Brain, mind and consciousness in the history of neuroscience

From Platonic and Galenic roots, the first well developed ventricular theory of brain function is due to Bishop Nemesius, fourth century C.E. Although more interested in the Christian concept of soul, St. Augustine, too addressed the question of the location of the soul, a problem that has endured in various guises to the present day. Other notable contributions to ventricular psychology are the ninth century C.E. Arabic writer, Qusta ibn Lūqā, and an early European medical text written by the twelfth century C.E. author, Nicolai the Physician. By the time of Albertus Magnus, so-called medieval cell doctrine was a well-developed model of brain function. By the sixteenth century, Vesalius no longer understands the ventricles to be imaginary cavities designed to provide a physical basis for faculty psychology but as fluid-filled spaces in the brain whose function is yet to be determined

Multicolour nonlinearly bound chirped dissipative solitons

The dissipative soliton regime is one of the most advanced ways to generate high-energy femtosecond pulses in mode-locked lasers. On the other hand, the stimulated Raman scattering in a fibre laser may convert the excess energy out of the coherent dissipative soliton to a noisy Raman pulse, thus limiting its energy. Here we demonstrate that intracavity feedback provided by re-injection of a Raman pulse into the laser cavity leads to formation of a coherent Raman dissipative soliton. Together, a dissipative soliton and a Raman dissipative soliton (of the first and second orders) form a two (three)-colour stable complex with higher total energy and broader spectrum than those of the dissipative soliton alone. Numerous applications can benefit from this approach, including frequency comb spectroscopy, transmission lines, seeding femtosecond parametric amplifiers, enhancement cavities and multiphoton fluorescence microscopy.

Carbon nanotubes for ultrafast fibre lasers

Carbon nanotubes (CNTs) possess both remarkable optical properties and high potential for integration in various photonic devices. We overview, here, recent progress in CNT applications in fibre optics putting particular emphasis on fibre lasers. We discuss fabrication and characterisation of different CNTs, development of CNT-based saturable absorbers (CNT-SA), their integration and operation in fibre laser cavities putting emphasis on state-of-the-art fibre lasers, mode locked using CNT-SA. We discuss new design concepts of high-performance ultrafast operation fibre lasers covering ytterbium (Yb), bismuth (Bi), erbium (Er), thulium (Tm) and holmium (Ho)-doped fibre lasers.

A compact polymer optical fibre ultrasound detector

Polymer optical fibre (POF) is a relatively new and novel technology that presents an innovative approach for ultrasonic endoscopic applications. Currently, piezo electric transducers are the typical detectors of choice, albeit possessing a limited bandwidth due to their resonant nature and a sensitivity that decreases proportionally to their size. Optical fibres provide immunity from electromagnetic interference and POF in particular boasts more suitable physical characteristics than silica optical fibre. The most important of these are lower acoustic impedance, a reduced Young's Modulus and a higher acoustic sensitivity than single-mode silica fibre at both 1 MHz and 10 MHz. POF therefore offers an interesting alternative to existing technology. Intrinsic fibre structures such as Bragg gratings and Fabry-Perot cavities may be inscribed into the fibre core using UV lasers. These gratings are a modulation of the refractive index of the fibre core and provide the advantages of high reflectivity, customisable bandwidth and point detection. We present a compact in fibre ultrasonic point detector based upon a POF Bragg grating (POFBG) sensor. We demonstrate that the detector is capable of leaving a laboratory environment by using connectorised fibre sensors and make a case for endoscopic ultrasonic detection through use of a mounting structure that better mimics the environment of an endoscopic probe. We measure the effects of water immersion upon POFBGs and analyse the ultrasonic response for 1, 5 and 10 MHz.

Mode-locking intracavity dynamics:modeling nonlinear power and energy fluctuations

Modern high-power, pulsed lasers are driven by strong intracavity fluctuations. Critical in driving the intracavity dynamics is the nontrivial phase profiles generated and their periodic modification from either nonlinear mode-coupling, spectral filtering or dispersion management. Understanding the theoretical origins of the intracavity fluctuations helps guide the design, optimization and construction of efficient, high-power and high-energy pulsed laser cavities. Three specific mode-locking component are presented for enhancing laser energy: waveguide arrays, spectral filtering and dispersion management. Each component drives a strong intracavity dynamics that is captured through various modeling and analytic techniques.

Raman fiber lasers with a random distributed feedback based on Rayleigh scattering

We demonstrate lasing based on a random distributed feedback due to the Raman amplified Rayleigh backscattering in different types of cavities with and without conventional point-action reflectors. Quasistationary generation of a narrowband spectrum is achieved despite the random nature of the feedback. The generated spectrum is localized at the reflection or gain spectral maxima in schemes with and without point reflectors, respectively. The length limit for a conventional cavity and the minimal pump power required for the lasing based purely on a random distributed feedback are determined. © 2010 The American Physical Society.

Hydrogeophysical characterization of anisotropy in the Biscayne Aquifer using geophysical methods

The anisotropy of the Biscayne Aquifer which serves as the source of potable water for Miami-Dade County was investigated by applying geophysical methods. Electrical resistivity imaging, self potential and ground penetration radar techniques were employed in both regional and site specific studies. In the regional study, electrical anisotropy and resistivity variation with depth were investigated with azimuthal square array measurements at 13 sites. The observed coefficient of electrical anisotropy ranged from 1.01 to 1.36. The general direction of measured anisotropy is uniform for most sites and trends W-E or SE-NW irrespective of depth. Measured electrical properties were used to estimate anisotropic component of the secondary porosity and hydraulic anisotropy which ranged from 1 to 11% and 1.18 to 2.83 respectively. 1-D sounding analysis was used to models the variation of formation resistivity with depth. Resistivities decreased from NW (close to the margins of the everglades) to SE on the shores of Biscayne Bay. Porosity calculated from Archie's law, ranged from 18 to 61% with higher values found along the ridge. Higher anisotropy, porosities and hydraulic conductivities were on the Atlantic Coastal Ridge and lower values at low lying areas west of the ridge. The cause of higher anisotropy and porosity is attributed to higher dissolution rates of the oolitic facies of the Miami Formation composing the ridge. The direction of minimum resistivity from this study is similar to the predevelopment groundwater flow direction indicated in published modeling studies. Detailed investigations were carried out to evaluate higher anisotropy at West Perrine Park located on the ridge and Snapper Creek Municipal well field where the anisotropy trend changes with depth. The higher anisotropy is attributed to the presence of solution cavities oriented in the E-SE direction on the ridge. Similarly, the change in hydraulic anisotropy at the well field might be related to solution cavities, the surface canal and groundwater extraction wells.^

Cardiac Neural Crest Cells Affect the Development of the Myocardium and Conduction System in the Mouse

Neural crest cells originate from the dorsal most region of the embryonic neural tube. These cells migrate into several embryonic locations and differentiate into a variety of cell types. Cardiac neural crest (CNC) cells are a set of neural crest progenitors that aid in the proper formation of the cardiac septum, which separates the pulmonary from the systemic circulation. We have used Splotch mice to investigate whether the murine CNC cells play a role during the development oft he myocardium and the conduction system. Splotch mice carry a mutation in the P AX3 transcription factor, and display a problem in CNC cell migration. A scanning-electron-microscopy analysis of Splotch mutant-embryonic-hearts reveals abnormalities in the interventricular septum. In addition, the right and left ventricular cavities appear dilated relative to a wild type heart. Hoechst nuclei staining of Splotch heart cryosections demonstrates a decreased number of cardiomyocytes and a corresponding thinner ventricular wall. The absence of Connexin 40 in the ventricles of Splotch mutants, suggests conduction system defects. These results support the evidence that CNC cell signaling plays a role in modulating the growth and development of murine cardiomyocytes and their differentiation into conductile cells.

Conformational dynamics associated with ligand binding to vertebrate hexa-coordinate hemoglobins

Neuroglobin (Ngb) and cytoglobin (Cygb) are two new additions to the globin family, exhibiting heme iron hexa-coordination, a disulfide bond and large internal cavities. These proteins are implicated in cytoprotection under hypoxic-ischemic conditions, but the molecular basis of their cytoprotective function is unclear. Herein, a photothermal and spectroscopic study of the interactions of diatomic ligands with Ngb, Cygb, myoglobin and hemoglobin is presented. The impact of the disulfide bond in Ngb and Cygb and role of conserved residues in Ngb His64, Val68, Cys55, Cys120 and Tyr44 on conformational dynamics associated with ligand binding/dissociation were investigated. Transient absorption and photoacoustic calorimetry studies indicate that CO photo-dissociation from Ngb leads to a volume expansion (13.4±0.9 mL mol-1), whereas a smaller volume change was determined for Ngb with reduced Cys (ΔV=4.6±0.3 mL mol-1). Furthermore, Val68 side chain regulates ligand migration between the distal pocket and internal hydrophobic cavities since Val68Phe geminate quantum yield is ∼2.7 times larger than that of WT Ngb. His64Gln and Tyr44Phe mutations alter the thermodynamic parameters associated with CO photo-release indicating that electrostatic/hydrogen binding network that includes heme propionate groups, Lys 67, His64, and Tyr 44 in Ngb modulates the energetics of CO photo-dissociation. In Cygb, CO escape from the protein matrix is fast (< 40 ns) with a ΔH of 18±2 kcal mol-1 in Cygbred, whereas disulfide bridge formation promotes a biphasic ligand escape associated with an overall enthalpy change of 9±4 kcal mol-1. Therefore, the disulfide bond modulates conformational dynamics in Ngb and Cygb. I propose that in Cygb with reduced Cys the photo-dissociated ligand escapes through the hydrophobic tunnel as occurs in Ngb, whereas the CO preferentially migrates through the His64 gate in Cygbox. To characterize Cygb surface 1,8-ANS interactions with Cygb were investigated employing fluorescence spectroscopy, ITC and docking simulations. Two 1,8-ANS binding sites were identified. One binding site is located close to the extended N-terminus of Cygb and was also identified as a binding site for oleate. Furthermore, guanidinium hydrochloride-induced unfolding studies of Cygb reveal that the disulfide bond does not impact Cygb stability, whereas binding of cyanide slightly increases the protein stability.

Chemical composition of hydrothermal carbonates and barites from the Deryugin Basin, Sea of Okhotsk

Data on hydrothermal activity in the Deryugin Basin (Sea of Okhotsk) are reviewed. Barites and carbonates found in sediment cores sampled at feet of hydrothermal mounds were subdivided into recycled and authigenic types. Recycled minerals were represented by crystals and aggregations of travertine-like barite and fragments of barite and carbonate tubes. Authigenic formations included: (1) carbonate nodules; (2) barite micronodules; (3) transparent colorless barite that generated numerous small nests and filled cavities in sediments; (4) yellow barite formed thin (0.5 mm) veins; and (5) white barite cemented small aggregations of coarse-grained sediments. A detailed examination of formation processes of authigenic minerals in the bottom sediment cores allowed to conclude that, there, hydrothermal activity is still going on today. This was confirmed by high methane concentration in near-bottom water above a field of hydrothermal barite minerals.

The critical role of intracavity dynamics in high-power mode-locked fiber lasers

We present a theoretical description of the generation of ultra-short, high-energy pulses in two laser cavities driven by periodic spectral filtering or dispersion management. Critical in driving the intra-cavity dynamics is the nontrivial phase profiles generated and their periodic modification from either spectral filtering or dispersion management. For laser cavities with a spectral filter, the theory gives a simple geometrical description of the intra-cavity dynamics and provides a simple and efficient method for optimizing the laser cavity performance. In the dispersion managed cavity, analysis shows the generated self-similar behavior to be governed by the porous media equation with a rapidly-varying, mean-zero diffusion coefficient whose solution is the well-known Barenblatt similarity solution with parabolic profile. © 2010 Copyright SPIE - The International Society for Optical Engineering.

Intracavity dynamics in mode-locked lasers

We present a theoretical description of the generation of ultra-short, high-energy pulses in two laser cavities driven by periodic spectral filtering or dispersion management. Critical in driving the intra-cavity dynamics is the nontrivial phase profiles generated and their periodic modification from either spectral filtering or dispersion management. For laser cavities with a spectral filter, the theory gives a simple geometrical description of the intra-cavity dynamics and provides a simple and efficient method for optimizing the laser cavity performance. In the dispersion managed cavity, analysis shows the generated self-similar behavior to be governed by the porous media equation with a rapidly-varying, mean-zero diffusion coefficient whose solution is the well-known Barenblatt similarity solution with parabolic profile. © 2010 American Institute of Physics.

Intracavity dynamics for power and energy enhancement in mode-locked lasers

We present a theoretical description of the generation of ultra-short, high-energy pulses in two laser cavities driven by periodic spectral filtering or dispersion management. Critical in driving the intra-cavity dynamics is the nontrivial phase profiles generated and their periodic modification from either spectral filtering or dispersion management. For laser cavities with a spectral filter, the theory gives a simple geometrical description of the intra-cavity dynamics and provides a simple and efficient method for optimizing the laser cavity performance. In the dispersion managed cavity, analysis shows the generated self-similar behavior to be governed by the porous media equation with a rapidly-varying, mean-zero diffusion coefficient whose solution is the well-known Barenblatt similarity solution with parabolic profile.

Near-field coupling and resonant cavity modes in plasmonic nanorod metamaterials

Plasmonic resonant cavities are capable of confining light at the nanoscale, resulting in both enhanced local electromagnetic fields and lower mode volumes. However, conventional plasmonic resonant cavities possess large Ohmic losses at metal-dielectric interfaces. Plasmonic near-field coupling plays a key role in a design of photonic components based on the resonant cavities because of the possibility to reduce losses. Here, we study the plasmonic near-field coupling in the silver nanorod metamaterials treated as resonant nanostructured optical cavities. Reflectance measurements reveal the existence of multiple resonance modes of the nanorod metamaterials, which is consistent with our theoretical analysis. Furthermore, our numerical simulations show that the electric field at the longitudinal resonances forms standing waves in the nanocavities due to the near-field coupling between the adjacent nanorods, and a new hybrid mode emerges due to a coupling between nanorods and a gold-film substrate. We demonstrate that this coupling can be controlled by changing the gap between the silver nanorod array and gold substrate.

Micro-Fabricated Surface Trap and Cavity Integration for Trapped Ion Quantum Computing

Atomic ions trapped in micro-fabricated surface traps can be utilized as a physical platform with which to build a quantum computer. They possess many of the desirable qualities of such a device, including high fidelity state preparation and readout, universal logic gates, long coherence times, and can be readily entangled with each other through photonic interconnects. The use of optical cavities integrated with trapped ion qubits as a photonic interface presents the possibility for order of magnitude improvements in performance in several key areas of their use in quantum computation. The first part of this thesis describes the design and fabrication of a novel surface trap for integration with an optical cavity. The trap is custom made on a highly reflective mirror surface and includes the capability of moving the ion trap location along all three trap axes with nanometer scale precision. The second part of this thesis demonstrates the suitability of small micro-cavities formed from laser ablated fused silica substrates with radii of curvature in the 300-500 micron range for use with the mirror trap as part of an integrated ion trap cavity system. Quantum computing applications for such a system include dramatic improvements in the photonic entanglement rate up to 10 kHz, the qubit measurement time down to 1 microsecond, and the measurement error rates down to the 10e-5 range. The final part of this thesis details a performance simulator for exploring the physical resource requirements and performance demands to scale such a quantum computer to sizes capable of performing quantum algorithms beyond the limits of classical computation.