Energy Minimization of Discrete Protein Titration State Models Using Graph Theory

There are several applications in computational biophysics which require the optimization of discrete interacting states; e.g., amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very time-consuming as it scales exponentially in the number of sites to be optimized. In this paper, we describe a new polynomial-time algorithm for optimization of discrete states in macromolecular systems. This algorithm was adapted from image processing and uses techniques from discrete mathematics and graph theory to restate the optimization problem in terms of "maximum flow-minimum cut" graph analysis. The interaction energy graph, a graph in which vertices (amino acids) and edges (interactions) are weighted with their respective energies, is transformed into a flow network in which the value of the minimum cut in the network equals the minimum free energy of the protein, and the cut itself encodes the state that achieves the minimum free energy. Because of its deterministic nature and polynomial-time performance, this algorithm has the potential to allow for the ionization state of larger proteins to be discovered

Constrained modelling of instrumental radial velocity drift in precision Radial Velocity Spectrometers: Application to HPF

For precise measurement of the radial velocity change in a star, the precision of the wavelength solution is 4 orders more important than accuracy of the wavelength solution. Since the absolute wavelength solution model of a multi-order echelle spectrographs require a large number of parameters, it is better to track the change in wavelength solution over time instead of refitting the complete wavelength solution without any constrains. For stabilized spectrographs like The Habitable-Zone Planet Finder (HPF) and NEID, these changes in wavelength solution are significantly low order and can be modeled with only a few parameters. Table 1, shows an example of low order changes to dispersion solution we expect from various physical mechanisms in HPF or NEID

Evidence for He I 10830 \AA~ absorption during the transit of a warm Neptune around the M-dwarf GJ 3470 with the Habitable-zone Planet Finder

Understanding the dynamics and kinematics of out-flowing atmospheres of hot and warm exoplanets is crucial to understanding the origins and evolutionary history of the exoplanets near the evaporation desert. Recently, ground based measurements of the meta-stable Helium atom's resonant absorption at 10830 \AA~has become a powerful probe of the base environment which is driving the outflow of exoplanet atmospheres. We report evidence for the He I 10830 \AA~in absorption (equivalent width $\sim$ $0.012 \pm 0.002$ \AA) in the exosphere of a warm Neptune orbiting the M-dwarf GJ 3470, during three transits using the Habitable Zone Planet Finder (HPF) near infrared spectrograph. This marks the first reported evidence for He I 10830 \AA\, atmospheric absorption for a planet orbiting an M-dwarf. Our detected absorption is broad and its blueshifted wing extends to -36 km/sec, the largest reported in the literature to date. We modelled the state of Helium atoms in the exosphere of GJ3470b based on assumptions on the UV and X-ray flux of GJ 3470, and found our measurement of flux-weighted column density of meta-stable state Helium $(N_{He^2_3S} = 2.4 \times 10^{10} \mathrm{cm^{-2}})$, derived from our transit observations, to be consistent with model, within its uncertainties. The methodology developed here will be useful to study and constrain the atmospheric outflow models of other exoplanets like GJ 3470b which are near the edge of the evaporation desert.Comment: Accepted in Ap

Impact of crosshatch patterns in H2RGs on high-precision radial velocity measurements: exploration of measurement and mitigation paths with the Habitable-Zone Planet Finder

Teledyne’s H2RG detector images suffer from crosshatch like patterns, which arise from subpixel quantum efficiency (QE) variation. We present our measurements of this subpixel QE variation in the Habitable-Zone Planet Finder’s H2RG detector. We present a simple model to estimate the impact of subpixel QE variations on the radial velocity and how a first-order correction can be implemented to correct for the artifact in the spectrum. We also present how the HPF’s future upgraded laser frequency comb will enable us to implement this correction

Solar Contamination in Extreme-precision Radial-velocity Measurements: Deleterious Effects and Prospects for Mitigation

Solar contamination, due to moonlight and atmospheric scattering of sunlight, can cause systematic errors in stellar radial velocity (RV) measurements that significantly detract from the ~10 cm s−1 sensitivity required for the detection and characterization of terrestrial exoplanets in or near habitable zones of Sun-like stars. The addition of low-level spectral contamination at variable effective velocity offsets introduces systematic noise when measuring velocities using classical mask-based or template-based cross-correlation techniques. Here we present simulations estimating the range of RV measurement error induced by uncorrected scattered sunlight contamination. We explore potential correction techniques, using both simultaneous spectrometer sky fibers and broadband imaging via coherent fiber imaging bundles, that could reliably reduce this source of error to below the photon-noise limit of typical stellar observations. We discuss the limitations of these simulations, the underlying assumptions, and mitigation mechanisms. We also present and discuss the components designed and built into the NEID (NN-EXPLORE Exoplanet Investigations with Doppler spectroscopy) precision RV instrument for the WIYN 3.5 m telescope, to serve as an ongoing resource for the community to explore and evaluate correction techniques. We emphasize that while "bright time" has been traditionally adequate for RV science, the goal of 10 cm s−1 precision on the most interesting exoplanetary systems may necessitate access to darker skies for these next-generation instruments

Improvements to the APBS biomolecular solvation software suite

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining p$K_a$ values, and an improved web-based visualization tool for viewing electrostatics

Impact of crosshatch patterns in H2RGs on high-precision radial velocity measurements: exploration of measurement and mitigation paths with the Habitable-Zone Planet Finder

Teledyne’s H2RG detector images suffer from crosshatch like patterns, which arise from subpixel quantum efficiency (QE) variation. We present our measurements of this subpixel QE variation in the Habitable-Zone Planet Finder’s H2RG detector. We present a simple model to estimate the impact of subpixel QE variations on the radial velocity and how a first-order correction can be implemented to correct for the artifact in the spectrum. We also present how the HPF’s future upgraded laser frequency comb will enable us to implement this correction

Potential effects of ionizing radiation on the evidentiary value of DNA, latent fingerprints, hair, and fibers: A comprehensive review and new results

An extensive literature review and new post-irradiation experimental results are presented of genotyping blood stains and hair, and physical examinations of latent fingerprints, hairs, and fibers. Results indicate that successful development of nuclear short tandem repeat (STR) and mitochondrial DNA sequence profiles from human blood and hair evidence is possible—up to a point—following exposure to gamma, neutron, beta, and alpha radiation at several levels that would most likely be present at this type of crime scene (i.e., a “dirty bomb,” etc.). Commencing at gamma radiation levels between 90 and 900 kGy, DNA analysis using conventional DNA techniques was unsuccessful. In general, irradiation negatively affected the quality of latent fingerprints. All four radiation types degraded most fingerprint samples at all doses; nevertheless, many fingerprints remained of value for potential use in comparison. Although variable from one hair to another, microscopic changes observed for all types and levels of irradiation could potentially result in false exclusions. Negligible microscopic changes were observed in papers and fibers (used as substrates for fingerprints and bloodstains) up to 90 kGy gamma, but fluorescence of fibers began to change above that dose. Paper and fibers, as well as plastic evidence enclosures, became extremely brittle leading to breakage after a gamma dose of 900 kGy

A solar feed for NEID

NEID is a radial velocity (RV) instrument including an ultra-stabilized fiber-fed spectrograph, installed in 2019 at the 3.5m WIYN telescope at Kitt Peak National Observatory. Accompanying it is a solar feed system built to supply the spectrograph with disk-integrated sunlight. Observing the Sun “as a star” is essential for developing and validating mitigation strategies for RV variations due to stellar activity and instrument systematics, thus enabling more-effective detections of lower-mass exoplanets. In this paper, we will detail the design of the NEID solar feed system and showcase early results addressing NEID systematics and solar RV variability