3D unknown view tomography via rotation invariants

In this paper, we study the problem of reconstructing a 3D point source model from a set of 2D projections at unknown view angles. Our method obviates the need to recover the projection angles by extracting a set of rotation-invariant features from the noisy projection data. From the features, we reconstruct the density map through a constrained nonconvex optimization. We show that the features have geometric interpretations in the form of radial and pairwise distances of the model. We further perform an ablation study to examine the effect of various parameters on the quality of the estimated features from the projection data. Our results showcase the potential of the proposed method in reconstructing point source models in various noise regimes

A Quantum Approach to the Discretizable Molecular Distance Geometry Problem

The Discretizable Molecular Distance Geometry Problem (DMDGP) aims to determine the three-dimensional protein structure using distance information from nuclear magnetic resonance experiments. The DMDGP has a finite number of candidate solutions and can be solved by combinatorial methods. We describe a quantum approach to the DMDGP by using Grover's algorithm with an appropriate oracle function, which is more efficient than classical methods that use brute force. We show computational results by implementing our scheme on IBM quantum computers with a small number of noisy qubits.Comment: 17 page

High mass accuracy analytical applications of Fourier transform ion cyclotron resonance mass spectrometry

The performance capabilities of Fourier transform ion cyclotron resonance (FTICR) mass spectrometry are higher than any other type of mass spectrometer, making this technique suitable for a range of analytical applications. Here, FTICR mass spectrometry has been used for the structural analysis of polyketides and nonribosomal peptides, and in the identification of peptide binding sites of ruthenium(II) arene anticancer complexes. In both these applications, methods have been developed involving complementary tandem mass spectrometry techniques, specifically collision activated dissociation (CAD), electron induced dissociation (EID), and electron capture dissociation. In particular, CAD and EID have been shown to be effective in the structural characterisation of polyketides, with a method developed for distinguishing between two isomers of the polyketide lasalocid A. This method has been optimised and extended for application to non-ribosomal peptides enabling detailed structural information to be obtained with very high accuracy. Using CAD and ECD has enabled the identification of amino acids involved in binding ruthenium(II) complexes. Binding to phenylalanine and glutamic acid was observed in this work for the first time; coordination by histidine and methionine was also observed and is in agreement with previous work. Overall, new methods for highly accurate structural characterisation and binding site identification have been successfully designed and implemented

팁-증강 라만 효과를 이용한 나노컨파인드 물의 수소결합 구조 측정

학위논문(박사) -- 서울대학교대학원 : 자연과학대학 물리·천문학부(물리학전공), 2023. 2. 제원호.Confinement change interfacial energy and entropy of molecule within by reducing degrees of freedom. The properties of confined water are also changed like any other molecules. For example, macroscopic properties of confined water such as elastic modulus, friction coefficient, viscosity, and dielectric constant are changed with respect to bulk water. The origin of the peculiar properties of confined water has been thought to be closely related to the hydrogen bond (HB) network since the unique properties of water are mainly attributed to the HB network. Many simulation studies and spectroscopy study report that nanoscale confined water has a different HB network from the bulk phase. However, experimental demonstration of the HB network of confined water found in simulation is not achieved yet. In the spectroscopy study, the fine control of the confinement is difficult and demonstration of the correlation of the HB network with the macroscopic properties is not easy. Meanwhile, experiments to measure changes in the mechanical properties of confined water were mainly conducted using atomic force microscopy (AFM) or a surface force apparatus (SFA), but these force-measuring instruments could not observe the HB network. To simultaneously measure both the HB network and the mechanical property of confined water, we establish tip-enhanced Raman spectroscopy (TERS) by combining the quartz tuning forks (QTF) based AFM and the confocal Raman spectroscopy. TERS is the near-field optical technique that realizes to overcome optical diffraction limits by the enhanced local field at the apex of the metallic tip. The enhancement factor (EF) of TERS, indicating the amount of signal magnification compared to micro-Raman, is achieved up to 10^9 in ambient conditions. Thus, employment of the TERS is essential to investigate a very small amount of water molecules because of the small scattering crosssection of a water molecule. we establish stable nano-confined water by creating a capillary condensed nano-meniscus between the tip and the substrate. As a result, confined water at weak confinement behaves like supercooled water, while confined water at strong confinement has the same HB structure as ice-VII, a high-pressure ice phase at room temperature. We also observe the correlation between the Raman signal and the mechanical relaxation time of confined water, which strongly indicates that the enhanced solidity of confined water near the substrate is caused by the increased portion of ice-VII within confined water. Water is the most important liquid on earth that is closely involved in many atmospheric processes and biochemical reactions. Furthermore, confined water plays a major role in initial cloud formation or DNA-protein interaction rather than bulk water. In this study, we investigate the physical and chemical properties of confined water. In particular, we focused on the HB network because it gives the unique features of water. Our result will help to understand the origin of the peculiar properties of confined water such as sluggish behaviour and will provide experimental evidence of the unique HB structure under confinement.컨파인드 상태에서는 자유도가 감소하기 때문에 컨파인먼트 내부 물질의 표면 에너지와 엔트로피 등이 변화하게 된다. 물도 예외는 아니며 컨파인드 물의 탄성 계수, 마찰 계수, 점성, 유전 상수 등과 같은 거시적 성질들이 벌크 물과 비교하여 달라진다고 알려져있다. 물은 수소결합 네트워크를 가지고 있고 물이 가지는 특이한 성질들은 대부분 수소결합과 밀접한 관련이 있다. 따라서 컨파인드 물의 성질변화 또한 수소결합 네트워크 변화와 아주 밀접한 관련이 있을것으로 생각되었고 여러 시뮬레이션과 분광 실험에서도 컨파인드 물이 특이한 수소결합 구조를 가지고 있다는 것을 확인 할 수 있었다. 그러나 시뮬레이션 결과에서 관측한 특이한 수소결합 구조들은 실험적으로 검증되지 않았다. 또한 분광실험에서는 충분히 작은 크기의 컨파인드를 구현하기 어려웠으며 그 결과를 거시적 성질과 동시에 측정시킬 수 없었다. 한편 컨파인드 물의 거시적 성질 변화를 측정하는 실험들 은 주로 원자 힘 현미경(Atomic force microscopy) 혹은 표면 힘 측정기(Surface Force Apparatus)를 이용하여 진행되었는데 이러한 힘 측정 장비들에서는 수소 결합 네트워크를 측정할 수 없었다. 우리는 컨파인드 물의 수소결합과 그 기계적 특성을 동시에 측정하기 위하여, 수정진동자 기반의 원자 힘 현미경과 공초점 라만 분광장비를 결합하여 팁-증강 라만 분광 장비를 자체 제작하였다. 일반적인 라만분광의 효율로는 약 3000개 미만의 적은 수의 물 분자들의 수소결합을 측정할 수 없기 때문에 금속 팁의 끝에서 국부 전기장의 세기가 증폭되는 팁-증강 라만 분광장비가 필요하였다. 팁도 자체 제작을 하였으며 E-beam evaporation, Sputter coating을 통해 은(Ag)을 코팅하거나 은 와이어를 에칭하여 제작하였다. 팁과 바닥 표면사이에 모세관 응축을 통해 나노 물 기둥을 형성하였으며 팁과 바닥 표면사이의 거리를 조절함으로서 컨파인먼트 정도를 조절하며 라만 신호를 측정 하였다. 그 결과 약한 컨파인먼트 조건에서는 컨파인드 물이 과냉각수 처럼 행동하였으며 강한 컨파인먼트 조건에서는 수소결합 구조가 상온 고압 얼음인 아이스 VII과 유사한 구조를 가진다는 것을 알 수 있었다. 또한 같은 시스템에서 측정한 기계적 이완 시간은 라만신호와 상관관계를 보였으며 강한 컨파인먼트 조건에서 증가하는 양상을 보였다. 이는 컨파인먼트가 강해질 때 내부에 위치한 시료의 고체성이 증가했음을 의미한다. 이러한 점을 통해 강한 컨파인먼트 조건은 표면으로 부터 약 2 나노미터이하의 영역으로 정의할 수 있었다. 물은 지구환경 및 생명활동에서 중요한 역할을 하는 액체이다. 또한 많은 경우에 나노미터 수준으로 갇혀있는 물 환경에서 생명반응이 일어나거나 컨파인드 물의 매개하에 대기 미세입자 들이 형성된다. 따라서 본 연구에서는 컨파인드 물의 성질, 그 중에서도 물의 가장 독특하고 중요한 성질인 수소결합 성질에 대한 연구를 진행하였다. 이 연구 결과는 컨파인드 물이 가지는 여러 독특한 성질들의 기원을 수소결합적인 측면에서 설명할수 있을 것이며, 현재까지는 시뮬레이션 연구 분야였던 초기 얼음핵 구조 연구에 실험적인 증거를 제공한다.1 Introduction 1 1.1 Motivation 1 1.2 Outline of this work 4 2 Theoretical background 6 2.1 Capillary condensation 6 2.1.1 Kelvin equation 7 2.1.2 Young-Laplace equation 7 2.2 Atomic force microscopy 8 2.2.1 Operating modes of AFM 10 2.3 Raman spectroscopy 13 2.3.1 Classical picture of Raman scattering 14 2.3.2 Intensity of Raman scattering 17 2.3.3 Selection rules 17 2.4 Surface-enhanced Raman spectroscopy 20 2.4.1 Enhancement mechanism 20 2.5 Tip-enhanced Raman spectroscopy 25 2.5.1 Enhancement factor 26 3 Experimental setup 28 3.1 System overview 28 3.2 QTF-based atomic force microscopy 32 3.2.1 AFM controller 32 3.2.2 Preamplifier for QTF 36 3.2.3 Mechanical modes of QTF 42 3.2.4 Mechanical amplitude calibration 44 3.3 Raman spectroscopy 46 3.4 Tip fabrication 49 3.4.1 Enhancement factor 55 3.5 Sample preparation 57 4 Hydrogen bond network of nano-confined water 62 4.1 Introduction 62 4.2 Previous works on HB network of confined water 65 4.3 Experimental procedure 68 4.4 Zero-point determination 73 4.5 RH dependent force-distance curves 75 4.6 Comparison of hotspot size to nanomeniscus 78 4.7 OH-stretching band signal of confined water 79 4.7.1 Full spectrum 84 4.7.2 Tip dependence 87 4.8 Peak assignment 89 4.8.1 Spectral assignment 89 4.8.2 Spatial assignment 89 4.9 Peak Behavior 94 4.9.1 Transition between two DDAAs 94 4.9.2 Other peak behavior 96 4.10 Origin of the ice-VII 101 5 Conclusion 106 A Probe aspect ratio dependent approach curve 111 B Tip shape vs etching voltage 114 C Tip quality table 117 D Airtight metal chamber specification 119 Bibliography 122 초록 143박

Surface-Enhanced Raman Scattering: Substrate Development and Applications in Analytical Detection

To advance the capabilities of surface-enhanced Raman scattering (SERS), we developed a silver modified polypropylene filter (AgPPF) substrate which acts as a pseudo stationary phase in harvesting SERS signatures of so called phytochemical estrogens and other environmentally significant chemicals. To augment electron beam lithography (EBL) in SERS research, we also introduced an interesting nanotransfer printing (nTP) technique which could circumvent the low throughput and extremely high resolution (\u3c 10 nm) limitations of EBL in designing advanced SERS substrates. In our study, a nominal average thickness of 10 nm silver on the polypropylene microfiber produced nanoglobules of less than 100 nm in diameter. This noble metal nanoroughened layer allowed AgPPF to serve as a SERS active substrate, onto which the noted endocrine disrupting chemicals were passed through and harvested. The intense, multifeatured vibrational Raman spectra of very rarely SERS studied chemical species collected indicates the potential for useful detection via this approach of creating SERS substrates. AgPPF substrates were also used in characterizing the adsorption behavior of hydroxyl complexes of uranium. Interestingly, hydroxyl group on the uranium complexes showed slow sorption kinetics on the nanostructured silver surfaces. Understanding the adsorption behavior of aqueous solution of uranium on nanostructured silver surfaces has opened up the possibilities of SERS detection of these environmental and non-proliferation concerned species without any surface modifications. nTP is a high resolution printing technique and relies on interfacial chemistries to control the transfer of thin metal film from a stamp to a substrate . In our research, high-aspect-ratio AutoCAD designed nanopatterns were created on silicon wafers using e-beam lithography and reactive ion etching. Silicon relief pillars based stamps were then used to integrate a variety of nanostructures on different dielectric materials. Thus created nanopatterns have shown their promise to hold their inherent SERS activity. For its simplicity, cost-effectiveness, and ease of operation, this hyphenated nTP-SERS technique is impressive in the selection of suitable supporting-films for better SERS enhancements and also to manipulate gap between nanodiscs (gap-plasmonic SERS effect)

Recent Developments in Atomic Force Microscopy and Raman Spectroscopy for Materials Characterization

This book contains chapters that describe advanced atomic force microscopy (AFM) modes and Raman spectroscopy. It also provides an in-depth understanding of advanced AFM modes and Raman spectroscopy for characterizing various materials. This volume is a useful resource for a wide range of readers, including scientists, engineers, graduate students, postdoctoral fellows, and scientific professionals working in specialized fields such as AFM, photovoltaics, 2D materials, carbon nanotubes, nanomaterials, and Raman spectroscopy

Nonlinear Optics

This book examines nonlinear optical effects in nonlinear nanophotonics, plasmonics, and novel materials for nonlinear optics. It discusses different types of plasmonic excitations such as volume plasmons, localized surface plasmons, and surface plasmon polaritons. It also examines the specific features of nonlinear optical phenomena in plasmonic nanostructures and metamaterials. Chapters cover such topics as applications of nanophotonics, novel materials for nonlinear optics based on nanoparticles, polymers, and photonic glasses

Diffusion of tin from TEC-8 conductive glass into mesoporous titanium dioxide in dye sensitized solar cells

The photoanode of a dye sensitized solar cell is typically a mesoporous titanium dioxide thin film adhered to a conductive glass plate. In the case of TEC-8 glass, an approximately 500 nm film of tin oxide provides the conductivity of this substrate. During the calcining step of photoanode fabrication, tin diffuses into the titanium dioxide layer. Scanning Electron Microscopy and Electron Dispersion Microscopy are used to analyze quantitatively the diffusion of tin through the photoanode. At temperatures (400 to 600 °C) and times (30 to 90 min) typically employed in the calcinations of titanium dioxide layers for dye sensitized solar cells, tin is observed to diffuse through several micrometers of the photoanode. The transport of tin is reasonably described using Fick\u27s Law of Diffusion through a semi-infinite medium with a fixed tin concentration at the interface. Numerical modeling allows for extraction of mass transport parameters that will be important in assessing the degree to which tin diffusion influences the performance of dye sensitized solar cells