Liang Dong, Ph.D. - US grants

Intellectual Merit: The objective of this research is to develop a programmable, reconfigurable, and tunable photonic circuit platform and to explore its smart sensor applications. The platform will allow one to dynamically configure/reconfigure, tune/detune, and erase/rewrite photonic circuits on a single chip upon demand. The approach is combining nano-electro-mechanical systems and planar photonic crystal technologies to manipulate light on the wavelength scale. Nanocantilevers are fabricated over air holes in a photonic crystal slab. Each nanocantilever is individually controllable to bend into an air hole via an electrostatic actuator addressed by electronic integrated circuits. Therefore, local effective refractive indices of photonic lattices can be tuned and programmed flexibly to form various photonic devices and circuits. The smart sensors can be realized by chemically modifying the surface of nanocantilevers on the photonic circuit platform, making it sensitive to specific analytes mechanically. Through dynamic tuning of the photonic platform, the sensors can be agile enough to tune their internal optical circuits to adapt to different situations and requirements.

Broader Impacts: This research will provide an unprecedented photonic circuit platform with unique reconfigurablity, tunability and programmability to satisfy the demand for multipurpose and compact photonic chips. The proposed technology could revolutionize photonic circuit design, and open up drastically new possibilities in a broad range of areas, including photonic computing, optical communication, environmental monitoring, biochemical defense, and lab-on-a-chip technologies, thus having great potential economic impact. This research will generate broad educational opportunities for undergraduate and graduate students, benefit curriculum development, and provide opportunities for students to work on research projects at both university and industrial laboratories. A pyramid structure for educational outreach will be established to provide an efficient way to introduce micro/nanotechnology into high schools, middle schools, and grade schools of Iowa. Women and minority students will be attracted into science and engineering through year-round open-lab tours, summer internships, and in-class presentations.

Objective: The objective of the program is to develop an integrated droplet-based microfluidic system for parallel screening of phenotypic changes in nematode worms within droplet microenvironments of varying chemical compositions. This work aims to provide a radical translation from existing low-throughput worm motility assays to a truly high-throughput, whole-organism assay for testing multi-drug compounds against nematodes.

Intellectual Merit: The intellectual merit is to provide a powerful lab-on-a-chip assay system for biological studies on whole-animal models with unprecedented high throughput. The system will uniquely combine automated generation and modulation of drug-coded pharmacological droplet libraries, guided movement stimulation, locomotion assay, and electrophysiological recording for single organisms inside droplets. This research is transformative because the system can provide unique details of neurophysiological changes in nematodes with drug exposures, facilitating experiments that are impossible by current techniques. The proposed technology is generic because the system can be adapted to test a wide range of important nematodes and drug compounds.

Broader Impacts: The proposed research will help answer fundamental questions in diagnosing, controlling and predicting drug resistance in nematode parasites, thereby unraveling complex mechanisms of host-parasite interactions. This research will generate broad educational opportunities for both undergraduate and graduate students, and benefit curriculum development for a new Undergraduate Bioengineering Minor Program of the Iowa State. Women and minority students, and middle school students will be attracted into science and engineering through open-lab tours, and in-class presentations. High school science teachers will be collaborated to develop K-12 instructional materials in the topics of micro/nanotechnology and bioengineering.

The project will address Cyber-Enabled Nutrient Management for Sustainable Agriculture through precise spatial/temporal control of agricultural inputs for optimized resource utilization and minimized environmental impact. There is a critical need for the development of cyber technologies in production agriculture that allow automated collection of real-time spatial soil and crop data while advancing a deeper understanding of the fertilizer inputs and nitrogen (N) cycling. This project aims to develop: (1) In-situ, accurate, self-calibrating, self-localizing soil sensors for monitoring soil properties such as soil moisture and nitrates, (2) Small antenna technologies for underground communication so the sensors do not interfere with agricultural operations, (3) Effective techniques for broadband energy-harvesting from vibrational sources (eg., thunder and farming operations); (4) Modeling and analysis methods for understanding the underlying nitrogen cycling at high spatial/temporal resolutions, and information management and decision-making tools for precise agricultural control.

Managing the nitrogen Cycle is one of the grand challenges identified by the National Academies. Nitrogen fertilizers from farm fields are major source of water quality impairment and the leading contributor to hypoxia. The project is a step towards developing deeper understanding of agricultural N cycling process while developing precise controls over N fertilizer inputs that are key to sustainable agriculture. To enhance educational and workforce development efforts, the PIs will contribute to a graduate minor in Sustainable Agriculture by introducing new curriculum material on Bio-Chemical Sensors. PhD students of the funded research will enroll in the Sustainable Agriculture minor, thus developing a new generation of workforce trained in the aspects of cybersystems, agroecosystems, environmental monitoring, and sustainable cultivation. To achieve wider awareness and reception, PIs will work closely with industry and government organizations in the agricultural sector, several of whom have expressed interest through supporting letters.

An award is made to Iowa State University to develop a high-throughput, large-scale plant phenotyping instrumentation for knowledge discovery in plant phenomics area. Characterization of the complete plant phenome has posed a difficult challenge due to the large number of genes in the genomes, and changeable environmental conditions that influence plant phenotypes. Analyzing plant phenotypes on a large and multi-scale level with sufficient throughput and resolution has thus been difficult and expensive. This project will lead to the development of microsystem technology based plant phenotyping instrumentation, and therefore will constitute a transformative leap in throughput and information content over existing phenotype assays. The core of the instrumentation is an integrated plant growth system consisting of an array of miniature greenhouses, microfluidic plant chips, and microfluidic control logic. The plant growth system can provide maximal environmental flexibility in large- and multi-scale study of plant-environment interactions. The miniature greenhouses will flexibly regulate relative humidity, carbon dioxide level, and light intensity. The microfluidic plant chips will be designed to be sliding chip-like disposable components for use inside the greenhouses. Each plant chip will not only allow a number of plants to simultaneously grow for a desired period of time, but be able to automatically trap individual seeds, change growth temperature, regulate chemical concentration, and introduce biological species to the plant growth regions. A programmable imaging system will be designed to collect images of plant seeds, roots, shoots, and cells. To quantify morphological traits and determine phenotypic differences in a high throughput manner, an automated algorithm will be developed to extract and analyze images acquired during plant growth and development. Arabidopsis thaliana will be used as a model plant for biological verification of the instrumentation.

The project will contribute to systematic analysis of plant phenotypes with a wide range of applications in gene identification, functional genomics, and genotype-to-phenotype correlations. Large and multi-scale phenotyping of plants, in concert with changeable growth environmental influences, has broad implications in applied and basic plant biology. The proposed instrumentation will make breakthrough toward solving grand challenging large-scale problems in the field of phenomics, will build resources to benefit plant biology researchers, and will create a paradigm shift in the plant phenomics area by placing powerful data analysis capability in the hands of researchers. The education plans include providing an interdisciplinary opportunity to three doctoral students and four undergraduate students including two female and minority students, creating a one-credit seminar course for the Undergraduate Bioengineering Minor Program, and adding a new lab to existing undergraduate and graduate courses at Iowa State. The dissemination plan includes providing phenotying services to plant biologists at Iowa State and beyond through extensive collaborations, organizing Plant Phenomics workshop, partnering with national laboratories to disseminate phenotying services, and commercializing the instrumentation through the small business innovation research or small business technology transfer mechanism.

Roots interact with and respond to the biotic and abiotic environment in which they live (the rhizosphere) by qualitatively and quantitatively modulating material exuded by roots. These exudates use the language of chemistry to communicate between and among the biotic and abiotic components. Powerful DNA sequencing platforms and analytical tools for identifying chemical components are now available for profiling these interactions among the rhizosphere and the root components. The integrated application of these analytical strategies is limited by the ability to access and isolate exudates from roots and the rhizosphere. Existing exudate sampling tools are bulky, require large amounts of soil, and significantly alter the soil structure. This difficulty of sampling exudates has slowed the process of linking plant genetic determinants to rhizosphere microbiome genomic and metabolic features. This project addresses key design, fabrication, integration, and operation problems faced in developing next-generation root exudate sampling tools. The research will develop greatly-needed tools for probing the chemical exchange between plants and the micro- and macro-organisms in the rhizosphere. The root exudates are critical drivers of microbiome assembly and plant-pest/pathogen outcomes. The dynamic and environmentally responsive nature of root exudates illustrates the importance of developing sampling tools that are functional in a real-world situation, rather than the current tools that are limited to use in primarily artificial hydroponic and polymer-embedded systems. The samplers that will be developed will significantly impact the pace of research on rhizosphere microbiome by enabling continuous, spatially-resolved sampling of the microbes and exudates on roots grown in real-world conditions. This enhanced capability will meet societal needs to increase agricultural productivity for an increasing global population in the face of the uncertainties associated with climate-change, and thus develop new strategies to impact gains in agricultural productivity. This research will enhance interdisciplinary STEM workforce development by hosting at least two under-represented students in an undergraduate Howard Hughes Medical Institute summer internship program, providing research opportunities to four undergraduate senior students, and providing hands-on workshops to a high school Science Bound program to engage students in tech-transfer endeavors, while highlighting plant-microbe contributions to agriculture and global food security.

This project will elaborate advanced technology for gathering high spatiotemporal resolution data of metabolites and microbes in the rhizosphere. This objective will be met by developing a modular toolkit for the localized sampling of rhizosphere exudates from roots grown in soil matrices. This toolkit will consist of (i) a single site exudate sampler, which will serve as a building block of more complex modular sampling systems; (ii) distributed exudate samplers able to extract exudates from key locations with high spatial resolution; (iii) spine-like flexible exudate samplers, providing conformational fitting at the root-soil interface, which will maximize sampling at this crucial interface; and (iv) parallel gradient samplers positioned radially outward from a root, providing access to radial gradients of exudates. These samplers will be uniquely coupled with microfluidic sorters to enable automated separation and isolation of microbes from the collected exudates for simultaneous analysis of both the microbes and the soluble exudates. Furthermore, these samplers will integrate miniature tensiometers, which will allow monitoring of local soil potential condition at the sampling sites, and trigger the automatic start of sampling. Rendering such a "smart" device will improve temporal resolution of sampling. Validating the utility of these integrated devices will involve installing them, collecting and sorting samples, and analyzing the interactions between the rhizosphere and genetically specified maize roots, grown under gnotobiotic conditions with and without microbes. The multidisciplinary research has drawn expertise ranging from microsystems design and construction, microbiome and metabolomics, to address the proposed goal and deliver on the specific aims.

This PFI: AIR Technology Translation project focuses on translating agricultural soil sensor development research into accurate monitoring of spatio-temporal variation of soil properties of agricultural interest. The development of the proposed soil sensors is important because they can enable the real-time, in-place monitoring of soil moisture, salinity, and nutrients in production agriculture, thus enabling precise nutrient management. This project will result in a feasible design/prototype of an in-situ soil sensor for agricultural application. This soil sensor has the unique features that it can measure the soil properties mentioned above in real-time when deployed in an underground grid configuration with support for wireless interaction. Current sensing systems do not support continual in-situ monitoring and also require manual operation, while the proposed system is a fully-automated solution, capable of continual in-situ monitoring and wireless transport.

This project addresses technical gaps as it translates from research discovery toward commercial application in soil sensors for agriculture. Specifically in this project, sensor prototypes, using dielectric-based moisture/salinity sensing and electrophoretic nitrate sensing packaged with signal processing and wireless capability for underground deployment, will be tested and evaluated.

In addition, personnel involved in this project, namely the two PhD students, will receive innovation and technology translation experiences through soil sensor development and evaluation research, regular participation in interactions with the Iowa State Office of Intellectual Property and Technology Transfer for disclosures and patents, and further interactions with agricultural domain industries for licensing, technology transfer and commercialization.

The project engages Microwaves by the Weber, Inc. as a consultant with experience in product design, development and commercialization to augment the team's research capability, and guide commercialization aspects in this technology translation effort from research discovery toward commercial reality.

Liquid biopsy has significant advantages over traditional tumor biopsies, because it is minimally invasive and uses biofluids, such as blood and urine, to diagnose cancer and other diseases in their early stages. Exosomes, which are actively secreted from cancer cells, carry molecular constituents of their originating cells. Because these membranous extracellular vesicles can serve as cellular surrogates, exosomes have emerged as a new type of potent biomarkers. However, conventional exosome analysis methods such as immunoblotting or enzyme-linked immunosorbent assays are costly and require approximately twelve hours and excessive volumes of serum to detect transmembrane proteins on the surface of exosomes. Exosome separation requires complex steps to remove debris or cellular components that will confound downstream analysis. High-throughput molecular profiling of exosomes using miniature label-free biosensors is not available. The goal of this project is to develop a new capability to rapidly screen and profile exosomes based on both molecular and size characteristics. This research will lead to a transformative change in exosome analysis by integrating two state-of-the-art technologies on a single silicon chip. In addition, this research will be integrated with education through adding new lab modules to existing undergraduate biomedical engineering minor program curriculum, recruiting female students, and providing summer internship opportunities to African-American students to participate in the project at Iowa State University, and developing a new undergraduate-level course related to nanobiotechnology at Arizona State University.

The project will lead to an integrated silicon-based nano-opto-fluidic platform for rapidly and continuously profiling of both molecular and size features of exosomes. Cascaded nanoscale deterministic lateral displacement pillar arrays will be developed to simplify the isolation and size profiling of exosomes. The exosomes will be effectively separated from interference molecules present in the fluid sample. High-performance lateral flow-through optical biosensors will be developed to quantify the separated exosomes. The exosome samples can flow through the nanoscale biosensor and be immobilized and enriched on the functionalized sensor surface. Because both the separation and detection modules have the features of lateral flow designs, they can be integrated on a single silicon chip using the nanoimprint lithography process. The integration of these two functions will lead to an unprecedented ability to continuously streamline exosome separation, enrichment and detection processes to profile multi-dimensional molecular and size information for multiple protein markers within one hour. The biological validation plan of the project will be carried out using the proposed device to sort and sense exosomes released from a parasitic nematode and etiological agent of the human disease, Lymphatic Filariasis. The proposed technology is advantageous over the lab-based methods in terms of cost, sample consumption, and throughput, and could be extended to the profiling of circulating exocellular exosomes in human or animal biofluids to diagnose a variety of diseases, identify companion biomarkers that are important for drug discovery, and monitor the progress of a therapy.

This PFI: AIR Technology Translation project focuses on translating agricultural soil sensor development research into accurate monitoring of spatio-temporal variation of soil properties of agricultural interest. The development of the proposed soil sensors is important because they can enable the real-time, in-place monitoring of soil moisture, salinity, and nutrients in production agriculture, thus enabling precise nutrient management. This project will result in a feasible design/prototype of an in-situ soil sensor for agricultural application. This soil sensor has the unique features that it can measure the soil properties mentioned above in real-time when deployed in an underground grid configuration with support for wireless interaction. Current sensing systems do not support continual in-situ monitoring and also require manual operation, while the proposed system is a fully-automated solution, capable of continual in-situ monitoring and wireless transport.

This project addresses technical gaps as it translates from research discovery toward commercial application in soil sensors for agriculture. Specifically in this project, sensor prototypes, using dielectric-based moisture/salinity sensing and electrophoretic nitrate sensing packaged with signal processing and wireless capability for underground deployment, will be tested and evaluated.

In addition, personnel involved in this project, namely the two PhD students, will receive innovation and technology translation experiences through soil sensor development and evaluation research, regular participation in interactions with the Iowa State Office of Intellectual Property and Technology Transfer for disclosures and patents, and further interactions with agricultural domain industries for licensing, technology transfer and commercialization.

The project engages Microwaves by the Weber, Inc. as a consultant with experience in product design, development and commercialization to augment the team's research capability, and guide commercialization aspects in this technology translation effort from research discovery toward commercial reality.

Non-technical:

The development of three-dimensional (3D) printing has allowed custom manufacturing of complex objects with millimeter resolution. Recent advances have enabled 3D patterning of the critical dimensions of materials and devices to the submicron scale. This project will acquire a Nanoscribe Photonic Professional GT2 system to be deployed at the Microelectronic Research Center of Iowa State University. The Nanoscribe is a computer-controlled pattern generator coupled with a 3D printer to produce accurate materials, structures, and devices with a minimum feature size five hundred times smaller than the diameter of a human hair. The Nanoscribe will allow researchers to conduct transformative research in diverse science and engineering areas, such as biomedicine, agriculture, energy, photonics, defense, and advanced manufacturing. This instrument will also promote the integration of research and teaching by using the Nanoscribe in multiple laboratory classes taught by the investigators. The instrument will enrich programs that develop the next-generation STEM workforce and help to broaden the participation of undergraduate and graduate students and postdoctoral researchers. Many undergraduates will participate in the research through REU projects and as part of their senior design projects. There will be a strong emphasis on recruiting women and students from underrepresented minorities in STEM. The education of students in STEM disciplines will be aided by hands-on demonstrations and by providing high school teachers the opportunity to use the instrument and conduct research.

Technical:

The Nanoscribe instrument will enable an array of new research projects in the area of micro-nano science and technology, including multimodal wearable sensors to monitor critical parameters in precision agriculture, portable exosome-based biomarker screening devices integrated with micro-optics, photonic crystals and CMOS imaging sensors, metamaterials and metadevices with functionalities attained through the exploitation of sub-wavelength scale structures to manipulate lights, biodegradable nerve regeneration structures for efficient peripheral nerve repairs, engineered cell microenvironment, soft matter-based electronics, bioinspired adhesives, microrobotic actuators, photovoltaic devices with printed high-aspect-ratio microgrooves, high-efficiency triboelectric energy harvesting materials, and high-performance X-ray collimator with nanogrooves. The instrument will promote multidisciplinary collaborations between engineers and scientists within the departments, across Iowa State University, and beyond the institution. The capabilities of the instrument will become apparent to undergraduate and graduate students and postdoc researchers in the areas of advanced manufacturing, internet-of-things sensors, energy harvesting materials and devices, biomedical devices and instruments, soft electronics, and condensed matter physics at Iowa State University. The instrument will help Iowa State University to become a regional hub for high-resolution 3D printing support to researchers in the State of Iowa.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

In the US, agricultural drainage infrastructure benefits >22.6 Mha of cropland and is valued at ~$100B. As a proportion of total croplands, drained croplands produce a disproportionately large amount of grain but also release a disproportionately large amount of eutrophying nutrients to aquatic ecosystems. Drainage systems include individually-owned field drains that depend on the function of community-owned main drains. Climate change and agricultural intensification are causing farmers to increase the extent and intensity of drainage leading to a pressing need to balance productivity, profitability, and environmental quality when making drainage decisions. Further, because drainage systems include individually-owned and community-owned drains, decision-making involves complex techno-economic social issues together with understanding biophysical processes and requires balancing the needs of individual farmers, drainage communities, and surrounding regions. This project will develop an integrated decision-making platform to facilitate community decision making for precise prediction and management of drainage effects on water flow, crop production, farm net returns, and nutrient loss. The platform data will be made possible by new agricultural sensors and robots, innovations in behavioral economics and analytics tools. Development of the drainage decision-making platform will be guided by farmer stakeholders—including, the Iowa and Illinois Drainage Districts Associations, a national-level agricultural drainage management coalition, and directly with farmers—forming a continuous learning environment across scientists and farmers that fosters adoption of new technologies and transfer of the research process to the next generation of scientists, engineers, and agricultural professionals.

The project will build upon a suite of biophysical and social science advances in multiple areas, including bioinspired robotic snake sensors, in-situ soil nutrient sensors, computational modeling, and socioeconomics. The snake sensors will navigate through agricultural drainage networks to generate a high spatial resolution data stream about flow rates and nitrate concentrations throughout the belowground network. The soil sensors will enable continuous monitoring of nitrate dynamics. Process-based ecohydrological models, subsurface water transport models, and multiple spatiotemporal sensor outputs will be integrated to obtain high-resolution information about distributions of water and nitrate. Biophysical scenario analyses will assist decision-making for different agricultural management scenarios to balance resource use efficiency, profitability, and environmental performance. Socioeconomic science innovations will be integrated by learning how current systems are managed in the context of various heterogeneities across individuals and drainage districts, such as demographics, farm size, and presence of wetlands, and how new information provided by the proposed infrastructure interacts with human incentives and choices and consequent policy making.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.