Light shifts in atomic Bragg diffraction

Bragg diffraction of an atomic wave packet in a retroreflective geometry with two counterpropagating optical lattices exhibits a light shift induced phase. We show that the temporal shape of the light pulse determines the behavior of this phase shift: In contrast to Raman diffraction, Bragg diffraction with Gaussian pulses leads to a significant suppression of the intrinsic phase shift due to a scaling with the third power of the inverse Doppler frequency. However, for box-shaped laser pulses, the corresponding shift is twice as large as for Raman diffraction. Our results are based on approximate, but analytical expressions as well as a numerical integration of the corresponding Schr\"odinger equation.Comment: 6 pages, 5 figure

Peptide Retention in Hydrophilic Strong Anion Exchange Chromatography Is Driven by Charged and Aromatic Residues

Hydrophilic strong anion exchange chromatography (hSAX) is becoming a popular method for the prefractionation of proteomic samples. However, the use and further development of this approach is affected by the limited understanding of its retention mechanism and the absence of elution time prediction. Using a set of 59 297 confidentially identified peptides, we performed an explorative analysis and built a predictive deep learning model. As expected, charged residues are the major contributors to the retention time through electrostatic interactions. Aspartic acid and glutamic acid have a strong retaining effect and lysine and arginine have a strong repulsion effect. In addition, we also find the involvement of aromatic amino acids. This suggests a substantial contribution of cation−π interactions to the retention mechanism. The deep learning approach was validated using 5-fold cross-validation (CV) yielding a mean prediction accuracy of 70% during CV and 68% on a hold-out validation set. The results of this study emphasize that not only electrostatic interactions but rather diverse types of interactions must be integrated to build a reliable hSAX retention time predictor

Fracture toughness of thermal barrier coatings determined by micro cantilever bending tests

To investigate the local fracture toughness of thin coatings new small scale methods like FIB milling of micro cantilever are used. Webler et al. used this technique for measuring the fracture toughness of NiAl bond [1]. This method can also be used to investigate the local fracture toughness of thermal barrier coatings. The fracture toughness of ceramic coatings can be determined by different indentation techniques [2]. The drawback of these methods is the analysis of the KIc-value without the specific knowledge of the crack front propagation, which can only be determined after the experiment. By using micro-cantilever produced by ion beam milling it is possible to measure the local fracture toughness with freestanding micro-cantilever independent of the substrate. Therefore two yttrium stabilized zirconia (YSZ) top coats with a thickness of 250μm, which were deposited by suspension plasma spraying on a layer of Amdry 9954 bond coat and IN 738 substrate with different standoff distances of about 70 and 100 mm, were investigated. Figure 1. shows the micro-cantilever with the initial crack (a) before testing. Please click Additional Files below to see the full abstract

Regimes of atomic diffraction: Raman versus Bragg diffraction in retroreflective geometries

We provide a comprehensive study of atomic Raman and Bragg diffraction when coupling to a pair of counterpropagating light gratings (double diffraction) or to a single one (single diffraction) and discuss the transition from one case to the other in a retroreflective geometry as the Doppler detuning changes. In contrast to single diffraction, double Raman loses its advantage of high diffraction efficiency for short pulses and has to be performed in a Bragg-type regime. Moreover, the structure of double diffraction leads to further limitations for broad momentum distributions on the efficiency of mirror pulses, making the use of (ultra) cold ensembles essential for high diffraction efficiency.Comment: 16 pages, 14 figure

Retention time prediction using neural networks increases identifications in crosslinking mass spectrometry

Crosslinking mass spectrometry has developed into a robust technique that is increasingly used to investigate the interactomes of organelles and cells. However, the incomplete and noisy information in the mass spectra of crosslinked peptides limits the numbers of protein–protein interactions that can be confidently identified. Here, we leverage chromatographic retention time information to aid the identification of crosslinked peptides from mass spectra. Our Siamese machine learning model xiRT achieves highly accurate retention time predictions of crosslinked peptides in a multi-dimensional separation of crosslinked E. coli lysate. Importantly, supplementing the search engine score with retention time features leads to a substantial increase in protein–protein interactions without affecting confidence. This approach is not limited to cell lysates and multi-dimensional separation but also improves considerably the analysis of crosslinked multiprotein complexes with a single chromatographic dimension. Retention times are a powerful complement to mass spectrometric information to increase the sensitivity of crosslinking mass spectrometry analyses

A HT3 Platform for Rapid Prototyping and High Performance Reconfigurable Computing

FPGAs as reconfigurable devices play an important role in both rapid prototyping and high performance reconfigurable computing. Usually, FPGA vendors help the users with pre-designed cores, for instance for various communication protocols. However, this is only true for widely used protocols. In the use case described here, the target application may benefit from a tight integration of the FPGA in a computing system. Typical commodity protocols like PCI Express may not fulfill these demands. HyperTransport (HT), on the other hand, allows connecting directly and without intermediate bridges or protocol conversion to a processor interface. As a result, communication costs between the FPGA unit and both processor and main memory are minimal. In this paper we present an HT3 interface for Stratix IV based FPGAs, which allows for minimal latencies and high bandwidths between processor and device and main memory and device. Designs targeting a HT connection can now be prototyped in real world systems. Furthermore, this design can be leveraged for acceleration tasks, with the minimal communication costs allowing fine-grain work deployment and the use of cost-efficient main memory instead of size-limited and costly on-device memory

Leveraging parameter dependencies in high-field asymmetric waveform ion-mobility spectrometry and size exclusion chromatography for proteome-wide cross-linking mass spectrometry

[Image: see text] Ion-mobility spectrometry shows great promise to tackle analytically challenging research questions by adding another separation dimension to liquid chromatography–mass spectrometry. The understanding of how analyte properties influence ion mobility has increased through recent studies, but no clear rationale for the design of customized experimental settings has emerged. Here, we leverage machine learning to deepen our understanding of field asymmetric waveform ion-mobility spectrometry for the analysis of cross-linked peptides. Knowing that predominantly m/z and then the size and charge state of an analyte influence the separation, we found ideal compensation voltages correlating with the size exclusion chromatography fraction number. The effect of this relationship on the analytical depth can be substantial as exploiting it allowed us to almost double unique residue pair detections in a proteome-wide cross-linking experiment. Other applications involving liquid- and gas-phase separation may also benefit from considering such parameter dependencies

Atomic Raman scattering: Third-order diffraction in a double geometry

In a retroreflective scheme atomic Raman diffraction adopts some of the properties of Bragg diffraction due to additional couplings to off-resonant momenta. As a consequence, double Raman diffraction has to be performed in a Bragg-type regime. Taking advantage of this regime, double Raman allows for resonant higher-order diffraction. We study theoretically the case of third-order diffraction and compare it to first order as well as a sequence of first-order pulses giving rise to the same momentum transfer as the third-order pulse. In fact, third-order diffraction constitutes a competitive tool for the diffraction of ultracold atoms and interferometry based on large momentum transfer since it allows to reduce the complexity of the experiment as well as the total duration of the diffraction process compared to a sequence.Comment: 10 pages, 13 figure