Multi-functional, self-sensing and automated real-time non-contact liquid dispensing system

Liquid dispensing in the order of pico-liter has become more and more important in biology, electronics and micro-electronic-mechanical-system (MEMS) during the past two decades due to the rapid progress of researches on the deoxyribonucleic acid (DNA) microarray, compact and low-cost direct write technology (DWT), organic semiconductors and nano-particles. The existing approaches, commercialized or experimental, to liquid dispensing in minute amounts have one common shortcoming: open loop control, i.e., they have no direct control on the quality of dispensed liquid. In contrast, the SmartPin has intrinsic self-sensing capability to not only control the process of liquid dispensing, but also the results of the dispensed liquid in real time. The dual purpose fiber optics sensor/plunger is able to detect the status of liquid morphology under dispensing, in real time, by the internal light sensor and control both the amount and the manner of liquid dispensing by its plunger-like movements. This dissertation work has implemented, with the SmartPin technology, a frilly automated DNA microarrayer based on the first generation prototype developed at NJIT\u27s Real Time Control Laboratory. This new DNA microarrayer fulfills all requirements in each step of DNA microarray fabrication, such as thorough cleaning to avoid cross contamination and clogging, aspiration of tiny amount of DNA samples, spotting on multiple slides, and flexible in stream change of DNA samples. Experiment results shows that this DNA microarrayer compares favorably with its commercialized counterpart OmniGrid 100 with SMP3 pins. As a verification of robust implementation and on-the-fly control of spot morphology, high volume of spots (120 K) have been made, from which the corresponding experiment data has been obtained, categorized and normalized as template database. In addition, this dissertation research explores the patterned microline-drawing capability of the SmartPin. Two approaches, spot sequence and liquid-column sweeping, are proposed and implemented. Experiment results show that the SmartPin is promising in the area of patterning of large area organic electronics. Besides the experimental research, computational fluid dynamics (CFD) simulation of the liquid dispensing process has been done by utilizing GAMBIT and FLUENT, which are state-of-the-art computer programs for modeling fluid flow and heat transfer in complex geometries. The CFD simulation results, validated by experimental results, offer a guide to the design of control system for different tasks of liquid dispensation, such as fabrication of protein microarray

BioMEMS

As technological advancements widen the scope of applications for biomicroelectromechanical systems (BioMEMS or biomicrosystems), the field continues to have an impact on many aspects of life science operations and functionalities. Because BioMEMS research and development require the input of experts who use different technical languages and come from varying disciplines and backgrounds, scientists and students can avoid potential difficulties in communication and understanding only if they possess a skill set and understanding that enables them to work at the interface of engineering and biosciences. Keeping this duality in mind throughout, BioMEMS: Science and Engineering Perspectives supports and expedites the multidisciplinary learning involved in the development of biomicrosystems. Divided into nine chapters, it starts with a balanced introduction of biological, engineering, application, and commercialization aspects of the field. With a focus on molecules of biological interest, the book explores the building blocks of cells and viruses, as well as molecules that form the self-assembled monolayers (SAMs), linkers, and hydrogels used for making different surfaces biocompatible through functionalization. The book also discusses: Different materials and platforms used to develop biomicrosystems Various biological entities and pathogens (in ascending order of complexity) The multidisciplinary aspects of engineering bioactive surfaces Engineering perspectives, including methods of manufacturing bioactive surfaces and devices Microfluidics modeling and experimentation Device level implementation of BioMEMS concepts for different applications. Because BioMEMS is an application-driven field, the book also highlights the concepts of lab-on-a-chip (LOC) and micro total analysis system (μTAS), along with their pertinence to the emerging point-of-care (POC) and point-of-need (PON) applications

BioMEMS

As technological advancements widen the scope of applications for biomicroelectromechanical systems (BioMEMS or biomicrosystems), the field continues to have an impact on many aspects of life science operations and functionalities. Because BioMEMS research and development require the input of experts who use different technical languages and come from varying disciplines and backgrounds, scientists and students can avoid potential difficulties in communication and understanding only if they possess a skill set and understanding that enables them to work at the interface of engineering and biosciences. Keeping this duality in mind throughout, BioMEMS: Science and Engineering Perspectives supports and expedites the multidisciplinary learning involved in the development of biomicrosystems. Divided into nine chapters, it starts with a balanced introduction of biological, engineering, application, and commercialization aspects of the field. With a focus on molecules of biological interest, the book explores the building blocks of cells and viruses, as well as molecules that form the self-assembled monolayers (SAMs), linkers, and hydrogels used for making different surfaces biocompatible through functionalization. The book also discusses: Different materials and platforms used to develop biomicrosystems Various biological entities and pathogens (in ascending order of complexity) The multidisciplinary aspects of engineering bioactive surfaces Engineering perspectives, including methods of manufacturing bioactive surfaces and devices Microfluidics modeling and experimentation Device level implementation of BioMEMS concepts for different applications. Because BioMEMS is an application-driven field, the book also highlights the concepts of lab-on-a-chip (LOC) and micro total analysis system (μTAS), along with their pertinence to the emerging point-of-care (POC) and point-of-need (PON) applications

SuNS : fabricating nano/bio devices using DNA as a movable type

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2007.Includes bibliographical references.When a useful device is developed, it always requires a mass-production technique to industrialize it. In the era of nano/biotechnology, the development of printing techniques has not followed the speed of the inventions of novel devices. One of the main challenges is handling at the same time the resolution and the chemical complexity of these nano/bio-devices. Here a new stamping technique, Supramolecular Nano-Stamping, SuNS, capable of reproducing surfaces containing DNA-features is presented and discussed. SuNS is based on the combination of contact and supramolecular interaction between complementary DNA strands. It can replicate in a single cycle features made of DNA of arbitrary chemical complexity. SuNS is a versatile technique, masters can be fabricated with various fabrication techniques, ranging from hard lithography to soft lithography. It was used to print on multiple substrates, hard (gold, silicon), soft (Poly-methyl-methacylate or Poly-dimethyl-siloxane) or even liquid. The technical specifications of the printing process depend on the substrate material.(cont.) As an example SuNS can achieve state-of-art printing feature and point-to-point resolution ( 25 cm2) when printing onto a liquid prepolymer. In SuNS a copy has the potential to be used as another master to generate more copies. Lastly and most importantly, SuNS can replicates features composed of DNA of different sequences in a single printing cycle while keeping the chemical differences between the patterns. SuNS is still in its infancy and far from complete, it is expected that it will be extended/improved in the future.y Arum Amy Yu.Ph.D

다조성계 플라즈몬 나노 구조의 화학 및 전기적 산란 신호 조절

학위논문(박사) -- 서울대학교대학원 : 자연과학대학 화학부, 2022.2. 남좌민.Plasmon resonance, which is a coherent collective oscillation of conductive electrons in the presence of an external electromagnetic field, effectively enhances various optical processes by means of strong light-matter interactions. Especially, plasmonic nanomaterials scatter light with extraordinary efficiency and the increased far-field radiation intensity can be exploited for the advanced design of biosensors, colorimetric methods for naked-eye detection, and smart displays. However, the full potential of the scattering from plasmonic nanomaterials cannot be fully realized by single component-based nanostructures with monotonic and confined properties. On the contrary, multi-component-based systems exhibit diverse properties and opportunities owing to the synergistically combined physicochemical functions of individual components or new features arising from the integrated structures. In this thesis, I present a chemical and an electrical strategy to modulate scattering response of plasmonic multi-component nanostructures and optimal examples of which showing benefits from the multicomponent systems. Chapter 1 introduces plasmonic properties of multicomponent nanostructures and following advantages of enhanced and modulated plasmonic scattering on applications. In Chapter 2, I developed a highly specific, well-defined Cu polyhedral nanoshell (CuPN) overgrowth chemistry and introduced to enhance light-scattering signal of Au nanoparticle probes for bio-detection. The CuPNs are exclusively formed on the surface of Au nanoparticles in a controllable manner without any noticeable non-specific signal amplification. This newly developed polymer-mediated multicomponent core-shell formation chemistry was shown as a means of the development of the naked-eye-based highly sensitive and quantitative detections of DNA and viruses. Chapter 3 includes new-found anomalous electrochromic behaviors of Au nanocubes. Plasmon scattering of the nanocubes showed higher shift rate of resonance frequency at the highly negative potential range in reversible manner. This unexpected change beyond classical understandings was attributed to the material-specific quantum mechanical electronic structures of the plasmonic materials. The substantial role of quantum capacitance in plasmonic material, which can be derived from the density of states of the composing metals, was able to be verified for the first time by means of altering the surface element by forming Ag-Au core-shell nanocubes.플라즈몬 공명은 외부 전기장에 따른 전도성 전자들의 정합 진동이며, 물질과 빛의 강력한 상호작용을 통하여 다양한 광학적 과정을 효과적으로 증대한다. 특히 플라즈모닉 나노물질은 비범할 정도의 효율로 빛을 산란하며, 증가된 원거리장 방사 세기는 바이오센서, 육안 검출을 위한 비색분석, 스마트 디스플레이 등의 발전된 설계를 위해 활용할 수 있다. 그러나 단조롭고 제한된 특성을 보이는 단일 조성의 나노 구조만으로는 플라즈모닉 나노물질의 산란이 갖는 모든 잠재력을 충분히 발휘할 수 없다. 반면 다조성계 기반 체계에서는 개별 요소로부터 오는 물리 화학적 특성의 상승적 조합이나 결합된 구조로부터 오는 새로운 특성과 같은 다양한 성질과 가능성을 보일 수 있다. 이 논문에서는 플라즈모닉 다조성계 나노구조의 산란 신호를 조절하기 위한 화학적 및 전기적 전략과 다조성계 시스템의 이점을 보여주는 최적의 예를 제시한다. 제1 장에서는 다조성계 나노구조의 플라즈몬 특성과 이를 응용할 때 플라즈모닉 산란의 조절 및 증강으로부터 기대할 수 있는 장점을 소개한다. 제2 장에서는 매우 특이적이고 잘 정의된 구리 다면체 나노쉘(CuPN)의 과성장을 위한 화학적 접근법 개발을 소개한다. 새로운 과성장 법은 바이오 검지를 위해 사용되는 금 나노입자 프로브의 빛 산란에 적용하였다. CuPN은 금 나노입자 표면에서만 선택적이고 제어 가능하도록 형성되었으며 비 특이적 신호 증폭을 나타내지 않았다. 이렇게 새로 개발된 다조성계 코어-쉘을 형성하는 고분자 기반 화학적 합성법이 DNA와 바이러스의 정량 가능한 고감도 육안 검출법의 개발에 사용됨을 보였다. 제3 장은 금 나노 큐브의 색전현상에서 새롭게 발견한 비정상적 거동을 포함한다. 나노 큐브의 플라즈몬 산란은 높은 음전위 영역에서 더 높은 진동수 변화율을 보였다. 고전적인 이해를 벗어나는 이러한 예기치 않은 변화는 플라즈모닉 재료의 물질 특이적인 양자 역학적 전자 구조에 기인한다. 플라즈모닉 재료를 구성하는 금속의 상태 밀도로부터 유도될 수 있는 양자 정전용량의 상당한 역할은, 은-금 코어-쉘 나노 큐브를 형성하여 표면 원소를 바꾸는 방법을 통해 처음으로 증명할 수 있었다.Abstract i Self-Citations of the Prior Publications iv Chapter 1. Introduction: Plasmonic Scattering of Multicomponent Nanostructures 1 1.1. Light Scattering of Plasmonic Nanomaterials 2 1.2. Plasmonic Multicomponent Nanostructures 7 1.3. Plasmonic Scattering Modulation for Applications 14 Chapter 2. Polyhedral Cu Nanoshell Formation Chemistry for Bio-Detections 23 2.1. Introduction 24 2.2. Experimental Methods 28 2.3. Results and Discussion 40 2.4. Conclusion 66 Chapter 3. Unconventional Electrochromic Behaviors of Plasmonic Au and Au-Ag Core-Shell Nanocubes 71 3.1. Introduction 72 3.2. Experimental Methods 81 3.3. Results and Discussion 90 3.4. Conclusion 115 Bibliography 119 Abstract in Korean 126박

Upconverting diagnostics: Multiplex assays utilizing upconversion luminescence technology

Conventional diagnostics tests and technologies typically allow only a single analysis and result per test. The aim of this study was to propose robust and multiplex array-inwell test platforms based on oligonucleotide and protein arrays combining the advantages of simple instrumentation and upconverting phosphor (UCP) reporter technology. The UCPs are luminescent lanthanide-doped crystals that have a unique capability to convert infrared radiation into visible light. No autofluorescence is produced from the sample under infrared excitation enabling the development of highly sensitive assays. In this study, an oligonucleotide array-in-well hybridization assay was developed for the detection and genotyping of human adenoviruses. The study provided a verification of the advantages and potential of the UCP-based reporter technology in multiplex assays as well as anti-Stokes photoluminescence detection with a new anti- Stokes photoluminescence imager. The developed assay was technically improved and used to detect and genotype adenovirus types from clinical specimens. Based on the results of the epidemiological study, an outbreak of adenovirus type B03 was observed in the autumn of 2010. A quantitative array-in-well immunoassay was developed for three target analytes (prostate specific antigen, thyroid stimulating hormone, and luteinizing hormone). In this study, quantitative results were obtained for each analyte and the analytical sensitivities in buffer were in clinically relevant range. Another protein-based array-inwell assay was developed for multiplex serodiagnostics. The developed assay was able to detect parvovirus B19 IgG and adenovirus IgG antibodies simultaneously from serum samples according to reference assays. The study demonstrated that the UCPtechnology is a robust detection method for diverse multiplex imaging-based array-inwell assays.Perinteiset diagnostiset testit mahdollistavat vain yhden analyysin ja tuloksen määritystä kohden. Väitöskirjatyöni tavoitteena oli kehittää uudenlaisia järjestelmä kuopassa tyyppisiä mallintavia monianalyyttimäärityksiä, joissa yhdestä näytteestä yhdessä reaktiokaivossa voidaan mitata samanaikaisesti useita analyyttejä ja niiden pitoisuuksia. Kehitetyt monianalyyttimääritykset perustuvat sekä nukleiinihappojen että proteiinien mittaukseen hyödyntäen leimoina valoa tuottavia epäorgaanisia lantanidi-ioneja sisältäviä loisteainepartikkeleita (UCP). Näillä partikkeleilla on ainutlaatuinen kyky virittyä matalaenergisen infrapunavalon vaikutuksesta ja emittoida korkeaenergisen näkyvän valon aallonpituuksilla, mikä mahdollistaa autofluoresenssista vapaan mittauksen ja näin ollen herkkien määrityksien kehityksen. Väitöskirjatyössäni kehitin adenoviruksille DNA-tyypitysmäärityksen, joka perustui yksinauhaisen PCR-tuotteen ja adenovirus-tyyppispesifisten koettimien väliseen hybridisaatioreaktioon mikrotiitterilevyn kaivon pohjalla. Tulokset osoittivat, että UCP-leimateknologia ja uusi anti-Stokes luminesenssin kuvantamiseen kehitetty laite soveltuvat monianalyttimääritysten kvantitatiiviseen mittaukseen. Teknisesti parannettua adenovirusten DNA-tyypitysmenetelmää hyödynnettiin kliinisesti merkittävien adenovirustyyppien havaitsemisessa ja genotyypityksessä. Adenovirusinfektioiden epidemiologinen seuranta osoitti, että adenovirus tyyppi B03 aiheutti epidemian syksyllä 2010. Väitöskirjatyössäni kehitin myös kvantitatiivisen mallintavan monianalyytti-immunomäärityksen kolmelle antigeenille. Määrityksessä kaikille analyyteille saatiin kvantitatiivinen tulos, ja analyyttiset herkkyydet olivat kliinisesti merkittävällä alueella. Lisäksi väitöskirjatyössäni kehitin serologisen monianalyyttimäärityksen, jonka avulla mitattiin seerumista IgG-luokan adenovirusja parvovirus B19-vasta-aineita samanaikaisesti. Serologinen monianalyyttimääritys validoitiin näytepaneelilla ja tulokset korreloivat hyvin adenovirus IgG ja parvovirus B19 IgG referenssi-entsyymi-immunomäärityksien kanssa. Väitöskirjatyössäni osoitin, että UCP-teknologia soveltuu sekä oligonukleotidi- että proteiini-pohjaisten monianalyyttimääritysten kvantitatiiviseen kuvantamiseen.Siirretty Doriast

DEVELOPMENT OF NOVEL HIGH PERFORMANCE PROTEIN MICROARRAYS FOR DIAGNOSTIC APPLICATIONS

Several application of protein microarray technology in diagnostics have been published and a limited number of protein microarrays is currently available on the In Vitro Diagnostics (IVD) market. Albeit several advantages, related to the miniaturization, the multiplexing capability and the possibility of integrating the immunoassays in biosensing devices, microarrays may still lack of specificity or sensitivity. To overcome these limitations and expand the use of protein microarray platform in diagnostics, the present PhD research aimed at developing innovative approaches to increase the assay specificity and sensitivity, reaching very low detection limits, that are compatible with the use of the proposed devices in diagnostics. Furthermore, the use of protein microarrays has been applied to the characterization of emerging biomarkers: exosomes. First of all, surface immobilized hydrogels have been investigated as reagent reservoir for microarray reagents. They have been demonstrated to store reagents in a dry form, stable over days, in a format easy to transport and to preserve. Moreover, they also acted as chambers able to physically separate analytes or reagents which may cross-react with proteins on the printed arrays. In this way the solution was prevented from spreading over the surface and the assays provided sentitive performances, comparable to standard static incubations. In further studies, the complementarity of information provided by fluorescence-based, label-free IRIS and SP-IRIS microarray platforms has been applied to develop immunoassays useful in the diagnostics of Neurodegenerative Disorders. Specifically, two different assay formats have been exploited. The first part of the work focused on the development of a classical sandwich immunoassay able to detect physiological concentrations of Amyloid-beta peptides, biomarkers for Alzheimer\u2019s disease, in both artificial cerebrospinal fluid and real human samples. The second study was aimed at extending the concept of protein microarrays to extracellular vesicles (i.e., exosomes) detection through surface antigen-antibodies recognition. In this innovative application, the nanoparticles were detected with label-free IRIS (total biomass measurements) and SP-IRIS (particle counting and size distribution). In addition, individual particles were incubated with gold-labeled antibodies to identify biomarkers expressed on their surface

Trypanosoma brucei: Protein Expression Microarrays and Circulating miRNA during Infection

The last decades have been galvanized by efforts to reduce the ever widening gap that exist between functional genomics and proteomics. Assigning molecular functions to, and breaking through the complex networks in which each and every individual protein of the cellular proteome is involved is the breathtaking task that needs to be overcome in order to understand the molecular and physiological basis underlying health and disease. System-wide analysis is an approach that can permit a better understanding of the proteome, and there is need for robust and reliable platforms for such analysis to be developed. To contribute to current efforts, I have developed and optimized methods for the production of functional protein microarrays in a miniaturized form from cDNA products and genomic DNA as template source. I have further shown that such arrays are very useful and reliable in various applications such as protein-protein interactions, protein-RNA interactions, Kinase substrate identification and antibody selection. I have validated some data obtained from these arrays in vivo in a model organism, Trypanosoma brucei. This confirms that the platform can well contribute to the already existing proteomic tools in generating reliable biological data. Moreover, using cDNA products allow for the analysis of disease-related and rare transcripts as well as other spliced variants. Current diagnostic tools for human African trypanosomiases are very invasive and in some cases are not sensitive enough, and this is compounded by a highly heterogeneous seropositive patient population that is difficult to classify. To address this, I have equally analyzed the miRNA and mRNA expression pattern in the peripheral blood of patients in search for new markers. Thirteen differentially expressed miRNAs were identified, three of which (miRNA-199a-3p, miRNA-27b and miRNA-126*) were highly selective (>95%). These miRNAs have also been reported to be differentially regulated in other diseases and miRNA-199a-3p for example is used as a diagnostic biomarker. They are therefore not suitable as specific biomarkers in sleeping sickness. I have however shown that there is deregulation of miRNA expression following T. brucei infection, and most of the differentially regulated miRNAs are related to immune responses to infectious agents and other inflammatory responses influencing disease outcome