Multimode Analysis of Nanoscale Biomolecular Interactions

Biomolecular interactions, including protein-protein, protein-DNA, and protein-ligand interactions, are of special importance in all biological systems. These interactions may occer during the loading of biomolecules to interfaces, the translocation of biomolecules through transmembrane protein pores, and the movement of biomolecules in a crowded intracellular environment. The molecular interaction of a protein with its binding partners is crucial in fundamental biological processes such as electron transfer, intracellular signal transmission and regulation, neuroprotective mechanisms, and regulation of DNA topology. In this dissertation, a customized surface plasmon resonance (SPR) has been optimized and new theoretical and label free experimental methods with related analytical calculations have been developed for the analysis of biomolecular interactions. Human neuroglobin (hNgb) and cytochrome c from equine heart (Cyt c) proteins have been used to optimize the customized SPR instrument. The obtained Kd value (~13 µM), from SPR results, for Cyt c-hNgb molecular interactions is in general agreement with a previously published result. The SPR results also confirmed no significant impact of the internal disulfide bridge between Cys 46 and Cys 55 on hNgb binding to Cyt c. Using SPR, E. coli topoisomerase I enzyme turnover during plasmid DNA relaxation was found to be enhanced in the presence of Mg2+. In addition, a new theoretical approach of analyzing biphasic SPR data has been introduced based on analytical solutions of the biphasic rate equations. In order to develop a new label free method to quantitatively study protein-protein interactions, quartz nanopipettes were chemically modified. The derived Kd (~20 µM) value for the Cyt c-hNgb complex formations matched very well with SPR measurements (Kd ~16 µM). The finite element numerical simulation results were similar to the nanopipette experimental results. These results demonstrate that nanopipettes can potentially be used as a new class of a label-free analytical method to quantitatively characterize protein-protein interactions in attoliter sensing volumes, based on a charge sensing mechanism. Moreover, the molecule-based selective nature of hydrophobic and nanometer sized carbon nanotube (CNT) pores was observed. This result might be helpful to understand the selective nature of cellular transport through transmembrane protein pores.

Fibrillar Elastomeric Micropatterns Create Tunable Adhesion Even to Rough Surfaces

Acknowledgements V.B., N.K.G., and E.A. contributed with conception and experimental design. V.B. performed the experiments. V.B., R.H., A.G., and R.M.M. carried out analysis and interpretation of data. V.B., R.H., A.G., and E.A. wrote the manuscript. V.B. and R.H. contributed equally to this work. V.B. acknowledges funding by SPP 1420 of the German Science Foundation DFG. E.A., N.K.G., and R.H. acknowledge funding from the European Research Council under the European Union/ERC Advanced Grant “Switch2Stick,” Agreement No. 340929.

Understanding the twist-bend nematic phase: the characterisation of 1-(4-cyanobiphenyl-4'-yloxy)-6-(4-cyanobiphenyl-4'-yl) hexane (CB6OCB) and comparison with CB7CB

Acknowledgements The FFTEM data were obtained at the (Cryo) TEM facility at the Liquid Crystal Institute, Kent State University, supported by the Ohio Research Scholars Program Research Cluster on Surfaces in Advanced Materials. ODL acknowledges the support of NSF DMR-1410378 grant. The authors are grateful for financial support from MINECO/FEDER MAT2015-66208-C3-2-P and from the Gobierno Vasco (GI/IT-449-10)

Crystal structure of 1-benzylsulfonyl-1,2,3,4-tetrahydroquinoline

Peer reviewed

Multimode Atomic Pattern Formation via Enhanced Light-atom Interactions

The nonlinear interaction between light and atoms is an extensive field of study with a broad range of applications in quantum information science and condensed matter physics. Nonlinear optical phenomena occurring in cold atoms are particularly interesting because such slowly moving atoms can spatially organize into density gratings, which allows for studies involving optical interactions with structured materials. In this thesis, I describe a novel nonlinear optical effect that arises when cold atoms spatially bunch in an optical lattice. I show that employing this spatial atomic bunching provides access to a unique physical regime with reduced thresholds for nonlinear optical processes and enhanced material properties. Using this method, I observe the nonlinear optical phenomenon of transverse optical pattern formation at record-low powers. These transverse optical patterns are generated by a wave- mixing process that is mediated by the cold atomic vapor. The optical patterns are highly multimode and induce rich non-equilibrium atomic dynamics. In particular, I find that there exists a synergistic interplay between the generated optical pat- terns and the atoms, wherein the scattered fields help the atoms to self-organize into new, multimode structures that are not externally imposed on the atomic sample. These self-organized structures in turn enhance the power in the optical patterns. I provide the first detailed investigation of the motional dynamics of atoms that have self-organized in a multimode geometry. I also show that the transverse optical patterns induce Sisyphus cooling in all three spatial dimensions, which is the first observation of spontaneous three-dimensional cooling. My experiment represents a unique means by which to study nonlinear optics and non-equilibrium dynamics at ultra-low required powers.

Multistabilities and symmetry-broken one-color and two-color states in closely coupled single-mode lasers

We theoretically investigate the dynamics of two mutually coupled, identical single-mode semi-conductor lasers. For small separation and large coupling between the lasers, symmetry-broken one-color states are shown to be stable. In this case the light outputs of the lasers have significantly different intensities while at the same time the lasers are locked to a single common frequency. For intermediate coupling we observe stable symmetry-broken two-color states, where both lasers lase simultaneously at two optical frequencies which are separated by up to 150 GHz. Using a five-dimensional model, we identify the bifurcation structure which is responsible for the appearance of symmetric and symmetry-broken one-color and two-color states. Several of these states give rise to multistabilities and therefore allow for the design of all-optical memory elements on the basis of two coupled single-mode lasers. The switching performance of selected designs of optical memory elements is studied numerically.

Particle-in-cell simulation study of a lower-hybrid shock

The expansion of a magnetized high-pressure plasma into a low-pressure ambient medium is examined with particle-in-cell simulations. The magnetic field points perpendicular to the plasma's expansion direction and binary collisions between particles are absent. The expanding plasma steepens into a quasi-electrostatic shock that is sustained by the lower-hybrid (LH) wave. The ambipolar electric field points in the expansion direction and it induces together with the background magnetic field a fast E cross B drift of electrons. The drifting electrons modify the background magnetic field, resulting in its pile-up by the LH shock. The magnetic pressure gradient force accelerates the ambient ions ahead of the LH shock, reducing the relative velocity between the ambient plasma and the LH shock to about the phase speed of the shocked LH wave, transforming the LH shock into a nonlinear LH wave. The oscillations of the electrostatic potential have a larger amplitude and wavelength in the magnetized plasma than in an unmagnetized one with otherwise identical conditions. The energy loss to the drifting electrons leads to a noticeable slowdown of the LH shock compared to that in an unmagnetized plasma.

Intra-pulse transition between ion acceleration mechanisms in intense laser-foil interactions

Multiple ion acceleration mechanisms can occur when an ultrathin foil is irradiated with an intense laser pulse, with the dominant mechanism changing over the course of the interaction. Measurement of the spatial-intensity distribution of the beam of energetic protons is used to investigate the transition from radiation pressure acceleration to transparency-driven processes. It is shown numerically that radiation pressure drives an increased expansion of the target ions within the spatial extent of the laser focal spot, which induces a radial deflection of relatively low energy sheath-accelerated protons to form an annular distribution. Through variation of the target foil thickness, the opening angle of the ring is shown to be correlated to the point in time transparency occurs during the interaction and is maximized when it occurs at the peak of the laser intensity profile. Corresponding experimental measurements of the ring size variation with target thickness exhibit the same trends and provide insight into the intra-pulse laser-plasma evolution.

Charge migration induced by attosecond pulses in bio-relevant molecules

After sudden ionization of a large molecule, the positive charge can migrate throughout the system on a sub-femtosecond time scale, purely guided by electronic coherences. The possibility to actively explore the role of the electron dynamics in the photo-chemistry of bio-relevant molecules is of fundamental interest for understanding, and perhaps ultimately controlling, the processes leading to damage, mutation and, more generally, to the alteration of the biological functions of the macromolecule. Attosecond laser sources can provide the extreme time resolution required to follow this ultrafast charge flow. In this review we will present recent advances in attosecond molecular science: after a brief description of the results obtained for small molecules, recent experimental and theoretical findings on charge migration in bio-relevant molecules will be discussed.

Evaluation of strontium-site-deficient Sr2Fe1.4Co0.1Mo0.5O6-δ-based perovskite oxides as intermediate temperature solid oxide fuel cell cathodes

In this paper strontium-site-deficient Sr₂Fe_1.4Co_0.1Mo_0.5O_6-δ-based perovskite oxides (S_xFCM) were prepared and evaluated as the cathode materials for intermediate temperature solid oxide fuel cells (IT-SOFCs). All samples exhibited a cubic phase structure and the lattice shrinked with increasing the Sr-deficiency as shown in XRD patterns. XPS results determined that the transition elements (Co/Fe/Mo) in S_xFCM oxides were in a mixed valence state, demonstrating the small polaron hopping conductivity mechanism existed. Among the samples, S_1.950FCM presented the lowest coefficient of thermal expansion of 15.62 × 10^-6 K^-1, the highest conductivity value of 28 S cm^-1 at 500 °C, and the lowest interfacial polarization resistance of 0.093 Ω cm² at 800 °C, respectively. Furthermore, an anode-supported single cell with a S_1.950FCM cathode was prepared, demonstrating a maximum power density of 1.16 W cm^-2 at 800 °C by using wet H₂ (3% H₂O) as the fuel and ambient air as the oxidant. These results indicate that the introduction of Sr-deficiency can dramatically improve the electrochemical performance of Sr₂Fe_1.4Co_0.1Mo_0.5O_6-δ, showing great promise as a novel cathode candidate material for IT-SOFCs.

Facile synthesis of copper-manganese spinel anodes with high capacity and cycling performance for lithium-ion batteries

Copper-manganese spinel containing anodes were synthesized by a facile sol-gel method and evaluated in lithium-ion battery applications for the first time. The synergistic effects between copper-manganese and the aqueous binder (sodium carboxymethyl cellulose) provided a high specific capacity and excellent cycling performance. It was found that the specific capacity of the copper-manganese spinel remained at 608 mAh g⁻¹ after 100 cycles at a current density of 200 mA g⁻¹. Furthermore, a relatively high reversible capacity of 278 mAh g⁻¹ could be obtained at a current density of 2000 mA g⁻¹, indicating a good rate capability. These studies suggest that copper-manganese spinel is a promising material for lithium-ion battery applications due to a combination of good electrochemical performance and low cost.

An effective three-dimensional ordered mesoporous CuCo2O4 as electrocatalyst for Li-O2 batteries

Three-dimensional ordered mesoporous (3DOM) CuCo₂O₄ materials have been synthesized via a hard template and used as bifunctional electrocatalysts for rechargeable Li-O₂ batteries. The characterization of the catalyst by X-ray diffractometry and transmission electron microscopy confirms the formation of a single-phase, 3-dimensional, ordered mesoporous CuCo₂O₄ structure. The as-prepared CuCo₂O₄ nanoparticles possess a high specific surface area of 97.1 m² g^{- 1} and a spinel crystalline structure. Cyclic voltammetry demonstrates that mesoporous CuCo₂O₄ catalyst enhances the kinetics for either oxygen reduction reaction (ORR) or oxygen evolution reaction (OER). The Li-O₂ battery utilizing 3DOM CuCo₂O₄ shows a higher specific capacity of 7456 mAh g^{- 1} than that with pure Ketjen black (KB). Moreover, the CuCo₂O₄-based electrode enables much enhanced cyclability with a 610 mV smaller discharge-recharge voltage gap than that of the carbon-only cathode at a current rate of 100 mA g^{- 1}. Such excellent catalytic performance of CuCo₂O₄ could be associated with its larger surface area and 3D ordered mesoporous structure. The excellent electrochemical performances coupled with its facile and cost-effective way will render the 3D mesoporous CuCo₂O₄ nanostructures as attractive electrode materials for promising application in Li-O₂ batteries.

Improved electrochemical performance of Sr2Fe1.5Mo0.4Nb0.1O6-δ -Sm0.2Ce0.8O2-δ composite cathodes by a one-pot method for intermediate temperature solid oxide fuel cells

In this paper, Sr₂Fe_1.5Mo_0.4Nb_0.1O_6-δ (SFMNb)-xSm_0.2Ce_0.8O_2-δ (SDC) (x = 0, 20, 30, 40, 50 wt%) composite cathode materials were synthesized by a one-pot combustion method to improve the electrochemical performance of SFMNb cathode for intermediate temperature solid oxide fuel cells (IT-SOFCs). The fabrication of composite cathodes by adding SDC to SFMNb is conducive to providing extended electrochemical reaction zones for oxygen reduction reactions (ORR). X-ray diffraction (XRD) demonstrates that SFMNb is chemically compatible with SDC electrolytes at temperature up to 1100 °C. Scanning electron microscope (SEM) indicates that the SFMNb-SDC composite cathodes have a porous network nanostructure as well as the single phase SFMNb. The conductivity and thermal expansion coefficient of the composite cathodes decrease with the increased content of SDC, while the electrochemical impedance spectra (EIS) exhibits that SFMNb-40SDC composite cathode has optimal electrochemical performance with low polarization resistance (R_p) on the La_0.9Sr_0.1Ga_0.8Mg_0.2O₃ electrolyte. The R_p of the SFMNb-40SDC composite cathode is about 0.047 Ω cm² at 800 °C in air. A single cell with SFMNb-40SDC cathode also displays favorable discharge performance, whose maximum power density is 1.22 W cm^-2 at 800 °C. All results indicate that SFMNb-40SDC composite material is a promising cathode candidate for IT-SOFCs.

Synthesis of Pr0.6Sr0.4FeO 3-δ -xCe0.9Pr0.1O 2-δ cobalt-free composite cathodes by a one-pot method for intermediate-temperature solid oxide fuel cells

Cobalt-free composite cathodes consisting of Pr_0.6Sr_0.4FeO _3-δ -xCe_0.9Pr_0.1O _2-δ (PSFO-xCPO, x = 0-50 wt%) have been synthesized using a one-pot method. X-ray diffraction, scanning electron microscopy, thermal expansion coefficient, conductivity, and polarization resistance (R _P ) have been used to characterize the PSFO-xCPO cathodes. Furthermore the discharge performance of the Ni-SSZ/SSZ/GDC/PSFO-xCPO cells has been measured. The experimental results indicate that the PSFO-xCPO composite materials fully consist of PSFO and CPO phases and posses a porous microstructure. The conductivity of PSFO-xCPO decreases with the increase of CPO content, but R _P of PSFO-40CPO shows the smallest value amongst all the samples. The power density of single cells with a PSFO-40CPO composite cathode is significantly improved compared with that of the PSFO cathode, exhibiting 0.43, 0.75, 1.08 and 1.30 W cm^-2 at 650, 700, 750 and 800 °C, respectively. In addition, single cells with the PSFO-40CPO composite cathode show a stable performance with no obvious degradation over 100 h when operating at 750 °C.

Absolute cross sections for dissociative electron attachment to HCCCN

New absolute cross sections for dissociative electron attachment to HCCCN (cyanoacetylene or propiolonitrile) in the range of 0-10 eV electron energy are presented here, which have been determined from a new analysis of previously reported data (Graupner et al 2006 New J. Phys. 8 117). The highest cross sections are observed for the formation of CN^- at 5.3 eV and CCCN^- at 5.1 eV; approximately 0.06 Ų and 0.05 Ų respectively. As part of the re-analysis, it was necessary to determine absolute cross sections for electron-impact ionization of HCCCN with the binary-encounter Bethe method. These electron-impact ionization absolute cross sections for HCCCN are also presented here; the maximum value was found to be ∼6.6 Ų at ∼80 eV.