Calculations of Potential Energy Surfaces Using Monte Carlo Configuration Interaction

We apply the method of Monte Carlo configuration interaction (MCCI) to calculate ground-state potential energy curves for a range of small molecules and compare the results with full configuration interaction. We show that the MCCI potential energy curve can be calculated to relatively good accuracy, as quantified using the non-parallelity error, using only a very small fraction of the FCI space. In most cases the potential curve is of better accuracy than its constituent single-point energies. We finally test the MCCI program on systems with basis sets beyond full configuration interaction: a lattice of fifty hydrogen atoms and ethylene. The results for ethylene agree fairly well with other computational work while for the lattice of fifty hydrogens we find that the fraction of the full configuration interaction space we were able to consider appears to be too small as, although some qualitative features are reproduced, the potential curve is less accurate.Comment: 14 pages, 22 figure

Monte Carlo configuration interaction applied to multipole moments, ionisation energies and electron affinities

The method of Monte Carlo configuration interaction (MCCI) [1,2] is applied to the calculation of multipole moments. We look at the ground and excited state dipole moments in carbon monoxide. We then consider the dipole of NO, the quadrupole of the nitrogen molecule and of BH. An octupole of methane is also calculated. We consider experimental geometries and also stretched bonds. We show that these non-variational quantities may be found to relatively good accuracy when compared with FCI results, yet using only a small fraction of the full configuration interaction space. MCCI results in the aug-cc-pVDZ basis are seen to generally have reasonably good agreement with experiment. We also investigate the performance of MCCI when applied to ionisation energies and electron affinities of atoms in an aug-cc-pVQZ basis. We compare the MCCI results with full configuration-interaction quantum Monte Carlo [3,4] and `exact' non-relativistic results [3,4]. We show that MCCI could be a useful alternative for the calculation of atomic ionisation energies however electron affinities appear much more challenging for MCCI. Due to the small magnitude of the electron affinities their percentage errors can be high, but with regards to absolute errors MCCI performs similarly for ionisation energies and electron affinities.Comment: 12 pages, 20 figure

Prevalence of drug-drug interactions in oncology patients enrolled on National Clinical Trials Network oncology clinical trials

Abstract Background Drug-drug interactions (DDIs) in subjects enrolling in clinical trials can impact not only safety of the patient but also study drug outcomes and data validity. This makes it critical to adequately screen and manage DDIs. The study objective was to determine the prevalence of DDIs involving study medications in subjects enrolling in National Clinical Trials Network (NCTN) clinical trials at a single institution. DDIs were evaluated based on study protocol recommendations for concomitant medication use (i.e. exclude, avoid or use caution), screening via DDI tool, and pharmacist review. Methods Subjects enrolled in NCTN trials of commercially available agents between January 2013 and August 2017 were included if a complete medication list was available. Complete medication lists were collected from the date of enrollment or the next available date then screened utilizing protocol guidance and the DDI screening tool, Lexicomp® Drug Interactions (Wolters Kluwer, Hudson, OH). Interactions were reviewed for clinical relevance: defined as a DDI that would require a medication change to ensure study agent safety and efficacy at enrollment. Results One hundred and twenty-eight subjects enrolled in 35 clinical trials were included. Protocol guidance detected 15 unique DDI pairs that should be avoided or used with caution in 10.2% (13/128) of subjects. The majority of these subjects did not have a clinically relevant DDI (69.2%, 9/13) based on pharmacist review. Lexicomp® detected moderate to major DDIs in 24.2% (31/128) of subjects, with 9.4% (12/128) having a clinically relevant DDI. Conclusions This study confirms a high prevalence of DDIs present in subjects enrolling in oncology clinical trials. Further efforts should be made to improve methods to detect and manage DDIs in patients enrolling on clinical trials to ensure patient safety and trial data validity.https://deepblue.lib.umich.edu/bitstream/2027.42/146516/1/12885_2018_Article_5076.pd

Evolution of trace gases and particles emitted by a chaparral fire in California

Biomass burning (BB) is a major global source of trace gases and particles. Accurately representing the production and evolution of these emissions is an important goal for atmospheric chemical transport models. We measured a suite of gases and aerosols emitted from an 81 hectare prescribed fire in chaparral fuels on the central coast of California, US on 17 November 2009. We also measured physical and chemical changes that occurred in the isolated downwind plume in the first ~4 h after emission. The measurements were carried out onboard a Twin Otter aircraft outfitted with an airborne Fourier transform infrared spectrometer (AFTIR), aerosol mass spectrometer (AMS), single particle soot photometer (SP2), nephelometer, LiCor CO_2 analyzer, a chemiluminescence ozone instrument, and a wing-mounted meteorological probe. Our measurements included: CO_2; CO; NO_x; NH_3; non-methane organic compounds; organic aerosol (OA); inorganic aerosol (nitrate, ammonium, sulfate, and chloride); aerosol light scattering; refractory black carbon (rBC); and ambient temperature, relative humidity, barometric pressure, and three-dimensional wind velocity. The molar ratio of excess O_3 to excess CO in the plume (ΔO_3/ΔCO) increased from −5.13 (±1.13) × 10^(−3) to 10.2 (±2.16) × 10^(−2) in ~4.5 h following smoke emission. Excess acetic and formic acid (normalized to excess CO) increased by factors of 1.73 ± 0.43 and 7.34 ± 3.03 (respectively) over the same time since emission. Based on the rapid decay of C_2H_4 we infer an in-plume average OH concentration of 5.27 (±0.97) × 10^6 molec cm^(−3), consistent with previous studies showing elevated OH concentrations in biomass burning plumes. Ammonium, nitrate, and sulfate all increased over the course of 4 h. The observed ammonium increase was a factor of 3.90 ± 2.93 in about 4 h, but accounted for just ~36% of the gaseous ammonia lost on a molar basis. Some of the gas phase NH_3 loss may have been due to condensation on, or formation of, particles below the AMS detection range. NO_x was converted to PAN and particle nitrate with PAN production being about two times greater than production of observable nitrate in the first ~4 h following emission. The excess aerosol light scattering in the plume (normalized to excess CO_2) increased by a factor of 2.50 ± 0.74 over 4 h. The increase in light scattering was similar to that observed in an earlier study of a biomass burning plume in Mexico where significant secondary formation of OA closely tracked the increase in scattering. In the California plume, however, ΔOA/ΔCO_2 decreased sharply for the first hour and then increased slowly with a net decrease of ~20% over 4 h. The fraction of thickly coated rBC particles increased up to ~85% over the 4 h aging period. Decreasing OA accompanied by increased scattering/particle coating in initial aging may be due to a combination of particle coagulation and evaporation processes. Recondensation of species initially evaporated from the particles may have contributed to the subsequent slow rise in OA. We compare our results to observations from other plume aging studies and suggest that differences in environmental factors such as smoke concentration, oxidant concentration, actinic flux, and RH contribute significantly to the variation in plume evolution observations

Distance to the SNR CTB 109/AXP 1E 2259+586 by HI absorption and self-absorption

We suggest a revised distance to the supernova remnant (SNR) G109.1-1.0 (CTB 109) and its associated anomalous X-ray pulsar (AXP) 1E 2259+586 by analyzing 21cm HI-line and 12CO-line spectra of CTB 109, HII region Sh 152, and the adjacent molecular cloud complex. CTB 109 has been established to be interacting with a large molecular cloud (recession velocity at v=-55 km s^-1). The highest radial velocities of absorption features towards CTB 109 (-56 km s^-1) and Sh 152 (-65 km s^-1) are larger than the recombination line velocity (-50 km s^-1) of Sh 152 demonstrating the velocity reversal within the Perseus arm. The molecular cloud has cold HI column density large enough to produce HI self-absorption (HISA) and HI narrow self-absorption (HINSA) if it was at the near side of the velocity reversal. Absence of both HISA and HINSA indicates that the cloud is at the far side of the velocity reversal within the Perseus Arm, so we obtain a distance for CTB 109 of 4+/-0.8 kpc. The new distance still leads to a normal explosion energy for CTB 109/AXP 1E 2259+586.Comment: 5 pages, 3 figures. Accepted by MNRAS Letter

Improvement Initiative to Develop and Implement a Tool for Detecting Drug-Drug Interactions During Oncology Clinical Trial Enrollment Eligibility Screening

Objectives Screening subjects for drug-drug interactions (DDIs) before enrollment in oncology clinical trials is integral to ensuring safety, but standard procedures or tools are not readily available to screen DDI in this setting. Our objectives were to develop a DDI screening tool for use during oncology clinical trial enrollment and to test usability in single-center and multicenter pilot studies. Methods A multistage approach was used for this quality improvement intervention. Semistructured interviews with individuals responsible for DDI screening were conducted to develop a prototype tool. The tool was used for screening DDI in subjects enrolling in National Clinical Trials Network trials of commercially available agents during a single-center 3-month pilot. Improvements were made, and a 3-month multicenter pilot was conducted at volunteer SWOG Cancer Research Network sites. Participants were surveyed to determine tool usability and efficiency. Results A tool was developed from semistructured interviews. A critical feature was reporting which medications had specific pharmacokinetic and pharmacodynamic characteristics including transporter and cytochrome P450 substrates, inhibitors, or inducers and QT prolongation. In the 12-site study, average (SD) DDI screening time for each patient decreased by 15.7 (10.2) minutes (range, 3–35 minutes; P \u3c 0.001). Users reported the tool highly usable, with \u3e90% agreeing with all positive usability characterizations and disagreeing with all negative complexity characterizations. Conclusions A DDI screening tool for oncology clinical trial enrollment was created and its usability confirmed. Further testing with more diverse investigator sites and study drugs during eligibility screening is warranted to improve safety and data accuracy within clinical trials

Size-dependent wet removal of black carbon in Canadian biomass burning plumes

Wet deposition is the dominant mechanism for removing black carbon (BC) from the atmosphere and is key in determining its atmospheric lifetime, vertical gradient and global transport. Despite the importance of BC in the climate system, especially in terms of its ability to modulate the radiative energy budget, there are few quantitative case studies of wet removal in ambient environments. We present a case study of BC wet removal by examining aerosol size distributions and BC coating properties sampled in three Canadian boreal biomass burning plumes, one of which passed through a precipitating cloud. This depleted the majority of the plume’s BC mass, and the largest and most coated BCcontaining particles were found to be preferentially removed, suggesting that nucleation scavenging was likely the dominant mechanism. Calculated single-scattering albedo (SSA) showed little variation, as a large number of non-BC particles were also present in the precipitation-affected plume. The remaining BC cores were smaller than those observed in previous studies of BC in post-precipitation outflow over Asia, possibly due to the thick coating by hydrophilic compounds associated with the Canadian biomass burning particles. This study provides measurements of BC size, mixing state and removal efficiency to constrain model parameterisations of BC wet removal in biomass burning regions, which will help to reduce uncertainty in radiative forcing calculations

XMM-Newton observations of the Galactic Supernova Remnant CTB 109 (G109.1-1.0)

We present the analysis of the X-ray Multi-Mirror Mission (XMM-Newton) European Photon Imaging Camera (EPIC) data of the Galactic supernova remnant (SNR) CTB 109 (G109.1-1.0). CTB 109 is associated with the anomalous X-ray pulsar (AXP) 1E 2259+586 and has an unusual semi-circular morphology in both the X-ray and the radio, and an extended X-ray bright interior region known as the `Lobe'. The deep EPIC mosaic image of the remnant shows no emission towards the west where a giant molecular cloud complex is located. No morphological connection between the Lobe and the AXP is found. We find remarkably little spectral variation across the remnant given the large intensity variations. All spectra of the shell and the Lobe are well fitted by a single-temperature non-equilibrium ionization model for a collisional plasma with solar abundances (kT = 0.5 - 0.7 keV, tau = n_e t = 1 - 4 x 10^11 s cm^-3, N_H = 5 - 7 x 10^21 cm^-2). There is no indication of nonthermal emission in the Lobe or the shell. We conclude that the Lobe originated from an interaction of the SNR shock wave with an interstellar cloud. Applying the Sedov solution for the undisturbed eastern part of the SNR, and assuming full equilibration between the electrons and ions behind the shock front, the SNR shock velocity is derived as v_s = 720 +/- 60 km s^-1, the remnant age as t = (8.8 +/- 0.9) x 10^3 d_3 yr, the initial energy as E_0 = (7.4 +/- 2.9) x 10^50 d_3^2.5 ergs, and the pre-shock density of the nuclei in the ambient medium as n_0 = (0.16 +/- 0.02) d_3^-0.5 cm^-3, at an assumed distance of D = 3.0 d_3 kpc. Assuming CTB 109 and 1E 2259+586 are associated, these values constrain the age and the environment of the progenitor of the SNR and the pulsar.Comment: Accepted for publication in ApJ. 9 figures. Figs. 1 + 2 are in color (fig1.jpg, fig2.jpg

Evolution of Trace Gases and Particles Emitted by a Chaparral Fire in California

Biomass burning (BB) is a major global source of trace gases and particles. Accurately representing the production and evolution of these emissions is an important goal for atmospheric chemical transport models. We measured a suite of gases and aerosols emitted from an 81 hectare prescribed fire in chaparral fuels on the central coast of California, US on 17 November 2009. We also measured physical and chemical changes that occurred in the isolated down-wind plume in the first similar to 4 h after emission. The measurements were carried out onboard a Twin Otter aircraft outfitted with an airborne Fourier transform infrared spectrometer (AFTIR), aerosol mass spectrometer (AMS), single particle soot photometer (SP2), nephelometer, LiCor CO2 analyzer, a chemiluminescence ozone instrument, and a wing-mounted meteorological probe. Our measurements included: CO2; CO; NOx; NH3; non-methane organic compounds; organic aerosol (OA); inorganic aerosol (nitrate, ammonium, sulfate, and chloride); aerosol light scattering; refractory black carbon (rBC); and ambient temperature, relative humidity, barometric pressure, and three-dimensional wind velocity. The molar ratio of excess O-3 to excess CO in the plume (Delta O-3/Delta CO) increased from -5.13 (+/- 1.13) x 10(-3) to 10.2 (+/- 2.16) x 10(-2) in similar to 4.5 h following smoke emission. Excess acetic and formic acid (normalized to excess CO) increased by factors of 1.73 +/- 0.43 and 7.34 +/- 3.03 (respectively) over the same time since emission. Based on the rapid decay of C2H4 we infer an in-plume average OH concentration of 5.27 (+/- 0.97) x 10(6) molec cm(-3), consistent with previous studies showing elevated OH concentrations in biomass burning plumes. Ammonium, nitrate, and sulfate all increased over the course of 4 h. The observed ammonium increase was a factor of 3.90 +/- 2.93 in about 4 h, but accounted for just similar to 36% of the gaseous ammonia lost on a molar basis. Some of the gas phase NH3 loss may have been due to condensation on, or formation of, particles below the AMS detection range. NOx was converted to PAN and particle nitrate with PAN production being about two times greater than production of observable nitrate in the first similar to 4 h following emission. The excess aerosol light scattering in the plume (normalized to excess CO2) increased by a factor of 2.50 +/- 0.74 over 4 h. The increase in light scattering was similar to that observed in an earlier study of a biomass burning plume in Mexico where significant secondary formation of OA closely tracked the increase in scattering. In the California plume, however, Delta OA/Delta CO2 decreased sharply for the first hour and then increased slowly with a net decrease of similar to 20% over 4 h. The fraction of thickly coated rBC particles increased up to similar to 85% over the 4 h aging period. Decreasing OA accompanied by increased scattering/particle coating in initial aging may be due to a combination of particle coagulation and evaporation processes. Recondensation of species initially evaporated from the particles may have contributed to the subsequent slow rise in OA. We compare our results to observations from other plume aging studies and suggest that differences in environmental factors such as smoke concentration, oxidant concentration, actinic flux, and RH contribute significantly to the variation in plume evolution observations

Investigating the links between ozone and organic aerosol chemistry in a biomass burning plume from a prescribed fire in California chaparral

Within minutes after emission, complex photochemistry in biomass burning smoke plumes can cause large changes in the concentrations of ozone (O_3) and organic aerosol (OA). Being able to understand and simulate this rapid chemical evolution under a wide variety of conditions is a critical part of forecasting the impact of these fires on air quality, atmospheric composition, and climate. Here we use version 2.1 of the Aerosol Simulation Program (ASP) to simulate the evolution of O_3 and secondary organic aerosol (SOA) within a young biomass burning smoke plume from the Williams prescribed fire in chaparral, which was sampled over California in November 2009. We demonstrate the use of a method for simultaneously accounting for the impact of the unidentified intermediate volatility, semi-volatile, and extremely low volatility organic compounds (here collectively called "SVOCs") on the formation of OA (using the Volatility Basis Set – VBS) and O_3 (using the concept of mechanistic reactivity). We show that this method can successfully simulate the observations of O_3, OA, NO_x, ethylene (C_2H_4), and OH to within measurement uncertainty using reasonable assumptions about the average chemistry of the unidentified SVOCs. These assumptions were (1) a reaction rate constant with OH of ~ 10^(-11) cm^3 s^(−1); (2) a significant fraction (up to ~ 50 %) of the RO_2 + NO reaction resulted in fragmentation, rather than functionalization, of the parent SVOC; (3) ~ 1.1 molecules of O_3 were formed for every molecule of SVOC that reacted; (4) ~ 60 % of the OH that reacted with the unidentified non-methane organic compounds (NMOC) was regenerated as HO_2; and (5) that ~ 50 % of the NO that reacted with the SVOC peroxy radicals was lost, presumably to organic nitrate formation. Additional evidence for the fragmentation pathway is provided by the observed rate of formation of acetic acid (CH_3COOH), which is consistent with our assumed fragmentation rate. However, the model overestimates peroxyacetyl nitrate (PAN) formation downwind by about 50 %, suggesting the need for further refinements to the chemistry. This method could provide a way for classifying different smoke plume observations in terms of the average chemistry of their SVOCs, and could be used to study how the chemistry of these compounds (and the O_3 and OA they form) varies between plumes