Ablation and ultrafast dynamics of zinc selenide under femtosecond laser irradiation

The ablation in zinc selenide (ZnSe) crystal is studied by using 150-fs, 800-nm laser system. The images of the ablation pit measured by scanning electronic microscope (SEM) show no thermal stress and melting dynamics. The threshold fluence is measured to be 0.7 J/cm2. The ultrafast ablation dynamics is studied by using pump and probe method. The result suggests that optical breakdown and ultrafast melting take place in ZnSe irradiated under femtosecond laser pulses.

Dynamics and scaling of self-excited passive vortex generators for underwater propulsion

A series of experiments was conducted on the use of a device to passively generate vortex rings, henceforth a passive vortex generator (PVG). The device is intended as a means of propulsion for underwater vehicles, as the use of vortex rings has been shown to decrease the fuel consumption of a vehicle by up to 40% Ruiz (2010).

The PVG was constructed out of a collapsible tube encased in a rigid, airtight box. By adjusting the pressure within the airtight box while fluid was flowing through the tube, it was possible to create a pulsed jet with vortex rings via self-excited oscillations of the collapsible tube.

A study of PVG integration into an existing autonomous underwater vehicle (AUV) system was conducted. A small AUV was used to retrofit a PVG with limited alterations to the original vehicle. The PVG-integrated AUV was used for self-propelled testing to measure the hydrodynamic (Froude) efficiency of the system. The results show that the PVG-integrated AUV had a 22% increase in the Froude efficiency using a pulsed jet over a steady jet. The maximum increase in the Froude efficiency was realized when the formation time of the pulsed jet, a nondimensional time to characterize vortex ring formation, was coincident with vortex ring pinch-off. This is consistent with previous studies that indicate that the maximization of efficiency for a pulsed jet vehicle is realized when the formation of vortex rings maximizes the vortex ring energy and size.

The other study was a parameter study of the physical dimensions of a PVG. This study was conducted to determine the effect of the tube diameter and length on the oscillation characteristics such as the frequency. By changing the tube diameter and length by factors of 3, the frequency of self-excited oscillations was found to scale as f~D_0^{-1/2} L_0^0, where D_0 is the tube diameter and L_0 the tube length. The mechanism of operation is suggested to rely on traveling waves between the tube throat and the end of the tube. A model based on this mechanism yields oscillation frequencies that are within the range observed by the experiment.

Capturing protein dynamics with time-resolved luminescence spectroscopy

The presented doctoral research utilizes time-resolved spectroscopy to characterize protein dynamics and folding mechanisms. We resolve millisecond-timescale folding by coupling time-resolved fluorescence energy transfer (trFRET) to a continuous flow microfluidic mixer to obtain intramolecular distance distributions throughout the folding process. We have elucidated the folding mechanisms of two cytochromes---one that exhibits two-state folding (cytochrome cb₅₆₂) and one that has both a kinetic refolding intermediate ensemble and a distinct equilibrium unfolding intermediate (cytochrome c₅₅₂). Our data reveal that the distinct structural features of cytochrome c₅₅₂ contribute to its thermostability.

We have also investigated intrachain contact dynamics in unfolded cytochrome cb₅₆₂ by monitoring electron transfer, which occurs as the heme collides with a ruthenium photosensitizer, covalently bound to residues along the polypeptide. Intrachain diffusion for chemically denatured proteins proceeds on the microsecond timescale with an upper limit of 0.1 microseconds. The power-law dependence (slope = -1.5) of the rate constants on the number of peptide bonds between the heme and Ru complex indicate that cytochrome cb₅₆₂ is minimally frustrated.

In addition, we have explored the pathway dependence of electron tunneling rates between metal sites in proteins. Our research group has converted cytochrome b₅₆₂ to a c-type cytochrome with the porphyrin covalently bound to cysteine sidechains. We have investigated the effects of the changes to the protein structure (i.e., increased rigidity and potential new equatorial tunneling pathways) on the electron transfer rates, measured by transient absorption, in a series of ruthenium photosensitizer-modified proteins.

Dynamics of cell–matrix mechanical interactions in three dimensions

The forces cells apply to their surroundings control biological processes such as growth, adhesion, development, and migration. In the past 20 years, a number of experimental techniques have been developed to measure such cell tractions. These approaches have primarily measured the tractions applied by cells to synthetic two-dimensional substrates, which do not mimic in vivo conditions for most cell types. Many cell types live in a fibrous three-dimensional (3D) matrix environment. While studying cell behavior in such 3D matrices will provide valuable insights for the mechanobiology and tissue engineering communities, no experimental approaches have yet measured cell tractions in a fibrous 3D matrix.

This thesis describes the development and application of an experimental technique for quantifying cellular forces in a natural 3D matrix. Cells and their surrounding matrix are imaged in three dimensions with high speed confocal microscopy. The cell-induced matrix displacements are computed from the 3D image volumes using digital volume correlation. The strain tensor in the 3D matrix is computed by differentiating the displacements, and the stress tensor is computed by applying a constitutive law. Finally, tractions applied by the cells to the matrix are computed directly from the stress tensor.

The 3D traction measurement approach is used to investigate how cells mechanically interact with the matrix in biologically relevant processes such as division and invasion. During division, a single mother cell undergoes a drastic morphological change to split into two daughter cells. In a 3D matrix, dividing cells apply tensile force to the matrix through thin, persistent extensions that in turn direct the orientation and location of the daughter cells. Cell invasion into a 3D matrix is the first step required for cell migration in three dimensions. During invasion, cells initially apply minimal tractions to the matrix as they extend thin protrusions into the matrix fiber network. The invading cells anchor themselves to the matrix using these protrusions, and subsequently pull on the matrix to propel themselves forward.

Lastly, this thesis describes a constitutive model for the 3D fibrous matrix that uses a finite element (FE) approach. The FE model simulates the fibrous microstructure of the matrix and matches the cell-induced matrix displacements observed experimentally using digital volume correlation. The model is applied to predict how cells mechanically sense one another in a 3D matrix. It is found that cell-induced matrix displacements localize along linear paths. These linear paths propagate over a long range through the fibrous matrix, and provide a mechanism for cell-cell signaling and mechanosensing. The FE model developed here has the potential to reveal the effects of matrix density, inhomogeneity, and anisotropy in signaling cell behavior through mechanotransduction.

Direct visualization of the dynamics of membrane-anchor proteins in living cells

Dynamic properties of proteins have crucial roles in understanding protein function and molecular mechanism within cells. In this paper, we combined total internal reflection fluorescence microscopy with oblique illumination fluorescence microscopy to observe directly the movement and localization of membrane-anchored green fluorescence proteins in living cells. Total internal reflect illumination allowed the observation of proteins in the cell membrane of living cells since the penetrate depth could be adjusted to about 80 nm, and oblique illumination allowed the observation of proteins both in the cytoplasm and apical membrane, which made this combination a promising tool to investigate the dynamics of proteins through the whole cell. Not only individual protein molecule tracks have been analyzed quantitatively but also cumulative probability distribution function analysis of ensemble trajectories has been done to reveal the mobility of proteins. Finally, single particle tracking has acted as a compensation for single molecule tracking. All the results exhibited green fluorescence protein dynamics within cytoplasm, on the membrane and from cytoplasm to plasma membrane.

Role of feedback and dynamics in a gene regulatory network

Cells exhibit a diverse repertoire of dynamic behaviors. These dynamic functions are implemented by circuits of interacting biomolecules. Although these regulatory networks function deterministically by executing specific programs in response to extracellular signals, molecular interactions are inherently governed by stochastic fluctuations. This molecular noise can manifest as cell-to-cell phenotypic heterogeneity in a well-mixed environment. Single-cell variability may seem like a design flaw but the coexistence of diverse phenotypes in an isogenic population of cells can also serve a biological function by increasing the probability of survival of individual cells upon an abrupt change in environmental conditions. Decades of extensive molecular and biochemical characterization have revealed the connectivity and mechanisms that constitute regulatory networks. We are now confronted with the challenge of integrating this information to link the structure of these circuits to systems-level properties such as cellular decision making. To investigate cellular decision-making, we used the well studied galactose gene-regulatory network in \textit{Saccharomyces cerevisiae}. We analyzed the mechanism and dynamics of the coexistence of two stable on and off states for pathway activity. We demonstrate that this bimodality in the pathway activity originates from two positive feedback loops that trigger bistability in the network. By measuring the dynamics of single-cells in a mixed sugar environment, we observe that the bimodality in gene expression is a transient phenomenon. Our experiments indicate that early pathway activation in a cohort of cells prior to galactose metabolism can accelerate galactose consumption and provide a transient increase in growth rate. Together these results provide important insights into strategies implemented by cells that may have been evolutionary advantageous in competitive environments.

Flight dynamics in Drosophila through a dynamically-scaled robotic approach

Flies are particularly adept at balancing the competing demands of delay tolerance, performance, and robustness during flight, which invites thoughtful examination of their multimodal feedback architecture. This dissertation examines stabilization requirements for inner-loop feedback strategies in the flapping flight of Drosophila, the fruit fly, against the backdrop of sensorimotor transformations present in the animal. Flies have evolved multiple specializations to reduce sensorimotor latency, but sensory delay during flight is still significant on the timescale of body dynamics. I explored the effect of sensor delay on flight stability and performance for yaw turns using a dynamically-scaled robot equipped with a real-time feedback system that performed active turns in response to measured yaw torque. The results show a fundamental tradeoff between sensor delay and permissible feedback gain, and suggest that fast mechanosensory feedback provides a source of active damping that compliments that contributed by passive effects. Presented in the context of these findings, a control architecture whereby a haltere-mediated inner-loop proportional controller provides damping for slower visually-mediated feedback is consistent with tethered-flight measurements, free-flight observations, and engineering design principles. Additionally, I investigated how flies adjust stroke features to regulate and stabilize level forward flight. The results suggest that few changes to hovering kinematics are actually required to meet steady-state lift and thrust requirements at different flight speeds, and the primary driver of equilibrium velocity is the aerodynamic pitch moment. This finding is consistent with prior hypotheses and observations regarding the relationship between body pitch and flight speed in fruit flies. The results also show that the dynamics may be stabilized with additional pitch damping, but the magnitude of required damping increases with flight speed. I posit that differences in stroke deviation between the upstroke and downstroke might play a critical role in this stabilization. Fast mechanosensory feedback of the pitch rate could enable active damping, which would inherently exhibit gain scheduling with flight speed if pitch torque is regulated by adjusting stroke deviation. Such a control scheme would provide an elegant solution for flight stabilization across a wide range of flight speeds.

Dynamics of rotationally resolved multiphoton ionization processes in molecules

This dissertation presents the results of studies of several rotationally- resolved resonance enhanced multiphoton ionization (REMPI) processes in some simple molecular systems. The objective of these studies is to quantitatively identify the underlying dynamics of this highly state-specific process which utilizes the narrow bandwidth radiation of a laser to ionize a molecule by first preparing an excited state via multiphoton absorption and subsequently ionizing that state before it can decay. Coupled with high-resolution photoelectron spectroscopy, REMPI is clearly an important probe of molecular excited states and their photoioniza tion dynamics.

A key feature of our studies is that they are carried out using accurate Hartree-Fock orbitals to describe the photoelectron orbitals of the molecular ions. The use of such photoelectron orbitals is important in rotationally-resolved studies where the angular momentum coupling in the photoelectron orbital plays a significant role in the photoionization dynamics. In these studies the Hartree-Fock molecular molecular photoelectron orbitals are obtained by numerical solution of a Lippmann-Schwinger integral equation.

Studies reported here include investigations of (i) ionic rotational branching ratios and their energy dependence for REMPI via the A^2Σ^+(3sσ) and D^2Σ^+(3pσ)states of NO, (ii) the influence of angular momentum constraints on branching ratios at low photoelectron energies for REMPI via low-J levels of the resonant intermediate state, (iii) the strong dependence of photoelectron angular distributions on final ionic rotational state and on the alignment in REMPI of the A^2Σ^+ state of NO, (iv) vibrational state dependence of ionic rotational branching ratios arising from rapid orbital evolution in resonant states (E'^2Σ^+(3pσ) of CH), (v) the influence of rovibronic interactions on the rotational branching ratios seen in REMPI via the D^2Σ^+(3pσ) state of NO, and (vi) effects of laser intensity on the photoionization dynamics of REMPI.

An Alternative View of the US Price-Dividend Ratio Dynamics

As a necessary condition for the validity of the present value model, the price-dividend ratio must be stationary. However, significant market episodes seem to provide evidence of prices significantly drifting apart from dividends while other episodes show prices anchoring back to dividends. This paper investigates the stationarity of this ratio in the context of a Markov- switching model à la Hamilton (1989) where an asymmetric speed of adjustment towards a unique attractor is introduced. A three-regime model displays the best regime identification and reveals that the first part of the 90’s boom (1985-1995) and the post-war period are characterized by a stationary state featuring a slow reverting process to a relatively high attractor. Interestingly, the latter part of the 90’s boom (1996-2000), characterized by a growing price-dividend ratio, is entirely attributed to a stationary regime featuring a highly reverting process to the attractor. Finally, the post-Lehman Brothers episode of the subprime crisis can be classified into a temporary nonstationary regime.

Ultrafast dynamics in ZnO thin films irradiated by femtosecond lasers

The damage morphologies, threshold fluences in ZnO films were studied with femtosecond laser pulses. Time-resolved reflectivity and transmissivity have been measured by the pump-probe technique at different pump fluences and wavelengths. The results indicate that two-phase transition is the dominant damage mechanism, which is similar to that in narrow band gap semiconductors. The estimated energy loss rate of conduction electrons is 1.5 eV/ps. (c) 2005 Elsevier Ltd. All rights reserved.

Dynamics of femtosecond laser pulse induced damage in multilayers

We report the single-shot damage thresholds of MgF2/ZnS onmidirectional reflector for laser pulse durations from 50 A to 900 fs. A coupled dynamic model is applied to study the damage mechanisms, in which we consider not only the electronic excitation of the material, but also the influence of this excitation-induced changes in the complex refractive index of material on the laser pulse itself. The results indicate that this feedback effect plays a very important role during the damage of material. Based on this model, we calculate the threshold fluences and the time-resolved excitation process of the multiplayer. The theoretical calculations agree well with our experimental results. (c) 2005 Elsevier B.V. All rights reserved.

Investigations of charge-carrier dynamics at semiconductor/liquid interfaces

Theoretical and experimental investigations of charge-carrier dynamics at semiconductor/liquid interfaces, specifically with respect to interfacial electron transfer and surface recombination, are presented.

Fermi's golden rule has been used to formulate rate expressions for charge transfer of delocalized carriers in a nondegenerately doped semiconducting electrode to localized, outer-sphere redox acceptors in an electrolyte phase. The treatment allows comparison between charge-transfer kinetic data at metallic, semimetallic, and semiconducting electrodes in terms of parameters such as the electronic coupling to the electrode, the attenuation of coupling with distance into the electrolyte, and the reorganization energy of the charge-transfer event. Within this framework, rate constant values expected at representative semiconducting electrodes have been determined from experimental data for charge transfer at metallic electrodes. The maximum rate constant (i.e., at optimal exoergicity) for outer-sphere processes at semiconducting electrodes is computed to be in the range 10^-17-10^-16 cm⁴ s^-1, which is in excellent agreement with prior theoretical models and experimental results for charge-transfer kinetics at semiconductor/liquid interfaces.

Double-layer corrections have been evaluated for semiconductor electrodes in both depletion and accumulation conditions. In conjuction with the Gouy-Chapman-Stern model, a finite difference approach has been used to calculate potential drops at a representative solid/liquid interface. Under all conditions that were simulated, the correction to the driving force used to evaluate the interfacial rate constant was determined to be less than 2% of the uncorrected interfacial rate constant.

Photoconductivity decay lifetimes have been obtained for Si(111) in contact with solutions of CH₃OH or tetrahydrofuran containing one-electron oxidants. Silicon surfaces in contact with electrolyte solutions having Nernstian redox potentials > 0 V vs. SCE exhibited low effective surface recombination velocities regardless of the different surface chemistries. The formation of an inversion layer, and not a reduced density of electrical trap sites on the surface, is shown to be responsible for the long charge-carrier lifetimes observed for these systems. In addition, a method for preparing an air-stable, low surface recombination velocity Si surface through a two-step, chlorination/alkylation reaction is described.

Two-colour laser-induced electron dynamics in two-level quantum system

To attempt to control the quantum state of a physical system with a femtosecond two-colour laser field, a model for the two-level system is analysed as a first step. We investigate the coherent control of the two-colour laser pulses propagating in a two-level medium. Based on calculating the influence of the laser field with various laser parameters on the electron dynamics, it is found the electronic state can be changed up and down by choosing the appropriate laser pulses and the coherent control of the two-colour laser pulses can substantially modify the behaviour of the electronic dynamics: a quicker change of two states can be produced even for small pulse duration. Moreover, the oscillatory structures around the resonant frequency and the propagation features of the laser pulses depend sensitively on the relative phase of the two-colour laser pulses. Finally, the influence of a finite lifetime of the upper level is discussed in brief.