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Encapsulating Co and Pd Nanoparticles as Spatially Separated Dual Active Sites for Heterogeneous Persulfate Activation: Synergistic Catalysis and Switching of the Primary Reaction Pathway
No full textThis study demonstrates that the carbon encapsulation of Pd and Co as spatially isolated redox-active sites can synergistically enhance the activation of peroxymonosulfate (PMS) and peroxydisulfate (PDS) and enable persulfate precursor-sensitive degradation routes. The superiority of bimetal-carbon composites (i.e., Pd/Co@NC) was confirmed based on a higher efficiency of Pd/Co@NC with varying Pd/Co ratios for persulfate activation than the sum of efficiencies of single metal-component catalysts applied at corresponding dosages. Treatment performances of Pd/Co@NC with different metal compositions aligned with the dependence of electrical conductivity and binding affinity of Pd/Co@NC on the relative metal content. Reflecting differential reactivity of monometallic components toward persulfate, the primary degradation pathway was switched, depending on the persulfate type. Pd/Co@NC caused radical-induced oxidation upon PMS addition while initiating nonradical PDS activation through electron-transfer mediation, based on retarding effects of radical scavengers, reactivity toward multiple organics, Koutecký-Levich plots, electron paramagnetic spectral features, and product distribution. The fabrication strategy to enable the separate carbon encapsulation of two metallic sites with different catalytic reactivity created metal-carbon composites that retained the advantages of radical and nonradical persulfate activation under realistic treatment conditions; i.e., treatability of a wide spectrum of organics and minimal interference of background compounds in complex water matrices. © 2025 American Chemical Society.FALSEscopu
Recognition of two hydrophobic pockets in the KIX domain of CBP by FOXO4 transactivation domain
No full textThe transcription machinery is assembled via interactions of DNA-bound transcriptional activators and coactivators. When the eukaryotic RNA polymerase II complex is formed, cAMP-regulated transcription factor (CREB) binding protein (CBP) acts as a general coactivator bridging the transcriptional apparatus. Forkhead box protein O4 (FOXO4), a transcription factor, has been reported to bind to the KIX domain of CBP (CBP-KIX). Although the CR3 of FOXO4 (FOXO4-CR3) binds as expected to the MLL and c-Myb sites of CBP-KIX, its substantially higher affinity for CBP, compared to its homolog FOXO3a, cannot be explained by a single conserved Phi XX Phi Phi binding motif. Here, we found that a second Phi XX Phi Phi motif in FOXO4-CR3 provides an additional point of contact for CBP-KIX. Isothermal titration calorimetry and chemical shift perturbation analyses revealed a difference in binding affinity and confirmed that different binding patterns occur at the two hydrophobic pockets of CBP-KIX. Increased helicity of FOXO4-CR3 upon KIX MLL site binding was demonstrated by circular dichroism and C alpha chemical shifts. Paramagnetic relaxation enhancement and docking simulations suggested FOXO4-CR3 orientation is not restrained in the KIX-CR3 complex. Our study provides information about the unique binding properties of FOXO4-CR3 and CBP-KIX, expanding our understanding of CBP recruitment via KIX-transactivation domain binding.TRUEsciescopu
Study of Interlayer Charge Transfer in h-BN/MoS₂ Heterostructures by Fluorination of the h-BN Wrapping Layer
No full text2차원 전이금속 칼코겐화합물(TMDs)의 대표적인 물질인 단층 이황화몰리브덴(MoS₂)은 원자 수준의 얇은 구조와 우수한 반도체 특성으로 인해 차세대 반도체 소자로서 높은 잠재력을 보입니다. 본 연구에서는 h-BN/MoS₂ 이종구조에서, h-BN래핑층의 플루오린화를 통해 MoS₂의 전자 및 광학적 특성을 정밀하게 조절할 수 있음을 보고합니다. 플루오린화는 h-BN 층에 강한 전자 끌어당김 효과를 부여하여, 유기 흡착제 없이도 안정적인 층간 전하 이동을 유도하며, MoS₂ 채널에서 강력한 p형 도핑을 가능하게 합니다. 최적의 플루오린화 수준(7.3 at. %)에서 광발광(PL) 강도는 최대 16배 증가하였고, 광자 에너지는 약 30 meV 청색 이동하며, 밴드갭은 1.85 eV에서 1.88 eV로 증가하는 특성을 보였습니다. 이러한 변화는 트라이온(trion) 형성 억제 및 중성 엑시톤(neutral exciton) 재결합 촉진에 기인한 것으로 분석됩니다. 그러나 플루오린화 농도가 과도하게 증가할 경우(>11 at. %), MoS₂ 층에서 구조적 손상이 발생하여 플루오린화 수준의 정밀한 제어가 필요함을 확인하였습니다. 라만(Raman) 분광 및 X-선 광전자 분광(XPS) 분석을 통해 h-BN 층 내에서 B-F 및 N-F 공유 결합의 형성을 확인하였으며, MoS₂와의 화학적 결합은 관찰되지 않았음을 증명하였습니다.
결론적으로, 본 연구는 플루오린화 공정을 통한 2차원 재료의 전자적·광학적 특성 조절 방법을 제안하며, 이를 통해 조절 가능한 p-형 도핑 효과를 구현할 수 있음을 증명하였습니다. 본 연구에서 개발된 플루오린화된 h-BN/MoS₂ 이종구조는 차세대 나노 전자 및 광전자 소자 응용에 있어 유망한 플랫폼으로 활용될 수 있을 것입니다.|Transition metal dichalcogenides (TMDs), such as monolayer molybdenum disulfide (MoS₂), are promising alternatives to silicon for semiconductor applications due to their atomically thin structure and exceptional semiconducting properties. In this work, we demonstrate precise modulation of the optoelectronic and electrical properties of h-BN/MoS₂ heterostructures through fluorination of the h-BN wrapping layer. Fluorination introduces a strong electron-withdrawing effect, enabling stable interlayer charge transfer and inducing pronounced p-type doping in the MoS₂ channel without the need for organic adsorbents. At optimal fluorination levels (7.3 at. %), optical characterizations reveal up to a 16-fold enhancement in photoluminescence (PL) intensity, a ~30-meV blue shift in photon energy, and a bandgap increase from 1.85 eV to 1.88 eV, attributed to suppressed trion formation and enhanced neutral exciton recombination. Excessive fluorination (>11 at. %) leads to structural degradation, underscoring the importance of precise control. XPS analysis confirm covalent B-F and N-F bond formation in h-BN, with no chemical bonding to MoS₂.
Overall, this fluorination-based approach offers a scalable and controllable method to modulate properties in 2D heterostructures. By achieving stable and tunable charge transfer effects while preserving structural integrity under optimal conditions, fluorinated h-BN/MoS₂ heterostructures present a promising platform for next-generation nanoelectronics and optoelectronic device applications.MasterList of Contents
Abstract i
List of Figures iv
List of Tables v
1. Introduction １
1. 1. Background of Two-dimensional Materials ２
1. 1. 1. Crystal Structure of MoS2, WSe2, and h-BN ４
1. 1. 2. Electronic Structure and Properties ５
1. 1. 3. Optical Properties (Raman and Photoluminescence) ９
1. 2. Preparation of Two-Dimensional Materials １０
1. 2. 1. Mechanical Exfoliation １０
1. 2. 2. Chemical Vapor Deposition １０
1. 3. Surface Charge Transfer for Two-Dimensional Materials １５
1. 4. Interlayer Charge Transfer １７
1. 5. Fluorination of h-BN １９
2. Experimental Section ２１
2. 1. Synthesis of Monolayer MoS2 Using CVD ２１
2. 2. Synthesis of h-BN Film on Platinum Foil Using CVD ２１
2. 3. The Transfer Methods of MoS2 Using Polystyrene ２２
2. 4. The Transfer Methods of h-BN to the Target Substrate ２２
2. 5. Fabrication of h-BN/MoS2 Heterostructures ２３
2. 6. Fluorination Process ２３
2. 7. Characterization ２３
3. Results and Discussion ２４
3. 1. Interlayer Charge Transfer by Fluorination of h-BN/MoS2 ２４
3. 2. Characterization of interlayer charge transfer in h-BN/MoS2 by fluorination ２８
3. 3. XPS Analysis of Fluorination of h-BN/MoS2 Heterostructures ３４
4. Conclusion ３８
5. Reference ３９
6. Abstract in Korean ４
Temperature-driven molecular aggregation and phase behavior in sec-butyl alcohol/water mixtures
No full textThe miscibility and phase behavior of binary liquid mixtures are strongly regulated by temperature, often leading to liquid-liquid phase separation under conditions defined by an upper critical solution temperature (UCST), lower critical solution temperature (LCST), or closed-loop miscibility gaps. In this work, the temperature-driven aggregation behavior and spatial distribution of alcohol and water molecules in sec-butyl alcohol (SBA)/water mixtures, exhibiting a closed-loop miscibility gap across LCST and UCST points, were examined utilizing molecular dynamics (MD) simulations, graph theory, and spatial inhomogeneity analysis. The radial distribution function (RDF) and graph theoretical analysis in the binary liquid mixture reveal that small SBA aggregates at lower temperatures are formed due to the strong interaction of alcohol with water, which is well-mixed with liquid water, promoting a homogeneous mixture. However, at intermediate temperatures, enhanced alcohol-alcohol interaction causes the formation of larger SBA aggregates, which are incompatible with water, triggering liquid-liquid phase separation in the aqueous mixture. At higher temperatures, these large alcohol aggregates are fragmented into small ones due to increased thermal motion, which is compatible with the water H-bond network, restoring homogeneity in the single-phase state. The spatial distribution analysis highlights that at lower temperatures, low h -values reflect a uniform distribution of constituent molecules with small-sized alcohol aggregates. In contrast, as temperature rises, large SBA aggregates with high h -values indicate spatial inhomogeneity and the emergence of water-incompatible aggregates, resulting in the phase separation in binary liquid mixtures. At elevated temperatures, decreasing h -values signify restored homogeneity as alcohol aggregates disassemble, re-establishing a single-phase state in the two-component system. These investigations on temperature-induced aggregation behaviors are anticipated to critically contribute to the broader understanding of LCST, UCST, and reentrant phase behaviors in binary liquid mixtures as well as the liquid-liquid phase separation phenomena in biological systems. © 2025 Elsevier B.V.sciescopu
Disulfide-stabilized diabodies enable near-atomic cryo-EM imaging of small proteins: A case study of the bacterial Na+/citrate symporter CitS
No full textDiabodies are engineered antibody fragments with two antigen-binding Fv domains. Previously, we demonstrated that they are often highly flexible but can be rigidified by introducing a disulfide bond at the Fv interface. In this study, we explored the potential of disulfide-bridged, bispecific diabodies for near-atomic cryoelectron microscopy (cryo-EM) imaging of small proteins because they can predictably link target proteins to “structural marker” proteins. As a case study, we used the bacterial citrate transporter CitS as the target protein, and the horseshoe-shaped ectodomain of human Toll-like receptor 3 (TLR3) as the marker. We show that diabodies containing one or two disulfide bonds enabled the 3D reconstruction of CitS at resolutions of 3.3 Å and 3.1 Å, respectively. This resolution surpassed previous crystallographic results and allowed us to visualize the high-resolution structural features of the transporter. Our work expands the application of diabodies in structural biology to address a key limitation in the field. © 2025 Elsevier Inc.FALSEsciescopu
Tumor Size-Dependent Magnetic Hyperthermia Efficiency: A Simulation-Guided In Vivo Study
No full textMagnetic hyperthermia has shown promise as a localized cancer treatment, but optimizing the injection dose of magnetic nanoparticles (MNPs) remains a major challenge, particularly in tumors with different sizes. In this study, we present a simulation-guided and in vivo validated framework for injection dose planning based on the tumor volume. Specific loss power (SLP) of PEG-coated Synomag-D MNPs was estimated under immobilized conditions using tissue-mimicking agarose phantoms and incorporated into a three-dimensional COMSOL model of pancreatic tumors. Simulations were conducted for a wide range of tumor sizes (80-700 mm3) to identify the required MNP concentration to reach therapeutic temperatures (45 degrees C). The results revealed a nonlinear relationship between the tumor volume and required MNP amount, characterized by a critical size that separates two treatment regimes: small tumors requiring a minimum injection (MI) to compensate for high relative heat loss and large tumors where dose scales linearly with volume-Tumor Volume-Normalized Injection (TVNI). This two-regime hypothesis was validated in vivo using 31 pancreatic tumor mouse models divided into five groups. Complete tumor regression was achieved in groups treated with appropriately matched dosing strategies, while a mismatched protocol failed to reach therapeutic temperatures. With further analysis, we linked the critical size to fundamental thermal diffusion limits, which provided a theoretical basis for defining dosing strategies based on tumor volume. Our findings underscore the need for size-specific dosing strategies, which are necessary and offer practical insights into tailoring MNP dosing for improved treatment outcomes, particularly for early stage or small-volume tumors that are known to be difficult to treat. However, regardless of the tumor size or type, minimizing the injection dose is always desirable for biosafety, and our findings further highlight the importance of enhancing MNPs' SLP by tuning their intrinsic magnetic properties-particularly to meet the disproportionate demands of small tumors without compromising safety.FALSEsciescopu
The study of Rab GTPase mediated regulation of the endoplasmic reticulum structure
No full textThe intricate mesh-like structure of endoplasmic reticulum (ER) tubules is maintained by homotypic membrane fusion between ER tubules, mediated by the evolutionarily conserved dynamin-like GTPase, atlastin. Although a subset of Rab proteins, another family of GTPases, has been implicated in regulating ER structure, the relationship between atlastins and Rab GTPases in ER fusion remains unclear. This study reveals that Rab10, a Rab GTPase previously reported to regulate ER structure, participates in the atlastin-mediated ER fusion pathway. We demonstrate that Rab10 physically interacts with ATL2, a human atlastin protein predominantly expressed in non-neuronal cells. Fusion between ER microsomes isolated from HEK293 cells, where ATL2 is the major atlastin, is inhibited by anti-Rab10 antibodies. Furthermore, the co-reconstitution of Rab10 into liposomes markedly enhances the fusion of ATL2-containing liposomes. Our findings suggest that Rab10 functions as a crucial regulator of ATL2-mediated ER membrane fusion.MasterContents
Abstract································································································ i
Contents······························································································· ii
List of figures ······················································································· iii
I. Introduction································································································ 1
II. Materials and Methods
II-1. Protein preparation ··············································································· 3
II-2. Preparation of reconstituted atlastin-containing liposomes for the lipid mixing assay · 3
II-3. Lipid mixing assay ·············································································· 4
II-4. Co-Immunoprecipitation ········································································ 5
II-5. Cell culture and transfection ···································································· 5
II-6 Preparation of ER microsomes ·································································· 5
II-7 In vitro ER microsome fusion assay ···························································· 6
II-8 In vitro binding assay ············································································· 6
II-9. Microscopy ······················································································· 6
II-10. GTPase-Glo™ assay ············································································ 7
II-11. Statistical analysis ·············································································· 7
III. Results
III-1. ATL-dependent ER microsome fusion is sensitive to GDI, indicative of Rab involvement ····· 8
III-2. Identification of the interaction between Rab10 and ATL2 ······································· 8
III-3. Co-localization of ATL2 with Rab10 and the Influence of Rab10 on ER Morphology ·········· 9
III-4. Rab10 stimulates ATL2-mediated fusion ························································ 10
III-5. Rab10 Enhances ATL2 GTPase Activity to Facilitate GTP Hydrolysis ························· 11
IV. Discussion ······················································································· 12
V. References ······················································································· 31
VI. Abstract in Korean ··········································································· 34
Acknowledgement ············································································ 35
List of figures
Table 1. Plasmids used in this study ····································································· 15
Table 2. List of antibodies used in this study ····························································· 15
Figure 1. ATL-dependent ER microsome fusion is sensitive to GDI, indicative of Rab involvement. ······ 16
Figure 2. Rab10 directly interacts with the GTPase domain of ATL2. ···································· 18
Figure 3. ATL2 interacts with Rab10 in vivo. ···························································· 20
Figure 4. ATL2 interacts with Rab10 in vivo. ···························································· 22
Figure 5. Rab10 stimulates ATL2-dependent ER microsome fusion. ····································· 24
Figure 6. Rab10 stimulates lipid mixing between ATL2p-containing liposomes. ·························· 26
Figure 7. Rab10 enhances the GTP hydrolysis activity of ATL2. ······························· 28
Figure 8. Rab10's role in enhancing ATL2-mediated ER membrane fusion. ······························· 3
Composed Program Induction with Latent Program Lattice
No full textCompositional reasoning requires learning structure, inferring programs, and discovering refined primitives. Existing approaches either lack explicit decomposition mechanisms or rely
on hand-crafted primitives. We propose the Program Lattice Auto Encoder (PLAE), which
learns compositional transformations in a structured latent program space. PLAE trains
an encoder where program effects correspond to integer linear combinations of program
bases, forming a discrete program lattice. Program induction reduces to solving the Closest Vector Problem (CVP), enabling two complementary inference modes: fast System-1
reasoning via CVP and deliberate System-2 reasoning through stepwise lattice walks with
intermediate verification. The framework supports abstraction discovery through lattice
reduction, which refines primitive bases to uncover more fundamental components. This
work connects neural and symbolic reasoning by providing a mathematically principled
framework for compositional domains
Generalized Depth Perception from Everyday Sensors
No full textAccurate depth perception is one of the critical components for applications to au- tonomous driving, robotic navigation, and augmented reality. To obtain high-resolution, metric-scale depth information without relying on complex and expensive hardware, leveraging RGB images with corresponding sparse depth data from active sensors such as LiDAR and Kinect has become the most feasible solution, known as depth completion. This dissertation presents various approaches to enhance depth perception using commonly available sensors by addressing three fundamental challenges: (1) Better design of affinity map used for the depth completion, (2) Generalizable depth completion task motivated by prompt engineering, and (3) Data-efficient strategies to minimize the high costs associated with dense depth annotation. The first challenge arises from errors at object boundaries in conventional depth completion, where noise or smooth intensity changes in images cause ambiguity in the construction of pixel relationships. The conventional methods define an affinity map to explain the pixel relations in Euclidean space. They often struggle in such regions, leading to bleeding errors in depth perception, which occur when incorrect depth information spreads from one area to adjacent ones. To mitigate this, this dissertation redefines the representation space for the pixel relations from Euclidean to hyperbolic space, known for its effectiveness in capturing hierarchical relationships. Hyperbolic geometry allows us to make an affinity map with a more distinct separation between unrelated pixels by enlarging their distance, reducing the chance of incorrect depth information spreading between them. While the hyperbolic geometry-based affinity map significantly enhances pixel-level accuracy in depth completion, it is vital to address biases inherent in sensor measurements, as it can limit the effectiveness and applicability of dense depth perception in real-world scenarios. It is well-known that variations in sensor density, sensing patterns, and scan ranges lead to significant generalization issues. To overcome these limitations, this dissertation proposes a novel prompt engineering for depth input, enabling adaptable feature representations tailored to different depth distributions. By integrating this module into foundation models for monocular depth estimation, this dissertation allows these models to generate absolute scale depth maps without being constrained by specific sensor ranges, thereby enhancing their robustness and versatility. However, adapting these pretrained models remains challenging due to the significant differences between indoor and outdoor sensing environments. To further tackle the challenge of consistent depth estimation across diverse scenes and sensors, this dissertation defines a universal depth completion problem that acknowledges the significant data diversity between indoor and outdoor environments. This is crucial because variations in conditions, such as sudden snowfall, rain, or foggy situations, can drastically affect depth perception. To enable rapid adaptation, a baseline architecture is designed to estimate depth efficiently. It leverages a foundation model for monocular depth estimation to achieve a comprehensive understanding of 3D scene structures and incorporates a pixel-wise affinity map to align sensor-specific depth data with monocular depth estimates. By embedding features into hyperbolic space, this dissertation constructs implicit hierarchical structures of 3D data, thereby improving both adaptability and generalization, even in the face of limited examples.DoctorAbstract i
List of Contents iii
List of Tables v
List of Figures viii
1 Introduction 1
1.1 Problem Definition 1
1.2 Scope of the Research 3
1.2.1 Hierarchical Affinity Learning with Hyperbolic Geometry 4
1.2.2 Depth Perception with Diverse Commercial Sensors 5
1.2.3 Universal Depth Completion with Minimal Resources 6
1.3 Outline of Dissertation 6
2 Hierarchical Affinity Learning with Hyperbolic Geometry 8
2.1 Introduction 8
2.2 Related Works 11
2.3 Mathematical Preliminaries 12
2.3.1 Background of Hyperbolic Geometry 13
2.3.2 Rationale: Hyperbolic Representation for Affinity 14
2.3.3 Pixel-level Hyperbolicity 17
2.4 Hyperbolic Convolution Layer 17
2.5 Hyperbolic Affinity Learning Module 20
2.6 Learning Affinity with Hyperbolic Representation 22
2.7 Experimental Results and Analysis 23
2.7.1 Depth Completion 23
2.7.2 Semantic Segmentation 27
2.7.3 Ablation Study 31
2.7.4 Analysis 36
2.8 Conclusion 37
– iii –
3 Depth Perception with Diverse Commercial Sensors 38
3.1 Introduction 38
3.2 Related Works 41
3.3 Sensor Biases in Depth Perception: Exploring Diverse Sensor Bias Prob-
lems 44
3.4 Depth Prompting: Foundation Model & Prompting Engineering Method 45
3.5 Experimental Results and Analysis 50
3.5.1 Experiment Setup 50
3.5.2 Experimental Results 56
3.5.3 Case Studies: Sparsity, Pattern and Range Biases 59
3.5.4 Ablation Study 62
3.5.5 Few/Zero-shot Inference on Various Sensors 64
3.6 Conclusion 69
4 Universal Depth Completion with Minimal Resources 71
4.1 Introduction 72
4.2 Related Works 74
4.3 Baseline Architecture: Universal Few-shot Depth Perception 77
4.3.1 Rationale: Foundation Model Usage in Universal Depth Completion 77
4.3.2 Architecture Design 78
4.4 Advanced Architecture with Hyperbolic Geometry 80
4.4.1 Multi-scale Feature Fusion & Hyperbolic Curvature Generation 80
4.4.2 Sparse-to-Dense Conversion based on Hyperbolic Features 82
4.4.3 Depth Refinement in Multi-curvature Hyperbolic Space 83
4.5 Experimental Results and Analysis 86
4.5.1 Implementation Details 86
4.5.2 Experiment 89
4.6 Conclusion 93
5 Concluding Remark 94
References 97
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