Molecular Aspects of Transport in Thin Films of Controlled Architecture

Our laboratory focuses on developing spatially localized chemistries which can produce structures of controlled architecture on the supermolecular length scale -- structures which allow us to control the motion of molecular species with high spatial resolution, ultimately on nanometer length scales. Specifically, nanocapillary array membranes (NCAMs) contain an array of nanometer diameter pores connecting vertically separated microfluidic channels. NCAMs can manipulate samples with sub-femtoliter characteristic volumes and attomole sample amounts and are opening the field of chemical analysis of mass-limited samples, because they are capable of digital control of fluid switching down to sub-attoliter volumes; extension of analytical “unit operations” down to sub-femtomole sample sizes; and exerting spatiotemporal control over fluid mixing to enable studies of reaction dynamics. Digital flow switching mediated by nanocapillary array membranes can be controlled by bias, ionic strength, or pore diameter and is being studied by observing the temporal characteristics of transport across a single nanopore in thin PMMA membranes. The control of flow via nanopore surface characteristics, charge density and functional group presentation, is being studied by coupled conductivity and laser-induced fluorescence (LIF) measurements. Reactive mixing experiments previously established low millisecond mixing times for NCAM-mediated fluid transfer, and this has been exploited to demonstrate capture of mass-limited target species by Au colloids. Voltage and thermally-activated polymer switches have been developed for active control of transport in NCAMs. Thermally-switchable and size-selective transport was achieved by grafting poly(N-isopropylacrylamide) brushes onto the exterior surface of a Au-coated polycarbonate track-etched membrane, while the voltage-gated properties of poly(hydroxyethylmethacrylate) were characterized dynamically. Electrophoretic separations have been coupled to analyte sampling both by LIF and mass spectrometry. Detection of electrophoresis separation products by electrospray mass spectrometry was achieved through direct interfacing to an electrospray mass spectrometer. Pb(II) interactions with the DNAzyme have been realized in an NCAM-coupled integrated microfluidic structure allowing cation separations to be coupled to molecular beacon detection motifs for the determination of Pb(II) in an electroplating sludge reference material. By changing the DNAzyme to select for other compounds of interest, it is possible to incorporate multiple sensing systems within a single device, thereby achieving great flexibility

Reconstruction of eye movements during blinks

In eye movement research in reading, the amount of data plays a crucial role for the validation of results. A methodological problem for the analysis of the eye movement in reading are blinks, when readers close their eyes. Blinking rate increases with increasing reading time, resulting in high data losses, especially for older adults or reading impaired subjects. We present a method, based on the symbolic sequence dynamics of the eye movements, that reconstructs the horizontal position of the eyes while the reader blinks. The method makes use of an observed fact that the movements of the eyes before closing or after opening contain information about the eyes movements during blinks. Test results indicate that our reconstruction method is superior to methods that use simpler interpolation approaches. In addition, analyses of the reconstructed data show no significant deviation from the usual behavior observed in readers

Three Dimensional Molecular Imaging for Lignocellulosic Materials

The development of high efficiency, inexpensive processing protocols to render biomass components into fermentable substrates for the sequential processing of cell wall components into fuels and important feedstocks for the biorefinery of the future is a key goal of the national roadmap for renewable energy. Furthermore, the development of such protocols depends critically on detailed knowledge of the spatial and temporal infiltration of reagents designed to remove and separate the phenylpropenoid heteropolymer (lignin) from the processable sugar components sequestered in the rigid cell walls of plants. A detailed chemical and structural understanding of this pre-enzymatic processing in space and time was the focus of this program. We worked to develop new imaging strategies that produce real-time molecular speciation information in situ; extract sub-surface information about the effects of processing; and follow the spatial and temporal characteristics of the molecular species in the matrix and correlate this complex profile with saccharification. Spatially correlated SIMS and Raman imaging were used to provide high quality, high resolution subcellular images of Miscanthus cross sections. Furthermore, the combination of information from the mass spectrometry and Raman scattering allows specific chemical assignments of observed structures, difficult to assign from either imaging approach alone and lays the foundation for subsequent heterocorrelated imaging experiments targeted at more challenging biological systems, such as the interacting plant-microbe systems relevant to the rhizosphere

Single-molecule spectroelectrochemical cross-correlation during redox cycling in recessed dual ring electrode zero-mode waveguides

The ability of zero-mode waveguides (ZMW) to guide light into subwavelength-diameter nanoapertures has been exploited for studying electron transfer dynamics in zeptoliter-volume nanopores under single-molecule occupancy conditions

Observation of the superconducting proximity effect in Nb/InAs and NbNx/InAs by Raman scattering

URL:http://link.aps.org/doi/10.1103/PhysRevB.66.134530 DOI:10.1103/PhysRevB.66.134530High-quality thin Nb and NbN films (60-100 Å) are grown on (100) n+-InAs (n=1019cm-3) substrates by dc-magnetron sputter deposition. Studies of the electronic properties of interfaces between the superconductor and the semiconductor are done by Raman scattering measurements. The superconducting proximity effect at superconductor-semiconductor interfaces is observed through its impact on inelastic light scattering intensities originating from the near-interface region of InAs. The InAs longitudinal optical phonon LO mode (237cm-1) and the plasmon-phonon coupled modes L- (221cm-1) and L+ (1100 to 1350cm-1), for n+=1×1019-2×1019cm-3 are measured. The intensity ratio of the LO mode (associated with the near-surface charge accumulation region, in InAs) to that of the L- mode (associated with bulk InAs), is observed to increase by up to 40% below the superconducting transition temperature. This temperature-dependent change in light scattering properties is only observed with high quality superconducting films and when the superconductor and the semiconductor are in good electrical contact. A few possible mechanisms of the observed effect are proposed.We gratefully acknowledge support from the United States Department of Energy through Materials Research Laboratory~Grant No. DEFG02-96ER45439! ~I.V.R., A.C.A., L.H.G., T.A.T., J.F.D., P.W.B., J.F.K.!, and from the United States Department of Energy through Midwest Superconductivity Consortium ~MISCON! ~Grant No. DE FG02-90ER45427! and the NSF ~Grant No. DMR 96-23827! ~S.W.H., P.F.M.!. SEM, XRD, XPS, and RBS materials characterizations were performed at the Center for Microanalysis of Materials and Microfabrication Center at Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana- Champaign ~Grant No. DE FG02-96ER45439!. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin company, for the United States Department of Energy under Contract No. DE-AC04-94AL85000

Calculations of collisions between cold alkaline earth atoms in a weak laser field

We calculate the light-induced collisional loss of laser-cooled and trapped magnesium atoms for detunings up to 50 atomic linewidths to the red of the ^1S_0-^1P_1 cooling transition. We evaluate loss rate coefficients due to both radiative and nonradiative state-changing mechanisms for temperatures at and below the Doppler cooling temperature. We solve the Schrodinger equation with a complex potential to represent spontaneous decay, but also give analytic models for various limits. Vibrational structure due to molecular photoassociation is present in the trap loss spectrum. Relatively broad structure due to absorption to the Mg_2 ^1Sigma_u state occurs for detunings larger than about 10 atomic linewidths. Much sharper structure, especially evident at low temperature, occurs even at smaller detunings due to of Mg_2 ^1Pi_g absorption, which is weakly allowed due to relativistic retardation corrections to the forbidden dipole transition strength. We also perform model studies for the other alkaline earth species Ca, Sr, and Ba and for Yb, and find similar qualitative behavior as for Mg.Comment: 20 pages, RevTex, 13 eps figures embedde

Diffusion-Driven Looping Provides a Consistent Framework for Chromatin Organization

Chromatin folding inside the interphase nucleus of eukaryotic cells is done on multiple scales of length and time. Despite recent progress in understanding the folding motifs of chromatin, the higher-order structure still remains elusive. Various experimental studies reveal a tight connection between genome folding and function. Chromosomes fold into a confined subspace of the nucleus and form distinct territories. Chromatin looping seems to play a dominant role both in transcriptional regulation as well as in chromatin organization and has been assumed to be mediated by long-range interactions in many polymer models. However, it remains a crucial question which mechanisms are necessary to make two chromatin regions become co-located, i.e. have them in spatial proximity. We demonstrate that the formation of loops can be accomplished solely on the basis of diffusional motion. The probabilistic nature of temporary contacts mimics the effects of proteins, e.g. transcription factors, in the solvent. We establish testable quantitative predictions by deriving scale-independent measures for comparison to experimental data. In this Dynamic Loop (DL) model, the co-localization probability of distant elements is strongly increased compared to linear non-looping chains. The model correctly describes folding into a confined space as well as the experimentally observed cell-to-cell variation. Most importantly, at biological densities, model chromosomes occupy distinct territories showing less inter-chromosomal contacts than linear chains. Thus, dynamic diffusion-based looping, i.e. gene co-localization, provides a consistent framework for chromatin organization in eukaryotic interphase nuclei

A model for Escherichia coli chromosome packaging supports transcription factor-induced DNA domain formation

What physical mechanism leads to organization of a highly condensed and confined circular chromosome? Computational modeling shows that confinement-induced organization is able to overcome the chromosome's propensity to mix by the formation of topological domains. The experimentally observed high precision of separate subcellular positioning of loci (located on different chromosomal domains) in Escherichia coli naturally emerges as a result of entropic demixing of such chromosomal loops. We propose one possible mechanism for organizing these domains: regulatory control defined by the underlying E. coli gene regulatory network requires the colocalization of transcription factor genes and target genes. Investigating this assumption, we find the DNA chain to self-organize into several topologically distinguishable domains where the interplay between the entropic repulsion of chromosomal loops and their compression due to the confining geometry induces an effective nucleoid filament-type of structure. Thus, we propose that the physical structure of the chromosome is a direct result of regulatory interactions. To reproduce the observed precise ordering of the chromosome, we estimate that the domain sizes are distributed between 10 and 700 kb, in agreement with the size of topological domains identified in the context of DNA supercoiling

A carotenoid-deficient mutant in Pantoea sp. YR343, a bacteria isolated from the Rhizosphere of Populus deltoides, is defective in root colonization

The complex interactions between plants and their microbiome can have a profound effect on the health and productivity of the plant host. A better understanding of the microbial mechanisms that promote plant health and stress tolerance will enable strategies for improving the productivity of economically important plants. Pantoea sp. YR343 is a motile, rod-shaped bacterium isolated from the roots of Populus deltoides that possesses the ability to solubilize phosphate and produce the phytohormone indole-3-acetic acid (IAA). Pantoea sp. YR343 readily colonizes plant roots and does not appear to be pathogenic when applied to the leaves or roots of selected plant hosts. To better understand the molecular mechanisms involved in plant association and rhizosphere survival by Pantoea sp. YR343, we constructed a mutant in which the crtB gene encoding phytoene synthase was deleted. Phytoene synthase is responsible for converting geranylgeranyl pyrophosphate to phytoene, an important precursor to the production of carotenoids. As predicted, the ΔcrtB mutant is defective in carotenoid production, and shows increased sensitivity to oxidative stress. Moreover, we find that the ΔcrtB mutant is impaired in biofilm formation and production of IAA. Finally we demonstrate that the ΔcrtB mutant shows reduced colonization of plant roots. Taken together, these data suggest that carotenoids are important for plant association and/or rhizosphere survival in Pantoea sp. YR343.Work at the University of Notre Dame was supported by DOE grant SC0006642 (RM) and by a subcontract from Oak Ridge National Laboratory (SP).http://www.frontiersin.orgam2016Microbiology and Plant Patholog