Equivalence of domains for hyperbolic Hubbard-Stratonovich transformations

We settle a long standing issue concerning the traditional derivation of non-compact non-linear sigma models in the theory of disordered electron systems: the hyperbolic Hubbard-Stratonovich (HS) transformation of Pruisken-Schaefer type. Only recently the validity of such transformations was proved in the case of U(p,q) (non-compact unitary) and O(p,q) (non-compact orthogonal) symmetry. In this article we give a proof for general non-compact symmetry groups. Moreover we show that the Pruisken-Schaefer type transformations are related to other variants of the HS transformation by deformation of the domain of integration. In particular we clarify the origin of surprising sign factors which were recently discovered in the case of orthogonal symmetry.Comment: 30 pages, 3 figure

Diffusion limited reactions in confined environments

We study the effect of confinement on diffusion limited bimolecular reactions within a lattice model where a small number of reactants diffuse amongst a much larger number of inert particles. When the number of inert particles is held constant the rate of the reaction is slow for small reaction volumes due to limited mobility from crowding, and for large reaction volumes due to the reduced concentration of the reactants. The reaction rate proceeds fastest at an intermediate confinement corresponding to volume fraction near 1/2 and 1/3 in two and three dimensions, respectively. We generalize the model to off-lattice systems with hydrodynamic coupling and predict that the optimal reaction rate for monodisperse colloidal systems occurs when the volume fraction is ~0.18. Finally, we discuss the application of our model to bimolecular reactions inside cells as well as the dynamics of confined polymers.Comment: 4 pages, 3 figure

Building block libraries and structural considerations in the self-assembly of polyoxometalate and polyoxothiometalate systems

Inorganic metal-oxide clusters form a class of compounds that are unique in their topological and electronic versatility and are becoming increasingly more important in a variety of applications. Namely, Polyoxometalates (POMs) have shown an unmatched range of physical properties and the ability to form structures that can bridge several length scales. The formation of these molecular clusters is often ambiguous and is governed by self-assembly processes that limit our ability to rationally design such molecules. However, recent years have shown that by considering new building block principles the design and discovery of novel complex clusters is aiding our understanding of this process. Now with current progress in thiometalate chemistry, specifically polyoxothiometalates (POTM), the field of inorganic molecular clusters has further diversified allowing for the targeted development of molecules with specific functionality. This chapter discusses the main differences between POM and POTM systems and how this affects synthetic methodologies and reactivities. We will illustrate how careful structural considerations can lead to the generation of novel building blocks and further deepen our understanding of complex systems

Genetic noise control via protein oligomerization

Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling. While there have been numerous studies correlating the architecture of cellular reaction networks with noise tolerance, only a limited effort has been made to understand the dynamic role of protein-protein interactions. Here we have developed a fully stochastic model for the positive feedback control of a single gene, as well as a pair of genes (toggle switch), integrating quantitative results from previous in vivo and in vitro studies. We find that the overall noise-level is reduced and the frequency content of the noise is dramatically shifted to the physiologically irrelevant high-frequency regime in the presence of protein dimerization. This is independent of the choice of monomer or dimer as transcription factor and persists throughout the multiple model topologies considered. For the toggle switch, we additionally find that the presence of a protein dimer, either homodimer or heterodimer, may significantly reduce its random switching rate. Hence, the dimer promotes the robust function of bistable switches by preventing the uninduced (induced) state from randomly being induced (uninduced). The specific binding between regulatory proteins provides a buffer that may prevent the propagation of fluctuations in genetic activity. The capacity of the buffer is a non-monotonic function of association-dissociation rates. Since the protein oligomerization per se does not require extra protein components to be expressed, it provides a basis for the rapid control of intrinsic or extrinsic noise

Crossover between Thermally Assisted and Pure Quantum Tunneling in Molecular Magnet Mn12-Acetate

The crossover between thermally assisted and pure quantum tunneling has been studied in single crystals of high spin (S=10) uniaxial molecular magnet Mn12 using micro-Hall-effect magnetometry. Magnetic hysteresis and relaxation experiments have been used to investigate the energy levels that determine the magnetization reversal as a function of magnetic field and temperature. These experiments demonstrate that the crossover occurs in a narrow (0.1 K) or broad (1 K) temperature interval depending on the magnitude of the field transverse to the anisotropy axis.Comment: 5 pages, 4 figure

Trapping an Iron(VI) Water-Splitting Intermediate in Nonaqueous Media

We report in situ spectroscopic measurements in nonaqueous media designed to trap an exceptionally strong oxidant generated electrochemically from an iron-containing nickel layered double hydroxide ([NiFe]-LDH) material. Anodic polarization of this material in acetonitrile produces metal-oxo vibrational spectroscopic signatures along with an extremely narrow near-infrared luminescence peak that strongly indicate that the reactive intermediate is cis-dioxo-iron(VI). Chemical trapping experiments reveal that addition of H_2O to the polarized electrochemical cell produces hydrogen peroxide; and, most importantly, addition of HO– generates oxygen. Repolarization of the electrode restores the iron(VI) spectroscopic features, confirming that the high-valent oxo complex is active in the electrocatalytic water oxidation cycle

Trapping an Iron(VI) Water-Splitting Intermediate in Nonaqueous Media

We report in situ spectroscopic measurements in nonaqueous media designed to trap an exceptionally strong oxidant generated electrochemically from an iron-containing nickel layered double hydroxide ([NiFe]-LDH) material. Anodic polarization of this material in acetonitrile produces metal-oxo vibrational spectroscopic signatures along with an extremely narrow near-infrared luminescence peak that strongly indicate that the reactive intermediate is cis-dioxo-iron(VI). Chemical trapping experiments reveal that addition of H_2O to the polarized electrochemical cell produces hydrogen peroxide; and, most importantly, addition of HO– generates oxygen. Repolarization of the electrode restores the iron(VI) spectroscopic features, confirming that the high-valent oxo complex is active in the electrocatalytic water oxidation cycle

Infrared to millimetre photometry of ultra-luminous IR galaxies: new evidence favouring a 3-stage dust model

Infrared to millimetre spectral energy distributions have been obtained for 41 bright ultra-luminous infrared galaxies. The observations were carried out with ISOPHOT between 10 and 200 micron and supplemented for 16 sources with SCUBA at 450 and 850 micron and with SEST at 1.3 mm. In addition, seven sources were observed at 1.2 and 2.2 $\mu$m with the 2.2 m telescope on Calar Alto. These new SEDs represent the most complete set of infrared photometric templates obtained so far on ULIRGs in the local universe.Comment: 23 pages, 11 figures, accepted for publication in Astronomy & Astrophysic

Bacterial porin disrupts mitochondrial membrane potential and sensitizes host cells to apoptosis

The bacterial PorB porin, an ATP-binding beta-barrel protein of pathogenic Neisseria gonorrhoeae, triggers host cell apoptosis by an unknown mechanism. PorB is targeted to and imported by host cell mitochondria, causing the breakdown of the mitochondrial membrane potential (delta psi m). Here, we show that PorB induces the condensation of the mitochondrial matrix and the loss of cristae structures, sensitizing cells to the induction of apoptosis via signaling pathways activated by BH3-only proteins. PorB is imported into mitochondria through the general translocase TOM but, unexpectedly, is not recognized by the SAM sorting machinery, usually required for the assembly of beta-barrel proteins in the mitochondrial outer membrane. PorB integrates into the mitochondrial inner membrane, leading to the breakdown of delta psi m. The PorB channel is regulated by nucleotides and an isogenic PorB mutant defective in ATP-binding failed to induce delta psi m loss and apoptosis, demonstrating that dissipation of delta psi m is a requirement for cell death caused by neisserial infection

Spatial and topological organization of DNA chains induced by gene co-localization

Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into discrete spatial foci called transcription factories. However, the mechanisms underlying the formation of these foci and the resulting topological order of the chromosome remain to be elucidated. Here we consider a thermodynamic framework based on a worm-like chain model of chromosomes where sparse designated sites along the DNA are able to interact whenever they are spatially close-by. This is motivated by recurrent evidence that there exists physical interactions between genes that operate together. Three important results come out of this simple framework. First, the resulting formation of transcription foci can be viewed as a micro-phase separation of the interacting sites from the rest of the DNA. In this respect, a thermodynamic analysis suggests transcription factors to be appropriate candidates for mediating the physical interactions between genes. Next, numerical simulations of the polymer reveal a rich variety of phases that are associated with different topological orderings, each providing a way to increase the local concentrations of the interacting sites. Finally, the numerical results show that both one-dimensional clustering and periodic location of the binding sites along the DNA, which have been observed in several organisms, make the spatial co-localization of multiple families of genes particularly efficient.Comment: Figures and Supplementary Material freely available on http://dx.doi.org/10.1371/journal.pcbi.100067