arXiv subjects

Matthew Wood

Publications and source records attributed to Matthew Wood.

16 recordsLinked to original sources

arXiv2025

Helix-mRNA: A Hybrid Foundation Model For Full Sequence mRNA Therapeutics

mRNA-based vaccines have become a major focus in the pharmaceutical industry. The coding sequence as well as the Untranslated Regions (UTRs) of an mRNA can strongly influence translation efficiency, stability, degradation, and other factors that collectively determine a vaccine's effectiveness. However, optimizing mRNA sequences for those properties remains a complex challenge. Existing deep learning models often focus solely on coding region optimization, overlooking the UTRs. We present Helix-mRNA, a structured state-space-based and attention hybrid model to address these challenges. In addition to a first pre-training, a second pre-training stage allows us to specialise the model with high-quality data. We employ single nucleotide tokenization of mRNA sequences with codon separation, ensuring prior biological and structural information from the original mRNA sequence is not lost. Our model, Helix-mRNA, outperforms existing methods in analysing both UTRs and coding region properties. It can process sequences 6x longer than current approaches while using only 10% of the parameters of existing foundation models. Its predictive capabilities extend to all mRNA regions. We open-source the model (https://github.com/helicalAI/helical) and model weights (https://huggingface.co/helical-ai/helix-mRNA).

q-bio.GN↗

arXiv2022

Design and Performance of the Prototype Schwarzschild-Couder Telescope Camera

The prototype Schwarzschild-Couder Telescope (pSCT) is a candidate for a medium-sized telescope in the Cherenkov Telescope Array. The pSCT is based on a novel dual mirror optics design which reduces the plate scale and allows for the use of silicon photomultipliers as photodetectors. The prototype pSCT camera currently has only the central sector instrumented with 25 camera modules (1600 pixels), providing a 2.68$^{\circ}$ field of view (FoV). The camera electronics are based on custom TARGET (TeV array readout with GSa/s sampling and event trigger) application specific integrated circuits. Field programmable gate arrays sample incoming signals at a gigasample per second. A single backplane provides camera-wide triggers. An upgrade of the pSCT camera is in progress, which will fully populate the focal plane. This will increase the number of pixels to 11,328, the number of backplanes to 9, and the FoV to 8.04$^{\circ}$. Here we give a detailed description of the pSCT camera, including the basic concept, mechanical design, detectors, electronics, current status and first light.

astro-ph.IM↗

arXiv2017

Preliminary Results of the Fermi High-Latitude Extended Source Catalog

We report on preliminary results from the Fermi High-Latitude Extended Sources Catalog (FHES), a comprehensive search for spatially extended gamma-ray sources at high Galactic latitudes ($|b|>5^\circ$) based on data from the Fermi Large Area Telescope (LAT). While the majority of high-latitude LAT sources are extragalactic blazars that appear point-like within the LAT angular resolution, there are several physics scenarios that predict the existence of populations of spatially extended sources. If Dark Matter consists of Weakly Interacting Massive Particles, the annihilation or decay of these particles in subhalos of the Milky Way would appear as a population of unassociated gamma-ray sources with finite angular extent. Gamma-ray emission from blazars could also be extended (so-called pair halos) due to the deflection of electron-positron pairs in the intergalactic magnetic field (IGMF). The pairs are produced in the absorption of gamma rays in the intergalactic medium and subsequently up-scatter photons of background radiation fields to gamma-ray energies. Measurement of pair halos could provide constraints on the strength and coherence length scale of the IGMF. In a dedicated search, we find 21 extended sources and 16 sources not previously characterized as extended. Limits on the flux of the extended source components are used to derive constraints on the strength of the IGMF using spectral and spatial templates derived from Monte Carlo simulations of electromagnetic cascades. This allows us to constrain the IGMF to be stronger than $3\times10^{-16}\,$G for a coherence length $λ\gtrsim 10\,$kpc.

astro-ph.HE↗

arXiv2017

Gammapy - A prototype for the CTA science tools

Gammapy is a Python package for high-level gamma-ray data analysis built on Numpy, Scipy and Astropy. It enables us to analyze gamma-ray data and to create sky images, spectra and lightcurves, from event lists and instrument response information, and to determine the position, morphology and spectra of gamma-ray sources. So far Gammapy has mostly been used to analyze data from H.E.S.S. and Fermi-LAT, and is now being used for the simulation and analysis of observations from the Cherenkov Telescope Array (CTA). We have proposed Gammapy as a prototype for the CTA science tools. This contribution gives an overview of the Gammapy package and project and shows an analysis application example with simulated CTA data.

astro-ph.IM↗

arXiv2017

Fermipy: An open-source Python package for analysis of Fermi-LAT Data

Fermipy is an open-source python framework that facilitates analysis of data collected by the Fermi Large Area Telescope (LAT). Fermipy is built on the Fermi Science Tools, the publicly available software suite provided by NASA for the LAT mission. Fermipy provides a high-level interface for analyzing LAT data in a simple and reproducible way. The current feature set includes methods for extracting spectral energy distributions and lightcurves, generating test statistic maps, finding new source candidates, and fitting source position and extension. Fermipy leverages functionality from other scientific python packages including NumPy, SciPy, Matplotlib, and Astropy and is organized as a community-developed package following an open-source development model. We review the current functionality of Fermipy and plans for future development.

astro-ph.IM↗

arXiv2016

Open high-level data formats and software for gamma-ray astronomy

In gamma-ray astronomy, a variety of data formats and proprietary software have been traditionally used, often developed for one specific mission or experiment. Especially for ground-based imaging atmospheric Cherenkov telescopes (IACTs), data and software are mostly private to the collaborations operating the telescopes. However, there is a general movement in science towards the use of open data and software. In addition, the next-generation IACT instrument, the Cherenkov Telescope Array (CTA), will be operated as an open observatory. We have created a Github organisation at https://github.com/open-gamma-ray-astro where we are developing high-level data format specifications. A public mailing list was set up at https://lists.nasa.gov/mailman/listinfo/open-gamma-ray-astro and a first face-to-face meeting on the IACT high-level data model and formats took place in April 2016 in Meudon (France). This open multi-mission effort will help to accelerate the development of open data formats and open-source software for gamma-ray astronomy, leading to synergies in the development of analysis codes and eventually better scientific results (reproducible, multi-mission). This write-up presents this effort for the first time, explaining the motivation and context, the available resources and process we use, as well as the status and planned next steps for the data format specifications. We hope that it will stimulate feedback and future contributions from the gamma-ray astronomy community.

astro-ph.IM↗

arXiv2016

Sensitivity Projections for Dark Matter Searches with the Fermi Large Area Telescope

The nature of dark matter is a longstanding enigma of physics; it may consist of particles beyond the Standard Model that are still elusive to experiments. Among indirect search techniques, which look for stable products from the annihilation or decay of dark matter particles, or from axions coupling to high-energy photons, observations of the $γ$-ray sky have come to prominence over the last few years, because of the excellent sensitivity of the Large Area Telescope (LAT) on the Fermi Gamma-ray Space Telescope mission. The LAT energy range from 20 MeV to above 300 GeV is particularly well suited for searching for products of the interactions of dark matter particles. In this report we describe methods used to search for evidence of dark matter with the LAT, and review the status of searches performed with up to six years of LAT data. We also discuss the factors that determine the sensitivities of these searches, including the magnitudes of the signals and the relevant backgrounds, considering both statistical and systematic uncertainties. We project the expected sensitivities of each search method for 10 and 15 years of LAT data taking. In particular, we find that the sensitivity of searches targeting dwarf galaxies, which provide the best limits currently, will improve faster than the square root of observing time. Current LAT limits for dwarf galaxies using six years of data reach the thermal relic level for masses up to 120 GeV for the $b\bar{b}$ annihilation channel for reasonable dark matter density profiles. With projected discoveries of additional dwarfs, these limits could extend to about 250 GeV. With as much as 15 years of LAT data these searches would be sensitive to dark matter annihilations at the thermal relic cross section for masses to greater than 400 GeV (200 GeV) in the $b\bar{b}$ ($τ^+ τ^-$) annihilation channels.

astro-ph.HE↗

arXiv2016

Search for Gamma-ray Emission from Dark Matter Annihilation in the Small Magellanic Cloud with the Fermi Large Area Telescope

The Small Magellanic Cloud (SMC) is the second-largest satellite galaxy of the Milky Way and is only 60 kpc away. As a nearby, massive, and dense object with relatively low astrophysical backgrounds, it is a natural target for dark matter indirect detection searches. In this work, we use six years of Pass 8 data from the Fermi Large Area Telescope to search for gamma-ray signals of dark matter annihilation in the SMC. Using data-driven fits to the gamma-ray backgrounds, and a combination of N-body simulations and direct measurements of rotation curves to estimate the SMC DM density profile, we found that the SMC was well described by standard astrophysical sources, and no signal from dark matter annihilation was detected. We set conservative upper limits on the dark matter annihilation cross section. These constraints are in agreement with stronger constraints set by searches in the Large Magellanic Cloud and approach the canonical thermal relic cross section at dark matter masses lower than 10 GeV in the $b\bar{b}$ and $τ^+τ^-$ channels.

astro-ph.HE↗

arXiv2015

Prospects for Measuring the Positron Excess with the Cherenkov Telescope Array

The excess of positrons in cosmic rays above $\sim$10 GeV has been a puzzle since it was discovered. Possible interpretations of the excess have been suggested, including acceleration in a local supernova remnant or annihilation of dark matter particles. To discriminate between these scenarios, the positron fraction must be measured at higher energies. One technique to perform this measurement is using the Earth-Moon spectrometer: observing the deflection of positron and electron moon shadows by the Earth's magnetic field. The measurement has been attempted by previous imaging atmospheric Cherenkov telescopes without success. The Cherenkov Telescope Array (CTA) will have unprecedented sensitivity and background rejection that could make this measurement successful for the first time. In addition, the possibility of using silicon photomultipliers in some of the CTA telescopes could greatly increase the feasibility of making observations near the moon. Estimates of the capabilities of CTA to measure the positron fraction using simulated observations of the moon shadow will be presented.

astro-ph.IM↗

arXiv2015

Limits to dark matter properties from a combined analysis of MAGIC and Fermi-LAT observations of dwarf satellite galaxies

We present the first MAGIC/Fermi-LAT joint search for dark matter annihilation gamma-ray signals from dwarf satellite galaxies. We combine 158 hours of observations of Segue 1 by MAGIC with 6-years observations of 15 dwarf satellite galaxies by the Fermi-LAT. We obtain limits on the annihilation cross-section for dark matter particle masses between 10 GeV and 100 TeV - the widest mass range ever explored by a coherent and comprehensive analysis. Our new inclusive analysis approach is completely generic, and we propose to use it to perform a global, sensitivity-optimized dark matter search by combining data from present and future gamma-ray and neutrino detectors.

astro-ph.HE↗

arXiv2015

Dark Matter Searches with the Fermi-LAT in the Direction of Dwarf Spheroidals

The dwarf spheroidal satellite galaxies of the Milky Way are some of the most dark-matter-dominated objects known. Due to their proximity, high dark matter content, and lack of astrophysical backgrounds, dwarf spheroidal galaxies are widely considered to be among the most promising targets for the indirect detection of dark matter via gamma rays. Here we report on gamma-ray observations of Milky Way dwarf spheroidal satellite galaxies based on 6 years of Fermi Large Area Telescope data processed with the new Pass 8 reconstruction and event-level analysis. None of the dwarf galaxies are significantly detected in gamma rays, and we present upper limits on the dark matter annihilation cross section from a combined analysis of the 15 most promising dwarf galaxies. The constraints derived are among the strongest to date using gamma rays and lie below the canonical thermal relic cross section for WIMPs of mass $\lesssim 100~GeV$ annihilating via the $b \bar b$ and $τ^{+}τ^{-}$ channels.

astro-ph.HE↗

arXiv2015

Dark Matter in the Coming Decade: Complementary Paths to Discovery and Beyond

In this report we summarize the many dark matter searches currently being pursued through four complementary approaches: direct detection, indirect detection, collider experiments, and astrophysical probes. The essential features of broad classes of experiments are described, each with their own strengths and weaknesses. The complementarity of the different dark matter searches is discussed qualitatively and illustrated quantitatively in two simple theoretical frameworks. Our primary conclusion is that the diversity of possible dark matter candidates requires a balanced program drawing from all four approaches.

hep-ph↗

arXiv2014

Complementarity of Dark Matter Searches in the pMSSM

As is well known, the search for and eventual identification of dark matter in supersymmetry requires a simultaneous, multi-pronged approach with important roles played by the LHC as well as both direct and indirect dark matter detection experiments. We examine the capabilities of these approaches in the 19-parameter p(henomenological)MSSM which provides a general framework for complementarity studies of neutralino dark matter. We summarize the sensitivity of dark matter searches at the 7, 8 (and eventually 14) TeV LHC, combined with those by \Fermi, CTA, IceCube/DeepCore, COUPP, LZ and XENON. The strengths and weaknesses of each of these techniques are examined and contrasted and their interdependent roles in covering the model parameter space are discussed in detail. We find that these approaches explore orthogonal territory and that advances in each are necessary to cover the Supersymmetric WIMP parameter space. We also find that different experiments have widely varying sensitivities to the various dark matter annihilation mechanisms, some of which would be completely excluded by null results from these experiments.

hep-ph↗

arXiv2013

Dark Matter in the Coming Decade: Complementary Paths to Discovery and Beyond

In this Report we discuss the four complementary searches for the identity of dark matter: direct detection experiments that look for dark matter interacting in the lab, indirect detection experiments that connect lab signals to dark matter in our own and other galaxies, collider experiments that elucidate the particle properties of dark matter, and astrophysical probes sensitive to non-gravitational interactions of dark matter. The complementarity among the different dark matter searches is discussed qualitatively and illustrated quantitatively in several theoretical scenarios. Our primary conclusion is that the diversity of possible dark matter candidates requires a balanced program based on all four of those approaches.

hep-ph↗

arXiv2013

Prospects for Indirect Detection of Dark Matter with CTA

We discuss the prospects for indirect detection of dark matter (DM) with the Cherenkov Telescope Array (CTA), a future ground-based gamma-ray observatory that will be sensitive to gamma rays in the energy range from a few tens of GeV to 100 TeV. We consider the detectability of DM annihilation in different astrophysical targets with a focus on the Galactic Center (GC) region. With a deep observation of the GC, CTA will be sensitive to DM particles with mass greater than 100 GeV and an annihilation cross section close to the thermal relic value.

astro-ph.HE↗

arXiv2013

Search for Dark Matter Subhalos in the High-Energy Gamma-ray Band with Fermi and the Cherenkov Telescope Array

We discuss the potential for the detection of dark matter and the characterization of its particle nature via the observation of dark matter subhalos. Specifically, we discuss the search for dark matter Galactic subhalos in the gamma-ray band with the Large Area Telescope on-board the Fermi gamma-ray Space Telescope, and the future generation of imaging atmospheric Cherenkov telescopes, best represented by the planned Cherenkov Telescope Array.

astro-ph.HE↗