A Low Dimensional Approximation For Competence In Bacillus Subtilis

The behaviour of a high dimensional stochastic system described by a Chemical Master Equation (CME) depends on many parameters, rendering explicit simulation an inefficient method for exploring the properties of such models. Capturing their behaviour by low-dimensional models makes analysis of system behaviour tractable. In this paper, we present low dimensional models for the noise-induced excitable dynamics in Bacillus subtilis, whereby a key protein ComK, which drives a complex chain of reactions leading to bacterial competence, gets expressed rapidly in large quantities (competent state) before subsiding to low levels of expression (vegetative state). These rapid reactions suggest the application of an adiabatic approximation of the dynamics of the regulatory model that, however, lead to competence durations that are incorrect by a factor of 2. We apply a modified version of an iterative functional procedure that faithfully approximates the time-course of the trajectories in terms of a 2-dimensional model involving proteins ComK and ComS. Furthermore, in order to describe the bimodal bivariate marginal probability distribution obtained from the Gillespie simulations of the CME, we introduce a tunable multiplicative noise term in a 2-dimensional Langevin model whose stationary state is described by the time-independent solution of the corresponding Fokker-Planck equation.Comment: 12 pages, to be published in IEEE/ACM Transactions on Computational Biology and Bioinformatic

Direct Detection Constraints on Dark Photon Dark Matter

Dark matter detectors built primarily to probe elastic scattering of WIMPs on nuclei are also precise probes of light, weakly coupled particles that may be absorbed by the detector material. In this paper, we derive constraints on the minimal model of dark matter comprised of long-lived vector states V (dark photons) in the 0.01-100 keV mass range. The absence of an ionization signal in direct detection experiments such as XENON10 and XENON100 places a very strong constraint on the dark photon mixing angle, down to $O(10^{-15})$, assuming that dark photons comprise the dominant fraction of dark matter. This sensitivity to dark photon dark matter exceeds the indirect bounds derived from stellar energy loss considerations over a significant fraction of the available mass range. We also revisit indirect constraints from $V\to 3\gamma$ decay and show that limits from modifications to the cosmological ionization history are comparable to the updated limits from the diffuse gamma-ray flux.Comment: 10 pages, 4 figures; numerical bug in J-factor corrected; main results unchange

Directly Detecting MeV-scale Dark Matter via Solar Reflection

If dark matter (DM) particles are lighter than a few MeV/$c^2$ and can scatter off electrons, their interaction within the solar interior results in a considerable hardening of the spectrum of galactic dark matter received on Earth. For a large range of the mass vs. cross section parameter space, $\{m_e, \sigma_e\}$, the "reflected" component of the DM flux is far more energetic than the endpoint of the ambient galactic DM energy distribution, making it detectable with existing DM detectors sensitive to an energy deposition of $10-10^3$ eV. After numerically simulating the small reflected component of the DM flux, we calculate its subsequent signal due to scattering on detector electrons, deriving new constraints on $\sigma_e$ in the MeV and sub-MeV range using existing data from the XENON10/100, LUX, PandaX-II, and XENON1T experiments, as well as making projections for future low threshold direct detection experiments.Comment: 6 pages, 4 figures; improved treatment of reflection process; limits strengthened, conclusions otherwise unchange

Direct detection prospects of dark vectors with xenon-based dark matter experiments

Dark matter experiments primarily search for the scattering of WIMPs on target nuclei of well shielded underground detectors. The results from liquid scintillator experiments furthermore provide precise probes of very light and very weakly coupled particles that may be absorbed by electrons. In these proceedings we summarize previously obtained constraints on long-lived dark matter vector particles $V$ (dark photons) in the $0.01-100$ keV mass range. In addition, we provide a first projected sensitivity reach for the upcoming XENON1T dark matter search to detect dark photons.Comment: 5 pages, 1 figure; proceedings of the European Physical Society Conference on High Energy Physics 2015 (EPS-HEP 2015), Vienna, Austria; reference adde

Interference in Language Processing Reflects Direct-Access Memory Retrieval: Evidence from Drift-Diffusion Modeling

Many studies on memory retrieval in language processing have identified similarity-based interference as a key determinant of comprehension. The broad consensus is that similarity-based interference reflects erroneous retrieval of a non-target item that matches some of the retrieval cues. However, the mechanisms responsible for such effects remain debated. Activation-based models of retrieval (e.g., Lewis & Vasishth, 2005) claim that any differences in processing difficulty due to interference in standard RT measures and judgments reflect differences in the speed of retrieval (i.e., the amount of time it takes to retrieve a memory item). But this claim is inconsistent with empirical data showing that retrieval time is constant due to the use of a direct-access procedure (e.g., McElree, 2000, 2006). According to direct-access accounts, differences in judgments or RTs due to interference arise from differences in the quality or availability of the candidate memory representations, rather than differences in retrieval speed. To adjudicate between these accounts, we employed a novel methodology that combined a high-powered (N = 200) twoalternative forced-choice study on interference effects with drift diffusion modeling to disassociate the effects of retrieval speed and representation quality. Results showed that the presence of a distractor that matched some of the retrieval cues lowered asymptotic accuracy, reflecting an effect of representation quality, but did not affect retrieval speed, consistent with a direct-access procedure. These results suggest that the differences observed in RTs and judgment studies reflect differences in the ease of integrating the retrieved item back into the current processing stream, rather than differences in retrieval speed

Not All Phrases are Equally Attractive: New evidence for selective agreement attraction effects in comprehension

Research on memory retrieval during sentence comprehension suggests that similarity-based interference is mediated by the grammatical function of the distractor. For instance, Van Dyke and McElree (2011) observed interference during retrieval for subject-verb thematic binding when the distractor occurred as an oblique argument inside a prepositional phrase (PP), but not when it occurred as a core argument in direct object position. This contrast motivated the proposal that constituent encodings vary in the distinctiveness of their memory representations based on an argument hierarchy, which makes them differentially susceptible to interference. However, this hypothesis has not been explicitly tested. The present study uses an interference paradigm involving agreement attraction (e.g., Wagers et al., 2009) to test whether the argument status of the distractor determines susceptibility to interference. Results from two self-paced reading experiments show a clear contrast: agreement attraction is observed for oblique arguments (e.g., PP distractors), but attraction is nullified for core arguments (i.e., direct object and subject distractors). A follow-up experiment showed that this contrast cannot be reduced to the syntactic position of the distractor, favoring an account based on the semantic properties of the distractor. These findings support the proposal that interference is mediated by the argument status of the distractor and extend previous results by showing that the effect generalizes to a broader set of syntactic contexts and a wider range of syntactic dependencies. More generally, these results motivate a more nuanced account of real-time agreement processing that depends on both retrieval and encoding mechanisms

S8S_8 Tension in the Context of Dark Matter-Baryon Scattering

We explore the concordance of cosmological data in the context of dark matter (DM) that interacts with baryons. Using the effective theory of large-scale structure, we perform the first analysis of galaxy clustering data for this scenario and find a mild $\sim 3\sigma$ preference for velocity-independent DM-baryon scattering, assuming 10% of DM is interacting. Our results indicate that a broad power suppression on small scales is a generic feature that may help resolve $S_8$ tension between cosmological data sets. The validity of this interacting DM model will be critically tested with incoming survey data.Comment: 21 pages, 10 figures, submitted to PR