Tag Archives: Biological Physics

Photosynthesis Under a Red Sun: Predicting the absorption characteristics of an extraterrestrial light-harvesting antenna [EPA]

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http://arxiv.org/abs/2305.02067


Here we discuss the feasibility of photosynthesis on Earth-like rocky planets in close orbit around ultra-cool red dwarf stars. Stars of this type have very limited emission in the \textit{photosynthetically active} region of the spectrum ($400 – 700$ nm), suggesting that they may not be able to support oxygenic photosynthesis. However, photoautotrophs on Earth frequently exploit very dim environments with the aid of highly structured and extremely efficient antenna systems. Moreover, the anoxygenic photosynthetic bacteria, which do not need to oxidize water to source electrons, can exploit far red and near infrared light. Here we apply a simple model of a photosynthetic antenna to a range of model stellar spectra, ranging from ultra-cool (2300 K) to Sun-like (5800 K). We assume that a photosynthetic organism will evolve an antenna that maximizes the rate of energy input while also minimizing fluctuations. The latter is the ‘noise cancelling’ principle recently reported by Arp et al. 2020. Applied to the Solar spectrum this predicts optimal antenna configurations in agreement with the chlorophyll Soret absorption bands. Applied to cooler stars, the optimal antenna peaks become redder with decreasing stellar temperature, crossing to the typical wavelength ranges associated with anoxygenic photoautotrophs at $\sim 3300$ K. Lastly, we compare the relative input power delivered by antennae of equivalent size around different stars and find that the predicted variation is within the same order of magnitude. We conclude that low-mass stars do not automatically present light-limiting conditions for photosynthesis but they may select for anoxygenic organisms.

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C. Duffy, G. Canchon, T. Haworth, et. al.
Thu, 4 May 23
47/60

Comments: Resubmitted to MNRAS

Rebuilding the Habitable Zone from the Bottom Up with Computational Zones [EPA]

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http://arxiv.org/abs/2303.16111


Computation, if treated as a set of physical processes that act on information represented by states of matter, encompasses biological systems, digital systems, and other constructs, and may be a fundamental measure of living systems. The opportunity for biological computation, represented in the propagation and selection-driven evolution of information-carrying organic molecular structures, has been partially characterized in terms of planetary habitable zones based on primary conditions such as temperature and the presence of liquid water. A generalization of this concept to computational zones is proposed, with constraints set by three principal characteristics: capacity, energy, and instantiation (or substrate). Computational zones naturally combine traditional habitability factors, including those associated with biological function that incorporate the chemical milieu, constraints on nutrients and free energy, as well as element availability. Two example applications are presented by examining the fundamental thermodynamic work efficiency and Landauer limit of photon-driven biological computation on planetary surfaces and of generalized computation in stellar energy capture structures (a.k.a. Dyson structures). It is shown that computational zones involving nested structures or substellar objects could manifest unique observational signatures as cool far-infrared emitters. While this is an entirely hypothetical example, its simplicity offers a useful, complementary introduction to computational zones.

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C. Scharf and O. Witkowski
Wed, 29 Mar 23
27/73

Comments: 31 pages, 3 figures, submitted to The Astrobiology Journal

Venus, Phosphine and the Possibility of Life [EPA]

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http://arxiv.org/abs/2301.05160


The search for life elsewhere in the universe is one of the central aims of science in the 21st century. While most of this work is aimed at planets orbiting other stars, the search for life in our own Solar System is an important part of this endeavour. Venus is often thought to have too harsh an environment for life, but it may have been a more hospitable place in the distant past. If life evolved there in the past then the cloud decks of Venus are the only remaining niche where life as we know it might survive today. The discovery of the molecule phosphine, PH$_3$, in these clouds has reinvigorated research looking into the possibility of life in the clouds. In this review we examine the background to studies of the possibility of life on Venus, discuss the discovery of phosphine, review conflicting and confirming observations and analyses, and then look forward to future observations and space missions that will hopefully provide definitive answers as to the origin of phosphine on Venus and to the question of whether life might exist there.

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D. Clements
Fri, 13 Jan 23
7/72

Comments: Invited review, accepted for publication in Contemporary Physics

On the Role of $^{40}$K in the Origin of Terrestrial Life [CL]

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http://arxiv.org/abs/2210.13995


The abundance and biological role of potassium suggest that its unstable nuclide was present in all stages of terrestrial biogenesis. With its enhanced isotopic ratio in the Archean eon, $^{40}$K may have contributed to the special, perhaps unique, biogenetic conditions that were present in the primitive Earth. Compared to the U and Th radionuclides, $^{40}$K has a less disruptive radiochemical impact, which may drive a moderate, but persistent evolution of the structural and functional properties of proto-biological molecules. In the main $\beta$-decay route of $^{40}$K, the radiation dose generated by an Archean solution with potassium ions can be larger than the present background radiation on Earth by one to two orders of magnitude. Estimates of the rates of organic molecules indirectly affected by $\beta$ decays are provided for two schematic models of the propagation of secondary events in the solvent of prebiotic solutions. The left-handed $\beta^-$ particles emitted by $^{40}$K are the best candidates to trigger an enantiomeric excess of L-type amino acids via weak nuclear forces in the primitive Earth. The concentration-dependent radiation dose of $^{40}$K fits well in dry–wet scenarios of life’s origins and should be considered in realistic simulations of prebiotic chemical pathways.

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G. Vladilo
Wed, 26 Oct 22
40/73

Comments: 16 pages, 2 figures, published in Life 2022, 12, 1620

Letter of Interest: Ocean science with the Pacific Ocean Neutrino Experiment [CL]

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http://arxiv.org/abs/2209.14710


The Pacific Ocean Neutrino Experiment (P-ONE) is a proposed cubic-kilometer scale neutrino telescope planned to be installed in the deep-sea of the north-east Pacific Ocean. In collaboration with the optical deep-sea data and communications network operated by Ocean Networks Canada, an international collaboration of researchers plans to install an array of kilometer-long mooring lines in a depth of around 2660 m to the relatively flat deep-sea region called Cascadia Basin, around 300 miles West of Vancouver Island. With the design and development ongoing, the P-ONE collaboration is interested to initiate participation of fellow scientists of the oceanographic and marine science communities to provide expertise and experience towards deploying additional or inclusive instrumentation and measurement strategies for doing oceanographic research. In addition to the monitoring of optical bioluminescence and deep-ocean dynamics and thermodynamics, active and passive acoustics can be installed within the P-ONE array. This letter summarizes the P-ONE detector and a non-exhaustive list of potential topics of interest for oceanographic and marine research.

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F. Henningsen and L. Schumacher
Fri, 30 Sep 22
5/71

Comments: N/A

Biological Homochirality and the Search for Extraterrestrial Biosignatures [EPA]

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http://arxiv.org/abs/2205.01193


Most amino acids and sugars molecules occur in mirror, or chiral, images of each other, knowns as enantiomers. However, life on Earth is mostly homochiral: proteins contain almost exclusively L-amino acids, while only D-sugars appear in RNA and DNA. The mechanism behind this fundamental asymmetry of life remains unknown, despite much progress in the theoretical and experimental understanding of homochirality in the past decades. We review three potential mechanisms for the emergence of biological homochirality on primal Earth and explore their implications for astrobiology: the first, that biological homochirality is a stochastic process driven by local environmental fluctuations; the second, that it is driven by circularly-polarized ultraviolet radiation in star-forming regions; and the third, that it is driven by parity violation at the elementary particle level. We argue that each of these mechanisms leads to different observational consequences for the existence of enantiomeric excesses in our solar system and in exoplanets, pointing to the possibility that the search for life elsewhere will help elucidate the origins of homochirality on Earth.

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M. Gleiser
Wed, 4 May 22
23/48

Comments: arXiv admin note: text overlap with arXiv:0802.1446

Moosinesq Convection in the Cores of Moosive Stars [SSA]

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http://arxiv.org/abs/2204.00002


Stars with masses $\gtrsim 4 \times 10^{27}M_{\rm{moose}} \approx 1.1 M_\odot$ have core convection zones during their time on the main sequence. In these moosive stars, convection introduces many uncertainties in stellar modeling. In this Letter, we build upon the Boussinesq approximation to present the first-ever simulations of Moosinesq convection, which captures the complex geometric structure of the convection zones of these stars. These flows are bounded in a manner informed by the majestic terrestrial Alces alces (moose) and could have important consequences for the evolution of these stars. We find that Moosinesq convection results in very interesting flow morphologies and rapid heat transfer, and posit this as a mechanism of biomechanical thermoregulation.

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E. Anders, E. Bauer, A. Jermyn, et. al.
Mon, 4 Apr 22
9/50

Comments: 7 pages, 3 figures, 1 moose, no logic in this place

Taurine in Taurus. An Over-Caffeinated Search for Coffee in Space [EPA]

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http://arxiv.org/abs/2203.16598


Caffeination can open tired eyes and enhance focus. Over-caffeination, furthermore, can lead to errors but also to unexpected discoveries that might not have happened without 30 hours of sleep deprivation and 500mg of caffeine in our bodies. This paper presents exactly such a discovery. Upon much staring into our coffee cups, empty anew, the thought struck us: coffee in space. Caffeine may not be the only key. HL Tau, Taurus, bull… Taurine! We grinded some red bourbon for a new pour-over, and developed the new, coffee-groundsbreaking Large Astrocomical Taurine Tester Experiment (LATTE) in just 1/4 of a day. We felt bull-ish about our chances of making a great discovery! We installed LATTE, aimed it at the well-known young star HL Tau, and there it was: an abundance of taurine gas beautifully outlining a cup of cosmic flat white, with the ring structure of HL Tau turning out to be latte art performed by a skillful cosmic barista. The first Robusta discovery of coffee in space. Speaking of coffee, we hope you have a nice hot cup with you, and we encourage you to pun-tinue all the way to the end of this bean-grinding paper.

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C. Eistrup, &. Tychoniec, I. Nijman, et. al.
Fri, 1 Apr 22
82/85

Comments: 5 pages, 2 figures, submitted to Acta Prima Aprilia

Assessment of Microbial Habitability Across Solar System Targets [EPA]

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http://arxiv.org/abs/2203.03171


With a fleet of exploratory space missions on the horizon, the study of target specific biospheres is crucial for accurately determining the probability of the existence of microbial life on various planetary bodies and prioritising targets accordingly. Although previous studies have compared the potential habitability of objects in our solar system by bulk characteristics, it is less common that precise qualitative methods are developed for ranking candidates hospitable to microbial life on a local environment basis. In this review we create a planetary environmental database and use it to motivate a list of primary habitability candidates and essential criteria for microbial survival. We then propose a new method, the Microbial Habitability Index (MHI) which uses a metric of microbial survival factor values in target environments compared with appropriate Earth analogues to assess their potential for life. We arrive at a selection of eight primary candidates and from this set conclude that Europa, Mars, and Enceladus have the highest potential for facilitating microbial survival.

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D. Atri, T. Godderidge, D. Cirium, et. al.
Tue, 8 Mar 22
29/100

Comments: N/A

A Material-based Panspermia Hypothesis: The Potential of Polymer Gels and Membraneless Droplets [EPA]

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http://arxiv.org/abs/2201.06732


The Panspermia hypothesis posits that either life’s building blocks (molecular Panspermia) or life itself (organism-based Panspermia) may have been interplanetary transferred to facilitate the Origins of Life (OoL) on a given planet, complementing several current OoL frameworks. Although many spaceflight experiments were performed in the past to test for potential terrestrial organisms as Panspermia seeds, it is uncertain whether such organisms will likely “seed” a new planet even if they are able to survive spaceflight. Therefore, rather than using organisms, using abiotic chemicals as seeds has been proposed as part of the molecular Panspermia hypothesis. Here, as an extension of this hypothesis, we introduce and review the plausibility of a polymeric material-based Panspermia seed (M-BPS) theoretical concept, where the type of polymeric material that can function as a M-BPS must be able to: 1) survive spaceflight, and 2) “function”, i.e., contingently drive chemical evolution towards some form of abiogenesis once arriving on a foreign planet.
We use polymeric gels as a model example of a potential M-BPS. Polymeric gels that can be prebiotically synthesized on one planet (such as polyester gels) could be transferred to another planet via meteoritic transfer, where upon landing on a liquid bearing planet, can assemble into structures containing cellular-like characteristics and functionalities. Such features presupposed that these gels can assemble into compartments through phase separation to accomplish relevant functions such as encapsulation of primitive metabolic, genetic and catalytic materials, exchange of these materials, motion, coalescence, and evolution. All of these functions can result in the gels’ capability to alter local geochemical niches on other planets, thereby allowing chemical evolution to lead to OoL events.

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M. Sithamparam, N. Satthiyasilan, C. Chen, et. al.
Wed, 19 Jan 22
43/121

Comments: 21 pages, 2 figures

Origin of Chirality in the Molecules of Life [CL]

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http://arxiv.org/abs/2110.12232


Molecular chirality is inherent to biology and cellular chemistry. In this report, the origin of enantiomeric selectivity is analyzed from the viewpoint of the “RNA World” model, based on the autocatalytic self-replication of glyceraldehyde as a precursor for simple sugars, and in particular ribose, as promoted by the formose reaction. Autocatalytic coupling of formaldehyde and glycolaldehyde produces glyceraldehyde, which contains a chiral carbon center that is carried through in formation of the ribose ring. The parity non-conserving weak interaction is the only inherently handed property in nature and is herein shown to be sufficient to differentiate between two enantiomeric forms in an autocatalytic reaction performed over geologically relevant time scales, but only in the presence of a catalytic metal ion such as divalent calcium or higher Z alkaline earth elements. This work details calculations of the magnitude of the effect, the impact of various geologically-available metal ions, and the influence on evolution and dominance of chirality in the molecules of life.

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J. Cowan and R. Furnstahl
Tue, 26 Oct 21
102/109

Comments: 18 pages, 1 figures; supplementary material included with 9 pages, 4 figures

Nebula-Relay Hypothesis: The Chirality of Biological Molecules in Molecular Clouds [CL]

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http://arxiv.org/abs/2110.02524


The origin of chirality in the molecules of life is thought to be closely related to the origin of life and still an unsolved mystery for a long time. Previously, we proposed a new model of the origin of life, named Nebula-Relay Nebula-Relay, which assumed that the life on Earth originated at the planetary system of sun’s predecessor star and then filled in the pre-solar nebula after the its death. As primitive lives existed in the molecular cloud until the formation of solar system, does the chirality of biomolecules occured during this period? We explore such possibility in this work and find that the ultra-low temperature environment is very beneficial to generate the chiral polymer chain of biological molecules.

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L. Feng
Thu, 7 Oct 21
6/51

Comments: 8 pages, 2 figures

Polarized muons and the origin of biological homochirality [CL]

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http://arxiv.org/abs/2110.01975


While biologists have not yet reached a consensus on the definition of life, homochirality – the specific molecular handedness of biomolecules – is a phenomenon only produced by life. The unraveling of its origin requires interdisciplinary research, by exploring fundamental physics, chemistry, astrophysics and biology. Here, we consider the origin of biological homochirality in the context of astrophysics and particle physics. The weak force, one of the fundamental forces operating in nature, is parity-violating. On Earth, at ground level, most of our cosmic radiation dose comes from polarized muons formed in a decay involving the weak force. We discuss how the magnetic polarization is transmitted in cosmic showers within several different environments which are prime targets in the search for the origin of life. We consider how this polarization could have induced a biological preference for one type of chirality over the other, and discuss the implications for the search of life in other worlds.

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N. Globus, R. Blandford and A. Fedynitch
Wed, 6 Oct 21
35/56

Comments: Proceedings of the ICRC 2021 PoS(ICRC2021)031

Large-scale cortex-core structure formation in brain organoids [CL]

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http://arxiv.org/abs/2108.05824


Brain organoids recapitulate a number of brain properties, including neuronal diversity. However, do they recapitulate brain shape? Using a hydrodynamic description for cell nuclei as particles interacting via an attractive field generated by the surrounding active cell cytoskeleton, we quantify shape development in brain organoids. Regions of cell nuclei overdensity in the linear regime drive the initial seeding for cortex-core structures, which emerge in the non-linear regime with elongated cell nuclei and thus, cell shape, in the cortex. We then use an extended version of the buckling without bending morphogenesis model to predict foliations/folds of the cortex in the presence of a nonlinearity due to elongated cells actively regulating strain. In addition to laying new groundwork for the design of more familiar and less familiar brain shapes, our work provides an intriguing quantitative connection with large-scale structure formation in the universe.

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A. Borzou and J. Schwarz
Fri, 13 Aug 21
49/64

Comments: 14 pages, 9 figures. Comments are welcome

The Organization of Chaos into a Molecular Trap that Supervises Ligand-Interaction, Selection and Steric Guidance Similar to Events in Black Holes [CL]

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http://arxiv.org/abs/2108.01223


In the current study, we demonstrated that allostery transpires by entropy transference across time-spatial scales that actualize the conception of a molecular trap that supervises ligand interaction, selection, and migration into the amphipathic groove of the 14-3-3 {\zeta} docking protein. This transpires by steric guidance down a multi-dimensional trap constituted of superimposed chaotic, harmonic, and electromagnetic field gradients. The individual traps exist in discrete domains governed by disparate physics interconnected by their resonance states and are subjective to damping. Notably, the highly structured molecular entanglement was formed by the organization of white noise emitted by the anarchic motion of residues that comprised many of the common features of black holes.

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L. Davis
Wed, 4 Aug 21
38/66

Comments: 23 pages, 17 figures

Discovery of interstellar glycine in the hot molecular core G10.47+0.03 [GA]

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http://arxiv.org/abs/2106.11800


Amino acids are the essential keys in chemistry that contribute to the study of the formation of life. The complex organic molecule glycine (NH${2}$CH${2}$COOH) is the simplest amino acid that has been investigated in the interstellar medium for a long period to search for a potential connection between the Universe and the origin of life. Several attempts have failed to search for glycine in the last forty years, which made the researcher look for some glycine precursor in the interstellar medium as an alternative approach. We report the successful detection of the rotational emission lines of interstellar glycine with confirmer I and II in the hot molecular core G10.47+0.03 between the frequency range of $\nu$ = 158.6$-$160.4 GHz with Atacama Large Millimeter/Submillimeter Array (ALMA) observation. In hot molecular core G10.47+0.03, the fractional abundance of glycine is found between the range of (4.01$-$4.61)$\times$10$^{-10}$ which refers to the “medium warm-up” case. The detection of glycine in the interstellar medium is very complicated but many theoretical and laboratory studies indicated the possibilities of the presence of glycine and its precursors in hot molecular cores. We also detected the emission lines of complex organic molecules CHOCHOHCH${2}$OH, $^{13}$CH${2}$OHCHO, CHD(OH)CHO, CH${2}$OH$^{13}$CHO, cis-CH${2}$OHCHO, G$^{\prime}$Gg$^{\prime}$-CH${2}$(OH)CH(OH)CH${2}$OH, and CH$_{2}$DOH in the hot molecular core G10.47+0.03.

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A. Manna, S. Pal and S. Banerjee
Wed, 23 Jun 21
38/48

Comments: Comments are welcome

Chiral Selection, Isotopic Abundance Shifts, and Autocatalysis of Meteoritic Amino Acids [EPA]

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http://arxiv.org/abs/2106.01531


The discovery of amino acids in meteorites has presented two clues to the origin of their processing subsequent to their formation: a slight preference for left-handedness in some of them, and isotopic anomalies in some of their constituent atoms. In this article we present theoretical results from the Supernova Neutrino Amino Acid Processing (SNAAP) model, which uses electron anti-neutrinos and the magnetic fields from source objects such as supernovae or colliding neutron stars to selectively destroy one amino acid chirality and to create isotopic abundance shifts. For plausible magnetic fields and electron anti-neutrino fluxes, non-zero, positive enantiomeric excesses, $ee$s, defined to be the relative left/right asymmetry in an amino acid population, are reviewed for two amino acids, and conditions are suggested that would produce $ee>0$ for all of the $\alpha$-amino acids. The relatively high energy anti-neutrinos that produce the $ee$s would inevitably also produce isotopic anomalies. A nuclear reaction network was developed to describe the reactions resulting from them and the nuclides in the meteorites. At similar anti-neutrino fluxes, assumed recombination of the detritus from the anti-neutrino interactions is shown to produce appreciable isotopic anomalies in qualitative agreement with those observed for D/$^1$H and $^{15}$N/$^{14}$N. The isotopic anomalies for $^{13}$C/$^{12}$C are predicted to be small, as are also observed. Autocatalysis may be necessary for any model to produce the largest $ee$s observed in meteorites. This allows the constraints of the original SNAAP model to be relaxed, increasing the probability of meteoroid survival in sites where amino acid processing is possible. These results have obvious implications for the origin of life on Earth.

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M. Famiano, R. Boyd, T. Onaka, et. al.
Fri, 4 Jun 21
47/71

Comments: 24 pages, 8 figures, to be published in Physical Review Research

Biosignatures of the Earth I. Airborne spectropolarimetric detection of photosynthetic life [EPA]

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http://arxiv.org/abs/2106.00493


Context. Homochirality is a generic and unique property of life on Earth and is considered a universal and agnostic biosignature. Homochirality induces fractional circular polarization in the incident light that it reflects. Because this circularly polarized light can be sensed remotely, it can be one of the most compelling candidate biosignatures in life detection missions. While there are also other sources of circular polarization, these result in spectrally flat signals with lower magnitude. Additionally, circular polarization can be a valuable tool in Earth remote sensing because the circular polarization signal directly relates to vegetation physiology. Aims. While high-quality circular polarization measurements can be obtained in the laboratory and under semi-static conditions in the field, there has been a significant gap to more realistic remote sensing conditions. Methods. In this study, we present sensitive circular spectropolarimetric measurements of various landscape elements taken from a fast-moving helicopter. Results. We demonstrate that during flight, within mere seconds of measurements, we can differentiate (S/N>5) between grass fields, forests, and abiotic urban areas. Importantly, we show that with only nonzero circular polarization as a discriminant, photosynthetic organisms can even be measured in lakes. Conclusions. Circular spectropolarimetry can be a powerful technique to detect life beyond Earth, and we emphasize the potential of utilizing circular spectropolarimetry as a remote sensing tool to characterize and monitor in detail the vegetation physiology and terrain features of Earth itself.

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C. Patty, J. Kühn, P. Lambrev, et. al.
Wed, 2 Jun 21
36/48

Comments: 7 pages, 6 figures

ALMA detection of hydrogen cyanide and carbon monoxide in the atmosphere of Saturn [EPA]

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http://arxiv.org/abs/2104.10474


The hydrogen cyanide (HCN) molecule in the planetary atmosphere is key to the formation of building blocks of life. We present the spectroscopic detection of the rotational molecular line of nitrile species hydrogen cyanide (HCN) in the atmosphere of Saturn using the archival data of the Atacama Large Millimeter/Submillimeter Array (ALMA) in band 7 observation. The strong rotational emission line of HCN is detected at frequency $\nu$ = 354.505 GHz (>4$\sigma$ statistical significance). We also detect the rotational emission line of carbon monoxide (CO) at frequency $\nu$ = 345.795 GHz. The statistical column density of hydrogen cyanide and carbon monoxide emission line is N(HCN)$\sim$2.42$\times$10$^{16}$ cm$^{-2}$ and N(CO)$\sim$5.82$\times$10$^{17}$ cm$^{-2}$. The abundance of HCN and CO in the atmosphere of Saturn relative to the H$_{2}$ is estimated to be f(HCN)$\sim$1.02$\times$10$^{-9}$ and f(CO)$\sim$2.42$\times$10$^{-8}$. We discussed possible chemical pathways to the formation of the detected nitrile gas HCN in the atmosphere of Saturn.

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A. Manna and S. Pal
Thu, 22 Apr 2021
10/44

Comments: 6 pages, 4 figures, comments are welcome

ALMA detection of acetone, disulfur monoxide, and carbon monoxide in the Jupiter volcanic moon Io [EPA]

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http://arxiv.org/abs/2103.17018


The extremely thin atmosphere of the Jupiter volcanic moon Io primarily consists of sulfur (S), sodium (Na), and oxygen (O) molecules that are controlled by the combination of the sublimation and volcanic outgasses. We present the first spectroscopic detection of the two rotational emission lines of acetone (CH${3}$COCH${3}$), one single emission line of disulfur monoxide (S${2}$O), and a rotational absorptional line of CO at frequency $\nu$ = 346.539, 346.667, 346.543, and 345.795 GHz using high-resolution Atacama Large Millimeter/Submillimeter Array (ALMA) interferometer with band 7 observation. All molecular species are detected with $\ge$5$\sigma$ statistical significance. The Jupiter moon Io is the most volcanically active body in the solar system with a very thin and spatially variable atmosphere. The volcanic gas CH${3}$COCH${3}$, S${2}$O, and CO are mainly coming from volcanic plumes. The statistical column density of CH${3}$COCH${3}$ line is N(CH${3}$COCH${3}$) = 6.92$\times$10$^{16}$ cm$^{-2}$ but for the cases of S${2}$O and CO, the column densities are N(S${2}$O) = 2.63$\times$10$^{16}$ cm$^{-2}$ and N(CO) = 5.27$\times$10$^{15}$ cm$^{-2}$ respectively. The carbon monoxide gas is mainly formed by the photolysis of the volcanic gas acetone.

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A. Manna and S. Pal
Thu, 1 Apr 2021
7/71

Comments: 8 pages, 1 figure, comments are welcome

Theoretical constraints imposed by gradient detection and dispersal on microbial size in astrobiological environments [EPA]

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http://arxiv.org/abs/2102.05009


The capacity to sense gradients efficiently and acquire information about the ambient environment confers many advantages like facilitating movement toward nutrient sources or away from toxic chemicals. The amplified dispersal evinced by organisms endowed with motility is possibly beneficial in related contexts. Hence, the connections between information acquisition, motility, and microbial size are explored from an explicitly astrobiological standpoint. By using prior theoretical models, the constraints on organism size imposed by gradient detection and motility are elucidated in the form of simple heuristic scaling relations. It is argued that environments such as alkaline hydrothermal vents, which are distinguished by the presence of steep gradients, might be conducive to the existence of “small” microbes (with radii of $\gtrsim 0.1$ $\mu$m) in principle, when only the above two factors are considered; other biological functions (e.g., metabolism and genetic exchange) could, however, regulate the lower bound on microbial size and elevate it. The derived expressions are potentially applicable to a diverse array of settings, including those entailing solvents other than water; for example, the lakes and seas of Titan. The paper concludes with a brief exposition of how this formalism may be of practical and theoretical value to astrobiology.

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M. Lingam
Wed, 10 Feb 21
15/64

Comments: Accepted for publication in Astrobiology; 39 pages; 2 figures

Physical Constraints on Motility with Applications to Possible Life on Mars and Enceladus [EPA]

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http://arxiv.org/abs/2101.06876


Motility is a ubiquitous feature of microbial life on Earth and is widely regarded as a promising biosignature candidate. In the search for motile organisms, it is therefore valuable to have rough estimates for the number of such microbes that one might expect to find in a given area or volume. In this work, we explore this question by employing a simple theoretical model that takes into account the amount of free energy available in a given environment and the energetic cost of motility. We present heuristic upper bounds for the biomass density and the number density of motile lifeforms for the Martian subsurface and the ocean of Enceladus by presuming that the motile microbes in question derive their energy from methanogenesis. We consequently demonstrate that the resultant densities might be potentially comparable to, or much lower than, those documented in various extreme environments on Earth.

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M. Lingam and A. Loeb
Tue, 19 Jan 21
30/92

Comments: 6 pages; 3 figures

Wide Field Spectral Imaging with Shifted Excitation Raman Difference Spectroscopy Using the Nod and Shuffle Technique [CL]

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http://arxiv.org/abs/2011.13736


Wide field Raman imaging using the integral field spectroscopy approach was used as a fast, one shot imaging method for the simultaneous collection of all spectra composing a Raman image. For the suppression of autofluorescence and background signals such as room light, shifted excitation Raman difference spectroscopy (SERDS) was applied to remove background artifacts in Raman spectra. To reduce acquisition times in wide field SERDS imaging, we adapted the nod and shuffle technique from astrophysics and implemented it into a wide field SERDS imaging setup. In our adapted version, the nod corresponds to the change in excitation wavelength, whereas the shuffle corresponds to the shifting of charges up and down on a Charge-Coupled Device (CCD) chip synchronous to the change in excitation wavelength. We coupled this improved wide field SERDS imaging setup to diode lasers with 784.4/785.5 and 457.7/458.9 nm excitation and applied it to samples such as paracetamol and aspirin tablets, polystyrene and polymethyl methacrylate beads, as well as pork meat using multiple accumulations with acquisition times in the range of 50 to 200 ms. The results tackle two main challenges of SERDS imaging: gradual photobleaching changes the autofluorescence background, and multiple readouts of CCD detector prolong the acquisition time.

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F. Korinth, E. Schmälzlin, C. Stiebing, et. al.
Mon, 30 Nov 20
116/117

Comments: Accepted and Published by “Sensors” Journal, 19 pages, 8 figures

Spectropolarimetry of primitive phototrophs as global surface biosignatures [EPA]

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http://arxiv.org/abs/2010.02133


Photosynthesis is an ancient metabolic process that began on the early Earth, offering plentiful energy to organisms that utilize it, to the extent that they can achieve global significance. The potential exists for similar processes to operate on habitable exoplanets and result in observable biosignatures. Prior to the advent of oxygenic photosynthesis, the most primitive phototrophs, anoxygenic phototrophs, dominated surface environments on the planet. Here, we characterize surface polarization biosignatures associated with a diverse sample of anoxygenic phototrophs and cyanobacteria, examining both pure cultures and microbial communities from the natural environment. Polarimetry is a tool that can be used to measure the chiral signature of biomolecules. Chirality is considered a universal, agnostic biosignature that is independent of a planet’s biochemistry, receiving considerable interest as a target biosignature for life detection missions. In contrast to preliminary indications from earlier work, we show that there is a diversity of distinctive circular polarization signatures, including the magnitude of the polarization, associated with the variety of chiral photosynthetic pigments and pigment complexes of anoxygenic and oxygenic phototrophs. We also show that the apparent death and release of pigments from one of the phototrophs is accompanied by an elevation of the reflectance polarization signal by an order of magnitude, which may be significant for remotely detectable environmental signatures. This work and others suggest circular polarization signals up to ~1% may occur, significantly stronger than previously anticipated circular polarization levels. We conclude that global surface polarization biosignatures may arise from anoxygenic and oxygenic phototrophs, which have dominated nearly 80% of the history of our rocky, inhabited planet.

Read this paper on arXiv…

W. Sparks, M. Parenteau, R. Blankenship, et. al.
Tue, 6 Oct 2020
24/85

Comments: 26 pages, 8 figures. To be published in Astrobiology

A trampoline effect occurring in the stages of planetary reseeding [EPA]

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http://arxiv.org/abs/2005.09360


Impactors have hit the Earth ever since its formation and have continued to be infrequent guests throughout the Earth’s history. Although the early part of the Earth’s history was marked by these violent events, it is known that life was present early, possibly existing already in the Hadean Eon. It is possible that life can be, and still is, transported between the worlds of the solar system due to impacts leading material away from the impact region. In addition to this lithopanspermia theory, it has been suggested that ejected material can also return to its home planet and ‘reseed’ life after the world has recovered after a global impactor, thus restarting evolution, the so-called refugium hypothesis. Next to such impactors more frequent impacts from smaller non-sterilizing impactors existed during the Heavy Bombardment epoch, feeding material potentially harboring viable organisms into near Earth space. During the three stages of planetary reseeding the encapsulated bacterial population will experience abiotic stressors, specifically they will experience pressure and heat shock twice, in stage 1 and after a recovery phase in stage 2, again in stage 3.While many circumstances have played a role in lifes endurance in the early history of the Earth, a particular biological effect could potentially be conferred on a bacterial population in this scenario. Thus, the surviving population will not only experience an increase in the frequency of robust genotypes, but it can also be expected that their stress tolerance is enhanced compared to non-stressed organisms of the same species. Hence, the trampoline effect means that the mean robustness of the bacterial population towards these stressors is higher in stage 3, than at stage 1.In principle, the time between the impactor and the reimpactor need not be long before this trampoline effect appears.

Read this paper on arXiv…

I. Hegner
Wed, 20 May 20
2/66

Comments: N/A

Explaining the Variations in Isotopic Ratios in Meteoritic Amino Acids [EPA]

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http://arxiv.org/abs/2005.05540


Measurements of the isotopic abundances in meteoritic amino acids have found enhancements of $^2$H/H, $^{15}$N/$^{14}$N, and $^{13}$C/$^{12}$C in the amino acids in the meteorites studied. We show that they are consistent with the processing of the constituents of the meteorites by electron anti-neutrinos that would be expected from a core-collapse supernova or neutron-star merger. Using theoretical electron anti-neutrino cross sections we are able to predict these isotopic ratio variations depending on the time-integrated anti-neutrino flux at the site where the amino acids were processed.

Read this paper on arXiv…

M. Famiano, R. Boyd, T. Kajino, et. al.
Wed, 13 May 20
18/60

Comments: N/A

Revealing the Dark Threads of the Cosmic Web [GA]

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http://arxiv.org/abs/2003.04393


Modern cosmology predicts that matter in our Universe has assembled today into a vast network of filamentary structures colloquially termed the Cosmic Web. Because this matter is either electromagnetically invisible (i.e., dark) or too diffuse to image in emission, tests of this cosmic web paradigm are limited. Wide-field surveys do reveal web-like structures in the galaxy distribution, but these luminous galaxies represent less than 10% of baryonic matter. Statistics of absorption by the intergalactic medium (IGM) via spectroscopy of distant quasars support the model yet have not conclusively tied the diffuse IGM to the web. Here, we report on a new method inspired by the Physarum polycephalum slime mold that is able to infer the density field of the Cosmic Web from galaxy surveys. Applying our technique to galaxy and absorption-line surveys of the local Universe, we demonstrate that the bulk of the IGM indeed resides in the Cosmic Web. From the outskirts of Cosmic Web filaments, at approximately the cosmic mean matter density (rho_m) and approx. 5 virial radii from nearby galaxies, we detect an increasing H I absorption signature towards higher densities and the circumgalactic medium, to approx. 200 rho_m. However, the absorption is suppressed within the densest environments, suggesting shock-heating and ionization deep within filaments and/or feedback processes within galaxies.

Read this paper on arXiv…

J. Burchett, O. Elek, N. Tejos, et. al.
Wed, 11 Mar 20
54/65

Comments: Published in ApJL, 891, L35

Theory of chemical evolution of molecule compositions in the universe, in the Miller-Urey experiment and the mass distribution of interstellar and intergalactic molecules [CL]

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http://arxiv.org/abs/1806.06716


Chemical evolution is essential in understanding the origins of life. We present a theory for the evolution of molecule masses and show that small molecules grow by random diffusion and large molecules by a preferential attachment process leading eventually to life’s molecules. It reproduces correctly the distribution of molecules found via mass spectroscopy for the Murchison meteorite and estimates the start of chemical evolution back to 12.8 billion years following the birth of stars and supernovae. From the Frontier mass between the random and preferential attachment dynamics the birth time of molecule families can be estimated. Amino acids emerge about 165 million years after chemical elements emerge in stars. Using the scaling of reaction rates with the distance of the molecules in space we recover correctly the few days emergence time of amino acids in the Miller-Urey experiment. The distribution of interstellar and extragalactic molecules are both consistent with the evolutionary mass distribution, and their age is estimated to 108 and 65 million years after the start of evolution. From the model, we can determine the number of different molecule compositions at the time of the emergence of Earth to be 1.6 million and the number of molecule compositions in interstellar space to a mere 719 species.

Read this paper on arXiv…

S. Kauffman, D. Jelenfi and G. Vattay
Thu, 5 Dec 19
36/71

Comments: N/A

Similarities between Insect Swarms and Isothermal Globular Clusters [CL]

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http://arxiv.org/abs/1912.00395


Previous work has suggested that disordered swarms of flying insects can be well modeled as self-gravitating systems, as long as the “gravitational” interaction is adaptive. Motivated by this work we compare the predictions of the classic, mean-field King model for isothermal globular clusters to observations of insect swarms. Detailed numerical simulations of regular and adaptive gravity allow us to expose the features of the swarms’ density profiles that are captured by the King model phenomenology, and those that are due to adaptivity and short-range repulsion. Our results provide further support for adaptive gravity as a model for swarms.

Read this paper on arXiv…

D. Gorbonos, K. Vaart, M. Sinhuber, et. al.
Tue, 3 Dec 19
83/90

Comments: N/A

When did Life Likely Emerge on Earth in an RNA-First Process? [EPA]

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http://arxiv.org/abs/1908.11327


The widespread presence of ribonucleic acid (RNA) catalysts and cofactors in Earth’s biosphere today suggests that RNA was the first biopolymer to support Darwinian evolution. However, most “path-hypotheses” to generate building blocks for RNA require reduced nitrogen-containing compounds not made in useful amounts in the CO2-N2-H2O atmospheres of the Hadean. We review models for Earth’s impact history that invoke a single ~10^23 kg impactor (Moneta) to account for measured amounts of platinum, gold, and other siderophilic (“iron-loving”) elements on the Earth and Moon. If it were the last sterilizing impactor, Moneta would have reduced the atmosphere but not its mantle, opening a “window of opportunity” for RNA synthesis, a period when RNA precursors rained from the atmosphere to land holding oxidized minerals that stabilize advanced RNA precursors and RNA. Surprisingly, this combination of physics, geology, and chemistry suggests a time when RNA formation was most probable, ~120 +/- 100 million years after Moneta’s impact, or ~4.36 +/- 0.1 billion years ago. Uncertainties in this time are driven by uncertainties in rates of productive atmosphere loss and amounts of sub-aerial land.

Read this paper on arXiv…

S. Benner, E. Bell, E. Biondi, et. al.
Fri, 30 Aug 19
2/58

Comments: Paper accepted to ChemSystemsChem [this https URL] August 22, 2019

Circular spectropolarimetric sensing of vegetation in the field; possibilities for the remote detection of extraterrestrial life [EPA]

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http://arxiv.org/abs/1902.05859


Homochirality is a generic and unique property of all biochemical life and the fractional circular polarization it induces therefore constitutes an unambiguous biosignature. However, while high-quality circular polarimetric spectra can be easily and quickly obtained in the laboratory, accurate measurements in the field are much more challenging due to large changes in illumination and target movement. In this study we have measured various targets in the field, up to distances of a few kilometers, using the dedicated circular spectropolarimeter TreePol. We show how photosynthetic life can readily be distinguished from abiotic matter. We underline the potential of circular polarization signals as a remotely accessible means to characterize terrestrial life and detecting the presence of extraterrestrial life.

Read this paper on arXiv…

C. Patty, I. Kate, W. Buma, et. al.
Mon, 18 Feb 19
6/37

Comments: 24 pages, 6 figures

The Origin of RNA Precursors on Exoplanets [EPA]

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http://arxiv.org/abs/1808.02718


Given that the macromolecular building blocks of life were likely produced photochemically in the presence of ultraviolet (UV) light, we identify some general constraints on which stars produce sufficient UV for this photochemistry. We estimate how much light is needed for the UV photochemistry by experimentally measuring the rate constant for the UV chemistry (light chemistry', needed for prebiotic synthesis) versus the rate constants for the bimolecular reactions that happen in the absence of the UV light (dark chemistry’). We make these measurements for representative photochemical reactions involving SO$_3^{2-}$ and HS$^-$. By balancing the rates for the light and dark chemistry, we delineate the “abiogenesis zones” around stars of different stellar types based on whether their UV fluxes are sufficient for building up this macromolecular prebiotic inventory. We find that the SO$_3^{2-}$ ‘light chemistry’ is rapid enough to build up the prebiotic inventory for stars hotter than K5 (4400 K). We show how the abiogenesis zone overlaps with the liquid water habitable zone. Stars cooler than K5 may also drive the formation of these building blocks if they are very active. The HS$^-$ ‘light chemistry’ is too slow to work even for the Early Earth.

Read this paper on arXiv…

P. Rimmer, J. Xu, S. Thompson, et. al.
Thu, 9 Aug 18
5/57

Comments: 33 pages, 5 figures, preprint

The clock of chemical evolution [CL]

Posted on by

http://arxiv.org/abs/1806.06716


Chemical evolution is essential in understanding the origins of life. We present a theory for the evolution of molecule masses and show that small molecules grow by random diffusion and large molecules by a preferential attachment process leading eventually to life’s molecules. It reproduces correctly the distribution of molecules found via mass spectroscopy for the Murchison meteorite and estimates the start of chemical evolution back to 12.8 billion years following the birth of stars and supernovae. From the Frontier mass between the random and preferential attachment dynamics the birth time of molecule families can be estimated. Amino acids emerge about 165 million years after the start of evolution. Using the scaling of reaction rates with the distance of the molecules in space we recover correctly the few days emergence time of amino acids in the Miller-Urey experiment. The distribution of interstellar and extragalactic molecules are both consistent with the evolutionary mass distribution, and their age is estimated to 108 and 65 million years after the start of evolution. From the model, we can determine the number of different molecule compositions at the time of the creation of Earth to be 1.6 million and the number of molecule compositions in interstellar space to a mere 719.

Read this paper on arXiv…

S. Kauffman, D. Jelenfi and G. Vattay
Tue, 19 Jun 18
78/91

Comments: N/A

Role of stellar physics in regulating the critical steps for life [CL]

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http://arxiv.org/abs/1804.02271


We use the critical step model to study the major transitions in evolution on Earth. We find that a total of five steps represents the most plausible estimate, in agreement with previous studies, and use the fossil record to identify the potential candidates. We apply the model to Earth-analogs around stars of different masses by incorporating the constraints on habitability set by stellar physics including the habitable zone lifetime, availability of ultraviolet radiation for prebiotic chemistry, and atmospheric escape. The critical step model suggests that the habitability of Earth-analogs around M-dwarfs is significantly suppressed. The total number of stars with planets containing detectable biosignatures of microbial life is expected to be highest for K-dwarfs. In contrast, we find that the corresponding value for intelligent life (technosignatures) should be highest for solar-mass stars. Thus, our work may assist in the identification of suitable targets in the search for biosignatures and technosignatures.

Read this paper on arXiv…

M. Lingam and A. Loeb
Tue, 10 Apr 18
11/79

Comments: 34 pages; 5 figures

Sites That Can Produce Left-Handed Amino Acids in the Supernova Neutrino Amino Acid Processing Model [CL]

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http://arxiv.org/abs/1802.08285


The Supernova Neutrino Amino Acid Processing model, which uses electron anti-neutrinos and the magnetic field from a source object such as a supernova to selectively destroy one amino acid chirality, is studied for possible sites that would produce meteoroids having partially left-handed amino acids. Several sites appear to provide the requisite magnetic field intensities and electron anti-neutrino fluxes. These results have obvious implications for the origin of life on Earth.

Read this paper on arXiv…

R. Boyd, M. Famiano, T. Onaka, et. al.
Mon, 26 Feb 18
39/49

Comments: Accepted to ApJL

The Propitious Role of Solar Energetic Particles in the Origin of Life [EPA]

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http://arxiv.org/abs/1801.05781


We carry out 3-D numerical simulations to assess the penetration and bombardment effects of Solar Energetic Particles (SEPs), i.e. high-energy particle bursts during large flares and superflares, on ancient and current Mars. We demonstrate that the deposition of SEPs is non-uniform at the planetary surface, and that the corresponding energy flux is lower than other sources postulated to have influenced the origin of life. Nevertheless, SEPs may have been capable of facilitating the synthesis of a wide range of vital organic molecules (e.g. nucleobases and amino acids). Owing to the relatively high efficiency of these pathways, the overall yields might be comparable to (or even exceed) the values predicted for some conventional sources such as electrical discharges and exogenous delivery by meteorites. We also suggest that SEPs could have played a role in enabling the initiation of lightning. A notable corollary of our work is that SEPs may constitute an important mechanism for prebiotic synthesis on exoplanets around M-dwarfs, thereby mitigating the deficiency of biologically active ultraviolet radiation on these planets. Although there are several uncertainties associated with (exo)planetary environments and prebiotic chemical pathways, our study illustrates that SEPs represent a potentially important factor in understanding the origin of life.

Read this paper on arXiv…

M. Lingam, C. Dong, X. Fang, et. al.
Thu, 18 Jan 2018
55/58

Comments: published in The Astrophysical Journal; 14 pages; 2 figures

Time's arrow and life's origin [CEA]

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http://arxiv.org/abs/1801.01783


The thermodynamic arrow-of-time problem is thought to be resolved by the observation that our universe initially was—and still is—far from equilibrium. The psychological arrow-of-time problem is often attributed the same resolution, but the connection has not been thoroughly established. I argue that a compelling explanation of the psychological arrow requires an understanding of the physical conditions necessary for life to emerge from a prebiotic environment. A simple calculation illustrates how life-sustaining energy fluxes from the Sun and the Earth’s interior bias the development of life in the direction of the arrow inherited from cosmic initial conditions.

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L. Johns
Mon, 8 Jan 18
96/117

Comments: 5 pages, 2 figures

Terrestrial effects of moderately nearby supernovae [EPA]

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http://arxiv.org/abs/1712.02730


Recent data indicate one or more moderately nearby supernovae in the early Pleistocene, with additional events likely in the Miocene. This has motivated more detailed computations, using new information about the nature of supernovae and the distances of these events to describe in more detail the sorts of effects that are indicated at the Earth. This short communication/review is designed to describe some of these effects so that they may possibly be related to changes in the biota around these times.

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A. Melott and B. Thomas
Fri, 8 Dec 17
24/70

Comments: 2 figures; to be published in Lethaia

Multilevel Bayesian Parameter Estimation in the Presence of Model Inadequacy and Data Uncertainty [CL]

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http://arxiv.org/abs/1711.10599


Model inadequacy and measurement uncertainty are two of the most confounding aspects of inference and prediction in quantitative sciences. The process of scientific inference (the inverse problem) and prediction (the forward problem) involve multiple steps of data analysis, hypothesis formation, model construction, parameter estimation, model validation, and finally, the prediction of the quantity of interest. This article seeks to clarify the concepts of model inadequacy and bias, measurement uncertainty, and the two traditional classes of uncertainty: aleatoric versus epistemic, as well as their relationships with each other in the process of scientific inference. Starting from basic principles of probability, we build and explain a hierarchical Bayesian framework to quantitatively deal with model inadequacy and noise in data. The methodology can be readily applied to many common inference and prediction problems in science, engineering, and statistics.

Read this paper on arXiv…

A. Shahmoradi
Thu, 30 Nov 17
11/77

Comments: N/A

Percolation clusters of organics in interstellar ice grains as the incubators of life [EPA]

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http://arxiv.org/abs/1711.01945


Biomolecules can be synthesized in interstellar ice grains subject to UV radiation. Here I consider the processes in such ice grains from the perspective of getting to the machinery of life. I show that the large dose of UV radiation per molecule over sufficiently long time scales leads to the creation of large percolation clusters of organic molecules. The cluster will have a large network of pores traversing its entire length, which eventually collapses into small local networks (chambers).
During the formation of the solar system, some of these clusters would end up in proto-planets. The chambers of the cluster provided for micro-environments that are filtered versions of the outside environment, with the deeper chambers getting a more filtered environment. Periodic heating and chemical potential differences between chambers can drive processes involving systems of biomolecules replicating themselves.
The micro-environmental differences between chambers being small, allows such systems to get easily adapted to new higher level chambers, allowing them to eventually get adapted to the outside environment as it moves toward the outer regions of the cluster. Small clusters will likely be present inside such a system playing the role of reaction chambers. Such a system contained in a lipid membrane would be fully fledged microbe. A collision of a microbe containing proto-planet with the Moon could have led to chunks veering off back into space, microbes in small fragments can survive a subsequent impact with Earth.

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S. Mitra
Tue, 7 Nov 17
14/118

Comments: 10 pages

From Allometry to Dimensionally Homogenous `Laws': Reformulation of the Metabolic Rate Relation [CL]

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http://arxiv.org/abs/1707.02340


Meaningful laws of nature must be independent of the units employed to measure the variables. The principle of similitude (Rayleigh 1915) or dimensional homogeneity, states that only commensurable quantities (ones having the same dimension) may be compared, therefore, meaningful laws of nature must be homogeneous equations in their various units of measurement, a result which was formalized in the $\rm \Pi$ theorem (Vaschy 1892; Buckingham 1914). However, most relations in allometry do not satisfy this basic requirement, including the `3/4 Law’ (Kleiber 1932) that relates the basal metabolic rate and body mass, which it is sometimes claimed to be the most fundamental biological rate (Brown et al. 2004) and the closest to a law in life sciences (West \& Brown 2004). Using the $\rm \Pi$ theorem, here we show that it is possible to construct a unique homogeneous equation for the metabolic rates, in agreement with data in the literature. We find that the variations in the dependence of the metabolic rates on body mass are secondary, coming from variations in the allometric dependence of the heart frequencies. This includes not only different classes of animals (mammals, birds, invertebrates) but also different exercise conditions (basal and maximal). Our results demonstrate that most of the differences found in the allometric exponents (White et al. 2007) are due to compare incommensurable quantities and that our dimensionally homogenous formula, unify these differences into a single formulation. We discuss the ecological implications of this new formulation in the context of the Malthusian’s, Fenchel’s and Calder’s relations.

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A. Escala
Tue, 11 Jul 17
71/74

Comments: Submitted. Comments are welcome (andres.escala@aya.yale.edu)

From Blackbirds to Black Holes: Investigating Capture-Recapture Methods for Time Domain Astronomy [HEAP]

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http://arxiv.org/abs/1701.03801


In time domain astronomy, recurrent transients present a special problem: how to infer total populations from limited observations. Monitoring observations may give a biassed view of the underlying population due to limitations on observing time, visibility and instrumental sensitivity. A similar problem exists in the life sciences, where animal populations (such as migratory birds) or disease prevalence, must be estimated from sparse and incomplete data. The class of methods termed Capture-Recapture is used to reconstruct population estimates from time-series records of encounters with the study population. This paper investigates the performance of Capture-Recapture methods in astronomy via a series of numerical simulations. The Blackbirds code simulates monitoring of populations of transients, in this case accreting binary stars (neutron star or black hole accreting from a stellar companion) under a range of observing strategies. We first generate realistic light-curves for populations of binaries with contrasting orbital period distributions. These models are then randomly sampled at observing cadences typical of existing and planned monitoring surveys. The classical capture-recapture methods, Lincoln-Peterson, Schnabel estimators, related techniques, and newer methods implemented in the Rcapture package are compared. A general exponential model based on the radioactive decay law is introduced, and demonstrated to recover (at 95% confidence) the underlying population abundance and duty cycle, in a fraction of the observing visits (10-50%) required to discover all the sources in the simulation. Capture-Recapture is a promising addition to the toolbox of time domain astronomy, and methods implemented in R by the biostats community can be readily called from within Python.

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S. Laycock
Tue, 17 Jan 17
75/81

Comments: Accepted to New Astronomy. 11 pages, 8 figures (refereed version prior to editorial process)

Circular spectropolarimetric sensing of chiral photosystems in decaying leaves [CL]

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http://arxiv.org/abs/1701.01297


Circular polarization spectroscopy has proven to be an indispensable tool in photosynthesis research and (bio)-molecular research in general. Oxygenic photosystems typically display an asymmetric Cotton effect around the chlorophyll absorbance maximum with a signal $\leq 1 \%$. In vegetation, these signals are the direct result of the chirality of the supramolecular aggregates. The circular polarization is thus directly influenced by the composition and architecture of the photosynthetic macrodomains, and is thereby linked to photosynthetic functioning. Although ordinarily measured only on a molecular level, we have developed a new spectropolarimetric instrument, TreePol, that allows for both laboratory and in-the-field measurements. Through spectral multiplexing, TreePol is capable of fast measurements with a sensitivity of $\sim 1*10^{-4}$ and is therefore suitable of non-destructively probing the molecular architecture of whole plant leaves. We have measured the chiroptical evolution of \textit{Hedera helix} leaves for a period of 22 days. Spectrally resolved circular polarization measurements (450-900 nm) on whole leaves in transmission exhibit a strong decrease in the polarization signal over time after plucking, which we accredit to the deterioration of chiral macro-aggregates. Chlorophyll \textit{a} levels measured over the same period by means of UV-Vis absorption and fluorescence spectroscopy showed a much smaller decrease. With these results we are able to distinguish healthy from deteriorating leaves. Hereby we indicate the potency of circular polarization spectroscopy on whole and intact leaves as a nondestructive tool for structural and plant stress assessment. Additionally, we underline the establishment of circular polarization signals as remotely accessible means of detecting the presence of extraterrestrial life.

Read this paper on arXiv…

C. Patty, L. Visser, F. Ariese, et. al.
Fri, 6 Jan 17
5/46

Comments: 29 pages, 6 figures

Thermodynamic Explanation for the Cosmic Ubiquity of Organic Pigments [EPA]

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http://arxiv.org/abs/1608.08847


There is increasingly more evidence being accumulated for the occurrence of large amounts of organic material in the cosmos, particularly in the form of aromatic compounds. These molecules can be found on the surface of Earth and Mars, in the atmospheres of the larger planets and on many of their satellites, on asteroids, comets, meteorites, the atmospheres of red giant stars, interstellar nebulae, and in the spiral arms of galaxies. Many of these environments are expected to be of low temperature and pressure, implying that the Gibbs free energy for the formation of these complex molecules should be positive and large, suggesting that their existence could only be attributed to non-equilibrium thermodynamic processes. In this article we first review the evidence for the abundance of these molecules in the cosmos and then describe how the ubiquity can be explained from within the framework of non-equilibrium thermodynamics on the basis of the catalytic properties of these pigment molecules in dissipating photons of the ultraviolet and visible emission spectra of neighboring stars, leading to greater local entropy production. A relation between the maximum wavelength of absorption of these organic pigments and the corresponding stellar photon environment, provides a guide to determining which aromatic compounds are most probable in a given stellar neighborhood, a postulate that can be verified on Earth. It is suggested that at least some of the baryonic dark matter may be associated with these molecules which emit in the extreme infrared with many, but weak, emission lines, thus so far escaping detection. This thermodynamic explanation for the ubiquity of these organic molecules also has relevance to the possibility of life, both as we know it, and as we may not know it, throughout the universe.

Read this paper on arXiv…

K. Michaelian and A. Simeonov
Thu, 1 Sep 16
26/74

Comments: 23 pages, no figures

Modeling Stellar Proton Event-induced particle radiation dose on close-in exoplanets [EPA]

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http://arxiv.org/abs/1606.07027


Kepler observations have uncovered the existence of a large number of close-in exoplanets and serendipitously of stellar superflares with emissions several orders of magnitude higher than those observed on the Sun. The interaction between the two and its implications on planetary habitability is of great interest to the community. Stellar Proton Events interact with the planetary atmosphere, generate secondary particles and increase the radiation dose on the surface. This effect is amplified for close-in exoplanets and can be a serious threat to potential planetary life. Using Monte Carlo simulations, we model the SPE-induced particle radiation dose on the surface of such exoplanets. We study the dependence of radiation dose on flare energy, planet’s orbital distance, magnetic field strength and atmospheric column density, and discuss its implications on constraining planetary habitability.

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D. Atri
Thu, 23 Jun 16
40/49

Comments: N/A

Curvature-induced dissipation [CL]

Posted on by

http://arxiv.org/abs/1511.08031


By inspecting the effect of curvature on a moving fluid, we find that local sources of curvature not only exert inertial forces on the flow, but also generate viscous stresses as a result of the departure of streamlines from the idealized geodesic motion. The curvature-induced viscous forces are shown to cause an indirect and yet appreciable energy dissipation. As a consequence, the flow converges to a stationary equilibrium state solely by virtue of curvature-induced dissipation. In addition, we show that flow through randomly-curved media satisfies a non-linear transport law, resembling Darcy-Forchheimer’s law, due to the viscous forces generated by the spatial curvature. It is further shown that the permeability can be characterized in terms of the average metric perturbation.

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J. Debus, M. Mendoza, S. Succi, et. al.
Fri, 11 Dec 15
33/71

Comments: N/A

Parking-garage structures in astrophysics and biophysics [CL]

Posted on by

http://arxiv.org/abs/1509.00410


A striking shape was recently observed for the cellular organelle endoplasmic reticulum consisting of stacked sheets connected by helical ramps. This shape is interesting both for its biological function, to synthesize proteins using an increased surface area for ribosome factories, and its geometric properties that may be insensitive to details of the microscopic interactions. In the present work, we find very similar shapes in our molecular dynamics simulations of the nuclear pasta phases of dense nuclear matter that are expected deep in the crust of neutron stars. There are dramatic differences between nuclear pasta and terrestrial cell biology. Nuclear pasta is 14 orders of magnitude denser than the aqueous environs of the cell nucleus and involves strong interactions between protons and neutrons, while cellular scale biology is dominated by the entropy of water and complex assemblies of biomolecules. Nonetheless the very similar geometry suggests both systems may have similar coarse-grained dynamics and that the shapes are indeed determined by geometrical considerations, independent of microscopic details. Many of our simulations self-assemble into flat sheets connected by helical ramps. These ramps may impact the thermal and electrical conductivities, viscosity, shear modulus, and breaking strain of neutron star crust. The interaction we use, with Coulomb frustration, may provide a simple model system that reproduces many biologically important shapes.

Read this paper on arXiv…

C. Horowitz, D. Berry, M. Caplan, et. al.
Wed, 2 Sep 15
28/87

Comments: 5 pages, 3 figures

The Habitable Zone of Inhabited Planets [EPA]

Posted on by

http://arxiv.org/abs/1405.4576


In this paper we discuss and illustrate the hypothesis that life substantially alters the state of a planetary environment and therefore, modifies the limits of the HZ as estimated for an uninhabited planet. This hypothesis lead to the introduction of the Habitable Zone for Inhabited planets (hereafter InHZ), defined here as the region where the complex interaction between life and its abiotic environment is able to produce plausible equilibrium states with the necessary physical conditions for the existence and persistence of life itself. We support our hypothesis of an InHZ with three theoretical arguments, multiple evidences coming from observations of the Earth system, several conceptual experiments and illustrative numerical simulations. Conceptually the diference between the InHZ and the Abiotic HZ (AHZ) depends on unique and robust properties of life as an emergent physical phenomenon and not necesarily on the particular life forms bearing in the planet. Our aim here is to provide conceptual basis for the development of InHZ models incorporating consistently life-environment interactions. Although previous authors have explored the effects of life on habitability there is a gap in research developing the reasons why life should be systematically included at determining the HZ limits. We do not provide here definitive limits to the InHZ but we show through simple numerical models (as a parable of an inhabited planet) how the limits of the AHZ could be modified by including plausible interactions between biota and its environment. These examples aim also at posing the question that if limits of the HZ could be modified by the presence of life in those simple dynamical systems how will those limits change if life is included in established models of the AHZ.

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J. Zuluaga, J. Salazar, P. Cuartas-Restrepo, et. al.
Tue, 20 May 14
18/62

Comments: Accepted for publication in Biogeosciences Discussion; 16 pages, 5 figures. Comments and discussion are welcomed at: this http URL

Real-Space x-ray tomographic reconstruction of randomly oriented objects with sparse data frames [CL]

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http://arxiv.org/abs/1311.1776


Schemes for X-ray imaging single protein molecules using new x-ray sources, like x-ray free electron lasers (XFELs), require processing many frames of data that are obtained by taking temporally short snapshots of identical molecules, each with a random and unknown orientation. Due to the small size of the molecules and short exposure times, average signal levels of much less than 1 photon/pixel/frame are expected, much too low to be processed using standard methods. One approach to process the data is to use statistical methods developed in the EMC algorithm (Loh & Elser, Phys. Rev. E, 2009) which processes the data set as a whole. In this paper we apply this method to a real-space tomographic reconstruction using sparse frames of data (below $10^{-2}$ photons/pixel/frame) obtained by performing x-ray transmission measurements of a low-contrast, randomly-oriented object. This extends the work by Philipp et al. (Optics Express, 2012) to three dimensions and is one step closer to the single molecule reconstruction problem.

Read this paper on arXiv…

Fri, 8 Nov 13
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