Jeremy I. Feldblyum

Viral genome sequencing by random priming methods

BackgroundMost emerging health threats are of zoonotic origin. For the overwhelming majority, their causative agents are RNA viruses which include but are not limited to HIV, Influenza, SARS, Ebola, Dengue, and Hantavirus. Of increasing importance therefore is a better understanding of global viral diversity to enable better surveillance and prediction of pandemic threats; this will require rapid and flexible methods for complete viral genome sequencing.ResultsWe have adapted the SISPA methodology [1–3] to genome sequencing of RNA and DNA viruses. We have demonstrated the utility of the method on various types and sources of viruses, obtaining near complete genome sequence of viruses ranging in size from 3,000–15,000 kb with a median depth of coverage of 14.33. We used this technique to generate full viral genome sequence in the presence of host contaminants, using viral preparations from cell culture supernatant, allantoic fluid and fecal matter.ConclusionThe method described is of great utility in generating whole genome assemblies for viruses with little or no available sequence information, viruses from greatly divergent families, previously uncharacterized viruses, or to more fully describe mixed viral infections.

Reconciling the discrepancies between crystallographic porosity and guest access as exemplified by Zn-HKUST-1.

There are several compounds for which there exists a disconnect between porosity as predicted by crystallography and porosity measured by gas sorption analysis. In this paper, the Zn-based analogue of Cu(3)(btc)(2) (HKUST-1), Zn(3)(btc)(2) (Zn-HKUST-1; btc = 1,3,5-benzenetricarboxylate) is investigated. Conventional analysis of Zn-HKUST-1 by powder X-ray diffraction and gas sorption indicates retention of crystalline structure but negligible nitrogen uptake at 77 K. By using positron annihilation lifetime spectroscopy, a densified surface layer preventing the entry of even small molecular species into the crystal framework is revealed. The material is shown to have inherent surface instability after solvent removal, rendering it impermeable to molecular guests irrespective of handling and processing methods. This previously unobserved surface instability may provide insight into the failure of other microporous coordination polymers to exhibit significant porosity despite crystal structures indicative of regular, interconnected, microporous networks.

Analysis of the operation of thin nanowire photoelectrodes for solar energy conversion

The solar energy conversion properties of thin Si and GaP nanowire photoelectrodes in photoelectrochemical cells have been examined through sets of finite-element simulations. A discussion describing the motivation behind nanostructured, high aspect ratio semiconductor photoelectrode designs and a brief survey of current experimental results reported for nanostructured semiconductor photoelectrodes in photoelectrochemical cells are presented first. An analysis is then shown that outlines the primary recombination pathways governing the steady-state current-potential behaviors of thin, cylindrical nanowire photoelectrodes, with explicit expressions detailing the differences between planar and cylindrical photoelectrodes arising from the solution of carrier fluxes in planar and cylindrical geometries. Results from finite-element simulations used to model the key features of thin nanowire photoelectrodes under low-level injection conditions are shown that illustrate which recombination pathway(s) is operative under various experimental conditions. Specifically, the respective effects of non-uniform doping, tapering along the length, variation in charge carrier mobilities and lifetimes, changes in nanowire radius, and changes in the density of surface defects on the observable photocurrent-potential responses are reported. These cumulative results serve as guides for future experimental work aimed at improving the attainable solar energy conversion efficiencies of doped semiconductor nanowire photoelectrodes. Lastly, separate simulations that model lightly doped nanowire photoelectrodes under high-level injection conditions are discussed. These results suggest discrete, ohmic-selective contacts may afford a way to circumvent the stringent doping requirements discussed herein for thin nanowire photoelectrodes.

H-Bonded Supramolecular Polymer for the Selective Dispersion and Subsequent Release of Large-Diameter Semiconducting Single-Walled Carbon Nanotubes

Semiconducting, single-walled carbon nanotubes (SWNTs) are promising candidates for applications in thin-film transistors, solar cells, and biological imaging. To harness their full potential, however, it is necessary to separate the semiconducting from the metallic SWNTs present in the as-synthesized SWNT mixture. While various polymers are able to selectively disperse semiconducting SWNTs, the subsequent removal of the polymer is challenging. However, many applications require semiconducting SWNTs in their pure form. Toward this goal, we have designed a 2-ureido-6[1H]-pyrimidinone (UPy)-based H-bonded supramolecular polymer that can selectively disperse semiconducting SWNTs. The dispersion purity is inversely related to the dispersion yield. In contrast to conventional polymers, the polymer described herein was shown to disassemble into monomeric units upon addition of an H-bond-disrupting agent, enabling isolation of dispersant-free, semiconducting SWNTs.

Non-interpenetrated IRMOF-8: synthesis, activation, and gas sorption

The synthesis and successful activation of IRMOF-8 (Zn(4)O(ndc)(3), ndc = naphthalene-2,6-dicarboxylate) is presented. Room temperature synthesis effectively suppresses interpenetration. Although conventional activation under reduced pressure leads to structural collapse, activation by flowing supercritical CO(2) yields a guest-free material with a BET surface area of 4461 m(2) g(-1).

Interpenetration, Porosity, and High-Pressure Gas Adsorption in Zn4O(2,6-naphthalene dicarboxylate)3

Microporous coordination polymers (MCPs) have emerged as strong contenders for adsorption-based fuel storage and delivery in large part because of their high specific surface areas. The strategy of increasing surface area by increasing organic linker length has shown only sporadic success; as demonstrated by many members of the iconic Zn4O-based IRMOF series, for example, accessible porosity is often limited by interpenetration or pore collapse upon guest removal. In this work, we focus on Zn4O(ndc)3 (IRMOF-8, ndc = 2,6-naphthalene dicarboxylate), which exhibits typical surface areas of only 1000-2000 m(2)/g even though a surface area of more than 4000 m(2)/g is expected from geometric analysis of the originally reported crystal structure. We recently showed that a high surface area could be produced with zinc and ndc by room-temperature synthesis followed by activation with flowing supercritical CO2. In this work, we investigate in detail the porosity of both the low- and high-surface-area materials. Positron annihilation lifetime spectroscopy (PALS) is used to show that the low-surface-area material suffers from near-complete interpenetration, explaining why traditional synthetic routes have failed to yield materials with the expected porosity. Furthermore, the high-pressure hydrogen and methane sorption properties of noninterpenetrated Zn4O(ndc)3 are examined, and PALS is used to show that pore filling is not operative during room-temperature CH4 sorption even at pressures approaching 100 bar. These results provide insight into how gas adsorbs in high-surface-area materials at high pressure and reinforce previous contentions that increasing surface area alone is not sufficient for the simultaneous optimization of deliverable gravimetric and volumetric gas uptake in MCPs.

Filling Pore Space in a Microporous Coordination Polymer to Improve Methane Storage Performance

A strategy that allows the tuning of pore size in microporous coordination polymers (MCPs) through modification of their organic linkers is presented. When large substituents are introduced onto the linker, these pendent groups partially occupy the pores, thus reducing pore size while serving as additional adsorption sites for gases. The approach takes advantage of the fact that, for methane storage materials, small pores (0.4-0.8 nm in diameter) are more desirable than large pores since small pores promote optimal volumetric capacity. This method was demonstrated with IRMOF-8, a MCP constructed from Zn4O metal clusters and 2,6-naphthalenedicarboxylate (NDC) linkers. The NDC was functionalized through the addition of substituents including tert-butylethynyl or phenylethynyl groups. High pressure methane uptake demonstrates that the IRMOF-8 derivatives have significantly better performance than the unfunctionalized material in terms of both excess volumetric uptake and deliverable capacity. Moreover, IRMOF-8 derivatives also give rise to stronger interactions with methane molecules as shown by higher heat of adsorption values.

Structural analysis of soft multicomponent nanoparticle clusters

Quantitative techniques are essential to analyze the structure of soft multicomponent nanobioclusters. Here, we combine electrospray differential mobility analysis (ES-DMA), which rapidly measures the size of the entire cluster, with transmission electron microscopy (TEM), which detects the hard components, to determine the presence and composition of the softer components. Coupling analysis of TEM and ES-DMA derived data requires the creation and use of analytical models to determine the size and number of constituents in nanoparticle complexes from the difference between the two measurements. Previous ES-DMA analyses have been limited to clusters of identical spherical particles. Here, we dramatically extend the ES-DMA analysis framework to accommodate more challenging geometries, including protein corona-coated nanorods, clusters composed of heterogeneously sized nanospheres, and nanobioclusters composed of both nanospheres and nanorods. The latter is critical to determining the number of quantum dots attached to lambda (λ) phage, a key element of a rapid method to detect bacterial pathogens in environmental and clinical samples.

Positronium emission spectra from self-assembled metal-organic frameworks

P. Crivelli, D. Cooke, B. Barbiellini, B. L. Brown, J. I. Feldblyum, 5 P. Guo, D. W. Gidley, L. Gerchow, and A. J. Matzger Institute for Particle Physics, ETH Zurich, Switzerland∗ Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA Department of Physics, Marquette University, Milwaukee, USA Department of Chemistry, University of Michigan, 48109, USA Macromolecular Science and Engineering, University of Michigan, 48109-2136, USA Department of Physics, University of Michigan, 48109, USA (Dated: May 22, 2014)

Concentrated mixed cation acetate “water-in-salt” solutions as green and low-cost high voltage electrolytes for aqueous batteries

Electrolyte solutions are a key component of energy storage devices that significantly impact capacity, safety, and cost. Recent developments in “water-in-salt” (WIS) aqueous electrolyte research have enabled the demonstration of aqueous Li-ion batteries that operate with capacities and cyclabilities comparable with those of commercial non-aqueous Li-ion batteries. Critically, the use of aqueous electrolyte mitigates safety risks associated with non-aqueous electrolytes. However, the high cost and potential toxicity of imide-based WIS electrolytes limit their practical deployment. In this report, we disclose the efficacy of inexpensive, non-toxic mixed cation electrolyte systems for Li-ion batteries that otherwise provide the same benefits as current WIS electrolytes: extended electrochemical stability window and compatibility with traditional intercalation Li-ion battery electrode materials. We take advantage of the high solubility of potassium acetate to achieve the WIS condition in a eutectic mixture of lithium and potassium acetate with water-to-cation ratio as low as 1.3. Our work suggests an important direction for the practical realization of safe, low-cost, and high-performance aqueous Li-ion batteries.