Controlling tetramer formation, subunit rotation and DNA ligation during Hin-catalyzed DNA inversion.

Two critical steps controlling serine recombinase activity are the remodeling of dimers into the chemically active synaptic tetramer and the regulation of subunit rotation during DNA exchange. We identify a set of hydrophobic residues within the oligomerization helix that controls these steps by the Hin DNA invertase. Phe105 and Met109 insert into hydrophobic pockets within the catalytic domain of the same subunit to stabilize the inactive dimer conformation. These rotate out of the catalytic domain in the dimer and into the subunit rotation interface of the tetramer. About half of residue 105 and 109 substitutions gain the ability to generate stable synaptic tetramers and/or promote DNA chemistry without activation by the Fis/enhancer element. Phe106 replaces Phe105 in the catalytic domain pocket to stabilize the tetramer conformation. Significantly, many of the residue 105 and 109 substitutions support subunit rotation but impair ligation, implying a defect in rotational pausing at the tetrameric conformer poised for ligation. We propose that a ratchet-like surface involving Phe105, Met109 and Leu112 within the rotation interface functions to gate the subunit rotation reaction. Hydrophobic residues are present in analogous positions in other serine recombinases and likely perform similar functions

Efficient Computation of Power, Force, and Torque in BEM Scattering Calculations

We present concise, computationally efficient formulas for several quantities of interest -- including absorbed and scattered power, optical force (radiation pressure), and torque -- in scattering calculations performed using the boundary-element method (BEM) [also known as the method of moments (MOM)]. Our formulas compute the quantities of interest \textit{directly} from the BEM surface currents with no need ever to compute the scattered electromagnetic fields. We derive our new formulas and demonstrate their effectiveness by computing power, force, and torque in a number of example geometries. Free, open-source software implementations of our formulas are available for download online

Chemical and electrochemical behavior of the Cr(3)/Cr(2) half cell in the NASA Redox Energy Storage System

The Cr(III) complexes in the NASA Redox Energy Storage System were isolated and identified as Cr(H2O)6(+3) and Cr(H2O)5Cl(+2) by ion exchange chromatography and visible spectrophotometry. The cell reactions during charge-discharge cycles were followed by means of visible spectrophotometry. The spectral bands were resolved into component peaks and concentrations calculated using Beer's Law. During the charge mode Cr(H2O)5Cl(+2) is reduced to Cr(H2O)5Cl(+) and during the discharge mode Cr(H2O)5Cl(+) is oxidized back to Cr(H2O)5Cl(+2). Both electrode reactions occur via a chloride-bridge inner-sphere reaction pathway. Hysteresis effects can be explained by the slow attainment of equilibrium between Cr(H2O)6(+3) and Cr(H2O)5Cl(+2)

Will This Paper Increase Your h-index? Scientific Impact Prediction

Scientific impact plays a central role in the evaluation of the output of scholars, departments, and institutions. A widely used measure of scientific impact is citations, with a growing body of literature focused on predicting the number of citations obtained by any given publication. The effectiveness of such predictions, however, is fundamentally limited by the power-law distribution of citations, whereby publications with few citations are extremely common and publications with many citations are relatively rare. Given this limitation, in this work we instead address a related question asked by many academic researchers in the course of writing a paper, namely: "Will this paper increase my h-index?" Using a real academic dataset with over 1.7 million authors, 2 million papers, and 8 million citation relationships from the premier online academic service ArnetMiner, we formalize a novel scientific impact prediction problem to examine several factors that can drive a paper to increase the primary author's h-index. We find that the researcher's authority on the publication topic and the venue in which the paper is published are crucial factors to the increase of the primary author's h-index, while the topic popularity and the co-authors' h-indices are of surprisingly little relevance. By leveraging relevant factors, we find a greater than 87.5% potential predictability for whether a paper will contribute to an author's h-index within five years. As a further experiment, we generate a self-prediction for this paper, estimating that there is a 76% probability that it will contribute to the h-index of the co-author with the highest current h-index in five years. We conclude that our findings on the quantification of scientific impact can help researchers to expand their influence and more effectively leverage their position of "standing on the shoulders of giants."Comment: Proc. of the 8th ACM International Conference on Web Search and Data Mining (WSDM'15

Modulation of HU-DNA interactions by salt concentration and applied force.

HU is one of the most abundant proteins in bacterial chromosomes and participates in nucleoid compaction and gene regulation. We report experiments using DNA stretching that study the dependence of DNA condensation by HU on force, salt and HU concentration. Previous experiments at sub-physiological salt levels revealed that low concentrations of HU could compact DNA, whereas larger HU concentrations formed a DNA-stiffening complex. Here we report that this bimodal binding behavior depends sensitively on salt concentration. Only the compaction mode was observed for 150 mM and higher NaCl levels, i.e. for physiological salt concentrations. Similar results were obtained for the more physiological salt K-glutamate. Real-time studies of dissociation kinetics revealed that HU unbound slowly (minutes to hours under the conditions studied) but completely for salt concentrations at or above 100 mM NaCl; the lifetime of HU complexes was observed to increase with the HU concentration at which the complexes were formed, and to decrease with salt concentration. Higher salt levels of 300 mM NaCl completely eliminated observable HU binding to DNA. Finally, we observed that the dissociation kinetics depend on force applied to the DNA: increased applied force in the sub-piconewton range accelerates dissociation, suggesting a mechanism for DNA tension to regulate chromosome structure and gene expression

Computation of Casimir Interactions between Arbitrary 3D Objects with Arbitrary Material Properties

We extend a recently introduced method for computing Casimir forces between arbitrarily--shaped metallic objects [M. T. H. Reid et al., Phys. Rev. Lett._103_ 040401 (2009)] to allow treatment of objects with arbitrary material properties, including imperfect conductors, dielectrics, and magnetic materials. Our original method considered electric currents on the surfaces of the interacting objects; the extended method considers both electric and magnetic surface current distributions, and obtains the Casimir energy of a configuration of objects in terms of the interactions of these effective surface currents. Using this new technique, we present the first predictions of Casimir interactions in several experimentally relevant geometries that would be difficult to treat with any existing method. In particular, we investigate Casimir interactions between dielectric nanodisks embedded in a dielectric fluid; we identify the threshold surface--surface separation at which finite--size effects become relevant, and we map the rotational energy landscape of bound nanoparticle diclusters

DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis.

The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequences in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. The affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions

Fluctuating surface-current formulation of radiative heat transfer: theory and applications

We describe a novel fluctuating-surface current formulation of radiative heat transfer between bodies of arbitrary shape that exploits efficient and sophisticated techniques from the surface-integral-equation formulation of classical electromagnetic scattering. Unlike previous approaches to non-equilibrium fluctuations that involve scattering matrices---relating "incoming" and "outgoing" waves from each body---our approach is formulated in terms of "unknown" surface currents, laying at the surfaces of the bodies, that need not satisfy any wave equation. We show that our formulation can be applied as a spectral method to obtain fast-converging semi-analytical formulas in high-symmetry geometries using specialized spectral bases that conform to the surfaces of the bodies (e.g. Fourier series for planar bodies or spherical harmonics for spherical bodies), and can also be employed as a numerical method by exploiting the generality of surface meshes/grids to obtain results in more complicated geometries (e.g. interleaved bodies as well as bodies with sharp corners). In particular, our formalism allows direct application of the boundary-element method, a robust and powerful numerical implementation of the surface-integral formulation of classical electromagnetism, which we use to obtain results in new geometries, including the heat transfer between finite slabs, cylinders, and cones