arXiv subjects

Gage Siebert

Publications and source records attributed to Gage Siebert.

6 recordsLinked to original sources

arXiv2026

Assembly Spaces: Formal Definitions and Fast Methods for Approximating Assembly Indices

Assembly theory is an experimental and theoretical framework that introduces a metrological approach to detecting life, with potential applications across diverse substrates. Its two central observables are assembly index and copy number. The assembly index is the minimum number of joining operations required to construct an object from its elementary parts; for molecules, it can be measured using mass spectrometry, infrared spectroscopy, and NMR. Copy number is the abundance of a given distinguishable object within a sample. A key empirical result of the theory is that high assembly index combined with high copy number constitutes a signature that cannot arise abiotically, and this has been validated experimentally in application to molecular biosignatures. The foundational theoretical concept underlying these results is the assembly space, which encodes the causal possibilities determinable from observed objects, with the assembly index the shortest path to them given the physical constraints of a given substrate. Here, we provide a generalized formalism to describe assembly spaces and tools for assembly index approximations. We begin by reviewing the applications of assembly theory across molecules, minerals and atmospheres, and then introduce a general, substrate-independent formal definition of assembly spaces and assembly indices. We develop a unified path hierarchy framework to clarify relationships among the various representations of assembly spaces and assembly paths that appear in the literature on molecular assembly. Finally, we show how formal grammar algorithms can be adapted to efficiently bound assembly index calculations and provide clarification on the utility of such approximations, with the goal to increase the accessibility of tools to explore this emerging area for a broader group of researchers across chemistry, biology, and complexity science.

cs.FL↗

arXiv2025

A Firefly-inspired Model for Deciphering the Alien

The Search for Extraterrestrial Intelligence (ETI) is, historically, a search for aliens like us, inspired by human centric ideas of intelligence and technology. However, humans are not the only instance of an intelligent, communicating species on Earth, and thus not guide to how we might think about ETI. Here, we explore the potential for the study of non-human species to inform new approaches in SETI research, using firefly communication patterns as an illustrative example. Fireflies communicate their presence through evolved flash patterns distinct from complex visual backgrounds. Extraterrestrial signals may also be identifiable not by their complexity or decodable content, but by the structural properties of the signal, as currently being explored in efforts to decode communication in non-human species across our biosphere. We present a firefly-inspired model for detecting potential technosignatures within environments dominated by ordered astronomical phenomena, such as pulsars. Using pulsar data from the Australia Telescope National Facility, we generate simulated signals that exhibit evolved dissimilarity from the surrounding pulsar population. This approach shifts focus from anthropocentric assumptions about intelligence toward recognizing communication through its fundamental structural properties, specifically, evolutionarily optimized contrast with natural backgrounds. Our model demonstrates that alien signals need not be inherently complicated nor need we decipher their meaning to identify them; rather, signals might be distinguishable as products of selection. We discuss implications for broadening SETI methodologies, leveraging the diverse forms of intelligence found on Earth.

astro-ph.IM↗

arXiv2024

Rapid Exploration of Assembly Chemical Space of Molecular Graphs

Quantifying how hard it is to build a molecular graph matters for biosignature detection, chemical complexity, and cheminformatics. We present an exact, scalable algorithm to compute the molecular assembly index (MA) which prioritizes the largest duplicate subgraphs, represents fragmentation with an 'assembly state' array of edge-lists, reuses states via hashing/DAGs, and prunes the search using a dynamic-programming branch-and-bound guided by a conditional-addition-chain lower bound. For organic molecules in the greater than 500 Da range our approach is up to six orders of magnitude faster than prior methods and yields exact MAs where previous algorithms would have timed out. We compute MAs to convergence for ~300k COCONUT natural products with <50 bonds, profiling time and memory scaling. Finally, we exploit the speed of our algorithm to calculate joint assembly spaces and introduce the Joint Assembly Overlap (JAO), a Jaccard-like metric that emphasizes global scaffold reuse and show that the JAO yields substantially different rankings from Tanimoto similarity with ECFP fingerprints and MCS (e.g. in steroids 270-380/Da and short peptides), accounting for substructural similarity beyond local environments. Together, these advances turn the molecular assembly index into a practical tool for large-scale exploration of chemical space.

cs.DS↗

arXiv2021

The Tianlai Dish Pathfinder Array: design, operation and performance of a prototype transit radio interferometer

The Tianlai Dish Pathfinder Array is a radio interferometer designed to test techniques for 21~cm intensity mapping in the post-reionization universe as a means for measuring large-scale cosmic structure. It performs drift scans of the sky at constant declination. We describe the design, calibration, noise level, and stability of this instrument based on the analysis of about $\sim 5 \%$ of 6,200 hours of on-sky observations through October, 2019. Beam pattern determinations using drones and the transit of bright sources are in good agreement, and compatible with electromagnetic simulations. Combining all the baselines, we make maps around bright sources and show that the array behaves as expected. A few hundred hours of observations at different declinations have been used to study the array geometry and pointing imperfections, as well as the instrument noise behaviour. We show that the system temperature is below 80~K for most feed antennas, and that noise fluctuations decrease as expected with integration time, at least up to a few hundred seconds. Analysis of long integrations, from 10 nights of observations of the North Celestial Pole, yielded visibilities with amplitudes of 20-30~mK, consistent with the expected signal from the NCP radio sky with $<10\,$mK precision for $1 ~\mathrm{MHz} \times 1~ \mathrm{min}$ binning. Hi-pass filtering the spectra to remove smooth spectrum signal yields a residual consistent with zero signal at the $0.5\,$mK level.

astro-ph.IM↗

arXiv2021

Overview and status of EXCLAIM, the experiment for cryogenic large-aperture intensity mapping

The EXperiment for Cryogenic Large-Aperture Intensity Mapping (EXCLAIM) is a balloon-borne far-infrared telescope that will survey star formation history over cosmological time scales to improve our understanding of why the star formation rate declined at redshift z < 2, despite continued clustering of dark matter. Specifically,EXCLAIM will map the emission of redshifted carbon monoxide and singly-ionized carbon lines in windows over a redshift range 0 < z < 3.5, following an innovative approach known as intensity mapping. Intensity mapping measures the statistics of brightness fluctuations of cumulative line emissions instead of detecting individual galaxies, thus enabling a blind, complete census of the emitting gas. To detect this emission unambiguously, EXCLAIM will cross-correlate with a spectroscopic galaxy catalog. The EXCLAIM mission uses a cryogenic design to cool the telescope optics to approximately 1.7 K. The telescope features a 90-cm primary mirror to probe spatial scales on the sky from the linear regime up to shot noise-dominated scales. The telescope optical elements couple to six μ-Spec spectrometer modules, operating over a 420-540 GHz frequency band with a spectral resolution of 512 and featuring microwave kinetic inductance detectors. A Radio Frequency System-on-Chip (RFSoC) reads out the detectors in the baseline design. The cryogenic telescope and the sensitive detectors allow EXCLAIM to reach high sensitivity in spectral windows of low emission in the upper atmosphere. Here, an overview of the mission design and development status since the start of the EXCLAIM project in early 2019 is presented.

astro-ph.IM↗

arXiv2020

Optical Design of the EXperiment for Cryogenic Large-Aperture Intensity Mapping (EXCLAIM)

This work describes the design and implementation of optics for EXCLAIM, the EXperiment for Cryogenic Large-Aperture Intensity Mapping. EXCLAIM is a balloon-borne telescope that will measure integrated line emission from carbon monoxide (CO) at redshifts $z<1$ and ionized carbon ([CII]) at redshifts $z = 2.5-3.5$ to probe star formation over cosmic time in cross-correlation with galaxy redshift surveys. The EXCLAIM instrument is designed to observe at frequencies of $420$--$540$ GHz using six microfabricated silicon integrated spectrometers with spectral resolving power $R = 512$ coupled to kinetic inductance detectors (KIDs). A completely cryogenic telescope cooled to a temperature below 5~K provides low-background observations between narrow atmospheric lines in the stratosphere. Off-axis reflective optics use a $90$-cm primary mirror to provide $4.2^\prime$ full-width at half-maximum (FWHM) resolution at the center of the EXCLAIM band over a field of view of $22.5^\prime$. Illumination of the $1.7$ K cold stop combined with blackened baffling at multiple places in the optical system ensure low ($< -40$ dB) edge illumination of the primary to minimize spill onto warmer elements at the top of the dewar.

astro-ph.IM↗