Precision manipulation of organic and inorganic nanoentities for enhanced optical biodetection at deterministic positions

In the last decade, considerable research interests are focused on applying semiconductor quantum dots (QDs) for bioimaging, sensing, and therapeutic delivery. Compared to traditional organic dyes, semiconductor QDs exhibit higher fluorescent brightness, better resistance to photo-bleaching, tunable sizes/colors, wider absorption peak and larger stokes shifts. However, the applications of QDs as biosensors are still largely conducted in bulk colloidal suspensions, which present considerable difficulties in sensing a minute amount of bioanalyte. It is highly desirable if the QDs can be registered at designated locations for position-predicable optical analysis and sensing. Raman scattering spectroscopy has been utilized to unambiguously identify molecules based on their intrinsic vibrational "fingerprint" states. However, due to the relatively small Raman scattering cross-section, the intensity of Raman signal is usually 1/10⁶ of that of Rayleigh scattering. The recent discovery of Surface enhanced Raman scattering (SERS) dramatically improves the Raman signal and rejuvenates this field. An enhancement factor (EF) as high as 10¹² have been reported, which can readily detect various single molecules, essential for early-stage disease detection, warfare agent detection, environmental pollutant detection, and biomolecule detection. However, SERS substrates with such high EF usually suffer from reproducibility and uniformity issues. Moreover, SERS detection is still largely conducted in a seek-and-find manner which substantially limits the detection efficiency. Most SERS detections are carried out by drying analyte solutions on SERS substrates to force molecules to attach to hotspots before the detection. The employed drying methods can be different among individual research groups. Quantitative comparison of these results should be conducted carefully. It is highly desirable to directly detect molecules in suspension to accurately evaluate the performances of different SERS substrates. However, when directly measuring SERS signals of molecules in suspension, due to the inefficient diffusion based binding process, much less molecules can closely interact with hot spots compared to those on dried SERS samples. As a result, direct SERS detection from suspension can often be less sensitive by a few orders of magnitudes compares to those in dried condition. It is of great interest to investigate new mechanisms to detect analyte molecules directly from analyte solutions with high sensitivity. In this research, I rationally designed and synthesized various types of nanostructures, including ZnO, Si, and Au nanowires, ZnO nanosuperstructures, and hybrid nanocapsules. Such materials have unique optical/plasmonic properties and could be used in various applications, particularly in biochemical sensing. Two types of optical nanobiosensors have been designed, fabricated, characterized, and investigated. They are fluorescence-based QD-on-nanowire assemblies and SERS-photonic-crystal hybrid nanosensors. The QD-on-nanowire florescent nanosensors operated uniquely by focusing analyte molecules to the assembled QDs on tips of nanowires before detection via specific biochemical conjugation. Molecules, such as biotin, can be revealed unambiguously in a location deterministic manner with substantially enhanced sensitivity. In the development of SERS-photonic-crystal hybrid nanosensors, two enhancement mechanisms, including guided-mode resonance (GMR) and electrokinetic effect, were studied and applied in improving the sensitivity and efficiency of molecule detection, respectively. Such a hybrid device has been proposed and studied for the first time, which can readily improve the detection sensitivity by a robust 4-5 times in addition to the 10⁹-10¹⁰ SERS enhancement. This dissertation work, exploring innovative materials design, synthesis, and manipulation, has made an important forward step in the next-generation biochemical detection platform.Materials Science and Engineerin

Extreme Food-Plant Specialisation in Megabombus Bumblebees as a Product of Long Tongues Combined with Short Nesting Seasons

© 2015 Huang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. http://creativecommons.org/licenses/by/4.0/ The attached file is the published version of the article

Computationally efficient offline demand calibration algorithms for large-scale stochastic traffic simulation models

Thesis: Ph. D. in Transportation, Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, 2018.Cataloged from PDF version of thesis.Includes bibliographical references (pages 168-181).This thesis introduces computationally efficient, robust, and scalable calibration algorithms for large-scale stochastic transportation simulators. Unlike a traditional "black-box" calibration algorithm, a macroscopic analytical network model is embedded through a metamodel simulation-based optimization (SO) framework. The computational efficiency is achieved through the analytical network model, which provides the algorithm with low-fidelity, analytical, differentiable, problem-specific structural information and can be efficiently evaluated. The thesis starts with the calibration of low-dimensional behavioral and supply parameters, it then addresses a challenging high-dimensional origin-destination (OD) demand matrix calibration problem, and finally enhances the OD demand calibration by taking advantage of additional high-resolution traffic data. The proposed general calibration framework is suitable to address a broad class of calibration problems and has the flexibility to be extended to incorporate emerging data sources. The proposed algorithms are first validated on synthetic networks and then tested through a case study of a large-scale real-world network with 24,335 links and 11,345 nodes in the metropolitan area of Berlin, Germany. Case studies indicate that the proposed calibration algorithms are computationally efficient, improve the quality of solutions, and are robust to both the initial conditions and to the stochasticity of the simulator, under a tight computational budget. Compared to a traditional "black-box" method, the proposed method improves the computational efficiency by an average of 30%, as measured by the total computational runtime, and simultaneously yields an average of 70% improvement in the quality of solutions, as measured by its objective function estimates, for the OD demand calibration. Moreover, the addition of intersection turning flows further enhances performance by improving the fit to field data by an average of 20% (resp. 14%), as measured by the root mean square normalized (RMSN) errors of traffic counts (resp. intersection turning flows).by Chao Zhang.Ph. D. in Transportatio

Spatial and temporal control of lipid-membrane morphology induced by sphingomyelinase

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2009.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (p. 195-201).Sphingomyelinase (SMase) has been shown to be involved in a variety of cell regulation processes. It can convert sphingomyelin (SM) to ceramide (Cer) and has been suggested to influence the cellular processes by reorganizing the cell membrane morphology. This thesis aims at a more comprehensive understanding of how sphingomyelinase (SMase) can regulate lipid membrane heterogeneity. We develop corralled model raft membranes in a microfluidic device to study the complex phase phenomena induced by SMase. The mass balance of lipid molecules in each confined corral greatly helps us to interpret results. By using the corralled membrane arrays, we are able to obtain the overall statistical distribution of the induction time of a slow domain nucleation and therefore fairly compare the membrane responses caused by different factors. In addition, the flow control by a microfluidic device solves the difficulty of distributing SMase uniformly to membrane systems. Furthermore, the laminar flow in a microchannel allows us to create model membrane arrays with a variety of lipid membrane compositions or solution conditions, which can serve as a screening tool to study a broad range of parameters associated with the interactions between lipid membranes and SMase or other peripheral proteins. We report that SMase can induce both a reaction-induced and a solvent-mediated phase transformation, causing switches of three stationary membrane morphologies and multiple-time-domain ceramide generation in model raft membranes.(cont.) During the reaction-induced phase transformation, the ceramide generated by SMase causes the disintegration of pre-existing rafts rich in sphingomyelin and cholesterol, and recruit sphingomyelin to form SM-enriched domains which are relatively inaccessible to SMase. Once most of the sphingomyelin is physically trapped in SM-enriched domains and the SM concentration in the SMase-accessible region becomes low, the morphology pauses. The pause situation is resolved after the formation of a 3-D feature, rich in SMase, sphingomyelin (SMase's substrate), and ceramide (SMase's product), which triggers the solvent-mediated phase transformation. This 3-D feature is hypothesized as a slowly nucleating SMase-enriched phase where SMase processes sphingomyelin at low concentration more efficiently. The disparate time-scales of the formation of these SMase-features and the SM-enriched domains allow for the development of a significant duration of the middle pause morphology between the two transformations. The results show that SMase can be actively involved in the lipid membrane phase changes. The SMase-induced multi-stage morphology evolution is not only due to the membrane compositional changes caused by SMase,but also due to the selective binding of SMase, and SMase's special phase behavior during the solvent-mediated phase transformation. We further demonstrate that lipid membrane composition and SMase concentration can be used to tune the two phase transformations and therefore the intervals and spatial patterns of Smase-induced multi-stage morphology evolution.(cont.) At a physiologically relevant concentration of SMase, we observe that membrane composition can influence the formation of SM-enriched domains and the nucleation of SMase-features at different extents of time scale and thus significantly tune the stable duration of the middle pause morphology. More importantly, the induction time of SMase-feature nucleation can be significantly decreased by increasing the supersaturating level of its three components in the membrane system. We further model the spatio-temporal morphology change during the solvent-mediated phase transformation. Three major kinetic processes are described in the model: the consumption of SM by the enzymatic reaction at an SMase-feature, the diffusion of SM from SM-enriched domains to an SMase-feature, and the release of SM due to the dissolution of SM-enriched domains. We combine MATLAB coding with Comsol, a software using finite element method to solve partial differential equations, to solve the model numerically due to the complex geometry and the moving boundary of our membrane systems. The non-dimensionality of the model allows the system to be characterized by three non-dimensional parameters. We show all of the possible scenarios of spatial pattern change during the phase transformation. The modeling results are shown to be consistent with our experimental results and can provide insights into the system parameters which are difficult to measure.by Ling Chao.Ph.D

Development of an immersion maskless lithography system

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005.Includes bibliographical references (p. 85-87).As lithography quickly approaches its limits with current technologies, a host of new ideas is being proposed in hopes of pushing lithography to new levels of performance. The work presented in this thesis explores the use of an immersion scheme to improve the performance of a maskless lithographic technique known as Zone-Plate-Array Lithography (ZPAL). This is believed to be the first implementation of an immersion scheme in a maskless lithography system. This thesis provides a complete description of the Immersion Zone-Plate-Array Lithography (iZPAL) system. Since the zone plate component of the system is largely responsible for its lithographic performance, a thorough analysis of zone plate theory, design, and fabrication is also presented. The focusing performance of an immersion zone plate is then characterized through the experimental reconstruction of its point spread function. Finally, lithography results obtained with the iZPAL system are compared to those obtained with the non-immersion ZPAL system, demonstrating the improvement in resolution, exposure latitude, and depth-of-focus achieved with the immersion scheme.by David Chao.S.M

Electronic and structural properties of vacancies on and below the GaP(110) surface

We have performed total-energy density-functional calculations using first-principles pseudopotentials to determine the atomic and electronic structure of neutral surface and subsurface vacancies at the GaP(110) surface. The cation as well as the anion surface vacancy show a pronounced inward relaxation of the three nearest neighbor atoms towards the vacancy while the surface point-group symmetry is maintained. For both types of vacancies we find a singly occupied level at mid gap. Subsurface vacancies below the second layer display essentially the same properties as bulk defects. Our results for vacancies in the second layer show features not observed for either surface or bulk vacancies: Large relaxations occur and both defects are unstable against the formation of antisite vacancy complexes. Simulating scanning tunneling microscope pictures of the different vacancies we find excellent agreement with experimental data for the surface vacancies and predict the signatures of subsurface vacancies.Comment: 10 pages, 6 figures, Submitted to Phys. Rev. B, Other related publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm

Numerical visualization and optimization on the core penetration in multi-cavity co-injection molding with a bifurcation runner structure

[[abstract]]Co-Injection Molding and multi-cavity molding are common processes for plastic products manufacturing. These two systems are sometimes combined and applied in the manufacture of bifurcation-structure products. In the previous literature results, the dynamic behavior of the core penetration in co-injection multi-cavity molding with a bifurcation structure is quite complicated and the behavior is sensitive to injection flow rates, different materials, and other process conditions. However, how these influential factors truly affect the core penetration behavior and the detailed mechanism of core penetration behavior has not yet been fully understood. In this study, we focused on studying the multi-cavity co-injection system with a bifurcation runner structure. The results showed that when the skin-to-core ratio is fixed (say 72/28), the melt flow behavior of a co-injection system, utilizing the same material for both skin and core, is very similar to that of a single shot injection molding. Specifically, the non-symmetrical bifurcation runner structure will influence the flow behavior greatly and cause the core distribution imbalance between different cavities. Due to the geometric nature of the bifurcation runner design, this core distribution imbalance problem will still persist even if we modify the melt temperature, mold temperature, or even change the plastic material. Furthermore, when the skin-to-core ratio is fixed (say 72/28), the changes of the flow rate have very little effect on the core penetration result in the final molded product; the final molded product will still have a core distribution imbalance issue. However, we observed that when the flow rate is increased, the core material will occupy more volume space in the upstream portion of the runner and the core penetration distance will be reduced in the flow direction downstream. This feature is very useful to further manipulate the skin-core interface in a multi-cavity system. Moreover, regarding how to improve a poor inter-cavity balance of core material distribution, using a suitable adjustment of the skin-to-core ratio will be greatly helpful. However, the core break-through defect can be a common problem in co-injection molding when an unsuitable skin-to-core ratio is used. To prevent the core break-through defect, increasing the flow rate properly can be one of the good options that we can use. Hence, we concluded that a suitable adjustment of the skin-to-core ratio and a proper flow rate control can be used to optimize the core material distribution in multi-cavity co-injection molding with a bifurcation runner structure. Lastly, in order to validate our inference and the effectiveness of our proposal to improve the inter-cavity imbalance and core break-through problem, a series of experimental studies were performed. And, all experimental results are in good agreement with those of our numerical predictions to further validate the feasibility of our proposed method to gain a better control of the core material distribution with a bifurcation runner structure in multi-cavity co-injection molding.[[notice]]補正完

Scanning tunneling microscopy and spectroscopy at low temperatures of the (110) surface of Te doped GaAs single crystals

We have performed voltage dependent imaging and spatially resolved spectroscopy on the (110) surface of Te doped GaAs single crystals with a low temperature scanning tunneling microscope (STM). A large fraction of the observed defects are identified as Te dopant atoms which can be observed down to the fifth subsurface layer. For negative sample voltages, the dopant atoms are surrounded by Friedel charge density oscillations. Spatially resolved spectroscopy above the dopant atoms and above defect free areas of the GaAs (110) surface reveals the presence of conductance peaks inside the semiconductor band gap. The appearance of the peaks can be linked to charges residing on states which are localized within the tunnel junction area. We show that these localized states can be present on the doped GaAs surface as well as at the STM tip apex.Comment: 8 pages, 8 figures, accepted for publication in PR

Center-of-Mass Properties of the Exciton in Quantum Wells

We present high-quality numerical calculations of the exciton center-of-mass dispersion for GaAs/AlGaAs quantum wells of widths in the range 2-20 nm. The k.p-coupling of the heavy- and light-hole bands is fully taken into account. An optimized center-of-mass transformation enhances numerical convergence. We derive an easy-to-use semi-analytical expression for the exciton groundstate mass from an ansatz for the exciton wavefunction at finite momentum. It is checked against the numerical results and found to give very good results. We also show multiband calculations of the exciton groundstate dispersion using a finite-differences scheme in real space, which can be applied to rather general heterostructures.Comment: 19 pages, 12 figures included, to be published in Phys. Rev.