Artificial-intelligence-driven scanning probe microscopy

Scanning probe microscopy (SPM) has revolutionized the fields of materials, nano-science, chemistry, and biology, by enabling mapping of surface properties and surface manipulation with atomic precision. However, these achievements require constant human supervision; fully automated SPM has not been accomplished yet. Here we demonstrate an artificial intelligence framework based on machine learning for autonomous SPM operation (DeepSPM). DeepSPM includes an algorithmic search of good sample regions, a convolutional neural network to assess the quality of acquired images, and a deep reinforcement learning agent to reliably condition the state of the probe. DeepSPM is able to acquire and classify data continuously in multi-day scanning tunneling microscopy experiments, managing the probe quality in response to varying experimental conditions. Our approach paves the way for advanced methods hardly feasible by human operation (e.g., large dataset acquisition and SPM-based nanolithography). DeepSPM can be generalized to most SPM techniques, with the source code publicly available

A Consistent Model of the Accretion Shock Region in Classical T Tauri Stars

We develop a consistent model of the accretion shock region in Classical T Tauri Stars (CTTSs). The initial conditions of the post-shock flow are determined by the irradiated shock precursor and the ionization state is calculated without assuming ionization equilibrium. Comparison with observations of the C IV resonance lines (λλ 1550 Å) for CTTSs indicate that the post-shock emission predicted by the model is too large, for a reasonable range of parameters. If the model is to reproduce the observations, C IV emission from CTTSs has to be dominated by pre-shock emission, for stars with moderate to large accretion rates. For stars with low accretion rates, the observations suggest a comparable contribution between the pre- and post-shock regions. These conclusions are consistent with previous results indicating that the post-shock will be buried under the stellar photosphere for moderate to large accretion rates

Theoretical Spectra and Light Curves of Close-in Extrasolar Giant Planets and Comparison with Data

We present theoretical atmosphere, spectral, and light-curve models for extrasolar giant planets (EGPs) undergoing strong irradiation for which {\it Spitzer} planet/star contrast ratios or light curves have been published (circa June 2007). These include HD 209458b, HD 189733b, TrES-1, HD 149026b, HD 179949b, and $\upsilon$ And b. By comparing models with data, we find that a number of EGP atmospheres experience thermal inversions and have stratospheres. This is particularly true for HD 209458b, HD 149026b, and $\upsilon$ And b. This finding translates into qualitative changes in the planet/star contrast ratios at secondary eclipse and in close-in EGP orbital light curves. Moreover, the presence of atmospheric water in abundance is fully consistent with all the {\it Spitzer} data for the measured planets. For planets with stratospheres, water absorption features invert into emission features and mid-infrared fluxes can be enhanced by a factor of two. In addition, the character of near-infrared planetary spectra can be radically altered. We derive a correlation between the importance of such stratospheres and the stellar flux on the planet, suggesting that close-in EGPs bifurcate into two groups: those with and without stratospheres. From the finding that TrES-1 shows no signs of a stratosphere, while HD 209458b does, we estimate the magnitude of this stellar flux breakpoint. We find that the heat redistribution parameter, P$_n$, for the family of close-in EGPs assumes values from $\sim$0.1 to $\sim$0.4. This paper provides a broad theoretical context for the future direct characterization of EGPs in tight orbits around their illuminating stars.Comment: Accepted to Ap. J., provided here in emulateapj format: 28 pages, 8 figures, many with multiple panel

Bovine digital dermatitis: natural lesion development and experimental induction

Bovine Digital Dermatitis (DD) is a leading cause of lameness in dairy cattle in the US with more than 70% of herds affected. Despite 40 years of research, the definitive etiologic agent(s) associated with the disease process is unknown. While clinical lesions have been well described, little is known about the macroscopic, microscopic, and bacterial changes associated with the early stages of lesion development from normal skin to clinical lesions. The goal of this dissertation was to describe the temporal changes associated with lesion development in Holstein dairy cattle, particularly early stage lesions, and develop a model for lesion induction. By following a cohort of Holstein dairy cows for a three year period, several important epidemiologic findings were recognized. In the absence of control measures, DD lesions developed at a rate of 4 lesions per 100 cow feet-months, with the average time for a lesion to develop being 133 days. From the recognition of the macroscopic changes that preceded clinical DD lesions, a novel scoring system was developed. While 20% of the feet observations had clinical DD lesions, an additional 55% of observations had lesions that were indicative of early DD lesion development. Biopsies from these different stages of lesion development were submitted for metagenomic analysis using next generation sequencing. The bacterial microbiota of these biopsies was found to progress through a systematic series of changes that correlate with the macroscopic lesion scoring system with the microbiota of each stage being statistically different from other stages. As one of the major goals for these studies was to gain a better understanding of the etiology of disease, an experimental model was needed to test candidate pathogens. Four preliminary studies were conducted to optimize conditions and methodologies for induction of DD lesions that led to a final consensus protocol that was able to induce DD lesions in 95% of Holstein calves within 28 days. The results of these studies support the hypothesis that DD is a polybacterial disease process that undergoes systematic macroscopic, microscopic, and bacterial changes as lesions develop

A high-Resolution Catalog of Cometary Emission Lines

Using high-resolution spectra obtained with the Hamilton echelle spectrograph at Lick Observatory, we have constructed a catalog of emission lines observed in comets Swift-Tuttle and Brorsen-Metcalf. The spectra cover the range between 3800 Å and 9900 Å with a spectral resolution of λ/Δλ~42000. In the spectra, we catalog 2997 emission lines of which we identify 2438. We find cometary lines due to H, O, C_2, CN, NH_2, C_3, H_2O^+, CH, and CH^+. We list 559 unidentified lines compiled from the two spectra and comment on possibilities for their origins

Non-detection of the OH Meinel system in comet P/Swift-Tuttle

We report a search for emissions from the OH Meinel system in high-resolution near-infrared spectra of comet P/Swift-Tuttle. Because of the large cometary heliocentric velocity and high resolution of the spectrograph, the cometary lines should be well separated from the bright OH sky lines. Contrary to the findings of Tozzi et al. (1994) - who report seeing cometary OH at intensities comparable to the sky emissions in their low-resolution spectra - we find no OH in these spectra with an upper limit of 5% the value of the night sky lines. The non-detection of these cometary lines is consistent with theoretical calculations of expected emission strengths from prompt and fluorescent emission from cometary OH

A Young Planet Search in Visible and IR Light: DN Tau, V836 Tau, and V827 Tau

In searches for low-mass companions to late-type stars, correlation between radial velocity variations and line bisector slope changes indicates contamination by large starspots. Two young stars demonstrate that this test is not sufficient to rule out starspots as a cause of radial velocity variations. As part of our survey for substellar companions to T Tauri stars, we identified the ~2 Myr old planet host candidates DN Tau and V836 Tau. In both cases, visible light radial velocity modulation appears periodic and is uncorrelated with line bisector span variations, suggesting close companions of several M_Jup in these systems. However, high-resolution, infrared spectroscopy shows that starspots cause the radial velocity variations. We also report unambiguous results for V827 Tau, identified as a spotted star on the basis of both visible light and infrared spectroscopy. Our results suggest that infrared follow up observations are critical for determining the source of radial velocity modulation in young, spotted stars.Comment: Accepted for publication in the Astrophysical Journal Letter

Regression or significance tests: What other choice is there?—An academic perspective

Both the no-observed-effect concentration and its null hypothesis significance testing foundation have drawn steady criticism since their inceptions [1–5]. Many in our field reasonably advocate regression to avoid conventional null hypothesis significance testing shortcomings; however, regression is compromised under commonly encountered conditions (Green, present Perspective’s Challenge). As the debate to favor null hypothesis significance testing or regression methods continues into the 21st century, a sensible strategy might be to take a moment to ask, Are there now other choices? Our goal is to sketch out 1 such choice

Joint Effects of Fragmentation and Mercury Contamination on Marsh Periwinkle (Littoraria irrorata) Movement

There are different ways contaminants can interact and enhance the effects of habitat fragmentation, such as modifying the movement of organisms. The present study tested the hypothesis that mercury exacerbates the effects offragmentation by affecting the movement of the marsh periwinkle Littoraria irrorata and reducing the probability of snails crossing fragmented microlandscape experimental systems. How these changes could affect the search efficiency of organisms in the long term was assessed using hidden Markov models and random walks simulations. Bayesian nonlinearmodels were used to analyze the effects of fragmentation and contamination on the mean speed and mean directional change of organisms. Snail movement for control and two mercury‐exposure treatments were recorded in microlandscapeswith six different levels of habitat cover and three landscape replicates. The results indicated that exposed organisms had lower probabilities of crossing the landscape, reduced speed, and shifts in step length distributions. Both mercury exposure and habitat fragmentation affected the movement of the marsh periwinkle. Mercury exacerbated the effects of habitat fragmentation by affecting the cognition (e.g., route planning, orientation, and spatial learning) and movement of L. irrorata. Hence, the interaction of these stressors could further reduce the functional connectivity of landscapes and reduce the searchefficiency of organisms

Magnetic fields of intermediate mass T Tauri stars

Aims. In this paper, we aim to measure the strength of the surface magnetic fields for a sample of five intermediate mass T Tauri stars and one low mass T Tauri star from late-F to mid-K spectral types. While magnetic fields of T Tauri stars at the low mass range have been extensively characterized, our work complements previous studies towards the intermediate mass range; this complementary study is key to evaluate how magnetic fields evolve during the transition from a convective to a radiative core. Methods. We studied the Zeeman broadening of magnetically sensitive spectral lines in the H-band spectra obtained with the CRIRES high-resolution near-infrared spectrometer. These data are modelled using magnetic spectral synthesis and model atmospheres. Additional constraints on non-magnetic line broadening mechanisms are obtained from modelling molecular lines in the K band or atomic lines in the optical wavelength region. Results. We detect and measure mean surface magnetic fields for five of the six stars in our sample: CHXR 28, COUP 107, V2062 Oph, V1149 Sco, and Par 2441. Magnetic field strengths inferred from the most magnetically sensitive diagnostic line range from 0.8 to 1.8 kG. We also estimate a magnetic field strength of 1.9 kG for COUP 107 from an alternative diagnostic. The magnetic field on YLW 19 is the weakest in our sample and is marginally detected, with a strength of 0.8 kG. Conclusions. We populate an uncharted area of the pre-main-sequence HR diagram with mean magnetic field measurements from high-resolution near-infrared spectra. Our sample of intermediate mass T Tauri stars in general exhibits weaker magnetic fields than their lower mass counterparts. Our measurements will be used in combination with other spectropolarimetric studies of intermediate mass and lower mass T Tauri stars to provide input into pre-main-sequence stellar evolutionary models.Comment: 8 pages, 8 figures, accepted for publication in Astronomy and Astrophysic