Surface Phase Diagrams from Nested Sampling

Atomic-scale modeling of surface phase equilibria often focuses on temperatures near zero Kelvin due to the difficulty in computing the free energy of surfaces at finite temperatures. The Bayesian-inference-based nested sampling (NS) algorithm allows modeling surface phase equilibria at arbitrary temperatures by directly and efficiently calculating the partition function, whose relationship with free energy is well known. In this work, we extend NS to calculate surface phase diagrams, including all relevant translational, rotational, and vibrational contributions to the free energy. We apply NS to the surfaces of the Lennard-Jones solid, recording energies through the iterative compression of surface phase space rather than a specific cooling schedule. We construct the partition function from these recorded energies to calculate ensemble averages of thermodynamic properties, such as the constant-volume heat capacity and temperature-dependent order parameters that characterize the surface structure. Key results include determining the nature of phase transitions on flat and stepped surfaces, which typically feature an enthalpy-driven condensation at higher temperatures and an entropy-driven reordering process at lower temperatures, and the presence of critical points on the phase diagrams of most of the flatter facets. Overall, we demonstrate the ability and potential of NS for surface modeling and, ultimately, materials discovery.Comment: 41 pages, 11 figures; figures in Sec. S5 are not included due to size restriction

Ab initio study of proton-exchanged LiNbO3(I): Structural, thermodynamic, dielectric, and optical properties

Using first principles calculations, we study the ground-state structure of bulk proton-exchanged lithium niobate, which is also called hydrogen niobate and is widely used in waveguides. Thermodynamics helps to establish the most favorable nonpolar surface as well as the water-deficient and water-rich phases under different ambient conditions, which we refer to as "dehydrated" and "rehydrated" phases, respectively. We compute the low-frequency dielectric response and the optical refractive indices of hydrogen niobate in different phases. The dielectric constant is greatly enhanced compared to lithium niobate. At shorter wavelengths, the refractive indices vary between each phase and have a sharp contrast to lithium niobate. Our study characterizes the structures and thermal instabilities of this compound and reveals its excellent dielectric and optical properties, which can be important in the future application in waveguides

Spawning and early development of captive yellowfin tuna (Thunnus albacares)

In this study we describe the courtship and spawning behaviors of captive yellowfin tuna (Thunnus albacares), their spawning periodicity, the influence of physical and biological factors on spawning and hatching, and egg and early-larval development of this species at the Achotines Laboratory, Republic of Panama, during October 1996 through March 2000. Spawning occurred almost daily over extended periods and at water temperatures from 23.3° to 29.7°C. Water temperature appeared to be the main exogenous factor controlling the occurrence and timing of spawning. Courtship and spawning behaviors were ritualized and consistent among three groups of broodstock over 3.5 years. For any date, the time of day of spawning (range: 1330 to 2130 h) was predictable from mean daily water temperature, and 95% of hatching occurred the next day between 1500 and 1900 h. We estimated that females at first spawning averaged 1.6−2.0 years of age. Over short time periods (<1 month), spawning females increased their egg production from 30% to 234% in response to shortterm increases in daily food ration of 9% to 33%. Egg diameter, notochord length (NL) at hatching, NL at first feeding, and dry weights of these stages were estimated. Water temperature was significantly, inversely related to egg size, egg-stage duration, larval size at hatching, and yolksac larval duration

Prevalence of Microvascular and Macrovascular Disease in the Glycemia Reduction Approaches in Diabetes - A Comparative Effectiveness (GRADE) Study Cohort

Aims: The Glycemia Reduction Approaches in Diabetes - A Comparative Effectiveness (GRADE) trial is a randomized clinical trial comparing glycemic effects of four diabetes medications added to metformin in type 2 diabetes (T2D). Microvascular and macrovascular diseases are secondary outcomes. We evaluated the prevalence and risk factor relationships for microvascular and macrovascular complications in the GRADE cohort at study entry. Methods: Complication prevalence and risk factors were analyzed based on data from screening in all consenting participants meeting GRADE eligibility. Logistic regression and Z-statistics were used to assess risk factor relationships with complications. Results: We enrolled 5047 T2D participants [mean age 57 years; 36% female; mean known T2D duration 4 years (all < 10 years); mean HbA1c 8.0% (∼64 mmol/mol) at screening]. Urinary albumin/creatinine ratio (ACR) ≥ 30 mg/gram was present in 15.9% participants; peripheral neuropathy (by Michigan Neuropathy Screening Instrument) in 21.5%; cardiovascular autonomic neuropathy by electrocardiography-derived indices in 9.7%; self-reported retinopathy in 1.0%. Myocardial infarction ascertained by self-report or electrocardiogram was present in 7.3%, and self-reported history of stroke in 2.0%. Conclusions: In the GRADE cohort with < 10 years of T2D and a mean HbA1c of 8.0%, diabetes complications were present in a substantial fraction of participants, more so than might otherwise have been expected

Monte Carlo of Trapped Ultracold Neutrons in the UCNτ Trap

In the UCNτ experiment, ultracold neutrons (UCN) are confined by magnetic fields and the Earth’s gravitational field. Field-trapping mitigates the problem of UCN loss on material surfaces, which caused the largest correction in prior neutron experiments using material bottles. However, the neutron dynamics in field traps differ qualitatively from those in material bottles. In the latter case, neutrons bounce off material surfaces with significant diffusivity and the population quickly reaches a static spatial distribution with a density gradient induced by the gravitational potential. In contrast, the field-confined UCN—whose dynamics can be described by Hamiltonian mechanics—do not exhibit the stochastic behaviors typical of an ideal gas model as observed in material bottles. In this report, we will describe our efforts to simulate UCN trapping in the UCNτ magneto-gravitational trap. We compare the simulation output to the experimental results to determine the parameters of the neutron detector and the input neutron distribution. The tuned model is then used to understand the phase space evolution of neutrons observed in the UCNτ experiment. We will discuss the implications of chaotic dynamics on controlling the systematic effects, such as spectral cleaning and microphonic heating, for a successful UCN lifetime experiment to reach a 0.01% level of precision

Large Scale Benchmark of Materials Design Methods

Lack of rigorous reproducibility and validation are major hurdles for scientific development across many fields. Materials science in particular encompasses a variety of experimental and theoretical approaches that require careful benchmarking. Leaderboard efforts have been developed previously to mitigate these issues. However, a comprehensive comparison and benchmarking on an integrated platform with multiple data modalities with both perfect and defect materials data is still lacking. This work introduces JARVIS-Leaderboard, an open-source and community-driven platform that facilitates benchmarking and enhances reproducibility. The platform allows users to set up benchmarks with custom tasks and enables contributions in the form of dataset, code, and meta-data submissions. We cover the following materials design categories: Artificial Intelligence (AI), Electronic Structure (ES), Force-fields (FF), Quantum Computation (QC) and Experiments (EXP). For AI, we cover several types of input data, including atomic structures, atomistic images, spectra, and text. For ES, we consider multiple ES approaches, software packages, pseudopotentials, materials, and properties, comparing results to experiment. For FF, we compare multiple approaches for material property predictions. For QC, we benchmark Hamiltonian simulations using various quantum algorithms and circuits. Finally, for experiments, we use the inter-laboratory approach to establish benchmarks. There are 1281 contributions to 274 benchmarks using 152 methods with more than 8 million data-points, and the leaderboard is continuously expanding. The JARVIS-Leaderboard is available at the website: https://pages.nist.gov/jarvis_leaderboar

Unusual Regulation of a Leaderless Operon Involved in the Catabolism of Dimethylsulfoniopropionate in Rhodobacter sphaeroides

Rhodobacter sphaeroides strain 2.4.1 is a widely studied bacterium that has recently been shown to cleave the abundant marine anti-stress molecule dimethylsulfoniopropionate (DMSP) into acrylate plus gaseous dimethyl sulfide. It does so by using a lyase encoded by dddL, the promoter-distal gene of a three-gene operon, acuR-acuI-dddL. Transcription of the operon was enhanced when cells were pre-grown with the substrate DMSP, but this induction is indirect, and requires the conversion of DMSP to the product acrylate, the bona fide co-inducer. This regulation is mediated by the product of the promoter-proximal gene acuR, a transcriptional regulator in the TetR family. AcuR represses the operon in the absence of acrylate, but this is relieved by the presence of the co-inducer. Another unusual regulatory feature is that the acuR-acuI-dddL mRNA transcript is leaderless, such that acuR lacks a Shine-Dalgarno ribosomal binding site and 5′-UTR, and is translated at a lower level compared to the downstream genes. This regulatory unit may be quite widespread in bacteria, since several other taxonomically diverse lineages have adjacent acuR-like and acuI-like genes; these operons also have no 5′ leader sequences or ribosomal binding sites and their predicted cis-acting regulatory sequences resemble those of R. sphaeroides acuR-acuI-dddL

Presynaptically Localized Cyclic GMP-Dependent Protein Kinase 1 Is a Key Determinant of Spinal Synaptic Potentiation and Pain Hypersensitivity

Electrophysiological and behavioral experiments in mice reveal that a cGMP-dependent kinase amplifies neurotransmitter release from peripheral pain sensors, potentiates spinal synapses, and leads to exaggerated pain

Local and regional components of aerosol in a heavily trafficked street canyon in central London derived from PMF and cluster analysis of single-particle ATOFMS spectra.

Positive matrix factorization (PMF) has been applied to single particle ATOFMS spectra collected on a six lane heavily trafficked road in central London (Marylebone Road), which well represents an urban street canyon. PMF analysis successfully extracted 11 factors from mass spectra of about 700,000 particles as a complement to information on particle types (from K-means cluster analysis). The factors were associated with specific sources and represent the contribution of different traffic related components (i.e., lubricating oils, fresh elemental carbon, organonitrogen and aromatic compounds), secondary aerosol locally produced (i.e., nitrate, oxidized organic aerosol and oxidized organonitrogen compounds), urban background together with regional transport (aged elemental carbon and ammonium) and fresh sea spray. An important result from this study is the evidence that rapid chemical processes occur in the street canyon with production of secondary particles from road traffic emissions. These locally generated particles, together with aging processes, dramatically affected aerosol composition producing internally mixed particles. These processes may become important with stagnant air conditions and in countries where gasoline vehicles are predominant and need to be considered when quantifying the impact of traffic emissions.This is the author accepted manuscript. The final version is available via ACS at http://pubs.acs.org/doi/abs/10.1021/es506249z