gebhart/patrepeval huggingface dataset:
Understanding CO<sub>2</sub> capture kinetics and energetics by ionic liquids with molecular dynamics simulation (2020)

Room temperature ionic liquids (ILs) are recognized to be potential media for CO<sub>2</sub> capture, but the interaction nature is less documented which hinders the future development of ILs with high CO<sub>2</sub> solvation capability. Here, through all atom molecular dynamics (MD) simulations, the solvation process of CO<sub>2</sub> with four representative ILs, [EMIM][BF<sub>4</sub>], [BMIM][BF<sub>4</sub>], [EMIM]CL and [BMIM]CL was systematically studied. Our data clearly reflect the fact that hydrophobic components from both cations and anions dominate CO<sub>2</sub> solvation because IL-CO<sub>2</sub> attraction is mainly driven by the van der Waals attractions. Consequently, cations with longer alkyl chain (for instance, [BMIM]<sup>+</sup> than [EMIM]<sup>+</sup>) and anions with higher hydrophobicity (for instance, [BF<sub>4</sub>]<sup>-</sup> than CL<sup>-</sup>) effectively enhance CO<sub>2</sub> solvation. For all the ILs under study, addition of water into ILs abates CO<sub>2</sub> solvation through regulating the anion-CO<sub>2</sub> interactions. Moreover, it is worth mentioning that ILs with a hydrophobic anion ([BF<sub>4</sub>]<sup>-</sup> in this study) are more resistant to the existence of water to capture CO<sub>2</sub> than ILs with a hydrophilic anion (Cl<sup>-</sup> in this study). Free energy decomposition analyses were conducted which support the above findings consistently. Generally, it is predicted that cations with long alkyl chain, anions with high hydrophobicity, and ILs with smaller surface tension are potentially effective CO<sub>2</sub> capturing media. Our present study helps the deep understanding of the CO<sub>2</sub> capturing mechanism by ILs and is expected to facilitate the future design and fabrication of a novel IL medium for gas capture and storage.
Design of arbitrarily shaped acoustic cloaks through PDE-constrained optimization satisfying sonic-metamaterial design requirements (2021)

We develop an optimization framework for the design of acoustic cloaks, with the aim of overcoming the limitations of usual transformation-based cloaks in terms of microstructure complexity and shape arbitrarity of the obstacle. This is achieved by recasting the acoustic cloaking design as a nonlinear optimal control problem constrained by a linear elliptic partial differential equation. In this setting, isotropic material properties' distributions realizing the cloak take the form of control functions and a system of first-order optimality conditions is derived accordingly. Such isotropic media can then be obtained in practice with simple hexagonal lattices of inclusions in water. For this reason, the optimization problem is directly formulated to take into account suitable partitions of the control domain Two types of inclusions are considered, and long-wavelength homogenization is used to define the feasible set of material properties that is employed as a constraint in the optimization problem. In this manner, we link the stage of material properties optimization with that of microstructure design, aiming at finding the optimal implementable solution. As a test benchmark, cloaking of the silhouette of a ship is considered, for various frequencies and directions of incidence. The resulting cloak is numerically tested via coupled structural/acoustic simulations.
The pair approach applied to kinetics in restricted geometries: strengths and weaknesses of the method (2003)

In the rapidly emerging field of nanotechnology, as well as in biology where chemical reaction phenomena take place in systems with characteristic length scales ranging from micrometer to the nanometer range, understanding of chemical kinetics in restricted geometries is of increasing interest. In particular, there is a need to develop more accurate theoretical methods. We used many-particle-density-function formalism (originally developed to study infinite systems) in its simplest form (pair approach) to study two-species A+B-&gt;0 reaction-diffusion model in a finite volume. For simplicity reasons, it is assumed that geometry of the system is one-dimensional (1d) and closed into the ring to avoid boundary effects. The two types of initial conditions are studied with (i) equal initial number of A and B particles N_{0,A}=N_{0,B} and (ii) initial number of particles is only equal in average =. In both cases it was assumed that in the initial state the particles are well mixed. It is found that particle concentration decays exponentially for both types of initial conditions. In the case of the type (ii) initial condition, the results of the pair-like analytical model agrees qualitatively with computer experiment (Monte Carlo simulation), while less agreement was obtained for the type (i) initial condition, and the reasons for such behavior are discussed.
Static resistivity image of a cubic saline phantom in magnetic resonance electrical impedance tomography (MREIT) (2003)

In magnetic resonance electrical impedance tomography (MREIT) we inject currents through electrodes placed on the surface of a subject and try to reconstruct cross-sectional resistivity (or conductivity) images using internal magnetic flux density as well as boundary voltage measurements. In this paper we present a static resistivity image of a cubic saline phantom (50 x 50 x 50 mm3) containing a cylindrical sausage object with an average resistivity value of 123.7 ohms cm. Our current MREIT system is based on an experimental 0.3 T MRI scanner and a current injection apparatus. We captured MR phase images of the phantom while injecting currents of 28 mA through two pairs of surface electrodes. We computed current density images from magnetic flux density images that are proportional to the MR phase images. From the current density images and boundary voltage data we reconstructed a cross-sectional resistivity image within a central region of 38.5 x 38.5 mm2 at the middle of the phantom using the J-substitution algorithm. The spatial resolution of the reconstructed image was 64 x 64 and the reconstructed average resistivity of the sausage was 117.7 ohms cm. Even though the error in the reconstructed average resistivity value was small, the relative L2-error of the reconstructed image was 25.5% due to the noise in measured MR phase images. We expect improvements in the accuracy by utilizing an MRI scanner with higher SNR and increasing the size of voxels scarifying the spatial resolution.
Characterization and simulation of cDNA microarray spots using a novel mathematical model (2007)

This study explains how various spot shapes can exist and suggests which parameters are to be adjusted for obtaining a good spot. This system is able to explore the cDNA microarray spotting process in a predictable, manageable and descriptive manner. We hope it can provide a way to predict the incidents that can occur during a real cDNA microarray experiment, and produce useful data for several research applications involving cDNA microarrays.
GASP -- A Genetic Algorithm for State Preparation (2023)

The efficient preparation of quantum states is an important step in the execution of many quantum algorithms. In the noisy intermediate-scale quantum (NISQ) computing era, this is a significant challenge given quantum resources are scarce and typically only low-depth quantum circuits can be implemented on physical devices. We present a genetic algorithm for state preparation (GASP) which generates relatively low-depth quantum circuits for initialising a quantum computer in a specified quantum state. The method uses a basis set of R_x, R_y, R_z, and CNOT gates and a genetic algorithm to systematically generate circuits to synthesize the target state to the required fidelity. GASP can produce more efficient circuits of a given accuracy with lower depth and gate counts than other methods. This variability of the required accuracy facilitates overall higher accuracy on implementation, as error accumulation in high-depth circuits can be avoided. We directly compare the method to the state initialisation technique based on an exact synthesis technique by implemented in IBM Qiskit simulated with noise and implemented on physical IBM Quantum devices. Results achieved by GASP outperform Qiskit's exact general circuit synthesis method on a variety of states such as Gaussian states and W-states, and consistently show the method reduces the number of gates required for the quantum circuits to generate these quantum states to the required accuracy.
Foreground prediction of volcanic-subvolcanic gas-liquid pyrite deposits in Anhui area along the Yangtze River (2011)

The Anhui area along the Yangtze River is an important locality of the pyrite in China,and the volcanic-subvolcanic gas-liquid pyrite is its main genetic type.Through summarizing the geological characteristics of the volcanic-subvolcanic gas-liquid pyrites and analyzing their pyrite-forming geological conditions,the research areas are divided into 246 statistic units with the grid of 5 km×5 km.First the multiple geological information(including stratum,rock mass,fault,etc) of 20 volcanic-subvolcanic gas-liquid pyrites is extracted,and then seven prediction variables are extracted according to the weight of metallogenic factors by the approach of characteristic analysis.Finally the possible location of the volcanic-subvolcanic gas-liquid pyrite is predicted.The perspective mineralization zones of three levels are obtained.The prediction results can provide a scientific basis for further volcanic-subvolcanic gas-liquid pyrite prospecting in Anhui area along the Yangtze River.
Varying spin state composition by the choice of capping ligand in a family of molecular chains: detailed analysis of magnetic properties of chromium(iii) horseshoes (2011)

We report a detailed physical analysis on a family of isolated, antiferro-magnetically (AF) coupled, chromium(III) finite chains, of general formula (Cr(RCO(2))(2)F)(n) where the chain length n = 6 or 7. Additionally, the chains are capped with a selection of possible terminating ligands, including hfac (= l,l,l,5,5,5-hexafluoropentane-2,4-dionate(l-)), acac (= pentane-2,4-dionate(l-)) or (F)(3). Measurements by inelastic neutron scattering (INS), magnetometery and electron paramagnetic resonance (EPR) spectroscopy have been used to study how the electronic properties are affected by n and capping ligand type. These comparisons allowed the subtle electronic effects the choice of capping ligand makes for odd member spin 3/2 ground state and even membered spin 0 ground state chains to be investigated. For this investigation full characterisation of physical properties have been performed with spin Hamiltonian parameterisation, including the determination of Heisenberg exchange coupling constants and single ion axial and rhombic anisotropy. We reveal how the quantum spin energy levels of odd or even membered chains can be modified by the type of capping ligand terminating the chain. Choice of capping ligands enables Cr-Cr exchange coupling to be adjusted by 0, 4 or 24%, relative to Cr-Cr exchange coupling within the body of the chain, by the substitution of hfac, acac or (F)(3) capping ligands to the ends of the chain, respectively. The manipulation of quantum spin levels via ligands which play no role in super-exchange, is of general interest to the practise of spin Hamilton modelling, where such second order effects are generally not considered of relevance to magnetic properties.
Photoinduced Divergent Deaminative Borylation and Hydrodeamination of Primary Aromatic Amines (2022)

We have developed the divergent deaminative borylation and hydrodeamination of primary aromatic amines using bis(pinacolato)diboron. These transformations can be switched by the reaction conditions. Mechanistic and computational studies have suggested that the cleavage of the C-N bond and the formation of C-B bond are unlikely to involve free aryl radical intermediates. However, hydrodeamination is shown to proceed via hydrogen atom transfer between the corresponding aryl radical and an ethereal solvent.
[High-resolution magnetic resonance imaging of pulmonary circulation; a prospect]. (1989)

A prospect on high-resolution magnetic resonance imaging of pulmonary circulation is presented, utilizing surface coils, ECG-gating, fast scan technique and breath-holding. A goal for MRI should be the blood-flow-related information, which can not be obtained by CT.
Absolute temperature measurements using a two-color QWIP focal plane array (2010)

The infrared photon flux emitted by an object depends not only on its temperature but also on a proportionality factor referred to as its emissivity. Since the latter parameter is usually not known quantitatively a priori, any temperature determination based on single-band radiometric measurements suffers from an inherent uncertainty. Recording photon fluxes in two separate spectral bands can in principle circumvent this limitation. The technique amounts to solving a system of two equations in two unknowns, namely, temperature and emissivity. The temperature derived in this manner can be considered absolute in the sense that it is independent of the emissivity, as long as that emissivity is the same in both bands. QmagiQ has previously developed a 320x256 midwave/longwave staring focal plane array which has been packaged into a dual-band laboratory camera. The camera in question constitutes a natural tool to generate simultaneous and independent emissivity maps and temperature maps of entire two-dimensional scenes, rather than at a single point on an object of interest. We describe a series of measurements we have performed on a variety of targets of different emissivities and temperatures. We examine various factors that affect the accuracy of the technique. They include the influence of the ambient radiation reflected off the target, which must be properly accounted for and subtracted from the collected signal in order to lead to the true target temperature. We also quantify the consequences of spectrally varying emissivities.
MOIRAI: a compact workflow system for CAGE analysis (2014)

The MOIRAI source code is freely available at http://sourceforge.net/projects/moirai/.
Alginate Polymerization and Modification Are Linked in Pseudomonas aeruginosa (2015)

This study provides new insights into the molecular mechanisms of the synthesis of the unique polysaccharide, alginate, which not only is an important virulence factor of the opportunistic human pathogen Pseudomonas aeruginosa but also has, due to its material properties, many applications in medicine and industry. Unraveling the assembly and composition of the alginate-synthesizing and envelope-spanning multiprotein complex will be of tremendous significance for the scientific community. We identified a protein-protein interaction network inside the multiprotein complex and studied its relevance with respect to alginate polymerization/modification as well as the c-di-GMP-mediated activation mechanism. A relationship between alginate polymerization and modification was shown. Due to the role of alginate in pathogenesis as well as its unique material properties harnessed in numerous applications, results obtained in this study will aid the design and development of inhibitory drugs as well as the commercial bacterial production of tailor-made alginates.
Large‐Area Graphene Nanodot Array for Plasmon‐Enhanced Infrared Spectroscopy (2016)

Graphene nanodot arrays (GNDAs) are fabricated by block copolymer lithography in a high-throughput manner. The GNDA shows strong broadband plasmonic resonances in the mid-IR region with high localized field enhancement, thus allowing plasmon-enhanced infrared spectroscopy with reliable sensitivity and selectivity to be performed.
Thermodynamics of the Inner Heliosheath (2022)

Abstract We derive annual sky maps of the proton temperature in the inner heliosheath (IHS), and track their temporal evolution over the years 2009–2016 of Interstellar Boundary Explorer observations. Other associated thermodynamic parameters also determined are the density, kappa (the parameter that characterizes kappa distributions), temperature rate, polytropic index, and entropy. We exploit the theory of kappa distributions and their connection with polytropes, to (i) express a new polytropic quantity Π that remains invariant along streamlines where temperature and density may vary, (ii) parameterize the proton flux in terms of the Π invariant and kappa, and (iii) derive the temperature and density, respectively, from the slope and intercept of the linear relationship between kappa and logarithm of Π. We find the following thermodynamic characteristics: (1) temperature sky maps and histograms shifted to their lowest values in 2012 and their highest in 2015; (2) temperature negatively correlated with density, reflecting the subisothermal polytropic behavior; (3) temperature positively correlated with kappa, revealing characteristics of the mechanism responsible for generating kappa distributions; (4) processes in IHS are subisothermal tending toward isobaric, consistent with previously published results; (5) linear relationship between kappa and polytropic indices, revealing characteristics of the particle potential energy; and (6) entropy positively correlated with polytropic index, aligned with the underlying theory that entropy increases toward the isothermal state where the kappa distribution reduces to the Maxwell–Boltzmann description.
Dark Matter Properties and the Structure of Galaxy Clusters (2003)

Laboratory experiments, large-scale computer simulations and observational cosmology have begun to make progress in the campaign to identify the particle responsible for gravitationally-inferred dark matter. We report results from an astrophysical program to measure dark matter particle properties. We use a sample of carefully-selected, highly-relaxed galaxy clusters to constrain the strength of dark matter self-interaction. We also report structural parameters for this cluster sample and discuss the implications for cold dark matter cosmology.
S1411 Acute Esophageal Necrosis in a 29-Year-Old Patient With ESRD (2020)

INTRODUCTION: Acute esophageal necrosis (AEN), or Gurvits Syndrome, is a rare disorder with an incidence of about 0.001-0.2% with males having a 4:1 predilection. It is diagnosed clinically with endoscopic visualization of sharply demarcated circumferential black necrotic tissue occurring in the distal 1/3rd of the esophagus; whilst sparing the GEJ. Patients with AEN often have other comorbidities; such as vascular compromise, ESRD, DKA, malignancy, and duodenal ulcers. In 90% of cases, initial presentation includes melena, coffee ground emesis or frank hematemesis. We present a case of AEN seen in a 29-year old male with ESRD; amongst other comorbidities. CASE DESCRIPTION/METHODS: Our patient is a 29-year-old African American male with a history of ESRD on HD, HTN, and poorly-controlled T2DM who presented for sepsis secondary to non-healing diabetic foot ulcer. Vitals were significant for T 100.9, P 100, BP 168/78. Labs were significant for wbc 31.49, Na 130, K 3.1, BUN 41, Cr 9.80, CRP 21. Patient was treated for presumed osteomyelitis. During hospitalization, patient underwent HD three times per weekly schedule. On day 6, 8, and 10, he became hypotensive during his HD sessions. On day 13, he was found unresponsive and hypotensive with large melenic stool. Upon stabilization, EGD showed black necrotic esophagus spanning the entire length until GEJ. Colonoscopy was unremarkable. Conservative management with NPO, IVF, pRBC and IV PPI was done. Repeat EGD two weeks later showed patchy areas of necrosis interspersed with exudate seen throughout the esophagus improved from prior EGD. He recovered remarkably well including tolerating an oral diet. DISCUSSION: Although the exact pathophysiology is unknown, a two hit hypothesis postulates the proposed mechanism for AEN formation. An initial event precipitates a lack of blood flow causing necrosis and vulnerability to insults that precipitate bleeding at the affected site. There is eventual reversal of necrosis with normalization of the tissue. Prognosis is poor and carries a high mortality rate from 15 to 35% and is dependent upon underlying disease. Some complications include esophageal perforation, stenosis and stricture, and mediastinitis. Management of AEN involves treating underlying disease along with supportive care. Although our patient was young, he had multiple comorbidities including ESRD, vascular compromise, DM and septic shock. This led to the development of ischemia and eventually necrosis especially in vulnerable areas of distal third of the esophagus.
Role of <i>Rhodobacter</i> sp. Strain PS9, a Purple Non-Sulfur Photosynthetic Bacterium Isolated from an Anaerobic Swine Waste Lagoon, in Odor Remediation (2003)

Temporal pigmentation changes resulting from the development of a purple color in anaerobic swine waste lagoons were investigated during a 4-year period. The major purple photosynthetic bacterium responsible for these color changes and the corresponding reductions in odor was isolated from nine photosynthetic lagoons. By using morphological, physiological, and phylogenetic characterization methods we identified the predominant photosynthetic bacterium as a new strain of Rhodobacter, designated Rhodobacter sp. strain PS9. Rhodobacter sp. strain PS9 is capable of photoorganotrophic growth on a variety of organic compounds, including all of the characteristic volatile organic compounds (VOC) responsible for the odor associated with swine production facilities (J. A. Zahn, A. A. DiSpirito, Y. S. Do, B. E. Brooks, E. E. Copper, and J. L. Hatfield, J. Environ. Qual. 30:624-634, 2001). The seasonal variations in airborne VOC emitted from waste lagoons showed that there was a 80 to 93% decrease in the concentration of VOC during a photosynthetic bloom. During the height of a bloom, the Rhodobacter sp. strain PS9 population accounted for 10% of the total community and up to 27% of the eubacterial community based on 16S ribosomal DNA signals. Additional observations based on seasonal variations in meteorological, biological, and chemical parameters suggested that the photosynthetic blooms of Rhodobacter sp. strain PS9 were correlated with lagoon water temperature and with the concentrations of sulfate and phosphate. In addition, the photosynthetic blooms of Rhodobacter sp. strain PS9 were inversely correlated with the concentrations of protein and fluoride.