Label-free detection of single biological molecules using microtoroid optical resonators

Being able to detect a single molecule without the use of labels has been a long standing goal of bioengineers and physicists. This would simplify applications ranging from single molecular binding studies to those involving public health and security, improved drug screening, medical diagnostics, and genome sequencing. One promising technique that has the potential to detect single molecules is the microtoroid optical resonator. The main obstacle to detecting single molecules, however, is decreasing the noise level of the measurements such that a single molecule can be distinguished from background. We have used laser frequency locking in combination with balanced detection and data processing techniques to reduce the noise level of these devices and report the detection of a wide range of nanoscale objects ranging from nanoparticles with radii from 100 to 2.5 nm, to exosomes, ribosomes, and single protein molecules (mouse immunoglobulin G and human interleukin-2). We further extend the exosome results towards creating a non-invasive tumor biopsy assay. Our results, covering several orders of magnitude of particle radius (100 nm to 2 nm), agree with the `reactive' model prediction for the frequency shift of the resonator upon particle binding. In addition, we demonstrate that molecular weight may be estimated from the frequency shift through a simple formula, thus providing a basis for an ``optical mass spectrometer'' in solution. We anticipate that our results will enable many applications, including more sensitive medical diagnostics and fundamental studies of single receptor-ligand and protein-protein interactions in real time. The thesis summarizes what we have achieved thus far and shows that the goal of detecting a single molecule without the use of labels can now be realized.

Simulation of shock-induced bubble collapse with application to vascular injury in shockwave lithotripsy

Shockwave lithotripsy is a noninvasive medical procedure wherein shockwaves are repeatedly focused at the location of kidney stones in order to pulverize them. Stone comminution is thought to be the product of two mechanisms: the propagation of stress waves within the stone and cavitation erosion. However, the latter mechanism has also been implicated in vascular injury. In the present work, shock-induced bubble collapse is studied in order to understand the role that it might play in inducing vascular injury. A high-order accurate, shock- and interface-capturing numerical scheme is developed to simulate the three-dimensional collapse of the bubble in both the free-field and inside a vessel phantom. The primary contributions of the numerical study are the characterization of the shock-bubble and shock-bubble-vessel interactions across a large parameter space that includes clinical shockwave lithotripsy pressure amplitudes, problem geometry and tissue viscoelasticity, and the subsequent correlation of these interactions to vascular injury. Specifically, measurements of the vessel wall pressures and displacements, as well as the finite strains in the fluid surrounding the bubble, are utilized with available experiments in tissue to evaluate damage potential. Estimates are made of the smallest injurious bubbles in the microvasculature during both the collapse and jetting phases of the bubble's life cycle. The present results suggest that bubbles larger than 1 μm in diameter could rupture blood vessels under clinical SWL conditions.

Biodiversity of macrozoobenthos in a large river, the Austrian Danube, including quantitative studies in a free-flowing stretch below Vienna: a short review

The Danube is ca. 2850 km in length and is the second largest river in Europe. The Austrian part of the Danube falls 156 metres in altitude over its 351 km length and, since the early 1950s, the river has been developed into a power-generating waterway, so that the continuity of the river is now interrupted by ten impounded areas. Only two stretches of the original free-flowing river are left, the Wachau region (above river-km 2005, west of Vienna) and the region downstream from the impoundment at Vienna (river-km 1921). Most of the recent theories and concepts related to invertebrates, in the context of the ecology of running waters, are based on studies on small streams, whereas investigations of large rivers have played a minor role for a long time, mainly due to methodological difficulties. The authors' recent detailed studies on macroinvertebrates in the free-flowing section of the Danube below Vienna, provide an excellent opportunity to survey or restate scientific hypotheses on the basis of a large river. In this review the main interest focuses on the investigation of biodiversity, i.e. the number of species and their relative proportions in the whole invertebrate community, as well as major governing environmental factors. The article summarises the species composition, the important environmental variables at the river cross-section and the effect of upstream impoundment on the riverbed and its fauna.

Neural and computational representations of decision variables

These studies explore how, where, and when representations of variables critical to decision-making are represented in the brain. In order to produce a decision, humans must first determine the relevant stimuli, actions, and possible outcomes before applying an algorithm that will select an action from those available. When choosing amongst alternative stimuli, the framework of value-based decision-making proposes that values are assigned to the stimuli and that these values are then compared in an abstract “value space” in order to produce a decision. Despite much progress, in particular regarding the pinpointing of ventromedial prefrontal cortex (vmPFC) as a region that encodes the value, many basic questions remain. In Chapter 2, I show that distributed BOLD signaling in vmPFC represents the value of stimuli under consideration in a manner that is independent of the type of stimulus it is. Thus the open question of whether value is represented in abstraction, a key tenet of value-based decision-making, is confirmed. However, I also show that stimulus-dependent value representations are also present in the brain during decision-making and suggest a potential neural pathway for stimulus-to-value transformations that integrates these two results.

More broadly speaking, there is both neural and behavioral evidence that two distinct control systems are at work during action selection. These two systems compose the “goal-directed system”, which selects actions based on an internal model of the environment, and the “habitual” system, which generates responses based on antecedent stimuli only. Computational characterizations of these two systems imply that they have different informational requirements in terms of input stimuli, actions, and possible outcomes. Associative learning theory predicts that the habitual system should utilize stimulus and action information only, while goal-directed behavior requires that outcomes as well as stimuli and actions be processed. In Chapter 3, I test whether areas of the brain hypothesized to be involved in habitual versus goal-directed control represent the corresponding theorized variables.

The question of whether one or both of these neural systems drives Pavlovian conditioning is less well-studied. Chapter 4 describes an experiment in which subjects were scanned while engaged in a Pavlovian task with a simple non-trivial structure. After comparing a variety of model-based and model-free learning algorithms (thought to underpin goal-directed and habitual decision-making, respectively), it was found that subjects’ reaction times were better explained by a model-based system. In addition, neural signaling of precision, a variable based on a representation of a world model, was found in the amygdala. These data indicate that the influence of model-based representations of the environment can extend even to the most basic learning processes.

Knowledge of the state of hidden variables in an environment is required for optimal inference regarding the abstract decision structure of a given environment and therefore can be crucial to decision-making in a wide range of situations. Inferring the state of an abstract variable requires the generation and manipulation of an internal representation of beliefs over the values of the hidden variable. In Chapter 5, I describe behavioral and neural results regarding the learning strategies employed by human subjects in a hierarchical state-estimation task. In particular, a comprehensive model fit and comparison process pointed to the use of "belief thresholding". This implies that subjects tended to eliminate low-probability hypotheses regarding the state of the environment from their internal model and ceased to update the corresponding variables. Thus, in concert with incremental Bayesian learning, humans explicitly manipulate their internal model of the generative process during hierarchical inference consistent with a serial hypothesis testing strategy.

Strong atom-light interactions along nanostructures: Transition from free-space to nanophotonic interfaces

An exciting frontier in quantum information science is the integration of otherwise "simple'' quantum elements into complex quantum networks. The laboratory realization of even small quantum networks enables the exploration of physical systems that have not heretofore existed in the natural world. Within this context, there is active research to achieve nanoscale quantum optical circuits, for which atoms are trapped near nano-scopic dielectric structures and "wired'' together by photons propagating through the circuit elements. Single atoms and atomic ensembles endow quantum functionality for otherwise linear optical circuits and thereby enable the capability of building quantum networks component by component. Toward these goals, we have experimentally investigated three different systems, from conventional to rather exotic systems : free-space atomic ensembles, optical nano fibers, and photonics crystal waveguides. First, we demonstrate measurement-induced quadripartite entanglement among four quantum memories. Next, following the landmark realization of a nanofiber trap, we demonstrate the implementation of a state-insensitive, compensated nanofiber trap. Finally, we reach more exotic systems based on photonics crystal devices. Beyond conventional topologies of resonators and waveguides, new opportunities emerge from the powerful capabilities of dispersion and modal engineering in photonic crystal waveguides. We have implemented an integrated optical circuit with a photonics crystal waveguide capable of both trapping and interfacing atoms with guided photons, and have observed the collective effect, superradiance, mediated by the guided photons. These advances provide an important capability for engineered light-matter interactions, enabling explorations of novel quantum transport and quantum many-body phenomena.

On the methods of determining size/weight characteristics of food organisms of fish. (Determination of the length of Copepoda in larval stages by egg-laying females of the free living freshwater Copepoda). [Translation from: Voprosy Ikhtiologii 14, 182-194, 1960. ]

As is known, copepods play an important role in the nutrition of fish. Therefore with a view to facilitating research on the study of the quantitative side of feeding, there have recently appeared a considerable number of papers devoted to the development of methods for determining the wet. weight of these crustaceans. For the further facilitating of research in the nutrition of fish it would be of great interest to clarify the problem, is there not some kind of rule in the growth of the crustaceans during metamorphosis, and if there is such a rule is it not possible, to determine the length of the larvae at each stage, not by measuring them, but by using the formulae derived on the basis of these rules. This article examines the growth curves of different species of freshwater Copepoda, obtained on the basis of experimental observations in cultures or by way of measurement of mass material at all stages of development in samples from water-bodies. The authors study in particular the ratio of the mean diameter of the eggs to the mean length of the egg-bearing females.

Free algebras in Von Neumann-Bernays-Gӧdel set theory and positive elementary inductions in reasonable structures

This thesis consists of two independent chapters. The first chapter deals with universal algebra. It is shown, in von Neumann-Bernays-Gӧdel set theory, that free images of partial algebras exist in arbitrary varieties. It follows from this, as set-complete Boolean algebras form a variety, that there exist free set-complete Boolean algebras on any class of generators. This appears to contradict a well-known result of A. Hales and H. Gaifman, stating that there is no complete Boolean algebra on any infinite set of generators. However, it does not, as the algebras constructed in this chapter are allowed to be proper classes. The second chapter deals with positive elementary inductions. It is shown that, in any reasonable structure ᶆ, the inductive closure ordinal of ᶆ is admissible, by showing it is equal to an ordinal measuring the saturation of ᶆ. This is also used to show that non-recursively saturated models of the theories ACF, RCF, and DCF have inductive closure ordinals greater than _ω.

Numerical Studies of Topological Phases

The topological phases of matter have been a major part of condensed matter physics research since the discovery of the quantum Hall effect in the 1980s. Recently, much of this research has focused on the study of systems of free fermions, such as the integer quantum Hall effect, quantum spin Hall effect, and topological insulator. Though these free fermion systems can play host to a variety of interesting phenomena, the physics of interacting topological phases is even richer. Unfortunately, there is a shortage of theoretical tools that can be used to approach interacting problems. In this thesis I will discuss progress in using two different numerical techniques to study topological phases.

Recently much research in topological phases has focused on phases made up of bosons. Unlike fermions, free bosons form a condensate and so interactions are vital if the bosons are to realize a topological phase. Since these phases are difficult to study, much of our understanding comes from exactly solvable models, such as Kitaev's toric code, as well as Levin-Wen and Walker-Wang models. We may want to study systems for which such exactly solvable models are not available. In this thesis I present a series of models which are not solvable exactly, but which can be studied in sign-free Monte Carlo simulations. The models work by binding charges to point topological defects. They can be used to realize bosonic interacting versions of the quantum Hall effect in 2D and topological insulator in 3D. Effective field theories of "integer" (non-fractionalized) versions of these phases were available in the literature, but our models also allow for the construction of fractional phases. We can measure a number of properties of the bulk and surface of these phases.

Few interacting topological phases have been realized experimentally, but there is one very important exception: the fractional quantum Hall effect (FQHE). Though the fractional quantum Hall effect we discovered over 30 years ago, it can still produce novel phenomena. Of much recent interest is the existence of non-Abelian anyons in FQHE systems. Though it is possible to construct wave functions that realize such particles, whether these wavefunctions are the ground state is a difficult quantitative question that must be answered numerically. In this thesis I describe progress using a density-matrix renormalization group algorithm to study a bilayer system thought to host non-Abelian anyons. We find phase diagrams in terms of experimentally relevant parameters, and also find evidence for a non-Abelian phase known as the "interlayer Pfaffian".

Observing the fractional Fourier transform by free-space Fresnel diffraction

The fractional Fourier transform of an object can be observed in the free-space Fresnel diffraction pattern of the object. (C) 1997 Optical Society of America

Relay lens-free birefringence-customized stackable beam-steering modules for optical interconnects

A previously suggested birefringence-customized modular optical interconnect technique is extended for lens-free relay operation. Various lens-free relay imaging models are developed. We claim that the lens-free relay system is important in simplifying an optical interconnect system whenever the imaging conditions permit. To verify the validity of various proposed concepts, we experimentally implemented some 8 x 8 optical permutation modules. High-power efficiency and low channel cross talk were experimentally observed. In general, the larger the channel spacing, the less the cross talk. A quantitative cross-talk measurement of the lens-free relay system shows that, for a fixed channel width of 0.5 mm and channel spacings of 0.5, 1, and 2 mm, a less than -20-dB cross-talk performance can be guaranteed for lens-free relay distances of 40, 280, and 430 mm, respectively. (C) 1998 Optical Society of America.

Norbornenyl- and nortricyclyl free radicals

The number, symmetry, and product-forming capabilities of the intermediates in the photoinitiated reductions of endo- and exo-5- bromonorbornene and 2-bromonortricyclene with tri-n-butyltin hydride at temperatures between -10° and 22° were investigated.

Three mechanisms were evaluated:

1. The 5-norbornenyl- and 2-nortricyclyl radicals isomerize reversibly with the former producing nortricyclene by abstraction of hydrogen from tri-n-butyltin hydride.

2. The 5-norbornenyl- and 2-nortricyclyl radicals isomerize reversibly, but some norbornene can be formed from the 2-nortricyclyl radical or some nortricyclene can be formed from the 5-norbornenyl radical by abstraction of hydrogen.

3. There is intervention of a "bridged" radical which may be for med reversibly or irreversibly from the 5-norbornenyl- and 2-nortricyclyl radicals.

Within small error limits, the ratios of norbornene to nortricyclene as a function of the concentration of tri-n-butyltin hydride are consistent with the first mechanism.

In the reductions with tri-n-butyltin deuteride, primary deuterium isotope effects of 2. 3 and 2. 1 for the abstraction of deuterium by the 2-nortricyclyl- and 5-norbornenyl radicals, respectively, were found. The primary deuterium isotope effects were invariant with the concentration of tri-n-butyltin deuteride, although the ratios of norbornene to nortricyclene changed appreciably over this range. This is consistent with the first mechanism, and can accommodate the formation of either product from more than one intermediate only if the primary kinetic deuterium isotope effects are nearly equal for all reactions leading to the single product.

The reduction of endo-5-bromonorbornene-5, 6, 6-d₃ with tri-n-butyltin hydride or tri-n-butyltin deuteride leads to both unrearranged and rearranged norbornenes. The ratios of unrearranged to rearranged norbornene require that the 5-norbornenyl-5, 6, 6-d₃ radical isomerize to an intermediate with the symmetry expected of a nortricyclyl free radical. The results are consistent with mechanism 1, but imply a surprising normal secondary kinetic deuterium isotope effect of about 1.25 for the abstraction of hydrogen by the 5-norbornenyl- 5, 6, 6-d₃ radical.

Approximate calculations show that there does not appear to be any substantial difference in the stabilities of the 5-norbornenyl and 2-nortricyclyl radicals.

Although the results can not exclude a small contribution by a mechanism other than mechanism 1, no such contribution is required to adequately explain the results.

Part I: Latent heat of vaporization of n-decane. Part II: Heat and mass transfer from a cylinder placed in a turbulent air stream - Sherwood and Frössling numbers as a function of free stream turbulence level and Reynolds number

Part I

The latent heat of vaporization of n-decane is measured calorimetrically at temperatures between 160° and 340°F. The internal energy change upon vaporization, and the specific volume of the vapor at its dew point are calculated from these data and are included in this work. The measurements are in excellent agreement with available data at 77° and also at 345°F, and are presented in graphical and tabular form.

Part II

Simultaneous material and energy transport from a one-inch adiabatic porous cylinder is studied as a function of free stream Reynolds Number and turbulence level. Experimental data is presented for Reynolds Numbers between 1600 and 15,000 based on the cylinder diameter, and for apparent turbulence levels between 1.3 and 25.0 per cent. n-heptane and n-octane are the evaporating fluids used in this investigation.

Gross Sherwood Numbers are calculated from the data and are in substantial agreement with existing correlations of the results of other workers. The Sherwood Numbers, characterizing mass transfer rates, increase approximately as the 0.55 power of the Reynolds Number. At a free stream Reynolds Number of 3700 the Sherwood Number showed a 40% increase as the apparent turbulence level of the free stream was raised from 1.3 to 25 per cent.

Within the uncertainties involved in the diffusion coefficients used for n-heptane and n-octane, the Sherwood Numbers are comparable for both materials. A dimensionless Frössling Number is computed which characterizes either heat or mass transfer rates for cylinders on a comparable basis. The calculated Frössling Numbers based on mass transfer measurements are in substantial agreement with Frössling Numbers calculated from the data of other workers in heat transfer.

Information collected in Teesdale concerning free-swimming stages of brown trout (Salmo trutta L.)

During 1978 and 1979, electrofishing surveys were made in Teesdale - both to provide background information for ecological work on the streams, and to provide data so that the influence of discharge regime on the fish population densities could be examined. The discharge regimes of the different streams were compared using the Base Flow Index (BFI) as developed by the Institute of Hydrology. (PDF contains 30 pages)