^2. Cross sections are presented for inclusive prompt photons and for those accompanied by a single jet in the range E_T^jet \geq 6 GeV and -1.5 \leq eta^jet < 1.8. Calculations at order alpha^3alpha_s describe the data reasonably well.Comment: 16 pages, 5 figure

Isolated tau leptons in events with large missing transverse momentum at HERA

A search for events containing isolated tau leptons and large missing transverse momentum, not originating from the tau decay, has been performed with the ZEUS detector at the electron-proton collider HERA, using 130 pb^-1 of integrated luminosity. A search was made for isolated tracks coming from hadronic tau decays. Observables based on the internal jet structure were exploited to discriminate between tau decays and quark- or gluon-induced jets. Three tau candidates were found, while 0.40 +0.12 -0.13 were expected from Standard Model processes, such as charged current deep inelastic scattering and single W-boson production. To search for heavy-particle decays, a more restrictive selection was applied to isolate tau leptons produced together with a hadronic final state with high transverse momentum. Two candidate events survive, while 0.20 +-0.05 events are expected from Standard Model processes.Comment: 28 pages, 4 figures, 3 tables, accepted by Phys. Lett. B. Updated with minor changes to the text requested by the journal refere