Structural analysis of proteins by isotope-edited FTIR spectroscopy

Structure determination of multidomain proteins or protein membrane complexes is one of the most challenging tasks in modern structural biology. High-resolution techniques, like NMR or X-ray crystallography, are limited to molecules of moderate size or those that can be crystallized easily. Both methods encounter serious technical obstacles in structural analysis of protein membrane systems. This work describes an emerging biophysical technique that combines segmental isotope labeling or proteins with Fourier transform infrared (FTIR) spectroscopy, which provides site-specific structural information on proteins and allows structural characterization of protein membrane complexes. Labeling of a segment of the protein with (13)C results in infrared spectral resolution of the labeled and unlabeled parts and thus allows identification of structural changes in specific domains/segments of the protein that accompany functional transitions. Segmental isotope labeling also allows determination of the precise configuration of protein membrane complexes by polarized attenuated total reflection FTIR (ATR-FTIR) spectroscopy. These new developments offer solutions to functionally important site-specific structural changes in proteins and protein membrane complexes that are hard to approach using conventional methods

Geometric expansion of the log-partition function of the anisotropic Heisenberg model

We study the asymptotic expansion of the log-partition function of the anisotropic Heisenberg model in a bounded domain as this domain is dilated to infinity. Using the Ginibre's representation of the anisotropic Heisenberg model as a gas of interacting trajectories of a compound Poisson process we find all the non-decreasing terms of this expansion. They are given explicitly in terms of functional integrals. As the main technical tool we use the cluster expansion method.Comment: 38 page

Reviewing GPU architectures to build efficient back projection for parallel geometries

Back-Projection is the major algorithm in Computed Tomography to reconstruct images from a set of recorded projections. It is used for both fast analytical methods and high-quality iterative techniques. X-ray imaging facilities rely on Back-Projection to reconstruct internal structures in material samples and living organisms with high spatial and temporal resolution. Fast image reconstruction is also essential to track and control processes under study in real-time. In this article, we present efficient implementations of the Back-Projection algorithm for parallel hardware. We survey a range of parallel architectures presented by the major hardware vendors during the last 10 years. Similarities and differences between these architectures are analyzed and we highlight how specific features can be used to enhance the reconstruction performance. In particular, we build a performance model to find hardware hotspots and propose several optimizations to balance the load between texture engine, computational and special function units, as well as different types of memory maximizing the utilization of all GPU subsystems in parallel. We further show that targeting architecture-specific features allows one to boost the performance 2–7 times compared to the current state-of-the-art algorithms used in standard reconstructions codes. The suggested load-balancing approach is not limited to the back-projection but can be used as a general optimization strategy for implementing parallel algorithms

Programmable heralded linear optical generation of two-qubit states

We have investigated the heralded generation of two-qubit dual-rail-encoded states by programmable linear optics. Two types of schemes generating the states from four single photons, which is the minimal possible to accomplish the task, have been considered. The schemes have different detection patterns heralding successful generation events, namely, one-mode heralding, in which the two auxiliary photons are detected in one mode, and two-mode heralding, in which single photons are detected in each of the two modes simultaneously. We have shown that the dependence of the schemes' success probabilities on the target state's degree of entanglement are essentially different. In particular, one-mode heralding yields better efficiency for highly-entangled states, if the programmable interferometers can explore the full space of the unitary transfer matrices,. It is reversed in case of weakly-entangled states where two-mode heralding is better. We have found a minimal decomposition of the scheme with two-mode heralding that is programmed by one variable phase shift. We infer that the linear optical schemes designed specifically for generation of two-qubit states are more efficient than schemes implementing gate-based circuits with known two-qubit linear optical gates. Our results yield substantial reduction of physical resources needed to generate two-qubit dual-rail-encoded photonic states

Differentiation state-specific mitochondrial dynamic regulatory networks are revealed by global transcriptional analysis of the developing chicken lens.

The mature eye lens contains a surface layer of epithelial cells called the lens epithelium that requires a functional mitochondrial population to maintain the homeostasis and transparency of the entire lens. The lens epithelium overlies a core of terminally differentiated fiber cells that must degrade their mitochondria to achieve lens transparency. These distinct mitochondrial populations make the lens a useful model system to identify those genes that regulate the balance between mitochondrial homeostasis and elimination. Here we used an RNA sequencing and bioinformatics approach to identify the transcript levels of all genes expressed by distinct regions of the lens epithelium and maturing fiber cells of the embryonic Gallus gallus (chicken) lens. Our analysis detected more than 15,000 unique transcripts expressed by the embryonic chicken lens. Of these, more than 3000 transcripts exhibited significant differences in expression between lens epithelial cells and fiber cells. Multiple transcripts coding for separate mitochondrial homeostatic and degradation mechanisms were identified to exhibit preferred patterns of expression in lens epithelial cells that require mitochondria relative to lens fiber cells that require mitochondrial elimination. These included differences in the expression levels of metabolic (DUT, PDK1, SNPH), autophagy (ATG3, ATG4B, BECN1, FYCO1, WIPI1), and mitophagy (BNIP3L/NIX, BNIP3, PARK2, p62/SQSTM1) transcripts between lens epithelial cells and lens fiber cells. These data provide a comprehensive window into all genes transcribed by the lens and those mitochondrial regulatory and degradation pathways that function to maintain mitochondrial populations in the lens epithelium and to eliminate mitochondria in maturing lens fiber cells