Formation of Cosmic Dust Bunnies

Planetary formation is an efficient process now thought to take place on a relatively short astronomical time scale. Recent observations have shown that the dust surrounding a protostar emits more efficiently at longer wavelengths as the protoplanetary disk evolves, suggesting that the dust particles are coagulating into fluffy aggregates, "much as dust bunnies form under a bed." One poorly understood problem in this coagulation process is the manner in which micron-sized, charged grains form the fractal aggregate structures now thought to be the precursors of protoplanetary disk evolution. This study examines the characteristics of such fractal aggregates formed by the collision of spherical monomers and aggregates where the charge is distributed over the aggregate structure. The aggregates are free to rotate due to collisions and dipole-dipole electrostatic interactions. Comparisons are made for different precursor size distributions and like-charged, oppositelycharged, and neutral grains

Approaching protein design with multisite λ dynamics: Accurate and scalable mutational folding free energies in T4 lysozyme

The estimation of changes in free energy upon mutation is central to the problem of protein design. Modern protein design methods have had remarkable success over a wide range of design targets, but are reaching their limits in ligand binding and enzyme design due to insufficient accuracy in mutational free energies. Alchemical free energy calculations have the potential to supplement modern design methods through more accurate molecular dynamics based prediction of free energy changes, but suffer from high computational cost. Multisite λ dynamics (MSλD) is a particularly efficient and scalable free energy method with potential to explore combinatorially large sequence spaces inaccessible with other free energy methods. This work aims to quantify the accuracy of MSλD and demonstrate its scalability. We apply MSλD to the classic problem of calculating folding free energies in T4 lysozyme, a system with a wealth of experimental measurements. Single site mutants considering 32 mutations show remarkable agreement with experiment with a Pearson correlation of 0.914 and mean unsigned error of 1.19 kcal/mol. Multisite mutants in systems with up to five concurrent mutations spanning 240 different sequences show comparable agreement with experiment. These results demonstrate the promise of MSλD in exploring large sequence spaces for protein design.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146479/1/pro3500_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146479/2/pro3500.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146479/3/pro3500-sup-0001-appendixS1.pd

Structure-Based Model of RNA Pseudoknot Captures Magnesium-Dependent Folding Thermodynamics

We develop a simple, coarse-grained approach for simulating the folding of the Beet Western Yellow Virus (BWYV) pseudoknot toward the goal of creating a transferable model that can be used to study other small RNA molecules. This approach combines a structure-based model (SBM) of RNA with an electrostatic scheme that has previously been shown to correctly reproduce ionic condensation in the native basin. Mg2+ ions are represented explicitly, directly incorporating ion-ion correlations into the system, and K+ is represented implicitly, through the mean-field generalized Manning counterion condensation theory. Combining the electrostatic scheme with a SBM enables the electrostatic scheme to be tested beyond the native basin. We calibrate the SBM to reproduce experimental BWYV unfolding data by eliminating overstabilizing backbone interactions from the molecular contact map and by strengthening base pairing and stacking contacts relative to other native contacts, consistent with the experimental observation that relative helical stabilities are central determinants of the RNA unfolding sequence. We find that this approach quantitatively captures the Mg2+ dependence of the folding temperature and generates intermediate states that better approximate those revealed by experiment. Finally, we examine how our model captures Mg2+ condensation about the BWYV pseudoknot and a U-tail variant, for which the nine 3' end nucleotides are replaced with uracils, and find our results to be consistent with experimental condensation measurements. This approach can be easily transferred to other RNA molecules by eliminating and strengthening the same classes of contacts in the SBM and including generalized Manning counterion condensation

Final targeting strategy for the sloan digital sky survey IV Apache Point Observatory galactic evolution experiment 2 North Survey

Artículo escrito por más de 60 autores.The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is a dual-hemisphere, near-infrared (NIR), spectroscopic survey with the goal of producing a chemodynamical mapping of the Milky Way. The targeting for APOGEE-2 is complex and has evolved with time. In this paper, we present the updates and additions to the initial targeting strategy for APOGEE-2N presented in Zasowski et al. (2017). These modifications come in two implementation modes: (i) “Ancillary Science Programs” competitively awarded to Sloan Digital Sky Survey IV PIs through proposal calls in 2015 and 2017 for the pursuit of new scientific avenues outside the main survey, and (ii) an effective 1.5 yr expansion of the survey, known as the Bright Time Extension (BTX), made posible through accrued efficiency gains over the first years of the APOGEE-2N project. For the 23 distinct ancillary programs, we provide descriptions of the scientific aims, target selection, and how to identify these targets within the APOGEE-2 sample. The BTX permitted changes to the main survey strategy, the inclusion of new programs in response to scientific discoveries or to exploit major new data sets not available at the outset of the survey design, and expansions of existing programs to enhance their scientific success and reach. After describing the motivations, implementation, and assessment of these programs, we also leave a summary of lessons learned from nearly a decade of APOGEE-1 and APOGEE-2 survey operations. A companion paper, F. Santana et al. (submitted; AAS29036), provides a complementary presentation of targeting modifications relevant to APOGEE-2 operations in the Southern Hemisphere

Excited state electron and energy relays in supramolecular dinuclear complexes revealed by ultrafast optical and X-ray transient absorption spectroscopy

The kinetics of photoinduced electron and energy transfer in a family of tetrapyridophenazine-bridged heteroleptic homo- and heterodinuclear copper(I) bis(phenanthroline)/ruthenium(II) polypyridyl complexes were studied using ultrafast optical and multi-edge X-ray transient absorption spectroscopies. This work combines the synthesis of heterodinuclear Cu(I)–Ru(II) analogs of the homodinuclear Cu(I)–Cu(I) targets with spectroscopic analysis and electronic structure calculations to first disentangle the dynamics at individual metal sites by taking advantage of the element and site specificity of X-ray absorption and theoretical methods. The excited state dynamical models developed for the heterodinuclear complexes are then applied to model the more challenging homodinuclear complexes. These results suggest that both intermetallic charge and energy transfer can be observed in an asymmetric dinuclear copper complex in which the ground state redox potentials of the copper sites are offset by only 310 meV. We also demonstrate the ability of several of these complexes to effectively and unidirectionally shuttle energy between different metal centers, a property that could be of great use in the design of broadly absorbing and multifunctional multimetallic photocatalysts. This work provides an important step toward developing both a fundamental conceptual picture and a practical experimental handle with which synthetic chemists, spectroscopists, and theoreticians may collaborate to engineer cheap and efficient photocatalytic materials capable of performing coulombically demanding chemical transformations

Measurement of Charging and Discharging of High Resistivity Materials Spacecraft Materials by Electron Beams

New instrumentation has been developed for in situ measurements of the electron beam- induced surface voltage of high resistivity spacecraft materials in an existing ultra-high vacuum electron emission analysis chamber. Design details, calibration and characterization measurements of the system are presented, showing sensitivity to a range of surface voltages from12000 V, with resolution surface, using a paddle attached to a vacuum compatible stepper motor mounted within a hemispherical grid retarding field analyzer. These electrodes formed one end of a floating charge transfer probe that enabled measurements to be made by a standard electrostatic field probe external to the vacuum chamber. Surface voltage measurements were also made periodically during the electron beam charging process and as the surface discharged to a grounded substrate after exposure. Analysis of the measured curves provides information on the material electron yields and bulk resistivity

Long-time Low-latency Quantum Memory by Dynamical Decoupling

Quantum memory is a central component for quantum information processing devices, and will be required to provide high-fidelity storage of arbitrary states, long storage times and small access latencies. Despite growing interest in applying physical-layer error-suppression strategies to boost fidelities, it has not previously been possible to meet such competing demands with a single approach. Here we use an experimentally validated theoretical framework to identify periodic repetition of a high-order dynamical decoupling sequence as a systematic strategy to meet these challenges. We provide analytic bounds-validated by numerical calculations-on the characteristics of the relevant control sequences and show that a "stroboscopic saturation" of coherence, or coherence plateau, can be engineered, even in the presence of experimental imperfection. This permits high-fidelity storage for times that can be exceptionally long, meaning that our device-independent results should prove instrumental in producing practically useful quantum technologies.Comment: abstract and authors list fixe

The Nature of the Long-Lived Excited State in a Ni^(II) Phthalocyanine Complex Investigated by X-Ray Transient Absorption Spectroscopy

The nature of the photoexcited state of octabutoxy nickel(II) phthalocyanine (NiPcOBu₈) with a 500 ps lifetime was investigated by X‐ray transient absorption (XTA) spectroscopy. Previous optical, vibrational, and computational studies have suggested that this photoexcited state has a ligand‐to‐metal charge transfer (LMCT) nature. By using XTA, which provides unambiguous information on the local electronic and nuclear configuration around the Ni center, the nature of the excited state of NiPcOBu₈ was reassessed. Using X‐ray probe pulses from a synchrotron source, the ground‐ and excited‐state X‐ray absorption spectra of NiPcOBu8 were measured. Based on the results, we identified that the excited state exhibits spectral features that are characteristic of a Ni^(1, 3)(3d_(z²), 3d_(x²-y²)) state rather than a LMCT state with a transiently reduced Ni center. This state resembles the (d,d) state of nickel(II) tetramesitylphorphyrin. The XTA features are rationalized based on the inherent cavity sizes of the macrocycles. These results may provide useful guidance for the design of photocatalysts in the future