28 results on '"Tzu-Jen Lin"'
Search Results
2. Non-photochromic solar energy storage in carbon nitride surpassing blue radicals for hydrogen production
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Pei-Shan Wu, Tzu-Jen Lin, Sheng-Shu Hou, Chih-Chia Chen, Dai-Ling Tsai, Kuan-Hsiang Huang, and Jih-Jen Wu
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Renewable Energy, Sustainability and the Environment ,General Materials Science ,General Chemistry - Abstract
This study demonstrates nonphotochromic solar energy storage in the in-plan short-range-ordered KPHI, which photoelectron storage and catalytic activity surpass the blue radicals derived from conventional crystalline KPHIs.
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- 2022
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3. Optimization of acetamide based deep eutectic solvents with dual cations for high performance and low temperature-tolerant aqueous zinc ion batteries via tuning the ratio of co-solvents
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Ting-Yu Chen, Tzu-Jen Lin, Balaraman Vedhanarayanan, Hsin-Hui Shen, and Tsung-Wu Lin
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Biomaterials ,Colloid and Surface Chemistry ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials - Abstract
In this work, a novel acetamide-based deep eutectic solvent (DES) with Zn
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- 2022
4. Influence of P,S,O-Doping on g-C3N4 for hydrogel formation and photocatalysis: An experimental and theoretical study
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Yi Ching Chu, Tzu-Jen Lin, Chechia Hu, Wei Lun Chiu, Ba Son Nguyen, and Yan-Ru Lin
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Heptazine ,Methyl blue ,Doping ,Graphitic carbon nitride ,chemistry.chemical_element ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Photochemistry ,01 natural sciences ,Sulfur ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Self-healing hydrogels ,Photocatalysis ,Water splitting ,General Materials Science ,0210 nano-technology - Abstract
Photocatalysis is a facile and eco-friendly approach for the removal of dyes and organic compounds, water splitting, and CO2 reduction and fixation. Herein we report the first use of P,S,O-co-doped graphitic carbon nitride (g-C3N4) to produce a photocatalyst hydrogel. The hydrogels are generated by photoinitiated crosslinking of N,N-dimethylacrylamide and N,N-methylenebis(acrylamide) with modified g-C3N4 materials and the photocatalytic activity is evaluated by monitoring the degradation of methyl blue (MB) solutions. S- or O-doping creates C‒S or C‒O bonds, respectively, by replacement N atoms, while P-doping produces P‒N bonds by substitution of C in the heptazine rings of g-C3N4. Based on a combination of theoretical calculations and experimental analyses, phosphorus, sulfur, and oxygen doping considerably facilitates charge separation across the heptazine rings and attracts photoexcited electrons, thus contributing to enhanced photocatalytic activity of doped g-C3N4. The P,S,O-co-doped g-C3N4 hydrogel exhibited high photocatalytic activity for MB removal under simulated solar irradiation and could be easily isolated and cleaned for reuse. Thus, this study reports the formation of a state-of-the-art photocatalyst hydrogel from P,S,O-co-doped g-C3N4 with enhanced photocatalytic activity and demonstrated reusability.
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- 2020
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5. Photoluminescence quenching of thermally treated waste-derived carbon dots for selective metal ion sensing
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You-Yu Chen, Ying-Chu Huang, Ke-Hsuan Wang, Tzu-Jen Lin, Chechia Hu, and Kun-Yi Andrew Lin
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Thermal oxidation ,Ions ,Materials science ,Photoluminescence ,Quenching (fluorescence) ,Metal ions in aqueous solution ,Analytical chemistry ,Quantum yield ,010501 environmental sciences ,01 natural sciences ,Biochemistry ,Carbon ,Ion ,Metal ,03 medical and health sciences ,0302 clinical medicine ,Spectrometry, Fluorescence ,Atomic electron transition ,Metals ,visual_art ,Quantum Dots ,visual_art.visual_art_medium ,030212 general & internal medicine ,0105 earth and related environmental sciences ,General Environmental Science - Abstract
In the present study, carbon-dots (CDs) were derived from the thermal oxidation of an agricultural waste, bitter tea residue, to obtain different sp2/sp3 ratios and electronic structures for metal sensing. The CDs obtained from calcination at 700 °C exhibited the highest photoluminescence (PL) quantum yield (QY) of 11.8% among all the samples treated at different temperatures. These CDs had a high degree of graphitization, which resulted in a strong π-π* electron transition, and hence in a high QY. The strong photoluminescence of the CDs could be used to sense the metal ions Ag+, Sr2+, Fe2+, Fe3+, Co2+, Ni2+, Cu2+, and Sn2+ by monitoring their PL intensity at an excitation wavelength of 320 nm. The metals inhibited the PL intensity in the order Ag+ > Fe2+, Fe3+, Ni2+ > Sr2+, Co2+, Cu2+, Sn2+, which demonstrated that the CDs exhibited high metal ion detection capability and selectivity. The detection of Fe3+ using CDs was performed in the range of 10–100 ppm with a LOD (limit of detection) value of 0.380 ppm. Theoretical calculations demonstrated that Ag+, Sr2+, and Sn2+ induced charge transfer excitation and that Fe2+ and Ni2+ induced d-d transitions via complexation with the sp2 clusters. The charge transfer excitation and d-d transitions hindered the π-π* transition of the sp2 clusters, leading to a quenching effect. On the other hand, Li+, Na+, and K+ ions did not alter the π-π* transition of the sp2 clusters, resulting in a negligible quenching effect. In summary, the oxidation level and electronic structure of CDs derived from bitter tea residue could be tailored, and the CDs were shown to be a facile, sustainable, and eco-friendly material for metal sensing.
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- 2020
6. Intense broad-band absorption and efficient blue-emitting SrCa2MgSi2O8:Eu2+ phosphor for high color-rendering white LED applications
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Haikun Liu, Wei-Ren Liu, Pin-Chun Lin, Libing Liao, Lufu Mei, Tzu-Jen Lin, and Jy-Chern Chang
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010302 applied physics ,Materials science ,business.industry ,Broad band ,Phosphor ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,Rendering (computer graphics) ,0103 physical sciences ,High color ,Blue emitting ,Optoelectronics ,General Materials Science ,0210 nano-technology ,Absorption (electromagnetic radiation) ,business - Published
- 2018
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7. Synthesis, luminescent properties and theoretical calculations of novel orange-red-emitting Ca2Y8(SiO4)6O2:Sm3+ phosphors for white light-emitting diodes
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Maxim S. Molokeev, Tzu-Jen Lin, Chun-Ting Chen, and Wei-Ren Liu
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Materials science ,Photoluminescence ,Rietveld refinement ,business.industry ,Process Chemistry and Technology ,General Chemical Engineering ,Analytical chemistry ,Phosphor ,02 engineering and technology ,Crystal structure ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Density of states ,Optoelectronics ,0210 nano-technology ,Luminescence ,Electronic band structure ,business ,Diode - Abstract
The novel orange-red-emitting Ca2Y8(SiO4)6O2:Sm3+ phosphors (CYSO:Sm3+) were synthesized via conventional a solid state reaction. The crystal structure and atomic coordinates of CYSO:Sm3+ was characterized by Rietveld refinement. Luminesce properties of as-synthesized CYSO:Sm3+ phosphors are carried out by PL/PLE, decay life time, thermal quenching as well as reflectance spectrometer and LED fabrications. The results indicates that composition-optimized CYSO:1%Sm3+ exhibits orange-red emission peaks located on 564, 601, 608 and 648 nm attributed to the transitions of 4G5/2 → 6H5/2, 4G5/2 → 6H7/2, 4G5/2 → 6H7/2 and 4G5/2 → 6H9/2, respectively. The decay lifetime of CYSO:Sm3+ phosphors was in the range of 0.37–1.10 ms. The temperature-dependent photoluminescence is decreased to 80% from room temperature to 150 °C, which is superior to that of commercial red phsophpr-Y2O3:Eu3+. The results of LED fabrication by combing 405 chips and blue/green phosphors are demonstrated in this study. Finally, from viewpoint of theoretical calculations, band structure and density of state for CYSO and CYSO:Sm3+ are studied by first principles calculations. All the results indicate that CYSO:Sm3+ phosphors could be a potential material for white light-emitting diodes.
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- 2018
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8. Graphene-induced tuning of the d-spacing of graphene oxide composite nanofiltration membranes for frictionless capillary action-induced enhancement of water permeability
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S. Ranil Wickramasinghe, Kueir-Rarn Lee, Arijit Sengupta, Tzu-Jen Lin, Juin-Yih Lai, Hsiao Yi-Chen, Yu-Hsuan Chiao, Wei-Song Hung, and Chien-Chieh Hu
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Materials science ,Renewable Energy, Sustainability and the Environment ,Graphene ,Magnesium ,Sodium ,Oxide ,chemistry.chemical_element ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,law.invention ,chemistry.chemical_compound ,Membrane ,chemistry ,Chemical engineering ,law ,Permeability (electromagnetism) ,General Materials Science ,Surface charge ,Nanofiltration ,0210 nano-technology - Abstract
While dispersing graphene in water is a formidable challenge, π–π stacking between graphene oxide (GO) and graphene is known to enable the dispersion of graphene in water. In this work, graphene-induced tuning of the d-spacing in GO composite membranes was performed by pressure-assisted self-assembly on a polysulphone inactive support. The physicochemical properties of the GO–graphene membranes were examined using numeric techniques, and the surface charges and hydrophilicities of the surfaces of GO–graphene membranes with different relative compositions of graphene were assessed. The incorporation of graphene into the GO layers was effective in inhibiting the swelling effect in the wet state; the different GO–graphene composite membranes also exhibited water permeability and salt rejection. The GO1graphene0.8 composite membrane demonstrated a water flux of 36 LMH; salt rejection values of 88.3% (sodium chloride), 91.03% (magnesium chloride), 97.6% (magnesium sulphate) and 98.26% (sodium sulphate); and a minimal free volume. Hence, this sample is considered the optimal membrane. GO-incorporated graphene influences membrane performance by converting the Donnan effect to the molecular sieve mechanism. The GO–graphene composite membranes were compared via theoretical and experimental studies.
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- 2018
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9. Yellowish and blue luminescent graphene oxide quantum dots prepared via a microwave-assisted hydrothermal route using H2O2 and KMnO4 as oxidizing agents
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Kuo-Lun Tung, Chien-Wei Chang, Chechia Hu, Tzu-Jen Lin, and Tzer-Rurng Su
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Photoluminescence ,Band gap ,Chemistry ,Graphene ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Photochemistry ,01 natural sciences ,Catalysis ,0104 chemical sciences ,law.invention ,X-ray photoelectron spectroscopy ,Quantum dot ,law ,Materials Chemistry ,Density functional theory ,Fourier transform infrared spectroscopy ,0210 nano-technology ,Luminescence - Abstract
Graphene oxide quantum dots (GOQDs) with different oxygenation levels were successfully prepared using a facile, rapid, and cost-effective microwave-assisted hydrothermal method under neutral conditions using hydrogen peroxide (MGOH) or potassium permanganate (MGOK) as an oxidizing agent. GOQDs with an average diameter of 7–12 nm for both MGOH and MGOK samples were observed using transmission electron microscopy (TEM). X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR) analyses revealed that MGOH exhibited a high quantity of C–O and CO groups in its structure, whereas MGOK consisted of highly ordered sp2/sp3 bonds in its aromatic unit and had less oxygenated functional groups. The photoluminescence measurements showed that MGOH and MGOK QDs emitted yellowish-green and blue light with quantum yields of 15.1% and 8.4%, respectively. The luminescence mechanisms of MOGK and MGOH were attributed to π–π* and n–π* electron transitions in C–C/CC bonds and in π* states to non-bonding oxygen states, respectively. Density functional theory calculations were employed to determine the optical absorption of GOQDs in terms of surface functional groups and oxygenation degrees. Theoretical calculations demonstrate that the high oxygenation degree of GOQDs resulted in band gap reduction and light absorption due to electron transitions. Our theoretical and experimental results suggested that GOQDs with high quantum yields can serve as promising materials in applications including biosensing, imaging, and labeling.
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- 2018
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10. Reliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF
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Amanda Garley, Hendrik Heinz, Tzu-Jen Lin, Jianwei Miao, C.C. Dharmawardhana, Krishan Kanhaiya, Marc R. Knecht, and Jihan Zhou
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Chemistry ,General Chemical Engineering ,Crystal growth ,Nanotechnology ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,Force field (chemistry) ,0104 chemical sciences ,Nanomaterials ,Molecular dynamics ,Modeling and Simulation ,Computational design ,General Materials Science ,Inorganic materials ,Nanometre ,0210 nano-technology ,Nanoscopic scale ,Information Systems - Abstract
The function of nanomaterials and biomaterials greatly depends on understanding nanoscale recognition mechanisms, crystal growth and surface reactions. The Interface Force Field (IFF) and surface m...
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- 2017
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11. Influence of nonmetal dopants on charge separation of graphitic carbon nitride by time-dependent density functional theory
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Cheng-chau Chiu and Tzu-Jen Lin
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Materials science ,Heptazine ,General Physics and Astronomy ,FOS: Physical sciences ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,chemistry.chemical_compound ,Condensed Matter::Materials Science ,Physics - Chemical Physics ,Condensed Matter::Superconductivity ,Physics::Atomic and Molecular Clusters ,Physical and Theoretical Chemistry ,HOMO/LUMO ,Chemical Physics (physics.chem-ph) ,Dopant ,Doping ,Graphitic carbon nitride ,Time-dependent density functional theory ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,chemistry ,Chemical physics ,Photocatalysis ,Density functional theory ,0210 nano-technology - Abstract
Photocatalysts are crucial materials for green energy production and environmental remediation. Nonmetal-doped graphitic carbon nitride (g-C3N4) has attracted much attention in recent years because of its low-cost and desired photocatalytic performances, such as a high charge separation efficiency and broad visible light absorption. In this study, we conducted time-dependent density functional theory calculations, and a wavefunction analysis to evaluate the charge separation characteristics of phosphorus-, oxygen- and sulfur-doped g-C3N4 upon photo-excitation. In particular, we examined the electron–hole pair distances, the electron–hole pair overlaps, and the amounts of transferred charge. The phosphorus, oxygen, and sulfur dopants shifted the lowest unoccupied molecular orbital of doped heptazine rings downward to facilitate the electron transfer upon photo-excitation. Generally, the phosphorus dopant triggers relatively high amounts of transferred charge, strong electron–hole pair separations, and low electron–hole overlaps compared to oxygen and sulfur dopants. At a low dopant concentration, the sulfur dopant showed a similar effect to that of the phosphorus dopant. The phosphorus dopants not only contributed to the electron–hole pair separation, but also attracted photo-excited electrons. The comparison of different dopant distributions on the heptazine rings of g-C3N4 showed that dopants concentrated on one heptazine ring exhibit better charge separation performance than dopants dispersed on different heptazine rings do. This indicates that the doping configuration has a stronger effect than the doping concentration on the charge separation efficiency in nonmetal-doped g-C3N4.
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- 2019
12. Accurate Force Field Parameters and pH Resolved Surface Models for Hydroxyapatite to Understand Structure, Mechanics, Hydration, and Biological Interfaces
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Hendrik Heinz and Tzu-Jen Lin
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chemistry.chemical_classification ,Materials science ,Biomolecule ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Force field (chemistry) ,Apatite ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,General Energy ,Chemical bond ,chemistry ,Chemical physics ,Ionic strength ,visual_art ,visual_art.visual_art_medium ,Physical and Theoretical Chemistry ,0210 nano-technology - Abstract
Mineralization of bone and teeth involves interactions between biomolecules and hydroxyapatite. Associated complex interfaces and processes remain difficult to analyze at the 1 to 100 nm scale using current laboratory techniques, and prior apatite models for atomistic simulations have been limited in the representation of chemical bonding, surface chemistry, and interfacial interactions. In this contribution, an accurate force field along with pH-resolved surface models for hydroxyapatite is introduced to represent chemical bonding, structural, surface, interfacial, and mechanical properties in quantitative agreement with experiment. The accuracy is orders of magnitude higher in comparison to earlier models and facilitates quantitative monitoring of inorganic-biological assembly. The force field is integrated into the AMBER, CHARMM, CFF, CVFF, DREIDING, GROMACS, INTERFACE, OPLS-AA, and PCFF force fields to enable realistic simulations of apatite-biological systems of any composition and ionic strength. Sp...
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- 2016
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13. Structure prediction of the solid forms of methanol: an ab initio random structure searching approach
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Ching-Ming Wei, Jer-Lai Kuo, Tzu-Jen Lin, and Cheng-Rong Hsing
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Phase transition ,010304 chemical physics ,Chemistry ,Hydrogen bond ,Ab initio ,General Physics and Astronomy ,02 engineering and technology ,Crystal structure ,021001 nanoscience & nanotechnology ,01 natural sciences ,Crystal ,chemistry.chemical_compound ,Crystallography ,Chemical physics ,Phase (matter) ,0103 physical sciences ,Density functional theory ,Methanol ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,0210 nano-technology ,Astrophysics::Galaxy Astrophysics - Abstract
Liquid methanol and methanol clusters have been comprehensively studied to reveal their local structure and hydrogen bond networks. However, our understanding of the crystal forms of methanol is rather limited. The known crystal structures of solid methanol, α, β, and γ, are composed of infinite hydrogen bond chains in their unit cell. The structural diversity of solid methanol is much less than that of liquid methanol, in which both chain and ring structures exist and have been confirmed by experiments. In this study, we employed ab initio random structure searching (AIRSS) to study possible solid methanol structures. AIRSS predicted known solid methanol phases as well as various ring structures that have not been considered. A new possible candidate structure for the δ phase was also discovered. The relative stability of known solid methanol phases and our newly discovered structures were also investigated through dispersion corrected density functional theory. The density functional calculation provides reliable phase transition pressures between the known phases and the searched structures compared with experimental suggestions. In addition, the simulation result indicated that CH⋯O hydrogen bonds play a major role in stabilizing the methanol crystals under high pressures.
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- 2016
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14. Structures and infrared spectra of calcium phosphate clusters by ab initio methods with implicit solvation models
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Tzu-Jen Lin and Cheng-chau Chiu
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Chemistry ,Implicit solvation ,Ab initio ,General Physics and Astronomy ,Infrared spectroscopy ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Molecular dynamics ,Crystallography ,Chemical physics ,Ab initio quantum chemistry methods ,Cluster (physics) ,Molecule ,Physical and Theoretical Chemistry ,Solvent effects ,0210 nano-technology - Abstract
Since the first detection of pre-nucleation clusters during the formation of calcium phosphate minerals, determining such clusters’ compositions and structures has become crucial for understanding the early-stage nucleation of these minerals in solutions. In previous experimental studies, the composition and sizes of pre-nucleation clusters have been calculated, but their structural information has been difficult to determine because they are very small (
- Published
- 2017
15. Hydrogen Bonding between the QB Site Ubisemiquinone and Ser-L223 in the Bacterial Reaction Center: A Combined Spectroscopic and Computational Perspective
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Colin A. Wraight, Sergei A. Dikanov, Amgalanbaatar Baldansuren, Tzu-Jen Lin, Patrick J. O'Malley, Erik W. Martin, and Rimma I. Samoilova
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Photosynthetic reaction centre ,biology ,Semiquinone ,Ubiquinone ,Chemistry ,Hydrogen bond ,Spectrum Analysis ,Photosynthetic Reaction Center Complex Proteins ,Electron Spin Resonance Spectroscopy ,Hydrogen Bonding ,Rhodobacter sphaeroides ,biology.organism_classification ,Photochemistry ,Biochemistry ,Molecular mechanics ,Article ,Quantum Theory ,Redistribution (chemistry) ,Spin density ,Spectroscopy - Abstract
In the Q(B) site of the Rhodobacter sphaeroides photosynthetic reaction center, the donation of a hydrogen bond from the hydroxyl group of Ser-L223 to the ubisemiquinone formed after the first flash is debatable. In this study, we use a combination of spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations to comprehensively explore this topic. We show that ENDOR, ESEEM, and HYSCORE spectroscopic differences between mutant L223SA and the wild-type sample (WT) are negligible, indicating only minor perturbations in the ubisemiquinone spin density for the mutant sample. Qualitatively, this suggests that a strong hydrogen bond does not exist in the WT between the Ser-L223 hydroxyl group and the semiquinone O(1) atom, as removal of this hydrogen bond in the mutant should cause a significant redistribution of spin density in the semiquinone. We show quantitatively, using QM/MM calculations, that a WT model in which the Ser-L223 hydroxyl group is rotated to prevent hydrogen bond formation with the O(1) atom of the semiquinone predicts negligible change for the L223SA mutant. This, together with the better agreement between key QM/MM calculated and experimental hyperfine couplings for the non-hydrogen-bonded model, leads us to conclude that no strong hydrogen bond is formed between the Ser-L223 hydroxyl group and the semiquinone O(1) atom after the first flash. The implications of this finding for quinone reduction in photosynthetic reaction centers are discussed.
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- 2012
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16. An ONIOM Study of the Spin Density Distribution of the QA Site Plastosemiquinone in the Photosystem II Reaction Center
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Patrick J. O'Malley and Tzu-Jen Lin
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Anions ,chemistry.chemical_classification ,ONIOM ,Photosynthetic reaction centre ,Binding Sites ,Semiquinone ,Photosystem II ,Plastoquinone ,Chemistry ,Hydrogen bond ,Iron ,Photosystem II Protein Complex ,Hydrogen Bonding ,Molecular Dynamics Simulation ,Photochemistry ,Surfaces, Coatings and Films ,Divalent ,Ion ,Electron Transport ,Crystallography ,Materials Chemistry ,Quantum Theory ,Physical and Theoretical Chemistry ,Oxidation-Reduction ,Hyperfine structure - Abstract
ONIOM (QM/MM) calculations are used to calculate the spin density distribution for the plastosemiquinone anion radical in the Q(A) binding site of photosystem II. A number of models are examined that explore the effect of iron depletion on the Q(A) site semiquinone spin density distribution and resultant hyperfine couplings. For a model system with a divalent metal ion in the nonheme site the calculated spin density in the Q(A) site model suggests that differential hydrogen-bonding strength to the O1 and O4 oxygen atoms of the radical results in an asymmetric spin density distribution in the semiquinone anion free radical form. The hydrogen bond to the proximal O1 atom is significantly stronger. This is similar to the situation shown to exist previously in the bacterial reaction center of Rba sphaeroides. Various models of depleted nonheme site metal show the profound effect that the presence of a divalent ion in this site has on the spin density distribution of the Q(A) site semiquinone. The variation in calculated spin density distribution of the Q(A) site plastosemiquinone as a function of the occupancy of the nonheme site needs to be taken into account in the interpretation of experimental paramagnetic resonance data. For Type II reaction centers a major role for Fe(2+) in the nonheme site may be the raising of the redox potential of the Q(A)/Q(A)(-) couple to ensure that electron transfer from the (bacterio)pheophytin anion free radical occurs at a sufficient rate to compete with wasteful back-reactions.
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- 2011
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17. Hydrogen Bonding and Spin Density Distribution in the QB Semiquinone of Bacterial Reaction Centers and Comparison with the QA Site
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Kupala V. Narasimhulu, Rimma I. Samoilova, Colin A. Wraight, Sergei A. Dikanov, Patrick J. O'Malley, Tzu-Jen Lin, and Erik W. Martin
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Models, Molecular ,Photosynthetic reaction centre ,Semiquinone ,Proton ,Protein Conformation ,Photosynthetic Reaction Center Complex Proteins ,Rhodobacter sphaeroides ,Photochemistry ,Biochemistry ,Article ,Catalysis ,Colloid and Surface Chemistry ,Benzoquinones ,Spin (physics) ,Hyperfine structure ,chemistry.chemical_classification ,Pulsed EPR ,Hydrogen bond ,Electron Spin Resonance Spectroscopy ,Hydrogen Bonding ,General Chemistry ,Electron acceptor ,Crystallography ,chemistry ,Quantum Theory ,Protons - Abstract
In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (Q(A)) and secondary (Q(B)) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the Q(A) and Q(B) sites, using samples of (15)N-labeled reaction centers, with the native high spin Fe(2+) exchanged for diamagnetic Zn(2+), prepared in (1)H(2)O and (2)H(2)O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the Q(A) SQ by Flores et al. (Biophys. J.2007, 92, 671-682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6-5.4 MHz. HYSCORE was then applied to the Q(B) SQ where we found proton lines corresponding to T ≈ 5.2, 3.7 MHz and T ≈ 1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the Q(B) site, were used to assign the observed couplings to specific hydrogen bonding interactions with the Q(B) SQ. These calculations allow us to assign the T = 5.2 MHz proton to the His-L190 N(δ)H···O(4) (carbonyl) hydrogen bonding interaction. The T = 3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the Q(B) site show less asymmetric distribution of unpaired spin density over the SQ than seen for the Q(A) site, consistent with available experimental data for (13)C and (17)O carbonyl hyperfine couplings. The implications of these interactions for Q(B) function and comparisons with the Q(A) site are discussed.
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- 2011
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18. An ONIOM study of the QA site semiquinone in the Rhodobacter sphaeroides photosynthetic reaction centre
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Patrick J. O'Malley and Tzu-Jen Lin
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chemistry.chemical_classification ,ONIOM ,Photosynthetic reaction centre ,biology ,Semiquinone ,Hydrogen bond ,Condensed Matter Physics ,biology.organism_classification ,Photochemistry ,Biochemistry ,Divalent ,Ion ,Rhodobacter sphaeroides ,chemistry ,Physical and Theoretical Chemistry ,Binding site - Abstract
ONIOM (QM/MM) calculations are performed to investigate the spin density distribution for the ubisemiquinone anion radical in the QA binding site of the photosynthetic bacterium Rhodobacter sphaeroides. The calculated spin density in the QA site model suggests that differential hydrogen bonding strength to the O1 and O4 oxygen atoms of the radical results in an asymmetric spin density distribution in the semiquinone anion free radical form. The origin of the spin density asymmetry is attributed to the presence of the divalent iron or zinc ion situated between the QA and QB sites.
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- 2008
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19. Solder Joint Reliability Analysis of WLCSP Based on Inelastic Analysis
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Chia Lung Chang, Tzu-Jen Lin, and Kenny Huang
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Materials science ,business.industry ,Mechanical Engineering ,Structural engineering ,Temperature cycling ,Stress (mechanics) ,Printed circuit board ,Mechanics of Materials ,Chip-scale package ,Soldering ,Shear stress ,General Materials Science ,Composite material ,business ,Material properties ,Joint (geology) - Abstract
Nonlinear finite element analysis is performed to evaluate the reliability of the solder joint of wafer level chip scale package (WLCSP) under accelerated temperature cycling test. The solder joint is subjected to the inelastic strain that is generated during the temperature cycling test due to the thermal expansion mismatch between the various materials of the package and PCB (printed circuit board). The equivalent stress, equivalent inelastic strain, total shear strain, and hysteresis loop of the solder joint are determined in the simulation. The equivalent inelastic strain and total shear strain range of the joint are obtained as damage criterion to predict the solder fatigue. Both Coffin-Manson and Modified Coffin-Manson fatigue life prediction models are used to estimate the thermal fatigue life of WLCSP solder joints under temperature cycling test. Also, the effects of the material properties of the stress buffer layer (SBL) on the fatigue life of the solder joint are discussed.
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- 2006
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20. Theoretical study on the torsional potential of alkyl, donor, and acceptor substituted bithiophene: the hidden role of noncovalent interaction and backbone conjugation
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Tzu-Jen Lin and Shiang-Tai Lin
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Steric effects ,chemistry.chemical_classification ,Substituent ,General Physics and Astronomy ,Conjugated system ,Ring (chemistry) ,Photochemistry ,Acceptor ,chemistry.chemical_compound ,Crystallography ,chemistry ,Side chain ,Thiophene ,Physical and Theoretical Chemistry ,Alkyl - Abstract
Side chain and substituent engineering of conjugated polymers are important to their backbone design. Of particular interest here is how side chains and substituents influence the coplanarity of conjugated backbones. Steric hindrance is usually considered as the principal factor influencing the coplanarity. In this study, we used proper first-principle density functional theories to analyze the change in the torsional potentials of substituted bithiophene with substituents of varying degrees of electron donating/accepting capabilities. Besides steric hindrance, the torsional potential of substituted bithiophene is also determined by other factors such as the position of substitution, non-covalent interactions between the substituents and thiophene ring, and electron conjugation in the backbone. There is no significant change in the torsional potential unless the substituent group is located at the head position of bithiophene. The bulkiness of the substituent group increases the torsional barrier at 0 and 180 degree (planar bithiophene), while the weak noncovalent interaction (such as CH-π, NH-π, and dispersion interactions) stabilizes the transition structure and decreases the barrier at 90 degree (two thiophene rings in perpendicular). Strong electron-withdrawing substituent groups (e.g., formyl or nitro groups) are found to reduce backbone conjugation resulting in reduced internal rotation barrier at 90 degree. Any of these factors deteriorates the coplanarity of bithiophene. On the other hand, the backbone conjugation can be enhanced by introducing electron-donating groups (e.g., methoxy) resulting in an increased internal rotational barrier and stabilized planar structure. The influence of through-space interactions such as S···O, S···N and CH···O interactions are found to play a minor role in the coplanarity of substituted bithiophene.
- Published
- 2015
21. Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field
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Hendrik Heinz, Tzu-Jen Lin, Ratan K. Mishra, and Fateme S. Emami
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Models, Molecular ,Nanostructure ,Chemistry ,Nanotechnology ,Surfaces and Interfaces ,Condensed Matter Physics ,Atomic units ,Force field (chemistry) ,Nanostructures ,Molecular recognition ,Inorganic Chemicals ,Compass ,Electrochemistry ,Humans ,Thermodynamics ,General Materials Science ,Inorganic organic ,Organic Chemicals ,Biology ,Spectroscopy - Abstract
The complexity of the molecular recognition and assembly of biotic-abiotic interfaces on a scale of 1 to 1000 nm can be understood more effectively using simulation tools along with laboratory instrumentation. We discuss the current capabilities and limitations of atomistic force fields and explain a strategy to obtain dependable parameters for inorganic compounds that has been developed and tested over the past decade. Parameter developments include several silicates, aluminates, metals, oxides, sulfates, and apatites that are summarized in what we call the INTERFACE force field. The INTERFACE force field operates as an extension of common harmonic force fields (PCFF, COMPASS, CHARMM, AMBER, GROMACS, and OPLS-AA) by employing the same functional form and combination rules to enable simulations of inorganic-organic and inorganic-biomolecular interfaces. The parametrization builds on an in-depth understanding of physical-chemical properties on the atomic scale to assign each parameter, especially atomic charges and van der Waals constants, as well as on the validation of macroscale physical-chemical properties for each compound in comparison to measurements. The approach eliminates large discrepancies between computed and measured bulk and surface properties of up to 2 orders of magnitude using other parametrization protocols and increases the transferability of the parameters by introducing thermodynamic consistency. As a result, a wide range of properties can be computed in quantitative agreement with experiment, including densities, surface energies, solid-water interface tensions, anisotropies of interfacial energies of different crystal facets, adsorption energies of biomolecules, and thermal and mechanical properties. Applications include insight into the assembly of inorganic-organic multiphase materials, the recognition of inorganic facets by biomolecules, growth and shape preferences of nanocrystals and nanoparticles, as well as thermal transitions and nanomechanics. Limitations and opportunities for further development are also described.
- Published
- 2013
22. Binding site influence on the electronic structure and electron paramagnetic resonance properties of the phyllosemiquinone free radical of photosystem I
- Author
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Patrick J. O'Malley and Tzu-Jen Lin
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ONIOM ,Models, Molecular ,Hydrogen ,Protein Conformation ,chemistry.chemical_element ,Electrons ,Electronic structure ,law.invention ,law ,Atom ,Materials Chemistry ,Benzoquinones ,Physics::Atomic Physics ,Physical and Theoretical Chemistry ,Electron paramagnetic resonance ,Hyperfine structure ,Binding Sites ,Photosystem I Protein Complex ,Hydrogen bond ,Electron Spin Resonance Spectroscopy ,Surfaces, Coatings and Films ,Quinone ,Crystallography ,chemistry ,Anisotropy ,Atomic physics - Abstract
Electronic structure calculations are performed on models of the phyllosemiquinone (PhSQ) free radical in the A(1A) and A(1B) sites of photo system I. Partial geometry optimization of each site is performed, and from the resultant geometry spin densities and hyperfine couplings are calculated. We exploit the ONIOM methodology to progressively build up a model of the A(1A) site and monitor the effect on the spin density distribution of the PhSQ and its hyperfine couplings. For the A(1A) site, we show that while the O1 atom of the PhSQ is not involved in direct hydrogen bonding, the (17)O anisotropic hyperfine coupling for this position is sensitive to interactions with neighboring groups, especially Trp A697 and Phe A689. The results obtained are in agreement with experimental determinations which indicate small differences in (17)O hyperfine couplings for both oxygen atoms. Good agreement between calculated and experimental (1)H and (13)C hyperfine couplings is also found. In addition, we find that a significant (14)N isotropic coupling of 1.4 MHz is calculated for the peptide NH group of Leu A722. The (14)N isotropic hyperfine coupling obtained for the indole nitrogen atom of Trp A697 is calculated to be zero in disagreement with a previous experimental assignment. The spin density distribution of the PhSQ in the A(1B) site is calculated to be very similar to that in the A(1A) site. The presence of just one relatively weak hydrogen bond to the photo system I quinone is proposed to contribute substantially to its relatively low redox potential when compared with the more strongly hydrogen bonded quinone acceptors present in type II reaction centers.
- Published
- 2011
23. Origin of Ferromagnetism in nitrogen embedded ZnO:N thin films
- Author
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Tzu-Jen Lin, Chang-Feng Yu, Shih-Jye Sun, and Hsiung Chou
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Condensed Matter - Materials Science ,Materials science ,Acoustics and Ultrasonics ,Condensed matter physics ,Strongly Correlated Electrons (cond-mat.str-el) ,Magnetism ,Dangling bond ,Materials Science (cond-mat.mtrl-sci) ,FOS: Physical sciences ,Condensed Matter Physics ,Polaron ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Pulsed laser deposition ,Ion ,symbols.namesake ,Condensed Matter::Materials Science ,Condensed Matter - Strongly Correlated Electrons ,Ferromagnetism ,symbols ,Condensed Matter::Strongly Correlated Electrons ,Thin film ,Raman spectroscopy - Abstract
Nitrogen embedded ZnO:N films prepared by pulsed laser deposition exhibit significant ferromagnetism. The nitrogen ions contained in ZnO confirmed by Secondary Ion Microscopic Spectrum and Raman experiments and the embedded nitrogen ions can be regarded as defects. According to the experiment results, a mechanism is proposed based on one of the electrons in the completely filled d-orbits of Zn that compensates the dangling bonds of nitrogen ions and leads to a net spin of one half in the Zn orbits. These one half spins strongly correlate with localized electrons that are captured by defects to form ferromagnetism. Eventually, the magnetism of nitrogen embedded ZnO:N films could be described by a bound magnetic polaron model., 7 pages, 6 figures
- Published
- 2007
24. Thermal Fatigue Prediction for Leadless Solder Joint of TFBGA
- Author
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Tzu-Jen Lin, Chia-Lung Chang, and Chih-Hao Lai
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Substrate (building) ,Materials science ,Strain (chemistry) ,Physics::Instrumentation and Detectors ,Soldering ,Metallurgy ,Temperature cycling ,Composite material ,Material properties ,Joint (geology) ,Thermal expansion ,Die (integrated circuit) ,Computer Science::Other - Abstract
Nonlinear finite element analysis was performed to predict the thermal fatigue for leadless solder joint of TFBGA Package under accelerated TCT (Temperature Cycling Test). The solder joint was subjected to the inelastic strain that was generated during TCT due to the thermal expansion mismatch between the package and PCB. The solder was modeled with elastic-plastic-creep property to simulate the inelastic deformation under TCT. The creep strain rate of solder was described by double power law. The furthest solder away from the package center induced the highest strain during TCT was considered as the critical solder ball to be most likely damaged. The effects of solder meshing on the damage parameters of inelastic strain range, accumulated creep strain and creep strain energy density were compared to assure the accuracy of the simulation. The life prediction equation based on the accumulated creep strain and creep strain energy density proposed by Syed was used to predict the thermal fatigue life in this study. The agreement between the prediction life and experimental mean life is within 25 per cent. The effect of die thickness and material properties of substrate on the life of solder was also discussed.Copyright © 2006 by ASME
- Published
- 2006
- Full Text
- View/download PDF
25. Reliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF.
- Author
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Dharmawardhana, Chamila C., Kanhaiya, Krishan, Tzu-Jen Lin, Garley, Amanda, Knecht, Marc R., Jihan Zhou, Jianwei Miao, and Hendrik Heinz
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NANOPARTICLE synthesis ,MOLECULAR recognition ,CRYSTAL growth ,BINDING energy ,MOLECULAR dynamics ,STACKING interactions ,DENSITY functional theory - Abstract
The function of nanomaterials and biomaterials greatly depends on understanding nanoscale recognition mechanisms, crystal growth and surface reactions. The Interface Force Field (IFF) and surface model database are the first collection of transferable parameters for inorganic and organic compounds that can be universally applied to all materials. IFF uses common energy expressions and achieves best accuracy among classical force fields due to rigorous validation of structural and energetic properties of all compounds in comparison to perpetually valid experimental data. This paper summarises key aspects of parameterisation, including atomic charges and transferability of parameters and current coverage. Examples of biomolecular recognition at metal and mineral interfaces, surface reactions of alloys, as well as new models for graphitic materials and pi-conjugated molecules are described. For several metal-organic interfaces, a match in accuracy of computed binding energies between of IFF and DFT results is demonstrated at ten million times lower computational cost. Predictive simulations of biomolecular recognition of peptides on phosphate and silicate surfaces are described as a function of pH. The use of IFF for reactive molecular dynamics is illustrated for the oxidation of Mo
3 Si alloys at high temperature, showing the development of specific porous silica protective layers. The introduction of virtual pi electrons in graphite and pi-conjugated molecules enables improvements in property predictions by orders of magnitude. The inclusion of such molecule-internal polarity in IFF can reproduce cation-pi interactions, pi-stacking in graphite, DNA bases, organic semiconductors and the dynamics of aqueous and biological interfaces for the first time. [ABSTRACT FROM AUTHOR]- Published
- 2017
- Full Text
- View/download PDF
26. Dependence of local structural and electrical properties of nitride doped zinc oxide films on growth temperature
- Author
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Tzu-Jen Lin, Chang-Feng Yu, Sy-Hann Chen, Yen-Ju Liu, and Ya-Chi Li
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Materials science ,business.industry ,Schottky barrier ,Doping ,Wide-bandgap semiconductor ,chemistry.chemical_element ,Nanotechnology ,Zinc ,Nitride ,Condensed Matter Physics ,Pulsed laser deposition ,chemistry ,Optoelectronics ,Electrical and Electronic Engineering ,business ,Nanoscopic scale ,Ohmic contact - Abstract
Conducting atomic force microscopy was utilized to study the nanoscale surface electrical properties of N-doped zinc oxide films that had been prepared by pulsed laser deposition at different substrate temperatures. Current-voltage measurements were made while the conducting tip was fixed at different contact current points after scanning for normal imaging. Experimental results indicated that changes in the substrate temperature caused the redistribution of n-type carrier (Ohmic contact) and p-type carrier (Schottky contact) regions on the surface. Such a microscopic measurement method can be adopted to observe precisely the variances in the local carriers on the surface of films, benefiting future studies of nanoscale p-n homojunctions.
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- 2009
- Full Text
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27. Hydrogen Bonding and Spin Density Distribution in the QB Semiquinone of Bacterial Reaction Centers and Comparison with the QA Site.
- Author
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Martin, Erik, Samoilova, Rimma I., Narasimhulu, Kupala V., Tzu-Jen Lin, O'Malley, Patrick J., Wraight, Colin A., and Dikanov, Sergei A.
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- 2011
- Full Text
- View/download PDF
28. Dependence of local structural and electrical properties of nitride doped zinc oxide films on growth temperature.
- Author
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Sy-Hann Chen, Chang-Feng Yu, Yen-Ju Liu, Tzu-Jen Lin, and Ya-Chi Li
- Subjects
ATOMIC force microscopy ,ZINC oxide ,PULSED laser deposition ,THIN films ,CERAMICS - Abstract
Conducting atomic force microscopy was utilized to study the nanoscale surface electrical properties of N-doped zinc oxide films that had been prepared by pulsed laser deposition at different substrate temperatures. Current-voltage measurements were made while the conducting tip was fixed at different contact current points after scanning for normal imaging. Experimental results indicated that changes in the substrate temperature caused the redistribution of n-type carrier (Ohmic contact) and p-type carrier (Schottky contact) regions on the surface. Such a microscopic measurement method can be adopted to observe precisely the variances in the local carriers on the surface of films, benefiting future studies of nanoscale p-n homojunctions. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
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