Publications

Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions

by Vazquez-Anderson, J; Mihailovic, MK; Baldridge, KC; Reyes, KG; Haning, K; Cho, SH; Amador, P; Powell, WB; Contreras, LM

Journal of Nucleic Acids Research; May 19 2017; Volume: 45; Issue: 9; Pages: 5523-5538; DOI: 10.1093/nar/gkx115

Current approaches to design efficient antisense RNAs (asRNAs) rely primarily on a thermodynamic understanding of RNA-RNA interactions. However, these approaches depend on structure predictions and have limited accuracy, arguably due to overlooking important cellular environment factors. In this work, we develop a biophysical model to describe asRNA-RNA hybridization that incorporates in vivo factors using large-scale experimental hybridization data for three model RNAs: a group I intron, CsrB and a tRNA. A unique element of our model is the estimation of the availability of the target region to interact with a given asRNA using a differential entropic consideration of suboptimal structures. We showcase the utility of this model by evaluating its prediction capabilities in four additional RNAs: a group II intron, Spinach II, 2-MS2 binding domain and glgC 5′ UTR. Additionally, we demonstrate the applicability of this approach to other bacterial species by predicting sRNA-mRNA binding regions in two newly discovered, though uncharacterized, regulatory RNAs.

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Using Mercury Isotopes To Understand Mercury Accumulation in the Montane Forest Floor of the Eastern Tibetan Plateau

by Wang, X; Luo, J; Yuan, W; Lin, CJ; Sommar, J; Feng, X; Wang, H; Lin, C

Journal of Environmental Science & Technology; Jan 17 2017; doi: 10.1021/acs.est.6b03806

Mercury accumulation in montane forested areas plays an important role in global Hg cycling. In this study, we measured stable Hg isotopes in soil and litter samples to understand Hg accumulation on the forest floor along the eastern fringe of the Tibetan Plateau (TP). The low atmospheric Hg inputs lead to the small Hg pool size (23 ± 9 mg m-2 in 0-60 cm soil horizon), up to 1 order of magnitude lower than those found at sites in Southwest China, North America, and Europe. The slightly negative Δ199Hg (-0.12 to -0.05‰) in the litter at low elevations (3100 to 3600 m) suggests an influence of local anthropogenic emissions, whereas the more significant negative Δ199Hg (-0.38 to -0.15‰) at high elevations (3700 to 4300 m) indicates impact from long-range transport. Hg input from litter is more important than wet deposition to Hg accumulation on the forest floor, as evidenced by the negative Δ199Hg found in the surface soil samples. Correlation analyses of Δ199Hg versus total carbon and leaf area index suggest that litter biomass production is a predominant factor in atmospheric Hg inputs to the forest floor. Precipitation and temperature show indirect effects on Hg accumulation by influencing litter biomass production in the eastern TP.

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Autocovariance-based MPC model mismatch with measurable disturbances USA estimation for systems

by Wang, SY; Simkoff, JM; Baldea, M; Chiang, LH; Castillo, I; Bindlish, R; Stanley, DB

JOURNAL OF PROCESS CONTROL; Jul 2017; Volume: 55; Pages: 42-54; DOI: 10.1016/j.jprocont.2017.03.002

In this paper, we propose a novel autocovariance-based plant-model mismatch estimation approach for linear MPC MIMO control loops with changing setpoints and, measurable disturbances. Assuming a noise model is available and that there are of periods of operating data where the active set of the controller is fixed and the plant-model mismatch is invariant, we establish an explicit relation between the autocovariance matrices of the mean-centered process outputs and the plant-model mismatch. We then formulate the mismatch estimation problem as an optimization aimed at minimizing the difference between the theoretical autocovariance, computed from the established relation, and actual output autocovariances, calculated from the plant data. We elaborate our results for step-response models typically used in MPC, as well as for parametric (transfer function models) in both continuous time and discrete time. A simulation case study for an unconstrained MPC controller with measurable disturbances is used to illustrate the theoretical results.

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Functionalized Polycyclic Aromatic Polymers for High Temperature Wireless Chemical Memory Threshold Sensors

by Leonhardt, B; Pasupathy, P; Trivedi, T; Zhang, S; Neikirk; Ekerdt, JG

JOURNAL OF INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH; May 17 2017; Volume: 56; Issue: 19; Pages: 5479-5482; DOI: 10.1021/acs.iecr.6b04541

A pair of new polymers, poly(di-t-butylacenaphthylene) (pTBAcN) and poly(dipropylacenaphthylene) (pPAcN), were made via Friedel-Crafts alkylation of polyacenaphthylene. These polymers exhibit thermal stability beyond 250 degrees C and solubility in excess of 25 wt % in aliphatic hydrocarbons. Films of pPAcN over 10 lam thick were successively applied to planar surfaces via brush coating. Chemical memory for a passive wire resonant sensor was utilized to detect aliphatic hydrocarbons in high temperature environments. The coated threshold sensor showed a lower, stable resonant frequency before and after exposure to water at 130 degrees C for 3 h and showed an increased triggered resonant frequency after aliphatic exposure, consistent with an uncoated sensor device.

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Monovalent and divalent ion sorption in a cation exchange membrane based on cross-linked poly (p-styrene sulfonate-co-divinylbenzene)

by Galizia, M; Benedetti, FM; Paul, DR; Freeman, BD

Journal of Membrane Science; Aug 1 2017; Volume: 535; Pages: 132-142; DOI: 10.1016/j.memsci.2017.04.007

Many fundamentals of ion sorption in ion exchange membranes (IEMs) are not fully understood, and few modern studies focus on multivalent ion sorption, despite the importance of divalent ion transport properties in water purification applications. Here, MgCl2 and CaCl2 sorption in a commercial cross-linked, styrene-divinylbenzene cation exchange membrane (CEM) with fixed sulfonate groups was measured and compared with NaCl, LiCl and KCl sorption in the same material. The data were correlated with counter-ion size and valence, as well as membrane water content. Divalent salts had higher sorption coefficients than monovalent salts, even though membrane water content significantly decreased in the presence of divalent counter-ions. The Donnan potential is weaker in the presence of multivalent counter-ions, which increases co-ion sorption, contributing to the observed increase in salt sorption coefficients for divalent salts. Ion activity coefficients in the membrane were calculated and compared to predictions of the recently proposed Manning-Donnan model. This model showed much better agreement with the experimental data than the ideal Donnan model, suggesting that ion nonideality in the membrane is important when analyzing ion sorption and transport in IEMs.

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High temperature stability and low adsorption of sub-100 nm magnetite nanoparticles grafted with sulfonated copolymers on Berea sandstone in high salinity brine

by Iqbal, M; Lyon, BA; Urena-Benavides, EE; Moaseri, E; Fei, YP; McFadden, C; Javier, KJ; Ellison, CJ; Pennell, KD; Johnston, KP

JOURNAL OF COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS; May 5 2017; Volume: 520; Pages: 257-267; DOI: 10.1016/j.colsurfa.2017.01.080

The synthesis of polymer grafted nanoparticles that are stable at high salinities and high temperature with low retention in porous media is of paramount importance for subsurface applications including electromagnetic imaging, enhanced oil recovery and environmental remediation. Herein, we present an improved approach to synthesize and purify sub-100 nm IONPs grafted with a random copolymer poly (AMPS-co-AA) (poly(2-acrylamido-3-methylpropanesulfonate-co-acrylic acid)) by means of catalyzed amide bond formation at room temperature. The improved and uniform polymer grafting of magnetic nanoparticles led to colloidal stability of IONPs at high temperature (120 degrees C) in API for a month. The transport behavior of the polymer grafted IONPs was investigated in crushed and in consolidated Berea sandstone. The high poly(AMPS-co-AA) polymer level on the surface (similar to 34%) provided electrosteric stabilization between the NPs and weak interactions of the NPs with anionic silica and sandstone surfaces. This behavior was enabled by low affinity of Ca2+ towards the highly acidic AMPS monomers thus enabling strong solvation in API brine. In crushed Berea sandstone, the retention was reduced by three fold and nine fold relative to our earlier studies, given the improvements in the grafted polymer layer. For intact core flood experiments in Berea sandstone carried out at elevated temperature (65 degrees C) and pressure (1000 psi net confining stress), the retention was 519 mu g/g, comparable to the value for crushed Berea sandstone. Furthermore, the addition of a relatively small amount (0.1% v/v) of commercially available sacrificial polymer (e.g., HEC-10) further reduced IONP retention to 252 gig or 0.17 mg/m(2) by blocking retentive sites.

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Influence of temperature on gas solubility in thermally rearranged (TR) polymers

by Stevens, KA; Smith, ZP; Gleason, KL; Galizia, M; Paul, DR; Freeman, BD

JOURNAL OF MEMBRANE SCIENCE; Jul 1 2017; Volume: 533; Pages: 75-83; DOI: 10.1016/j.memsci.2017.03.005

Thermally rearranged (TR) polymers have been the subject of many fundamental studies, but the effect of TR conversion on temperature-dependent transport properties is largely unexplored. Sorption isotherms for N-2, CH4, and CO2 in HAB-6FDA polyimide and its TR analogs were measured at temperatures ranging from -10 degrees C to 50 degrees C and pressures up to 27 atm. Solubilities increase with decreasing temperature for each gas and sample tested. At low TR conversions, the sorption process initially becomes less exothermic. However, enthalpies of sorption do not significantly change with TR conversion after the initial stages of rearrangement. Enthalpies of sorption in TR polymers are qualitatively similar to those of other high free volume materials. Solubility selectivity for CO2/CH4 at 10 atm did not change with temperature due to similar enthalpies of sorption for CO2 and CH4. Sorption data were fit to the dual mode model at different temperatures, and model parameters were correlated with polymer and penetrant properties.

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Probabilistic inverse design for self-assembling materials

by Jadrich, RB; Lindquist, BA; Truskett, TM

Journal of Chemical Physics; May 14 2017; Volume: 146; Issue: 18; Article Number: 184103; DOI: 10.1063/1.4981796

One emerging approach for the fabrication of complex architectures on the nanoscale is to utilize particles customized to intrinsically self-assemble into a desired structure. Inverse methods of statistical mechanics have proven particularly effective for the discovery of interparticle interactions suitable for this aim. Here we evaluate the generality and robustness of a recently introduced inverse design strategy [B. A. Lindquist et al., J. Chem. Phys. 145, 111101 (2016)] by applying this simulation-based machine learning method to optimize for interparticle interactions that self-assemble particles into a variety of complex microstructures as follows: cluster fluids, porous mesophases, and crystalline lattices. Using the method, we discover isotropic pair interactions that lead to the self-assembly of each of the desired morphologies, including several types of potentials that were not previously understood to be capable of stabilizing such systems. One such pair potential led to the assembly of the highly asymmetric truncated trihexagonal lattice and another produced a fluid containing spherical voids, or pores, of designed size via purely repulsive interactions. Through these examples, we demonstrate several advantages inherent to this particular design approach including the use of a parametrized functional form for the optimized interparticle interactions, the ability to constrain the range of said parameters, and compatibility of the inverse design strategy with a variety of simulation protocols (e.g., positional restraints).

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Fluid flow in UV nanoimprint lithography with patterned templates

by Jain, A; Spann, A; Cochrane, A; Schunk, PR; Bonnecaze, RT

Journal of Microelectronic Engineering; Apr 5 2017; Volume: 173; Pages: 62-70; DOI: 10.1016/j.mee.2017.04.001

Fluid flow in UV nanoimprint lithography with patterned template is simulated to study the effect of pattern directionality on droplet merging, throughput and defectivity. Flow in high density patterns is simulated by using an anisotropic permeability. A method to calculate the permeability for templates with line and space patterns is presented. It is found that the directionality of the pattern results in anisotropic spreading of the droplets. The droplets flow faster in the direction of the pattern resulting in channelized unfilled regions. These regions fill slowly because the permeability in the direction normal to the patterns is low. A modified hexagonal arrangement for droplet dispensing is proposed in which the filling time is lower than square and hexagonal droplet arrangements. Simulations are carried out with different multi-patterned template and droplet dispensing schemes. Dispensing droplets such that their volume is sufficient to fill the features locally is found to be the optimum dispensing scheme to minimize filling time.

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Enhanced Photoelectrochemical Performance of Porous Bi2MoO6 Photoanode by an Electrochemical Treatment

by Tang, D; Mabayoje, O; Lai, YQ; Liu, YX; Mullins, CB

JOURNAL OF THE ELECTROCHEMICAL SOCIETY; 2017; Volume: 164; Issue: 6; Pages: H299-H306; DOI: 10.1149/2.0271706jes

We report on the growth of porous Bi2MoO6 electrodes by first electrochemically depositing bismuth oxyiodide (BiOI) films and then thermally annealing the BiOI films with a molybdate solution. These Bi2MoO6 electrodes were tested as photoanodes for photoelectrochemical water oxidation. We found that the photoactivity of Bi2MoO6 electrode was largely improved after conducting a cyclic voltammetry treatment in 0.1 M phosphate buffer solution (pH 7.0). Through designed control experiments, XPS, FTIR and isoelectric point analyses, it was confirmed that phosphate anions (PO43-) modified the surface of Bi2MoO6 electrode during the cyclic voltammetry process and played a critical role in the enhancement of PEC performance. The performance improvement was attributed to the formation of a negative electrostatic field on the surface of Bi2MoO6 electrode after phosphate modification which resulted in the enhanced efficiency of charge separation.

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