Chiroptical spectroscopy of biomolecules using chiral plasmonic nanostructures

This thesis explores the potential of chiral plasmonic nanostructures for the ultrasensitive detection of protein structure. These nanostructures support the generation of fields with enhanced chirality relative to circularly polarised light and are an extremely incisive probe of protein structure. In chapter 4 we introduce a nanopatterned Au film (Templated Plasmonic Substrate, TPS) fabricated using a high through-put injection moulding technique which is a viable alternative to expensive lithographically fabricated nanostructures. The optical and chiroptical properties of TPS nanostructures are found to be highly dependent on the coupling between the electric and magnetic modes of the constituent solid and inverse structures. Significantly, refractive index based measurements of strongly coupled TPSs display a similar sensitivity to protein structure as previous lithographic nanostructures. We subsequently endeavour to improve the sensing properties of TPS nanostructures by developing a high through-put nanoscale chemical functionalisation technique. This process involves a chemical protection/deprotection strategy. The protection step generates a self-assembled monolayer (SAM) of a thermally responsive polymer on the TPS surface which inhibits protein binding. The deprotection step exploits the presence of nanolocalised thermal gradients in the water surrounding the TPS upon irradiation with an 8ns pulsed laser to modify the SAM conformation on surfaces with high net chirality. This allows binding of biomaterial in these regions and subsequently enhances the TPS sensitivity levels. In chapter 6 an alternative method for the detection of protein structure using TPS nanostructures is introduced. This technique relies on mediation of the electric/magnetic coupling in the TPS by the adsorbed protein. This phenomenon is probed through both linear reflectance and nonlinear second harmonic generation (SHG) measurements. Detection of protein structure using this method does not require the presence of fields of enhanced chirality whilst it is also sensitive to a larger array of secondary structure motifs than the measurements in chapters 4 and 5. Finally, a preliminary investigation into the detection of mesoscale biological structure is presented. Sensitivity to the mesoscale helical pitch of insulin amyloid fibrils is displayed through the asymmetry in the circular dichroism (CD) of lithographic gammadions of varying thickness upon adsorption of insulin amyloid fibril spherulites and fragmented fibrils. The proposed model for this sensitivity to the helical pitch relies on the vertical height of the nanostructures relative to this structural property as well as the binding orientation of the fibrils.

A thermal-elastic analysis on laser-induced reverse bulging and plugging in circular brass foil

A new failure mode is observed in circular brass foils induced by laser beam. The new failure is based on the following experimental facts : (1) the peripheries of the circular brass foils are fixed and the surfaces of the foils are radiated by laser beam ; (2) the laser beam used is considered to be non-Gaussian spatially, actually an approximately uniform distribution limited in a certain size spot ; (3) the pulse on time of laser beam should be 250 μs, i.e. so called long duration pulse laser. The failure process consists of three stages ; i.e. thermal bulging, localized shear deformation and perforation by plugging. The word reverse in reverse bulging and plugging mode means that bulging and plugging occur in the direction of incident laser beam. To study the newly-discovered type of failure quantitatively, analytical solutions for the axisymmetric temperature field and deflection curve are derived. The calculated results show that the newly discovered failure mode is attributed to the spatial structure effect of laser beam indeed.

Flow-induced vibrations of long circular cylinders modeled by coupled nonlinear oscillators

The dynamics of long slender cylinders undergoing vortex-induced vibrations (VIV) is studied in this work. Long slender cylinders such as risers or tension legs are widely used in the field of ocean engineering. When the sea current flows past a cylinder, it will be excited due to vortex shedding. A three-dimensional time domain model is formulated to describe the response of the cylinder, in which the in-line (IL) and cross-flow (CF) deflections are coupled. The wake dynamics, including in-line and cross-flow vibrations, is represented using a pair of non-linear oscillators distributed along the cylinder. The wake oscillators are coupled to the dynamics of the long cylinder with the acceleration coupling term. A non-linear fluid force model is accounted for to reflect the relative motion of cylinder to current. The model is validated against the published data from a tank experiment with the free span riser. The comparisons show that some aspects due to VIV of long flexible cylinders can be reproduced by the proposed model, such as vibrating frequency, dominant mode number, occurrence and transition of the standing or traveling waves. In the case study, the simulations show that the IL curvature is not smaller than CF curvature, which indicates that both IL and CF vibrations are important for the structural fatigue damage.

I. Studies on bacteriophage DNA's and minicircular DNA's in M. lysodeikticus and E. coli 15. II. Flow dichroism of DNA solutions

Part I

Chapter 1.....A physicochemical study of the DNA molecules from the three bacteriophages, N1, N5, and N6, which infect the bacterium, M. lysodeikticus, has been made. The molecular weights, as measured by both electron microscopy and sedimentation velocity, are 23 x 10⁶ for N5 DNA and 31 x 10⁶ for N1 and N6 DNA's. All three DNA's are capable of thermally reversible cyclization. N1 and N6 DNA's have identical or very similar base sequences as judged by membrane filter hybridization and by electron microscope heteroduplex studies. They have identical or similar cohesive ends. These results are in accord with the close biological relation between N1 and N6 phages. N5 DNA is not closely related to N1 or N6 DNA. The denaturation T_m of all three DNA's is the same and corresponds to a (GC) content of 70%. However, the buoyant densities in CsCl of Nl and N6 DNA's are lower than expected, corresponding to predicted GC contents of 64 and 67%. The buoyant densities in Cs₂SO₄ are also somewhat anomalous. The buoyant density anomalies are probably due to the presence of odd bases. However, direct base composition analysis of N1 DNA by anion exchange chromatography confirms a GC content of 70%, and, in the elution system used, no peaks due to odd bases are present.

Chapter 2.....A covalently closed circular DNA form has been observed as an intracellular form during both productive and abortive infection processes in M. lysodeikticus. This species has been isolated by the method of CsC1-ethidium bromide centrifugation and examined with an electron microscope.

Chapter 3.....A minute circular DNA has been discovered as a homogeneous population in M. lysodeikticus. Its length and molecular weight as determined by electron microscopy are 0.445 μ and 0.88 x 10⁶ daltons respectively. There is about one minicircle per bacterium.

Chapter 4.....Several strains of E. coli 15 harbor a prophage. Viral growth can be induced by exposing the host to mitomycin C or to uv irradiation. The coliphage 15 particles from E. coli 15 and E, coli 15 T^- appear as normal phage with head and tail structure; the particles from E. coli 15 TAU are tailless. The complete particles exert a colicinogenic activity on E.coli 15 and 15 T^-, the tailless particles do not. No host for a productive viral infection has been found and the phage may be defective. The properties of the DNA of the virus have been studied, mainly by electron microscopy. After induction but before lysis, a closed circular DNA with a contour length of about 11.9 μ is found in the bacterium; the mature phage DNA is a linear duplex and 7.5% longer than the intracellular circular form. This suggests the hypothesis that the mature phage DNA is terminally repetitious and circularly permuted. The hypothesis was confirmed by observing that denaturation and renaturation of the mature phage DNA produce circular duplexes with two single-stranded branches corresponding to the terminal repetition. The contour length of the mature phage DNA was measured relative to φX RFII DNA and λ DNA; the calculated molecular weight is 27 x 10⁶. The length of the single-stranded terminal repetition was compared to the length of φX 174 DNA under conditions where single-stranded DNA is seen in an extended form in electron micrographs. The length of the terminal repetition is found to be 7.4% of the length of the nonrepetitious part of the coliphage 15 DNA. The number of base pairs in the terminal repetition is variable in different molecules, with a fractional standard deviation of 0.18 of the average number in the terminal repetition. A new phenomenon termed "branch migration" has been discovered in renatured circular molecules; it results in forked branches, with two emerging single strands, at the position of the terminal repetition. The distribution of branch separations between the two terminal repetitions in the population of renatured circular molecules was studied. The observed distribution suggests that there is an excluded volume effect in the renaturation of a population of circularly permuted molecules such that strands with close beginning points preferentially renature with each other. This selective renaturation and the phenomenon of branch migration both affect the distribution of branch separations; the observed distribution does not contradict the hypothesis of a random distribution of beginning points around the chromosome.

Chapter 5....Some physicochemical studies on the minicircular DNA species in E. coli 15 (0.670 μ, 1.47 x 10⁶ daltons) have been made. Electron microscopic observations showed multimeric forms of the minicircle which amount to 5% of total DNA species and also showed presumably replicating forms of the minicircle. A renaturation kinetic study showed that the minicircle is a unique DNA species in its size and base sequence. A study on the minicircle replication has been made under condition in which host DNA synthesis is synchronized. Despite experimental uncertainties involved, it seems that the minicircle replication is random and the number of the minicircles increases continuously throughout a generation of the host, regardless of host DNA synchronization.

Part II

The flow dichroism of dilute DNA solutions (A₂₆₀≈0.1) has been studied in a Couette-type apparatus with the outer cylinder rotating and with the light path parallel to the cylinder axis. Shear gradients in the range of 5-160 sec.^-1 were studied. The DNA samples were whole, "half," and "quarter" molecules of T4 bacteriophage DNA, and linear and circular λb₂b₅c DNA. For the linear molecules, the fractional flow dichroism is a linear function of molecular weight. The dichroism for linear A DNA is about 1.8 that of the circular molecule. For a given DNA, the dichroism is an approximately linear function of shear gradient, but with a slight upward curvature at low values of G, and some trend toward saturation at larger values of G. The fractional dichroism increases as the supporting electrolyte concentration decreases.

A NEW WAKE OSCILLATOR MODEL FOR PREDICTING VORTEX INDUCED VIBRATION OF A CIRCULAR CYLINDER

This article proposes a new wake oscillator model for vortex induced vibrations of an elastically supported rigid circular cylinder in a uniform current. The near wake dynamics related with the fluctuating nature of vortex shedding is modeled based on the classical van der Pol equation, combined with the equation for the oscillatory motion of the body. An appropriate approach is developed to estimate the empirical parameters in the wake oscillator model. The present predicted results are compared to the experimental data and previous wake oscillator Model results. Good agreement with experimental results is found.

Electrical activity induced by nitric oxide in canine colonic circular muscle.

Nitric oxide generates slow electrical oscillations (SEOs) in cells near the myenteric edge of the circular muscle layer, which resemble slow waves generated by interstitial cells of Cajal (ICCs) at the submucosal edge of this muscle. The properties of SEOs were studied to determine whether these events are similar to slow waves. Rapid frequency membrane potential oscillations (MPOs; 16 +/- 1 cycles/min and 9.6 +/- 0.2 mV) were recorded from control muscles near the myenteric edge. Sodium nitroprusside (0.3 microM) reduced MPOs and initiated SEOs (1.3 +/- 0.3 cycles/min and 13.4 +/- 1.4 mV amplitude). SEOs were abolished by the guanylate cyclase inhibitor 1H-[1,2,4]-oxadiazolo-[4,3-a]-quinoxaline-1-one (10 microM). MPOs were abolished by nifedipine (1 microM), whereas SEO frequency increased and the amount of depolarization decreased. BAY K 8644 (1 microM) prolonged SEOs and reduced their frequency. SEOs were abolished by Ni(2+) (0.5 mM), low Ca(2+) solution (0.1 mM Ca(2+)), cyclopiazonic acid (10 microM), and the mitochondrial uncouplers antimycin (10 microM) and carbonyl cyanide p-trifluoromethoxyphenylhydrazone (1 microM). Oligomycin (10 microM) was without effect. These effects are similar to those described for colonic slow waves. Our results suggest that nitric oxide-induced SEOs are similar in mechanism to slow waves, an activity not previously thought to be generated by myenteric pacemakers.

Two-degree-of-freedom vortex-induced vibration of circular cylinders with very low aspect ratio and small mass ratio

The investigation of vortex-induced vibration on very short cylinders with two degrees of freedom has drawn the attention of a large number of researchers. Some investigations on such a problem are carried out in order to have a better understanding of the physics involved in vortex-induced motions of floating bodies such as offshore platforms. In this paper, experiments were carried out in a recirculating water channel over the range of Reynolds number 6000

Computational simulation of the flow-induced vibration of a circular cylinder subjected to wake interference

In this work, we considered the flow around two circular cylinders of equal diameter placed in tandem with respect to the incident uniform flow. The upstream cylinder was fixed and the downstream cylinder was completely free to move in the cross-stream direction, with no spring or damper attached to it. The centre-to-centre distance between the cylinders was four diameters, and the Reynolds number was varied from 100 to 645. We performed two- and three-dimensional simulations of this flow using a Spectral/hp element method to discretise the flow equations, coupled to a simple Newmark integration routine that solves the equation of the dynamics of the cylinder. The differences of the behaviours observed in the two- and three-dimensional simulations are highlighted and the data is analysed under the light of previously published experimental results obtained for higher Reynolds numbers.

Two-degree-of-freedom vortex-induced vibration of circular cylinders with very low aspect ratio and small mass ratio

The investigation of vortex-induced vibration on very short cylinders with two degrees of freedom has drawn the attention of a large number of researchers. Some investigations on such a problem are carried out in order to have a better understanding of the physics involved in vortex-induced motions of floating bodies such as offshore platforms. In this paper, experiments were carried out in a recirculating water channel over the range of Reynolds number 6000

Induced Damping on Vibrating Circular Plates Submerged in still Fluid

When a structure vibrates immersed in a fluid it is known that the dynamic properties of the system are modified. The surrounding fluid will, in general, contribute to the inertia, the rigidity and the damping coefficient of the coupled fluid-structure system. For light structures, like spacecraft antennas, even when the fluid is air the contribution to the dynamic properties can be important. For not so light structures the ratio of the equivalent fluid/structure mass and rigidity can be very small and the fluid contribution could be neglected. For the ratio of equivalent fluid/structure damping both terms are of the same order and therefore the fluid contribution must be studied. The working life of the spacecraft structure would be on space and so without any surrounding fluid. The response of a spacecraft structure on its operational life would be attenuated by the structural damping alone but when the structure is dynamically tested on the earth the dynamic modal test is performed with the fluid surrounding it. The results thus are contaminated by the effects of the fluid. If the damping added by the fluid is of the same order as the structural damping the response of the structure in space can be quite different to the response predicted on earth. It is therefore desirable to have a method able to determine the amount of damping induced by the fluid and that should be subtracted of the total damping measured on the modal vibration test. In this work, a method for the determination of the effect of the surrounding fluid on the dynamic characteristics of a circular plate has been developed. The plate is assumed to vibrate harmonically with the vacuum modes and the generalized forces matrix due to the fluid is thus computed. For a compressible fluid this matrix is formed by complex numbers including terms of inertia, rigidity and damping. The matrix due to the fluid loading is determined by a boundary element method (BEM). The BEM used is of circular rings on the plate surface so the number of elements to obtain an accurate result is very low. The natural frequencies of the system are computed by an iteration procedure one by one and also the damping fluid contribution. Comparisons of the present method with various experimental data and other theories show the efficiency and accuracy of the method for any support condition of the plate.

Binocular summation improves performance to defocus-induced blur

PURPOSE. To assess whether there are any advantages of binocular over monocular vision under blur conditions. METHODS. We measured the effect of defocus, induced by positive lenses, on the pattern reversal Visual Evoked Potential (VEP) and on visual acuity (VA). Monocular (dominant eye) and binocular VEPs were recorded from thirteen volunteers (average age: 28±5 years, average spherical equivalent: -0.25±0.73 D) for defocus up to 2.00 D using positive powered lenses. VEPs were elicited using reversing 10 arcmin checks at a rate of 4 reversals/second. The stimulus subtended a circular field of 7 degrees with 100% contrast and mean luminance 30 cd/m2. VA was measured under the same conditions using ETDRS charts. All measurements were performed at 1m viewing distance with best spectacle sphero-cylindrical correction and natural pupils. RESULTS. With binocular stimulation, amplitudes and implicit times of the P100 component of the VEPs were greater and shorter, respectively, in all cases than for monocular stimulation. Mean binocular enhancement ratio in the P100 amplitude was 2.1 in-focus, increasing linearly with defocus to be 3.1 at +2.00 D defocus. Mean peak latency was 2.9 ms shorter in-focus with binocular than for monocular stimulation, with the difference increasing with defocus to 8.8 ms at +2.00 D. As for the VEP amplitude, VA was always better with binocular than with monocular vision, with the difference being greater for higher retinal blur. CONCLUSIONS. Both subjective and electrophysiological results show that binocular vision ameliorates the effect of defocus. The increased binocular facilitation observed with retinal blur may be due to the activation of a larger population of neurons at close-to-threshold detection under binocular stimulation.

Photocytotoxic Lanthanum(III) and Gadolinium(III) Complexes of Phenanthroline Bases Showing Light-Induced DNA Cleavage Activity

Lanthanide complexes of formulation [La(B)(2)(NO3)(3)] (1-3) and [Gd(B)(2)(NO3)(3)] (4-6), where B is a N,N-donor phenanthroline base, namely, 1,10-phenanthroline (phen in 1, 4),dipyrido[3,2-d2',3'-f]quinoxaline (dpq in 2,5) and dipyrido[3,2-a2',3'-c]phenazine (dppz in 3, 6), have been prepared, characterized from physicochemical data, and their photoinduced DNA and protein cleavage activity studied The photocytotoxicity of the dppz complexes 3 and 6 has been studied using HeLa cancer cells. The complexes exhibitligand centered bands in the UV region The dppz complexes show thelowest energy band at 380 nm in N,N-dimethylformamide (DMF) The La(III)complexes are diamagnetic. The Gd(III) complexes (4-6) have magneticmoments that correspond to seven unpaired electrons The complexes are1(.)1 electrolytic in aqueous DMF The dpq and dppz complexes in DMFshow ligand-based reductions. The complexes display moderate binding propensity to calf thymus DNA giving binding constant values in the range of 5.7 x 10(4)-5.8 x 10(5) M-1 with a relative order. 3, 6 (dppz)> 2, 5 (dpq) > 1, 4 (phen) The binding data suggest DNA surface and/or groove binding nature of the complexes. The complexes do not show any hydrolytic cleavage of plasmid supercoiled pUC19 DNA. The dpq and dppz complexes efficiently cleave SC DNA to its nicked circular form onexposure to UV-A light of 365 nm at nanomolar complex concentration. Mechanistic studies reveal the involvement of singlet oxygen (O-1(2)) and hydroxyl radical (HO center dot) as the cleavage active species.The complexes show binding propensity to bovine serum albumin (BSA)protein giving K-BSA values of similar to 10(5) M-1. The dppz complexes 3 and 6 show BSA protein cleavage activity in UV-A light of 365 nm The dppz complexes 3 and 6 exhibit significant photocytotoxicity in HeLa cells giving respective IC50 values of 341 nM and 573 nM in UV-A light of 365 nm for an exposure time of 15 min (IC50 > 100 mu M in dark for both the complexes) Control experiments show significant dark and phototoxicity of the dppz base alone (IC50 = 413 nM in light with 4 h incubation in dark and 116 mu M in dark with 24 h incubation). A significant decrease in the dark toxicity of the dppz base is observedon binding to the lanthanide ions while retaining similar phototoxicity.

An experimental study of boundary layer transition induced by a cylinder wake

Boundary layer transition induced by the wake of a circular cylinder in the free stream has been investigated using the particle image velocimetry technique. Some differences between simulation and experimental studies have been reported in the literature, and these have motivated the present study. The appearance of spanwise vortices in the early stage is further confirmed here. Lambda spanwise vortex appears to evolve into a Lambda/hairpin vortex; the flow statistics also confirm such vortices. With increasing Reynolds number, based on the cylinder diameter, and with decreasing cylinder height from the plate, the physical size of these hairpin-like structures is found to decrease. Some mean flow characteristics, including the streamwise growth of the disturbance energy, in a wake-induced transition resemble those in bypass transition induced by free stream turbulence. Streamwise velocity streaks that are eventually generated in the late stage often undergo sinuous-type oscillations. Similar to other transitional flows, an inclined shear layer in the wall-normal plane is often seen to oscillate and shed vortices. The normalized shedding frequency of these vortices, estimated from the spatial spacing and the convection velocity of these vortices, is found to be independent of the Reynolds number, similar to that in ribbon-induced transition. Although the nature of free stream disturbance in a wake-induced transition and that in a bypass transition are different, the late-stage features including the flow breakdown characteristics of these two transitions appear to be similar.

Photo-induced DNA cleavage activity and remarkable photocytotoxicity of lanthanide(III) complexes of a polypyridyl ligand

Lanthanide(III) complexes [Ln(pyphen)(acac)(2)(NO3)] (1, 2), [Ln(pydppz)(acac)(2)(NO3)] (3, 4) and [La(pydppz)(anacac)(2)(NO3)] (5), where Ln is La(III) (in 1, 3, 5) and Gd(III) (in 2, 4), pyphen is 6-(2-pyridyl)-1,10-phenanthroline, pydppz is 6-(2-pyridyl)-dipyrido[3,2-a:2',3'-c] phenazine, anacac is anthracenylacetylacetonate and acac is acetylacetonate, were prepared, characterized and their DNA photocleavage activity and photocytotoxicity studied. The crystal structure of complex 2 displays a GdO6N3 coordination. The pydppz complexes 3-5 show an electronic spectral band at similar to 390 nm in DMF. The La(III) complexes are diamagnetic, while the Gd(III) complexes are paramagnetic with seven unpaired electrons. The molar conductivity data suggest 1 : 1 electrolytic nature of the complexes in aqueous DMF. They are avid binders to calf thymus DNA giving K-b in the range of 5.4 10(4)-1.2 x 10(6) M-1. Complexes 3-5 efficiently cleave supercoiled DNA to its nicked circular form in UV-A light of 365 nm via formation of singlet oxygen (O-1(2)) and hydroxyl radical (HO center dot) species. Complexes 3-5 also exhibit significant photocytotoxic effect in HeLa cancer cells giving respective IC50 value of 0.16(+/- 0.01), 0.15(+/- 0.01) and 0.26 +/-(0.02) mu M in UV-A light of 365 nm, while they are less toxic in dark with an IC50 value of >3 mu M. The presence of an additional pyridyl group makes the pydppz complexes more photocytotoxic than their dppz analogues. FACS analysis of the HeLa cells treated with complex 4 shows apoptosis as the major pathway of cell death. Nuclear localization of complex 5 having an anthracenyl moiety as a fluorophore is evidenced from the confocal microscopic studies.

Interaction-induced singular Fermi surface in a high-temperature oxypnictide superconductor

In the family of iron-based superconductors, LaFeAsO-type materials possess the simplest electronic structure due to their pronounced two-dimensionality. And yet they host superconductivity with the highest transition temperature T-c approximate to 55K. Early theoretical predictions of their electronic structure revealed multiple large circular portions of the Fermi surface with a very good geometrical overlap (nesting), believed to enhance the pairing interaction and thus superconductivity. The prevalence of such large circular features in the Fermi surface has since been associated with many other iron-based compounds and has grown to be generally accepted in the field. In this work we show that a prototypical compound of the 1111-type, SmFe0.92Co0.08AsO, is at odds with this description and possesses a distinctly different Fermi surface, which consists of two singular constructs formed by the edges of several bands, pulled to the Fermi level from the depths of the theoretically predicted band structure by strong electronic interactions. Such singularities dramatically affect the low-energy electronic properties of the material, including superconductivity. We further argue that occurrence of these singularities correlates with the maximum superconducting transition temperature attainable in each material class over the entire family of iron-based superconductors.