Air pollution control with semi-infinite programming

Environment issues are more than ever important in a modern society. Complying with stricter legal thresholds on pollution emissions raises an important economic issue. This paper presents some ideas in the use of optimization tools to help in the planning and control of stationary pollution sources. Three main semi-infinite programming approaches are described. The first consists in optimizing an objective function while the pollution level in a given region is kept bellow a given threshold. In the second approach the maximum pollution level in a given region is computed and in the third an air pollution abatement problem is considered. These formulations allow to obtain the best control parameters and the maxima pollution positions, where the sampling stations should be placed. A specific modeling language was used to code four academic problems. Numerical results computed with a semi-infinite programming solver are shown

Lifetimes of Confined Acoustic Phonons in Ultra-Thin Silicon Membranes

We study the relaxation of coherent acoustic phonon modes with frequencies up to 500 GHz in ultra-thin free-standing silicon membranes. Using an ultrafast pump-probe technique of asynchronous optical sampling, we observe that the decay time of the first-order dilatational mode decreases significantly from \sim 4.7 ns to 5 ps with decreasing membrane thickness from \sim 194 to 8 nm. The experimental results are compared with theories considering both intrinsic phonon-phonon interactions and extrinsic surface roughness scattering including a wavelength-dependent specularity. Our results provide insight to understand some of the limits of nanomechanical resonators and thermal transport in nanostructures

Primary stability of a press-fit cup in combination with impaction grafting in an acetabular defect model

The objectives of this study were to (a) assess primary stability of a press-fit cup in a simplified acetabular defect model, filled with compacted cancellous bone chips, and (b) to compare the results with primary stability of a press-fit cup combined with two different types of bone graft substitute in the same defect model. A previously developed acetabular test model made of polyurethane foam was used, in which a mainly medial contained defect was implemented. Three test groups (N = 6 each) were prepared: Cancellous bone chips (bone chips), tricalciumphosphate tetrapods + collagen matrix (tetrapods + coll), bioactive glass S53P4 + polyethylene glycol-glycerol matrix (b.a.glass + PEG). Each material was compacted into the acetabulum and a press-fit cup was implanted. The specimens were loaded dynamically in the direction of the maximum resultant force during level walking. Relative motion between cup and test model was assessed with an optical measurement system. At the last load step (3000 N), inducible displacement was highest for bone chips with median [25th percentile; 75th percentile] value of 113 [110; 114] µm and lowest for b.a.glass + PEG with 91 [89; 93] µm. Migration at this load step was highest for b.a.glass + PEG with 868 [845; 936] µm and lowest for tetrapods + coll with 491 [487; 497] µm. The results show a comparable behavior under load of tetrapods + coll and bone chips and suggest that tetrapods + coll could be an attractive alternative to bone chips. However, so far, this was found for one specific defect type and primary stability should be further investigated in additional/more severe defects

Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol.

Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from 13CO2 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived 13C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. 13C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 13C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 13C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities

Electronic interactions in fullerene spheres

The electron-phonon and Coulomb interactions inC$_{60}$, and larger fullerene spheres are analyzed. The coupling between electrons and intramolecular vibrations give corrections $\sim 1 - 10$ meV to the electronic energies for C$_{60}$, and scales as $R^{-4}$ in larger molecules. The energies associated with electrostatic interactions are of order $\sim 1 - 4$ eV, in C$_{60}$ and scale as $R^{-1}$. Charged fullerenes show enhanced electron-phonon coupling, $\sim 10$ meV, which scales as $R^{-2}$. Finally, it is argued that non only C$_{60}^{-}$, but also C$_{60}^{--}$ are highly polarizable molecules. The polarizabilities scale as $R^3$ and $R^4$, respectively. The role of this large polarizability in mediating intermolecular interactions is also discussed.Comment: 12 pages. No figure

A high-throughput \u3ci\u3ede novo\u3c/i\u3e sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

Abstract Background High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms. Results In this study, a new de novo sequencing algorithm, called Vonode, has been developed specifically for analysis of such high-resolution tandem mass spectra. To fully exploit the high mass accuracy of these spectra, a unique scoring system is proposed to evaluate sequence tags based primarily on mass accuracy information of fragment ions. Consensus sequence tags were inferred for 11,422 spectra with an average peptide length of 5.5 residues from a total of 40,297 input spectra acquired in a 24-hour proteomics measurement of Rhodopseudomonas palustris. The accuracy of inferred consensus sequence tags was 84%. According to our comparison, the performance of Vonode was shown to be superior to the PepNovo v2.0 algorithm, in terms of the number of de novo sequenced spectra and the sequencing accuracy. Conclusions Here, we improved de novo sequencing performance by developing a new algorithm specifically for high-resolution tandem mass spectral data. The Vonode algorithm is freely available for download at http://compbio.ornl.gov/Vonode webcite

Quantum control of proximal spins using nanoscale magnetic resonance imaging

Quantum control of individual spins in condensed matter systems is an emerging field with wide-ranging applications in spintronics, quantum computation, and sensitive magnetometry. Recent experiments have demonstrated the ability to address and manipulate single electron spins through either optical or electrical techniques. However, it is a challenge to extend individual spin control to nanoscale multi-electron systems, as individual spins are often irresolvable with existing methods. Here we demonstrate that coherent individual spin control can be achieved with few-nm resolution for proximal electron spins by performing single-spin magnetic resonance imaging (MRI), which is realized via a scanning magnetic field gradient that is both strong enough to achieve nanometric spatial resolution and sufficiently stable for coherent spin manipulations. We apply this scanning field-gradient MRI technique to electronic spins in nitrogen-vacancy (NV) centers in diamond and achieve nanometric resolution in imaging, characterization, and manipulation of individual spins. For NV centers, our results in individual spin control demonstrate an improvement of nearly two orders of magnitude in spatial resolution compared to conventional optical diffraction-limited techniques. This scanning-field-gradient microscope enables a wide range of applications including materials characterization, spin entanglement, and nanoscale magnetometry.Comment: 7 pages, 4 figure

Photon Statistics; Nonlinear Spectroscopy of Single Quantum Systems

A unified description of multitime correlation functions, nonlinear response functions, and quantum measurements is developed using a common generating function which allows a direct comparison of their information content. A general formal expression for photon counting statistics from single quantum objects is derived in terms of Liouville space correlation functions of the material system by making a single assumption that spontaneous emission is described by a master equation

Impact of Fatty-Acid Labeling of Bacillus subtilis Membranes on the Cellular Lipidome and Proteome

Developing cultivation methods that yield chemically and isotopically defined fatty acid (FA) compositions within bacterial cytoplasmic membranes establishes an in vivo experimental platform to study membrane biophysics and cell membrane regulation using novel approaches. Yet before fully realizing the potential of this method, it is prudent to understand the systemic changes in cells induced by the labeling procedure itself. In this work, analysis of cellular membrane compositions was paired with proteomics to assess how the proteome changes in response to the directed incorporation of exogenous FAs into the membrane of Bacillus subtilis. Key findings from this analysis include an alteration in lipid headgroup distribution, with an increase in phosphatidylglycerol lipids and decrease in phosphatidylethanolamine lipids, possibly providing a fluidizing effect on the cell membrane in response to the induced change in membrane composition. Changes in the abundance of enzymes involved in FA biosynthesis and degradation are observed; along with changes in abundance of cell wall enzymes and isoprenoid lipid production. The observed changes may influence membrane organization, and indeed the well-known lipid raft-associated protein flotillin was found to be substantially down-regulated in the labeled cells – as was the actin-like protein MreB. Taken as a whole, this study provides a greater depth of understanding for this important cell membrane experimental platform and presents a number of new connections to be explored in regard to modulating cell membrane FA composition and its effects on lipid headgroup and raft/cytoskeletal associated proteins

Inhibition of the MID1 protein complex: a novel approach targeting APP protein synthesis

Alzheimer's disease (AD) is characterized by two neuropathological hallmarks: senile plaques, which are composed of amyloid-β (Aβ) peptides, and neurofibrillary tangles, which are composed of hyperphosphorylated tau protein. Aβ peptides are derived from sequential proteolytic cleavage of the amyloid precursor protein (APP). In this study, we identified a so far unknown mode of regulation of APP protein synthesis involving the MID1 protein complex: MID1 binds to and regulates the translation of APP mRNA. The underlying mode of action of MID1 involves the mTOR pathway. Thus, inhibition of the MID1 complex reduces the APP protein level in cultures of primary neurons. Based on this, we used one compound that we discovered previously to interfere with the MID1 complex, metformin, for in vivo experiments. Indeed, long-term treatment with metformin decreased APP protein expression levels and consequently Aβ in an AD mouse model. Importantly, we have initiated the metformin treatment late in life, at a time-point where mice were in an already progressed state of the disease, and could observe an improved behavioral phenotype. These findings together with our previous observation, showing that inhibition of the MID1 complex by metformin also decreases tau phosphorylation, make the MID1 complex a particularly interesting drug target for treating AD