Revealing and modifying non-local variations in a single image

We present an algorithm for automatically detecting and visualizing small non-local variations between repeating structures in a single image. Our method allows to automatically correct these variations, thus producing an 'idealized' version of the image in which the resemblance between recurring structures is stronger. Alternatively, it can be used to magnify these variations, thus producing an exaggerated image which highlights the various variations that are difficult to spot in the input image. We formulate the estimation of deviations from perfect recurrence as a general optimization problem, and demonstrate it in the particular cases of geometric deformations and color variations.Israel Science Foundation (Grant 931/14)Shell Researc

Assembly and detection of viruses and biological molecules on inorganic surfaces

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2007.Includes bibliographical references.This work is composed of three distinct, albeit related, projects. Each project is an exploration of the ways in which interactions between inorganic surfaces and biological molecules can be advantageously exploited. The first project entitled, Biomolecular Recognition of Crystal Defects extended the phage display technique to the detection of crystal defects. The system used is based on the M13 bacteriophage with 7-residue constrained random sequence on protein III. After considerable experimentation a procedure described as 'Diffuse Selection' was developed for selecting defects on crystal surfaces. Challenges occur because it is difficult to drive phage display towards the selection of particular surface features as opposed to whole surfaces. After multiple iterations, diffuse selection was optimized and consensus sequences were achieved. Virus binding was characterized using Atomic Force Microscopy, Fluorescene Microscopy and Titration. Using a simple bimolecular model, the binding sequence identified through this work is shown to have a binding constant 100,000 times better than a random peptide sequence. The second project entitled, Surface Patterning of Genetically Programmed Viruses, developed a generalizable approach to patterning viruses regardless of the genetic modification made to the virus. Genetic modifications are made in order to create viruses which will construct inorganic materials on their bodies in the appropriate chemical environment. Three generalizable virus patterning approaches were developed based on hydrophobic, electrostatic and covalent binding approaches respectively. This work showed successful patterning using all three approaches, but only the covalent approach was shown to be an effective way to actually construct materials on the genetically programmed viruses.(cont.) The third and final project is entitled, A Kelvin Probe Biosensor. This project devised a label-free high-resolution scanning probe approach for detecting target biomolecules on nano-scaled features. In analogy to modern fluorescence microarrays, biological probes were patterned on a gold substrate. When the probes were exposed to a target analyte, the target would bind the probe and change the local surface potential. This change in surface potential could then be measured using Kelvin Probe Force Microscopy. This work represented the first example of detecting biological molecules on surface using KPFM at the nanoscale.by Asher Keeling Sinensky.Ph.D

나노다공성 인듐 주석 산화물 전극에서의 구조 효과 연구 및 바이폴라 전극 센서로의 응용

학위논문(박사)--서울대학교 대학원 :자연과학대학 화학부,2020. 2. 정택동.Along with the fast development of technology and the advent of environmental issues, the need for efficient and cost-effective electrocatalysts used in energy devices and sensors have increased greatly. Numerous researches have focused on improving the efficiency of electrocatalysts while reducing the contents of noble metals. In this context, fabricating nanostructured catalysts in order to enhance its catalytic activity has long been crucial in electrocatalyst development. In particular, nanoporous electrodes are widely utilized as competent catalysts due to its enlarged surface area and catalytic active surface characteristics. The catalytic contribution from an additional catalytic factor arising from the nanoporous morphology (nanoconfinement effects) has been suggested and investigated by several groups, most of which have utilized noble metal based nanoporous electrodes. In this thesis, nanoconfinement effects were investigated by employing low catalytic material with systematically varied nanoporous layer thickness. Furthermore, the effect of structure modification towards sensor sensitivity were demonstrated. In the first part of the thesis, the acceleration of electron transfer kinetics at the nanoporous indium tin oxide (ITO) electrodes were investigated. In this study, the catalytic activity of nanoporous electrodes was explored regarding the effects of confined morphology of the electrode towards heterogeneous electron transfer reactions. In order to observe the geometric contribution towards the electrocatalytic activity, ITO was chosen as the electrode material due to its low catalytic activity. Systematically varying the nanoporous ITO layer thickness allowed the exclusion of surface-originated catalytic effects of the nanoporous electrodes such as defect densities. Experimental results showed that the single electron transfer of Fe2+/3+ that involve no proton transfer is more facilitated with thickening ITO nanoporous layers, which have higher proportion of nanoconfined geometry. In the second part of the thesis, a novel indium-tin oxide (ITO) bipolar electrode (BPE) based sensor by the implementation of nanoporous ITO, is introduced. The nanoporous ITO layer implemented BPE showed markedly enhanced ECL signals compared to the planar ITO based BPE, enabling the detection of H2O2 even under a mild operating voltage. The ECL calibration curves towards H2O2 detection using BPEs of various nanoporous layer thicknesses exhibited lowered LODs and improved sensitivities with thickening nanoporous layers. We speculate that the nanopore morphologies may have spatially confined the analytes, thus leading to amplified ECL signals.효율적인 에너지 전환 장치 혹은 저장 장치, 그리고 센서 등에 대한 수요가 높아짐에 따라, 이들의 성능을 결정짓는 전기화학 촉매에 대한 연구가 활발히 진행되고 있다. 이러한 촉매 연구들은 촉매 효율을 최대한으로 끌어올리면서 동시에 귀금속 재료를 줄이는 방향으로 이루어지고 있다. 이러한 맥락에서 촉매들을 나노구조체로 제작하는 전략 또한 전극 표면적을 늘리거나 표면 자체의 촉매성을 높이려는 의도로 자주 쓰인다. 그 중에서도 나노다공성 구조의 전극들은 부피 대비 표면적 증가 및 표면 활성화 측면에서 주목받는 촉매 물질이다. 하지만 나노다공성 전극의 표면 성질로부터 파생되는 촉매 효과 외에도, 나노동공 구조 내부 반응종의 갇힘 효과에 의한 추가적인 촉매 효과가 있을 것이라는 주장이 제기된 바가 있다. 이러한 '나노 갇힘 효과' 연구들은 주로 귀금속 재료의 나노다공성 전극을 이용하여 연구가 진행되어 왔다. 본 연구에서는 낮은 촉매성을 가지는 인듐 주석 산화물 (indium tin oxide, ITO) 을 재료로 하여 나노다공성 층의 두께를 변화시켜가면서 나노 갇힘 효과를 관찰하였다. 또한 나노 갇힘 효과에 바탕한 구조 개조의 촉매 개발 응용 가능성을 센서 성능으로 보여주었다. 챕터 1 에서는 나노다공성 인듐 주석 산화물 전극을 도입하여 하나의 전자 전달이 가속화됨을 관찰하였고, 나노다공성 전극에서의 촉매 메커니즘을 구조 효과 측면에서 살펴보았다. 이를 위해, 촉매 효과가 느리다고 알려진 인듐 주석 산화물을 전극 재료로 택하였으며, 나노다공성 층 두께에 따른 전자전달 반응 빠르기를 관찰함으로써 전극 표면 성질로부터 파생되는 촉매 효과를 상쇄시킬 수 있었다. 이로부터 Fe2+/3+ 전자 전달 빠르기가 두꺼운 나노다공성 층에서 점차 증가하는 것을 보았으며, 이는 나노다공성 구조로부터 기인한 것으로 분석하였다. 챕터 2에서는 나노다공성 인듐 주석 산화물을 바이폴러 전극 (bipolar electrode, BPE) 센서에 도입함으로써 과산화수소에 대한 분석 능력이 향상됨을 관찰하였다. 과산화수소 농도에 따른 적정 곡선을 통해 BPE 센서에 나노다공성 구조를 도입할 경우, 그렇지 않은 평탄한 전극에 비해 감도가 매우 크게 향상하였으며, 약한 작동 전압에서도 효율적인 측정을 할 수 있었다.1. General Introduction 1 1.1 Background and overview 3 1.1.1 Conventional approaches in developing electrocatalysts 3 1.1.2 Chemistry in confined space 5 1.1.3 Molecular dynamics in confined space 6 1.1.4 Electron transfer models and rate formalism based on microscopic theories 8 1.2 Effect of confined space in electrochemistry 14 1.2.1 Electrochemical confinement effects 14 1.2.2 Nanoconfinement effects in nanoporous electrodes 17 1.2.3 Challenges in investigations of nanoconfinement effects 18 2. Investigation of Nanoconfinement effects at Nanoporous Indium Tin Oxide Electrodes 21 2.1 Introduction 23 2.2 Experimental 26 2.2.1 Reagents 26 2.2.2 Fabrication and Characterization of nanoporous Indium Tin Oxide electrodes with various thicknesses 26 2.2.3 Electrochemical Methods 28 2.3 Results and Discussion 29 2.3.1 Characterization of nanoporous Indium Tin Oxide electrodes 29 2.3.2 Measurements of Fe2+/3+ electrokinetics at nanoporous ITO electrodes 32 2.3.3 The surface area normalized rate constants of Fe2+/3+ at nanoporous ITO electrodes 39 2.3.4 Nanoconfinement effects as a function of temperature 43 2.4 Conclusion 48 3. Nanoporous ITO implemented Bipolar Electrode Sensor for enhanced Electrochemiluminescence 51 3.1 Introduction 53 3.2 Experimental 55 3.2.1 Chemicals and Materials 55 3.2.2 Instruments 56 3.2.3 Fabrication of Nanoporous Indium Tin Oxide BPEs 57 3.2.4 Optical Analysis 59 3.2.5 Electrochemical Methods 59 3.3 Results and Discussion 60 3.3.1 Design of the BPE microchip and the sensing system 60 3.3.2 Characterization of nanoporous Indium Tin Oxide layer 62 3.3.3 Optical analysis of H2O2 detection 67 3.3.4 Nanoconfinement effects of nanoporous structures towards H2O2 detection 72 3.4 Conclusion 75 4. Conclusions and Perspective 77 References 83 Abstract (in Korean) 95Docto

Doctor of Philosophy

dissertationThis dissertation focuses on the study of surface biomolecular interactions using second harmonic generation (SHG) spectroscopy, surface SHG imaging (SSHGI), and SH correlation spectroscopy (SHCS). The binding kinetics and energetics of four biotinbound proteins, avidin, streptavidin, neutrAvidin, and anti-biotin antibody were compared and data revealed significant differences in their apparent binding affinities and nonspecific binding. Specifically, protein-protein interactions were found to play an important role in the apparent binding affinity, making the streptavidin-biotin interaction the most energetically favorable. The details of the binding properties of these frequently employed tether/linker protein-biotin complexes provide valuable information for biosensors, immunoassays, and medical diagnostics. As most biosensor platforms are designed for high throughput detection, the resolution and planar wave-front of the SSHGI system was thoroughly analyzed. It was demonstrated that the coherent plane wave generated by SHG followed Gaussian beam propagation, enabling SSHGI to image without a lens system at rather long distances. Lens-less imaging simplifies the detection method, increases photon collection efficiency, and increases the detection area. These advantages could potentially make SSHGI a simple, label-free high throughput detection method for surface biomolecular interactions. The versatility and sensitivity of SHG were further probed by coupling SHG with correlation spectroscopy, a statistical fluctuation time-dependent method. SHCS was established as a viable and valuable option for the detection of surface binding kinetics for small molecule and protein-ligand interactions at the surface of lipid bilayers. First, the simple binding kinetics of a small molecule, (s)-(+)-1,1'-bi-2-napthol (SBN), incorporating into a lipid bilayer was determined using SHCS and results were statistically similar to those obtained from a traditional binding isotherm. Next, SHCS was used to examine the binding kinetics of a more complex interaction between the multivalent proteins, cholera toxin subunit b (CTb) and peanut agglutinin (PnA), and a GM1 doped lipid bilayer. SHCS was able to obtain the binding kinetics for these surface biomolecular interactions with more efficiency, less analyte, and less sensitivity to mass transport effects. Cumulatively, the studies of this dissertation showcase SHG, SSHGI, and SHCS as valuable label-free detection methods with incredible sensitivity for investigation of surface biomolecular interactions