Interacting single atoms with nanophotonics for chip-integrated quantum networks

Underlying matter and light are their building blocks of tiny atoms and photons. The ability to control and utilize matter-light interactions down to the elementary single atom and photon level at the nano-scale opens up exciting studies at the frontiers of science with applications in medicine, energy, and information technology. Of these, an intriguing front is the development of quantum networks where N >> 1 single-atom nodes are coherently linked by single photons, forming a collective quantum entity potentially capable of performing quantum computations and simulations. Here, a promising approach is to use optical cavities within the setting of cavity quantum electrodynamics (QED). However, since its first realization in 1992 by Kimble et al., current proof-of-principle experiments have involved just one or two conventional cavities. To move beyond to N >> 1 nodes, in this thesis we investigate a platform born from the marriage of cavity QED and nanophotonics, where single atoms at ~100 nm near the surfaces of lithographically fabricated dielectric photonic devices can strongly interact with single photons, on a chip. Particularly, we experimentally investigate three main types of devices: microtoroidal optical cavities, optical nanofibers, and nanophotonic crystal based structures. With a microtoroidal cavity, we realized a robust and efficient photon router where single photons are extracted from an incident coherent state of light and redirected to a separate output with high efficiency. We achieved strong single atom-photon coupling with atoms located ~100 nm near the surface of a microtoroid, which revealed important aspects in the atom dynamics and QED of these systems including atom-surface interaction effects. We present a method to achieve state-insensitive atom trapping near optical nanofibers, critical in nanophotonic systems where electromagnetic fields are tightly confined. We developed a system that fabricates high quality nanofibers with high controllability, with which we experimentally demonstrate a state-insensitive atom trap. We present initial investigations on nanophotonic crystal based structures as a platform for strong atom-photon interactions. The experimental advances and theoretical investigations carried out in this thesis provide a framework for and open the door to strong single atom-photon interactions using nanophotonics for chip-integrated quantum networks.

Coupled plasmonic systems and devices : applications in visible metamaterials, nanophotonic circuits, and CMOS imaging

With the size of transistors approaching the sub-nanometer scale and Si-based photonics pinned at the micrometer scale due to the diffraction limit of light, we are unable to easily integrate the high transfer speeds of this comparably bulky technology with the increasingly smaller architecture of state-of-the-art processors. However, we find that we can bridge the gap between these two technologies by directly coupling electrons to photons through the use of dispersive metals in optics. Doing so allows us to access the surface electromagnetic wave excitations that arise at a metal/dielectric interface, a feature which both confines and enhances light in subwavelength dimensions - two promising characteristics for the development of integrated chip technology. This platform is known as plasmonics, and it allows us to design a broad range of complex metal/dielectric systems, all having different nanophotonic responses, but all originating from our ability to engineer the system surface plasmon resonances and interactions. In this thesis, we demonstrate how plasmonics can be used to develop coupled metal-dielectric systems to function as tunable plasmonic hole array color filters for CMOS image sensing, visible metamaterials composed of coupled negative-index plasmonic coaxial waveguides, and programmable plasmonic waveguide network systems to serve as color routers and logic devices at telecommunication wavelengths.

Towards a Participatory Integrated Assessment Approach for Planning and Managing Natura 2000 Network Sites

36 p.

New climate scenario framework implementation in the GCAM integrated assessment model

48 p.

Temperature, organic matter and the sustainability of aquatic systems

Changes in sustainability of aquatic ecosystems are likely to be brought about by the global warming that has been widely predicted. In this article, the effects of water temperature on water-bodies (lakes, oceans and rivers) are reviewed followed by the effects of temperature on aquatic organisms. Almost all aquatic organisms require exogenous heat before they can metabolise efficiently. An organism that is adapted to warm temperatures will have a higher rate of metabolism of food organisms and this increases feeding rate. In addition, an increase in temperature raises the metabolism of food organisms, so food quality can be altered. Where populations have a different tolerance to temperature the result is habitat partitioning. One effect of prolonged high temperature is that it causes water to evaporate readily. In the marine littoral this is not an important problem as tides will replenish water in pools. Small rain pools are found in many tropical countries during the rainy season and these become incompletely dried at intervals. The biota of such pools must have resistant stages within the life cycle that enable them to cope with periods of drying. The most important potential effects of global warming include (i) the alteration of existing coastlines, (ii) the development of more deserts on some land masses, (iii) higher productivity producing higher crop production but a greater threat of algal blooms and (iv) the processing of organic matter at surface microlayers.

Development of Microfluidic Devices with the Use of Nanotechnology to Aid in the Analysis of Biological Systems Including Membrane Protein Separation, Single Cell Analysis, and Genetic Markers

Computation technology has dramatically changed the world around us; you can hardly find an area where cell phones have not saturated the market, yet there is a significant lack of breakthroughs in the development to integrate the computer with biological environments. This is largely the result of the incompatibility of the materials used in both environments; biological environments and experiments tend to need aqueous environments. To help aid in these development chemists, engineers, physicists and biologists have begun to develop microfluidics to help bridge this divide. Unfortunately, the microfluidic devices required large external support equipment to run the device. This thesis presents a series of several microfluidic methods that can help integrate engineering and biology by exploiting nanotechnology to help push the field of microfluidics back to its intended purpose, small integrated biological and electrical devices. I demonstrate this goal by developing different methods and devices to (1) separate membrane bound proteins with the use of microfluidics, (2) use optical technology to make fiber optic cables into protein sensors, (3) generate new fluidic devices using semiconductor material to manipulate single cells, and (4) develop a new genetic microfluidic based diagnostic assay that works with current PCR methodology to provide faster and cheaper results. All of these methods and systems can be used as components to build a self-contained biomedical device.

Design and implementation of fishery modules in integrated household surveys in developing countries

Fish and other aquatic animals contribute to the food security of citizens of developing countries, both as a source of income and as a component of healthy diets, yet fishing is not currently captured in most integrated household surveys. This sourcebook provides essential technical guidance on the design of statistical modules and questionnaires aimed at collecting fishery data at the household level. Background on the main policies important to the fishery sector, information on the data needed to analyze issues of policy relevance, and methodology on the construction of survey questions to collect necessary data are also provided. The document is organized to provide essential technical guidance on how to design statistical modules and questionnaires aimed at collecting fishery data at the household level. It includes an overview of the main technical and statistical challenges related to sampling fishery-dependent households. The document starts with an introductory section identifying the potential reasons why fisheries and in particular small-scale fisheries have not been adequately included in national statistical systems in a large number of countries. The report then proposes a succinct review of what is known (and what remains unknown) about small-scale fisheries and their contribution to the livelihoods of households in sub-Saharan Africa. It also provides readers with background on the main policies that are important to the fishery sector, information on the data needed to analyze issues of policy relevance, and methodology on the construction of survey questions to collect necessary data.

Aquatic Agricultural Systems: Annual report

The program on aquatic agricultural systems (AAS) aims to change the way the CGIAR engages with aquatic agricultural systems and the poor and vulnerable communities who depend upon them. To do so the program has focused on three primary lines of work in its first six months: (i) preparing for implementation of the program in focal countries and geographical hubs; (ii) harnessing the best of earlier and ongoing research that contributes to the science themes of the program and which we wish to see expanded and integrated into the program as it develops; (iii) establishing innovative governance and management arrangements that will guide and implement the program. This report summaries the achievements and reviews the progress of the AAS program.

Seasonality, labor and integration of aquaculture into southern African smallhold farming systems

Fish production on Malawian smallholdings is generally limited by the quantity and quality of inputs to the pond (Brummett and Noble 1995). The timing of labor availability and other farm activities limit the amount farmers put into their ponds resulting in lower growth rates and yields. There is potential for improving production and yields through modifications of production schedules to accommodate other farming activities. Limited material and labor inputs among farming system enterprises can be better allocated by considering seasonal availability of inputs and adapting the pond and fish farming technology to the farming system. This case from Malawi demonstrates that aquaculture technology that neglects the annual cycle of events and constraints on the farm will not be easily integrated into the farming system. Focusing on technology that maximizes fish production rather than facilitation of adoption and integration has been a feature of the majority of African smallholder agriculture/aquaculture projects. Farming Systems Research (FSR) must identify niches and opportunities for system improvement for it to be worth supporting as a development intervention.

Integration of freshwater prawn culture with rice farming in Kuttanad, India

The integration of paddy cultivation with prawn/fish culture can become a viable alternative to effectively utilize the vast area of derelict polders (embanked coastal flood plains) in Kuttanad, India. Nearly 55 000 ha of wetlands in Kuttanad are available for paddy cultivation year-round. Around 5 000 ha of the polders are utilized for Macrobrachium rosenbergii culture as a follow-up crop. Of the total area, about 250 ha of fallow polders are utilized for monoculture of M. rosenbergii from March to October, while in 4 750 ha polyculture with Indian and exotic carps is practiced from November to June. Stocking density is 15 000 to 60 000/ha for monoculture of M. rosenbergii, while in polyculture with carps, it is 5 000 to 20 000/ha of prawn and 5 000 to 10 000/ha of fish. Production from monoculture varies from 95 to 1 297 kg/ha whereas production from polyculture systems it is 70 to 500 kg/ha of prawn and 200 - 1 200 kg/ha of fish. Profits range from Rs. 5 000 to 20 000/ha. An evaluation is made of how the present polders of Kuttanad are best utilized for culture of M. rosenbergii following different systems of integrated farming and how the integration is useful in the aquaculture sustainability of Kuttanad, a tropical wetland ecosystem.

Sustainable utilization of inland water resources: an integrated program for research and management

In both developed and developing countries, there is increased competition for water resources, resulting in deficiencies in supply and in various forms of pollution. In developing countries, the nutritional potential of aquatic resources is very important. To realize this potential, integrated research and management for sustainable water resource use are needed. This requires a sound understanding of the structure and function of aquatic ecosystems. A programme is presented which stresses the interrelationships of the physical, chemical and biological components of aquatic systems and their catchments. The programme consists of 16 stages in 5 phases, which are as follows: System description; System functioning and modelling; Resource assessment/dynamics; Resource potential; and, Resource utilization for sustainability. This programme enables workers within different disciplines to identify how their expertise contributes to the overall research requirements to support resource development.

Perspectives from agriculture: advances in livestock breeding - implications for aquaculture genetics

In this paper we present livestock breeding developments that could be taken into consideration in the genetic improvement of farmed aquaculture species, especially in freshwater fish. Firstly, the current breeding objective in aquatic species has focused almost exclusively on the improvement of body weight at harvest or on growth related traits. This is unlikely to be sufficient to meet the future needs of the aquaculture industry. To meet future demands breeding programs will most likely have to include additional traits, such as fitness related ones (survival, disease resistance), feed efficiency, or flesh quality, rather than only growth performance. In order to select for a multi-trait breeding objective, genetic variation in traits of interest and the genetic relationships among them need to be estimated. In addition, economic values for these traits will be required. Generally, there is a paucity of data on variable and fixed production costs in aquaculture, and this could be a major constraint in the further expansion of the breeding objectives. Secondly, genetic evaluation systems using the restricted maximum likelihood method (REML) and best linear unbiased prediction (BLUP) in a framework of mixed model methodology could be widely adopted to replace the more commonly used method of mass selection based on phenotypic performance. The BLUP method increases the accuracy of selection and also allows the management of inbreeding and estimation of genetic trends. BLUP is an improvement over the classic selection index approach, which was used in the success story of the genetically improved farmed tilapia (GIFT) in the Philippines, with genetic gains from 10 to 20 per cent per generation of selection. In parallel with BLUP, optimal genetic contribution theory can be applied to maximize genetic gain while constraining inbreeding in the long run in selection programs. Thirdly, by using advanced statistical methods, genetic selection can be carried out not only at the nucleus level but also in lower tiers of the pyramid breeding structure. Large scale across population genetic evaluation through genetic connectedness using cryopreserved sperm enables the comparison and ranking of genetic merit of all animals across populations, countries or years, and thus the genetically superior brood stock can be identified and widely used and exchanged to increase the rate of genetic progress in the population as a whole. It is concluded that sound genetic programs need to be established for aquaculture species. In addition to being very effective, fully pedigreed breeding programs would also enable the exploration of possibilities of integrating molecular markers (e.g., genetic tagging using DNA fingerprinting, marker (gene) assisted selection) and reproductive technologies such as in-vitro fertilization using cryopreserved spermatozoa.