Probability distributed time delays: integrating spatial effects into temporal models

Background: In order to provide insights into the complex biochemical processes inside a cell, modelling approaches must find a balance between achieving an adequate representation of the physical phenomena and keeping the associated computational cost within reasonable limits. This issue is particularly stressed when spatial inhomogeneities have a significant effect on system's behaviour. In such cases, a spatially-resolved stochastic method can better portray the biological reality, but the corresponding computer simulations can in turn be prohibitively expensive.Results: We present a method that incorporates spatial information by means of tailored, probability distributed time-delays. These distributions can be directly obtained by single in silico or a suitable set of in vitro experiments and are subsequently fed into a delay stochastic simulation algorithm (DSSA), achieving a good compromise between computational costs and a much more accurate representation of spatial processes such as molecular diffusion and translocation between cell compartments. Additionally, we present a novel alternative approach based on delay differential equations (DDE) that can be used in scenarios of high molecular concentrations and low noise propagation.Conclusions: Our proposed methodologies accurately capture and incorporate certain spatial processes into temporal stochastic and deterministic simulations, increasing their accuracy at low computational costs. This is of particular importance given that time spans of cellular processes are generally larger (possibly by several orders of magnitude) than those achievable by current spatially-resolved stochastic simulators. Hence, our methodology allows users to explore cellular scenarios under the effects of diffusion and stochasticity in time spans that were, until now, simply unfeasible. Our methodologies are supported by theoretical considerations on the different modelling regimes, i.e. spatial vs. delay-temporal, as indicated by the corresponding Master Equations and presented elsewhere

MAGIC detection of short-term variability of the high-peaked BL Lac object 1ES 0806+524

The high-frequency-peaked BL Lac (HBL) 1ES 0806+524 (z = 0.138) was discovered in VHE $\gamma$ rays in 2008. Until now, the broad-band spectrum of 1ES 0806+524 has been only poorly characterized, in particular at high energies. We analysed multiwavelength observations from $\gamma$ rays to radio performed from 2011 January to March, which were triggered by the high activity detected at optical frequencies. These observations constitute the most precise determination of the broad-band emission of 1ES 0806+524 to date. The stereoscopic MAGIC observations yielded a $\gamma$-ray signal above 250 GeV of $(3.7 \pm 0.7)$ per cent of the Crab Nebula flux with a statistical significance of 9.9 $\sigma$. The multiwavelength observations showed significant variability in essentially all energy bands, including a VHE $\gamma$-ray flare that lasted less than one night, which provided unprecedented evidence for short-term variability in 1ES 0806+524. The spectrum of this flare is well described by a power law with a photon index of $2.97 \pm 0.29$ between $\sim$150 GeV and 1 TeV and an integral flux of $(9.3 \pm 1.9)$ per cent of the Crab Nebula flux above 250 GeV. The spectrum during the non-flaring VHE activity is compatible with the only available VHE observation performed in 2008 with VERITAS when the source was in a low optical state. The broad-band spectral energy distribution can be described with a one-zone Synchrotron Self Compton model with parameters typical for HBLs, indicating that 1ES 0806+524 is not substantially different from the HBLs previously detected.Comment: 12 pages, 8 figures, 3 tables, accepted 2015 April 20 for publication in Monthly Notices of the Royal Astronomical Society Main Journa

Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling

The Notch signaling pathway controls numerous cell fate decisions during development and adulthood through diverse mechanisms. Thus, whereas it functions as an oscillator during somitogenesis, it can mediate an all-or-none cell fate switch to influence pattern formation in various tissues during development. Furthermore, while in some contexts continuous Notch signaling is required, in others a transient Notch signal is sufficient to influence cell fate decisions. However, the signaling mechanisms that underlie these diverse behaviors in different cellular contexts have not been understood. Notch1 along with two downstream transcription factors hes1 and RBP-Jk forms an intricate network of positive and negative feedback loops, and we have implemented a systems biology approach to computationally study this gene regulation network. Our results indicate that the system exhibits bistability and is capable of switching states at a critical level of Notch signaling initiated by its ligand Delta in a particular range of parameter values. In this mode, transient activation of Delta is also capable of inducing prolonged high expression of Hes1, mimicking the “ON” state depending on the intensity and duration of the signal. Furthermore, this system is highly sensitive to certain model parameters and can transition from functioning as a bistable switch to an oscillator by tuning a single parameter value. This parameter, the transcriptional repression constant of hes1, can thus qualitatively govern the behavior of the signaling network. In addition, we find that the system is able to dampen and reduce the effects of biological noise that arise from stochastic effects in gene expression for systems that respond quickly to Notch signaling

Search for top squarks in events with a Higgs or Z boson using 139 fb−1 of pp collision data at √ s = 13 TeV with the ATLAS detector

This paper presents a search for direct top squark pair production in events with missing transverse momentum plus either a pair of jets consistent with Standard Model Higgs boson decay into b-quarks or a same-flavour opposite-sign dilepton pair with an invariant mass consistent with a Z boson. The analysis is performed using the proton–proton collision data at s=13 TeV collected with the ATLAS detector during the LHC Run-2, corresponding to an integrated luminosity of 139 fb- 1. No excess is observed in the data above the Standard Model predictions. The results are interpreted in simplified models featuring direct production of pairs of either the lighter top squark (t~ 1) or the heavier top squark (t~ 2), excluding at 95% confidence level t~ 1 and t~ 2 masses up to about 1220 and 875 GeV, respectively

Performance of the ATLAS RPC detector and Level-1 muon barrel trigger at √s = 13 TeV

The ATLAS experiment at the Large Hadron Collider (LHC) employs a trigger system consisting of a first-level hardware trigger (L1) and a software-based high-level trigger. The L1 muon trigger system selects muon candidates, assigns them to the correct LHC bunch crossing and classifies them into one of six transverse-momentum threshold classes. The L1 muon trigger system uses resistive-plate chambers (RPCs) to generate the muon-induced trigger signals in the central (barrel) region of the ATLAS detector. The ATLAS RPCs are arranged in six concentric layers and operate in a toroidal magnetic field with a bending power of 1.5 to 5.5 Tm. The RPC detector consists of about 3700 gas volumes with a total surface area of more than 4000 m^{2}. This paper reports on the performance of the RPC detector and L1 muon barrel trigger using 60.8 fb^{-1} of proton-proton collision data recorded by the ATLAS experiment in 2018 at a centre-of-mass energy of 13 TeV. Detector and trigger performance are studied using Z boson decays into a muon pair. Measurements of the RPC detector response, efficiency, and time resolution are reported. Measurements of the L1 muon barrel trigger efficiencies and rates are presented, along with measurements of the properties of the selected sample of muon candidates. Measurements of the RPC currents, counting rates and mean avalanche charge are performed using zero-bias collisions. Finally, RPC detector response and efficiency are studied at different high voltage and front-end discriminator threshold settings in order to extrapolate detector response to the higher luminosity expected for the High Luminosity LHC

Materials in particulate form for tissue engineering. 1 Basic concepts

For biomedical applications, materials small in size are growing in importance. In an era where ‘nano’ is the new trend, micro- and nano-materials are in the forefront of developments. Materials in the particulate form aim to designate systems with a reduced size, such as micro- and nanoparticles. These systems can be produced starting from a diversity of materials, of which polymers are the most used. Similarly, a multitude of methods are used to produce particulate systems, and both materials and methods are critically reviewed here. Among the varied applications that materials in the particulate form can have, drug delivery systems are probably the most prominent, as these have been in the forefront of interest for biomedical applications. The basic concepts pertaining to drug delivery are summarized, and the role of polymers as drug delivery systems conclude this review

Broadband Multi-wavelength Properties of M87 during the 2017 Event Horizon Telescope Campaign

Abstract: In 2017, the Event Horizon Telescope (EHT) Collaboration succeeded in capturing the first direct image of the center of the M87 galaxy. The asymmetric ring morphology and size are consistent with theoretical expectations for a weakly accreting supermassive black hole of mass ∼6.5 × 109 M ⊙. The EHTC also partnered with several international facilities in space and on the ground, to arrange an extensive, quasi-simultaneous multi-wavelength campaign. This Letter presents the results and analysis of this campaign, as well as the multi-wavelength data as a legacy data repository. We captured M87 in a historically low state, and the core flux dominates over HST-1 at high energies, making it possible to combine core flux constraints with the more spatially precise very long baseline interferometry data. We present the most complete simultaneous multi-wavelength spectrum of the active nucleus to date, and discuss the complexity and caveats of combining data from different spatial scales into one broadband spectrum. We apply two heuristic, isotropic leptonic single-zone models to provide insight into the basic source properties, but conclude that a structured jet is necessary to explain M87’s spectrum. We can exclude that the simultaneous γ-ray emission is produced via inverse Compton emission in the same region producing the EHT mm-band emission, and further conclude that the γ-rays can only be produced in the inner jets (inward of HST-1) if there are strongly particle-dominated regions. Direct synchrotron emission from accelerated protons and secondaries cannot yet be excluded