Symmetric angular momentum coupling, the quantum volume operator and the 7-spin network: a computational perspective

A unified vision of the symmetric coupling of angular momenta and of the quantum mechanical volume operator is illustrated. The focus is on the quantum mechanical angular momentum theory of Wigner's 6j symbols and on the volume operator of the symmetric coupling in spin network approaches: here, crucial to our presentation are an appreciation of the role of the Racah sum rule and the simplification arising from the use of Regge symmetry. The projective geometry approach permits the introduction of a symmetric representation of a network of seven spins or angular momenta. Results of extensive computational investigations are summarized, presented and briefly discussed.Comment: 15 pages, 10 figures, presented at ICCSA 2014, 14th International Conference on Computational Science and Application

The screen representation of vector coupling coefficients or Wigner 3j symbols: exact computation and illustration of the asymptotic behavior

The Wigner $3j$ symbols of the quantum angular momentum theory are related to the vector coupling or Clebsch-Gordan coefficients and to the Hahn and dual Hahn polynomials of the discrete orthogonal hyperspherical family, of use in discretization approximations. We point out the important role of the Regge symmetries for defining the screen where images of the coefficients are projected, and for discussing their asymptotic properties and semiclassical behavior. Recursion relationships are formulated as eigenvalue equations, and exploited both for computational purposes and for physical interpretations.Comment: 14 pages, 8 figures, presented at ICCSA 2014, 14th International Conference on Computational Science and Application

Photo-CIDNP 13C magic angle spinning NMR on bacterial reaction centres: exploring the electronic structure of the special pair and its surroundings

Solid state NMR/Biophysical Organic ChemistryBiological and Soft Matter Physic

Minimal knotted polygons in cubic lattices

An implementation of BFACF-style algorithms on knotted polygons in the simple cubic, face centered cubic and body centered cubic lattice is used to estimate the statistics and writhe of minimal length knotted polygons in each of the lattices. Data are collected and analysed on minimal length knotted polygons, their entropy, and their lattice curvature and writhe

Allergen-specific IgG+ memory B cells are temporally linked to IgE memory responses

BACKGROUND: Immunoglobulin E (IgE) are least abundant, tightly regulated and IgE producing B cells are rare. The cellular origin and evolution of IgE responses are poorly understood. OBJECTIVE: To investigate the cellular and clonal origin of IgE memory responses following mucosal allergen exposure by sublingual immunotherapy (SLIT). METHODS: In a randomized double-blind, placebo-controlled, time-course SLIT study, peripheral blood mononuclear cells (PBMCs) and nasal biopsies were collected from forty adults with seasonal allergic rhinitis at baseline, 4, 8, 16, 28 and 52 weeks. RNA was extracted from PBMCs, sorted B cells and nasal biopsies for VH repertoire sequencing. Moreover, monoclonal antibodies were derived from single B cell transcriptomes. RESULTS: Combining VH repertoire sequencing and single cell transcriptomics yielded direct evidence of a parallel boost of two clonally and functionally related B cell subsets of short-lived IgE+ plasmablasts and IgG+ memory B cells (termed IgGE). Mucosal grass pollen allergen exposure by SLIT resulted in highly diverse IgE and IgGE repertoires. These were extensively mutated and appeared relative stable as per heavy chain isotype, somatic hypermutations and clonal composition. Single IgGE + memory B cell and IgE+ pre-plasmablast transcriptomes encoded antibodies that were specific for major grass pollen allergens and were able to elicit basophil activation at very low allergen concentrations. CONCLUSION: For the first time, we have shown that upon mucosal allergen exposure, human IgE memory resides in allergen-specific IgG+ memory B cells. These rapidly switch isotype and expand into short-lived IgE+ plasmablasts and serve as a potential target for therapeutic intervention

Quantum physics meets biology

Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the last decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world view of quantum coherences, entanglement and other non-classical effects, has been heading towards systems of increasing complexity. The present perspective article shall serve as a pedestrian guide to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future quantum biology, its current status, recent experimental progress and also the restrictions that nature imposes on bold extrapolations of quantum theory to macroscopic phenomena.Comment: 26 pages, 4 figures, Perspective article for the HFSP Journa

Metabolite Damage and Damage Control in a Minimal Genome

Analysis of the genes retained in the minimized Mycoplasma JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes known to have such functions were identified and experimentally validated, including 5-formyltetrahydrofolate cycloligase, coenzyme A (CoA) disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and spontaneous side reactions. This extension revealed that several key metabolite damage control systems remain to be identified in JCVI-Syn3A, such as that for methylglyoxal. IMPORTANCE Metabolite damage and repair mechanisms are being increasingly recognized. We present here compelling genetic and biochemical evidence for the universal importance of these mechanisms by demonstrating that stripping a genome down to its barest essentials leaves metabolite damage control systems in place. Furthermore, our metabolomic and cheminformatic results point to the existence of a network of metabolite damage and damage control reactions that extends far beyond the corners of it that have been characterized so far. In sum, there can be little room left to doubt that metabolite damage and the systems that counter it are mainstream metabolic processes that cannot be separated from life itself

Observation of the solid-state photo-CIDNP effect in entire cells of cyanobacteria Synechocystis

Cyanobacteria are widely used as model organism of oxygenic photosynthesis due to being the simplest photosynthetic organisms containing both photosystem I and II (PSI and PSII). Photochemically induced dynamic nuclear polarization (photo-CIDNP) 13C magic-angle spinning (MAS) NMR is a powerful tool in understanding the photosynthesis machinery down to atomic level. Combined with selective isotope enrichment this technique has now opened the door to study primary charge separation in whole living cells. Here, we present the first photo-CIDNP observed in whole cells of the cyanobacterium Synechocystis