208 research outputs found
A systematic benchmark of the ab initio Bethe-Salpeter equation approach for low-lying optical excitations of small organic molecules
The predictive power of the ab initio Bethe-Salpeter equation (BSE) approach,
rigorously based on many-body Green's function theory but incorporating
information from density functional theory, has already been demonstrated for
the optical gaps and spectra of solid-state systems. Interest in photoactive
hybrid organic/inorganic systems has recently increased, and so has the use of
the BSE for computing neutral excitations of organic molecules. However, no
systematic benchmarks of the BSE for neutral electronic excitations of organic
molecules exist. Here, we study the performance of the BSE for the 28 small
molecules in Thiel's widely-used time-dependent density functional theory
benchmark set [M. Schreiber et al. J. Chem. Phys. 128, 134110 (2008)]. We
observe that the BSE produces results that depend critically on the mean-field
starting point employed in the perturbative approach. We find that this
starting point dependence is mainly introduced through the quasiparticle
energies obtained at the intermediate GW step, and that with a judicious choice
of starting mean-field, singlet excitation energies obtained from BSE are in
excellent quantitative agreement with higher-level wavefunction methods. The
quality of the triplet excitations is slightly less satisfactory
Effects of polarization on the band-structure of delafossite transparent conductive oxides
We use hybrid functionals and restricted self-consistent GW, state-of-the-art
theoretical approaches for quasiparticle band structures, to study the
electronic states of delafossite Cu(Al,In)O, the first p-type and bipolar
transparent conductive oxides. We show that self-consistent GW gives remarkably
wider band gaps than all the other approaches used so far. Accounting for
polaronic effects in the GW scheme we recover a very nice agreement with
experiments. Furthermore, the modifications with respect to the Kohn-Sham bands
are strongly k-dependent, which makes questionable the common practice of using
a scissor operator. Finally, our results support the view that the low energy
structures found in optical experiments, and initially attributed to an
indirect transition, are due to intrinsic defects in the samples.Comment: publishe
The XIIIth Banff Conference on Allograft Pathology: The Banff 2015 Heart Meeting Report: Improving Antibody-Mediated Rejection Diagnostics: Strengths, Unmet Needs, and Future Directions.
The 13th Banff Conference on Allograft Pathology was held in Vancouver, British Columbia, Canada from October 5 to 10, 2015. The cardiac session was devoted to current diagnostic issues in heart transplantation with a focus on antibody-mediated rejection (AMR) and small vessel arteriopathy. Specific topics included the strengths and limitations of the current rejection grading system, the central role of microvascular injury in AMR and approaches to semiquantitative assessment of histopathologic and immunophenotypic indicators, the role of AMR in the development of cardiac allograft vasculopathy, the important role of serologic antibody detection in the management of transplant recipients, and the potential application of new molecular approaches to the elucidation of the pathophysiology of AMR and potential for improving the current diagnostic system. Herein we summarize the key points from the presentations, the comprehensive, open and wide-ranging multidisciplinary discussion that was generated, and considerations for future endeavors
Mapping Myocardial Fiber Orientation Using Echocardiography-Based Shear Wave Imaging
The assessment of disrupted myocardial fiber arrangement may help to understand and diagnose hypertrophic or ischemic cardiomyopathy. We hereby proposed and developed shear wave imaging (SWI), which is an echocardiography-based, noninvasive, real-time, and easy-to-use technique, to map myofiber orientation. Five in vitro porcine and three in vivo open-chest ovine hearts were studied. Known in physics, shear wave propagates faster along than across the fiber direction. SWI is a technique that can generate shear waves travelling in different directions with respect to each myocardial layer. SWI further analyzed the shear wave velocity across the entire left-ventricular (LV) myocardial thickness, ranging between 10 (diastole) and 25 mm (systole), with a resolution of 0.2 mm in the middle segment of the LV anterior wall region. The fiber angle at each myocardial layer was thus estimated by finding the maximum shear wave speed. In the in vitro porcine myocardium (n=5), the SWI-estimated fiber angles gradually changed from +80° ± 7° (endocardium) to +30° ± 13° (midwall) and-40° ± 10° (epicardium) with 0° aligning with the circumference of the heart. This transmural fiber orientation was well correlated with histology findings (r2=0.91± 0.02, p<0.0001). SWI further succeeded in mapping the transmural fiber orientation in three beating ovine hearts in vivo. At midsystole, the average fiber orientation exhibited 71° ± 13° (endocardium), 27° ± 8° (midwall), and-26° ± 30° (epicardium). We demonstrated the capability of SWI in mapping myocardial fiber orientation in vitro and in vivo. SWI may serve as a new tool for the noninvasive characterization of myocardial fiber structure. © 2012 IEEE.published_or_final_versio
Assessment of the interplay between blood and skin vascular abnormalities in adult purpura fulminans
RATIONALE: Purpura fulminans in adults is a rare but devastating disease. Its pathophysiology is not well known. OBJECTIVES: To understand the pathophysiology of skin lesions in purpura fulminans, the interplay between circulating blood and vascular alterations was assessed. METHODS: Prospective multicenter study in four intensive care units. Patients with severe sepsis without skin lesions were recruited as control subjects. MEASUREMENTS AND MAIN RESULTS: Twenty patients with severe sepsis and purpura fulminans were recruited for blood sampling, and skin biopsy was performed in deceased patients. High severity of disease and mortality rates (80%) was observed. Skin biopsies in purpura fulminans lesions revealed thrombosis and extensive vascular damage: vascular congestion and dilation, endothelial necrosis, alteration of markers of endothelial integrity (CD31) and of the protein C pathway receptors (endothelial protein C receptor, thrombomodulin). Elevated plasminogen activating inhibitor-1 mRNA was also observed. Comparison with control patients showed that these lesions were specific to purpura fulminans. By contrast, no difference was observed for blood hemostasis parameters, including soluble thrombomodulin, activated protein C, and disseminated intravascular coagulation markers. Bacterial presence at the vascular wall was observed specifically in areas of vascular damage in eight of nine patients tested (including patients with Streptococcus pneumoniae, Neisseria meningitidis, Escherichia coli, and Pseudomonas aeruginosa infection). CONCLUSIONS: Thrombi and extensive vascular damage with multifaceted prothrombotic local imbalance are characteristics of purpura fulminans. A "vascular wall infection" hypothesis, responsible for endothelial damage and subsequent skin lesions, can be put forward
Colored-noise thermostats \`a la carte
Recently, we have shown how a colored-noise Langevin equation can be used in
the context of molecular dynamics as a tool to obtain dynamical trajectories
whose properties are tailored to display desired sampling features. In the
present paper, after having reviewed some analytical results for the stochastic
differential equations forming the basis of our approach, we describe in detail
the implementation of the generalized Langevin equation thermostat and the
fitting procedure used to obtain optimal parameters. We discuss in detail the
simulation of nuclear quantum effects, and demonstrate that, by carefully
choosing parameters, one can successfully model strongly anharmonic solids such
as neon. For the reader's convenience, a library of thermostat parameters and
some demonstrative code can be downloaded from an on-line repository
Quasiparticle interfacial level alignment of highly hybridized frontier levels: HO on TiO(110)
Knowledge of the frontier levels' alignment prior to photo-irradiation is
necessary to achieve a complete quantitative description of HO
photocatalysis on TiO(110). Although HO on rutile TiO(110) has been
thoroughly studied both experimentally and theoretically, a quantitative value
for the energy of the highest HO occupied levels is still lacking. For
experiment, this is due to the HO levels being obscured by hybridization
with TiO(110) levels in the difference spectra obtained via ultraviolet
photoemission spectroscopy (UPS). For theory, this is due to inherent
difficulties in properly describing many-body effects at the
HO-TiO(110) interface. Using the projected density of states (DOS) from
state-of-the-art quasiparticle (QP) , we disentangle the adsorbate and
surface contributions to the complex UPS spectra of HO on TiO(110). We
perform this separation as a function of HO coverage and dissociation on
stoichiometric and reduced surfaces. Due to hybridization with the TiO(110)
surface, the HO 3a and 1b levels are broadened into several peaks
between 5 and 1 eV below the TiO(110) valence band maximum (VBM). These
peaks have both intermolecular and interfacial bonding and antibonding
character. We find the highest occupied levels of HO adsorbed intact and
dissociated on stoichiometric TiO(110) are 1.1 and 0.9 eV below the VBM. We
also find a similar energy of 1.1 eV for the highest occupied levels of HO
when adsorbed dissociatively on a bridging O vacancy of the reduced surface. In
both cases, these energies are significantly higher (by 0.6 to 2.6 eV) than
those estimated from UPS difference spectra, which are inconclusive in this
energy region. Finally, we apply self-consistent QP (scQP1) to obtain
the ionization potential of the HO-TiO(110) interface.Comment: 12 pages, 12 figures, 1 tabl
Angiotensin-(1-7) and angiotensin-(1-9): function in cardiac and vascular remodeling
The renin angiotensin system (RAS) is integral to cardiovascular physiology, however, dysregulation of this system largely contributes to the pathophysiology of cardiovascular disease (CVD). It is well established that angiotensin II (Ang II), the main effector of the RAS, engages the angiotensin type 1 receptor and promotes cell growth, proliferation, migration and oxidative stress, all processes which contribute to remodeling of the heart and vasculature, ultimately leading to the development and progression of various CVDs including heart failure and atherosclerosis. The counter-regulatory axis of the RAS, which is centered on the actions of angiotensin converting enzyme 2 (ACE2) and the resultant production of angiotensin-(1-7) (Ang-(1-7) from Ang II, antagonizes the actions of Ang II via the receptor Mas, thereby providing a protective role in CVD. More recently, another ACE2 metabolite, Ang-(1-9), has been reported to be a biologically active peptide within the counter-regulatory axis of the RAS. This review will discuss the role of the counter-regulatory RAS peptides, Ang-(1-7) and Ang-(1-9) in the cardiovascular system, with a focus on their effects in remodeling of the heart and vasculature
Electronic Structure Calculation by First Principles for Strongly Correlated Electron Systems
Recent trends of ab initio studies and progress in methodologies for
electronic structure calculations of strongly correlated electron systems are
discussed. The interest for developing efficient methods is motivated by recent
discoveries and characterizations of strongly correlated electron materials and
by requirements for understanding mechanisms of intriguing phenomena beyond a
single-particle picture. A three-stage scheme is developed as renormalized
multi-scale solvers (RMS) utilizing the hierarchical electronic structure in
the energy space. It provides us with an ab initio downfolding of the global
band structure into low-energy effective models followed by low-energy solvers
for the models. The RMS method is illustrated with examples of several
materials. In particular, we overview cases such as dynamics of semiconductors,
transition metals and its compounds including iron-based superconductors and
perovskite oxides, as well as organic conductors of kappa-ET type.Comment: 44 pages including 38 figures, to appear in J. Phys. Soc. Jpn. as an
invited review pape
BerkeleyGW: A Massively Parallel Computer Package for the Calculation of the Quasiparticle and Optical Properties of Materials and Nanostructures
BerkeleyGW is a massively parallel computational package for electron
excited-state properties that is based on the many-body perturbation theory
employing the ab initio GW and GW plus Bethe-Salpeter equation methodology. It
can be used in conjunction with many density-functional theory codes for
ground-state properties, including PARATEC, PARSEC, Quantum ESPRESSO, OCTOPUS
and SIESTA. The package can be used to compute the electronic and optical
properties of a wide variety of material systems from bulk semiconductors and
metals to nanostructured materials and molecules. The package scales to
10,000's of CPUs and can be used to study systems containing up to 100's of
atoms
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