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A widely used adsorption energy scaling relation between OH* and OOH* intermediates in the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER), has previously been determined using density functional theory and shown to dictate a minimum thermodynamic overpotential for both reactions. Here, we show that the oxygen–oxygen bond in the OOH* intermediate is, however, not well described with the previously used class of exchange-correlation functionals. By quantifying and correcting the systematic error, an improved description of gaseous peroxide species versus experimental data and a reduction in calculational uncertainty is obtained. For adsorbates, we find that the systematic error largely cancels the vdW interaction missing in the original determination of the scaling relation. An improved scaling relation, which is fully independent of the applied exchange–correlation functional, is obtained and found to differ by 0.1 eV from the original. Lastly, this largely confirms that, although obtained with a method suffering from systematic errors, the previously obtained scaling relation is applicable for predictions of catalytic activity.
Computational investigations of heterogeneously catalyzed reactions using density functional theory (DFT) are often inaccurate, largely due to uncertainties in the choice of DFT functional (enthalpic uncertainty) and approximations for modeling adsorbate movement along the catalyst surface (entropic uncertainty). This work illustrates that both uncertainties are significant in the investigation of ethane dehydrogenation (EDH) and hydrogenolysis on Pt catalysts by considering the complete deconstruction of ethane on Pt(111), Pt(211), and Pt(100) using microkinetic modeling (MKM). Hence, this work uses both noncalibrated and Bayesian-calibrated MKMs to quantify and correct inaccuracies in macroscopic properties due to both uncertainties. A Bayesian approach to the correction of entropic errors was introduced using a “Modified Fermi Function (MFF)” to calibrate between the two bounds of entropy represented by the harmonic oscillator (HO) and free translator (FT) approximations. Regardless of enthalpic and entropic uncertainties, all three surfaces are capable of ethane activation; however, Pt(211) was found to be the most active and is largely responsible for methane production. Next, Pt(111) is largely responsible for acetylene production, and Pt(100) has the highest ethylene selectivity but is most susceptible to coking. By comparison of different calibrated models, the FT entropy approximation was found to better describe EDH under typical experimental conditions. Statistical evidence was found to support Pt(111) as the active site for EDH, assuming that one single site is responsible for the chemistry. On the three surfaces, competing second dehydrogenations to CH 2 CH 2 and CH 3 CH were observed as well as isomerization of CH 3 CH back to CH 2 CH 2 and deeper dehydrogenation of CH 3 CH. In conclusion, C–C cleavage was found to largely proceed via the CH 3 C intermediate on Pt(100) and Pt(111), while on Pt(211), it was via both CHC and CH 3 C.
We recently outlined an efficient multi-tiered parallel ab initio excitonic framework that utilizes time dependent density functional theory (TDDFT) to calculate ground and excited state energies and gradients of large supramolecular complexes in atomistic detail – enabling us to undertake non-adiabatic simulations which explicitly account for the coupled anharmonic vibrational motion of all the constituent atoms in a supramolecular system. Here we apply that framework to the 27 coupled bacterio-chlorophyll-a chromophores which make up the LH2 complex, using it to compute an on-the-fly nonadiabatic surface-hopping (SH) trajectory of electronically excited LH2. Part one of this article is focussed on calibrating our ab initio exciton Hamiltonian using two key parameters: a shift δ, which corrects for the error in TDDFT vertical excitation energies; and an effective dielectric constant ε, which describes the average screening of the transition-dipole coupling between chromophores. Using snapshots obtained from equilibrium molecular dynamics simulations (MD) of LH2, we tune the values of both δ and ε through fitting to the thermally broadened experimental absorption spectrum, giving a linear absorption spectrum that agrees reasonably well with experiment. In part two of this article, we construct a time-resolved picture of the coupled vibrational and excitation energy transfer (EET) dynamics in the sub-picosecond regime following photo-excitation. Assuming Franck–Condon excitation of a narrow eigenstate band centred at 800 nm, we use surface hopping to follow a single nonadiabatic dynamics trajectory within the full eigenstate manifold. Consistent with experimental data, this trajectory gives timescales for B800→B850 population transfer (τ B800→B850 ) between 650–1050 fs, and B800 population decay (τ 800→ ) between 10–50 fs. The dynamical picture that emerges is one of rapidly fluctuating LH2 eigenstates that are delocalized over multiple chromophores and undergo frequent crossing on a femtosecond timescale as a result of the atomic vibrations of the constituent chromophores. The eigenstate fluctuations arise from disorder that is driven by vibrational dynamics with multiple characteristic timescales. The scalability of our ab initio excitonic computational framework across massively parallel architectures opens up the possibility of addressing a wide range of questions, including how specific dynamical motions impact both the pathways and efficiency of electronic energy-transfer within large supramolecular systems.
Single ion solvation free energies are one of the most important properties of electrolyte solutions and yet there is ongoing debate about what these values are. Only the values for neutral ion pairs are known. Here, we use DFT interaction potentials with molecular dynamics simulation (DFT-MD) combined with a modified version of the quasi-chemical theory (QCT) to calculate these energies for the lithium and fluoride ions. A method to correct for the error in the DFT functional is developed and very good agreement with the experimental value for the lithium fluoride pair is obtained. Moreover, this method partitions the energies into physically intuitive terms such as surface potential, cavity and charging energies which are amenable to descriptions with reduced models. Here, our research suggests that lithium's solvation free energy is dominated by the free energetics of a charged hard sphere, whereas fluoride exhibits significant quantum mechanical behavior that cannot be simply described with a reduced model.
We have developed a high-pressure vessel and a cell for x-ray Compton scattering measurements of fluid alkali metals. Measurements have been successfully carried out for alkali metal rubidium at elevated temperatures and pressures using synchrotron radiation at SPring-8. The width of Compton profiles (CPs) of fluid rubidium becomes narrow with decreasing fluid density, which indicates that the CPs sensitively detect the effect of reduction in the valence electron density. At the request of all authors of the paper, and with the agreement of the Proceedings Editor, an updated version of this article was published on 10 September 2015. The original article supplied to AIP Publishing was not the final version and contained PDF conversion errors in Formulas (1) and (2). The errors have been corrected in the updated and re-published article.
RAON (Rare isotope Accelerator Of Newness) heavy ion accelerator of the rare isotope science project in Daejeon, Korea, has been designed to accelerate multiple-charge-state beams to be used for various science programs. In the RAON accelerator, the rare isotope beams which are generated by an isotope separation on-line system with a wide range of nuclei and charges will be transported through the post Low Energy Beam Transport (LEBT) section to the Radio Frequency Quadrupole (RFQ). In order to transport many kinds of rare isotope beams stably to the RFQ, the post LEBT should be devised to satisfy the requirement of the RFQ at the end of post LEBT, simultaneously with the twiss parameters small. We will present the recent lattice design of the post LEBT in the RAON accelerator and the results of the beam dynamics simulations from it. In addition, the error analysis and correction in the post LEBT will be also described.
InAs{sub x}P{sub 1-x}/InP quantum wells grown using metal organic vapor phase epitaxy are investigated for infrared detector applications. The structural parameters of the QWs are evaluated from high resolution x-ray diffraction. The electronic transition energies measured from surface photo voltage and photoconductivity confirms that these QWs can be used for fabricating IR detectors in the wide wavelength range, i.e. 0.9–1.46 µm by inter-band transitions and 7–18 µm by inter-sub-band transitions. Subsequently the functionality of one such fabricated InAs{sub x}P{sub 1-x}/InPQW detector is verified by measuring the photoluminescence of suitable semiconductor quantum well structure. At the request of all authors of the paper, and with the agreement of the Proceedings Editor, an updated version of this article was published on 24 June 2016. The original version supplied to AIP Publishing contained an error in the Figures 1 and 2 where the right side of the images were cutoff. The error has been corrected in the updated and re-published article.
Information on the lattice parameter of single crystals with known crystallographic structure allows for estimations of sample quality and composition. In many cases it is sufficient to determine one lattice parameter or the lattice spacing along a certain, high- symmetry direction, e.g. in order to determine the composition in a substitution series by taking advantage of Vegard’s rule. Here we present a guide to accurate measurements of single crystals with dimensions ranging from 200 μm up to several millimeter using a standard powder diffractometer in Bragg-Brentano geometry. The correction of the error introduced by the sample height and the optimization of the alignment are discussed in detail. Finally, in particular for single crystals with a plate-like habit, the described procedure allows for measurement of the lattice spacings normal to the plates with high accuracy on a timescale of minutes.
Due to an error in production, the error margins of many values were incorrectly published. Table 1 details the locations of the errors and their corrections.
Focal plane wave front sensing and control is a critical approach to reducing noncommon path errors between a conventional astronomical adaptive optics (AO) wave front sensor (WFS) detector and a science camera. However, in addition to mitigating noncommon path errors, recent focal plane wave front sensing techniques have been developed to operate at speeds fast enough to enable "multi-WFS" AO, where residual atmospheric errors are further corrected by a focal plane WFS. Although a number of such techniques have been recently developed for coronagraphic imaging, here we present one designed for noncoronagraphic imaging. Utilizing conventional AO system components, this concept additionally requires (1) a detector imaging the focal plane of the WFS light source and (2) a pupil plane optical chopper device that is the noncommon path to the first WFS and is synchronized to the focal plane imager readout. These minimal hardware requirements enable the temporal amplitude modulation to resolve the sine ambiguity of even wave-front modes for low, mid, and high wave front spatial frequencies. Similar capabilities have been demonstrated with classical phase diversity by defocusing the detector, but such techniques are incompatible with simultaneous science observations. This optical chopping technique, however, enables science imaging at up to 50% duty cycle. In conclusion, we present both simulations and laboratory validation of this concept on SEAL, the Santa Cruz Extreme AO Laboratory testbed.
Nucleic Acids Research, 46(13):6455–6469, https://doi.org/10.1093/nar/gky444. There was a typographical error on page 6458, column 1, line 12 and on page 6459, column 2, line 53. In both instances, dNTP concentrations should be listed as ‘5, 10, 25, 50, 100, 150, 250, 500 μM’. The same error has been corrected in the labels of Supplementary Figure S2. These typos do not affect the kinetics parameters listed in Table 2 and do not influence the results and conclusions of the article. The article and supplementary file have been updated.
Here, we study analytic solutions to the Bardeen-Cooper-Schrieffer (BCS) gap equation for isotropic superconductors with finite-range interaction potentials over the full range of temperatures from absolute zero to the superconducting critical temperature 0 ≤ T ≤ T c . Using these solutions Δ (ε,T), we provide a proof of the universality of the temperature dependence of the BCS gap ratio at the Fermi level Δ (ε = 0,T)/T c . Moreover, by examining the behavior of this ratio as a function of energy ε, we find that nonuniversal features emerge away from the Fermi level, and these features take the form of a temperature-independent multiplicative factor F(ε), which is equal to Δ (ε,T)/Δ(ε = 0,T) up to exponentially small corrections, i.e., the error terms vanish like e -1/λ in the weak-coupling limit λ → 0. We discuss the model-dependent features of both F(ε) and T c , and we illustrate their behavior focusing on several concrete examples of physically relevant finite-range potentials. Comparing these cases for fixed coupling constants, we highlight the importance of the functional form of the interaction potential in determining the size of the critical temperature and provide guidelines for choosing potentials which lead to higher values of T c . We also propose experimental signatures which could be used to probe the energy dependence of the gap and potentially shed light on the underlying mechanisms giving rise to superconductivity.
The study by Michels-Clark et al. (2013 [Michels-Clark, T. M., Lynch, V. E., Hoffmann, C. M., Hauser, J., Weber, T., Harrison, R. & Bürgi, H. B. (2013). J. Appl. Cryst. 46, 1616-1625.]) contains misleading errors which are corrected here. The numerical results reported in that paper and the conclusions given there are not affected and remain unchanged. The transition probabilities in Table 1 (rows 4, 5, 7, 8) and Fig. 2 (rows 1 and 2) of the original paper were different from those used in the numerical calculations. Corrected transition probabilities as used in the computations are given in Table 1 and Fig. 1 of this article. The Δ parameter in the stacking model expresses the preference for the fifth layer in a five-layer stack to be eclipsed with respect to the first layer. This statement corrects the original text on p. 1622, lines 4–7. In the original Fig. 2 the helicity of the layer stacks b L and b R in rows 3 and 4 had been given as opposite to those in rows 1, 2 and 5. Fig. 1 of this article shows rows 3 and 4 corrected to correspond to rows 1, 2 and 5.
In this work. we extend a canonical-thermodynamic method for computing intrinsic point defect concentrations as a function of chemical stoichiometry and temperature to include extrinsic defect contributions, while applying this method to study defects in CuInSe 2 . This technique relies on a large set of defect formation energies calculated from first principles, which require corrections for known errors arising from spurious interactions. Guided by recent experimental work exhibiting the complex interplay between Na, K, and Cd incorporation, we examine the behavior of dominant defects as the material composition varies under experimentally relevant conditions. In addition to identifying the regions of composition-parameter space relevant to the incorporation of impurities Na, K, and Cd, and stable against the formation of secondary compounds, we further study defect kinetics susceptible to the presence of these impurities. From this analysis, we propose a simple model for the enhanced diffusion of Cu-vacancies mediated by K, which could lead to the enhanced incorporation of Cd observed experimentally.
Purpose: Single-isocenter (SI) volumetric modulated arc therapy has been shown to be an effective and efficient approach to multiple metastasis radiosurgery. However, certain extreme cases raise the question of whether multiple-isocenter (MI) approaches can still generate superior plans. In this study, we ask this question with respect to a clinical case with two very widely separated lesions. Methods: A patient with two widely separated (d = 12cm) tumors was treated with SI-VMAT SRS using 10MV flattening filter free (FFF) beam with high-definition multi-leaf collimator (HD-MLC, 2.5/5mm) in two non-coplanar arcs using concentric rings to enforce steep gradient. Because of lesion positioning with respect to collimator angle selection, lesions were treated by 5mm leaves. We re-planned the case with a congruent arc arrangement but separate isocenter for each lesion. In this manner, lesions were treated by 2.5mm leaves. Conformity index (CI), V50%, and mean brain dose were compared. Results: Neither conformity (CI-SI = 1.12, CI-MI = 1.08) nor V50% (V50%-SI =8.82cc, V50%-MI =8.81cc) were improved by utilizing a separate isocenter for each lesion. Mean brain dose was slightly reduced (dmean-SI = 118.4 cGy, dmean-MI = 88.7 cGy) by using multiple isocenters. Conclusion: For this case with a lesion at the apex of the brain and another distantly located at the base of skull, employing a separate isocenter for each target did not meaningfully improve plan quality. Single-isocenter VMAT has been shown feasible and equivalent to multiple-isocenter VMAT for multiple metastasis cases in general. In this extreme case, single- and multiple- isocenter VMAT were also equivalent. If rotational setup errors are appropriately corrected, the increased delivery efficiency of the single-isocenter approach renders it preferable to the multiple isocenter approach. Dr’s Thomas, Popple, and Fiveash have all received honoraria from Varian Medical Systems for discussing their experiences with stereotactic radiosurgery.
Purpose: The conversion from Hounsfield units (HU) to stopping powers is a major source of range uncertainty in proton therapy (PT). Our contribution shows how proton radiographs (PR) acquired with a multi-layer ionization chamber in a PT center can be used for accurate patient positioning and subsequently for patient-specific optimization of the conversion from HU to stopping powers. Methods: A multi-layer ionization chamber was used to measure the integral depth-dose (IDD) of 220 MeV pencil beam spots passing through several anthropomorphic phantoms. The whole area of interest was imaged by repositioning the couch and by acquiring a 45×45 mm{sup 2} frame for each position. A rigid registration algorithm was implemented to correct the positioning error between the proton radiographs and the planning CT. After registration, the stopping power map obtained from the planning CT with the calibration curve of the treatment planning system was used together with the water equivalent thickness gained from two proton radiographs to generate a phantom-specific stopping power map. Results: Our results show that it is possible to make a registration with submillimeter accuracy from proton radiography obtained by sending beamlets separated by more than 1 mm. This was made possible by the complex shape of the IDD due to the presence of lateral heterogeneities along the path of the beam. Submillimeter positioning was still possible with a 5 mm spot spacing. Phantom specific stopping power maps obtained by minimizing the range error were cross-verified by the acquisition of an additional proton radiography where the phantom was positioned in a random but known manner. Conclusion: Our results indicate that a CT-PR registration algorithm together with range-error based optimization can be used to produce a patient-specific stopping power map. Sylvain Deffet reports financial funding of its PhD thesis by Ion Beam Applications (IBA) during the confines of the study and outside the submitted work. Francois Vander Stappen reports being employed by Ion Beam Applications (IBA) during the confines of the study and outside the submitted work.
The errors and associated corrections described in this document concerning the original manuscript were accountable to the production department handling this manuscript, and thus are no fault of the authors of this paper. Additionally, the online manuscript has now been updated with these corrections accordingly. In the original publication of this article, the title was displayed incorrectly as "Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134T, a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia". The genus name "Thermithiobacillus" was misspelt as "Thermithiobaclillus". This has now been corrected in the original article.