Pub Date : 2024-09-01DOI: 10.1016/j.fmre.2022.06.021
Quantum tunneling conductance of molecular junctions originates from the charge transport through the π-orbitals (π-transport) and the σ-orbitals (σ-transport) of the molecules, but the σ-transport can not be observed due to the more rapid decay of the tunneling conductance in the σ-system compared to that in the π-system. Here, we demonstrate that dominant σ-transport can be observed in π-conjugated molecular junctions at the sub-nanometer scale using the scanning tunneling microscope break junction technique (STM-BJ). We have found that the conductance of meta-connected picolinic acid, which mainly occurs by σ-transport, is ∼35 times higher than that of its para-isomer, which is entirely different from what is expected from π-transport through these systems. Flicker noise analysis reveals that the transport through the meta-connection exhibits more through-bond transport than the para-counterpart and density functional theory (DFT) shows that the σ-system provides the dominant transport path. These results reveal that the σ-electrons, rather than the π-electrons, can dominate charge transport through conjugated molecular junctions at the sub-nanometer scale, and this provides a new avenue toward the future miniaturization of molecular devices and materials.
{"title":"σ-dominated charge transport in sub-nanometer molecular junctions","authors":"","doi":"10.1016/j.fmre.2022.06.021","DOIUrl":"10.1016/j.fmre.2022.06.021","url":null,"abstract":"<div><div>Quantum tunneling conductance of molecular junctions originates from the charge transport through the π-orbitals (π-transport) and the σ-orbitals (σ-transport) of the molecules, but the σ-transport can not be observed due to the more rapid decay of the tunneling conductance in the σ-system compared to that in the π-system. Here, we demonstrate that dominant σ-transport can be observed in π-conjugated molecular junctions at the sub-nanometer scale using the scanning tunneling microscope break junction technique (STM-BJ). We have found that the conductance of <em>meta</em>-connected picolinic acid, which mainly occurs by σ-transport, is ∼35 times higher than that of its <em>para</em>-isomer, which is entirely different from what is expected from π-transport through these systems. Flicker noise analysis reveals that the transport through the <em>meta</em>-connection exhibits more through-bond transport than the <em>para</em>-counterpart and density functional theory (DFT) shows that the σ-system provides the dominant transport path. These results reveal that the σ-electrons, rather than the π-electrons, can dominate charge transport through conjugated molecular junctions at the sub-nanometer scale, and this provides a new avenue toward the future miniaturization of molecular devices and materials.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"4 5","pages":"Pages 1128-1136"},"PeriodicalIF":6.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43574050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1016/j.fmre.2024.01.007
During Fuel Cell Vehicle (FCV) operation, the liquid water in gas diffusion media (GDM) prevents the reaction gas from reaching the reaction zone and lead to output power fluctuation and reduce the lifespan of FCV. In the present research, hydrophobicity gradient settings of micro-porous layer (MPL) and gas diffusion layer (GDL) are optimized to improve the water removal ability of GDM. Computational fluid dynamics (CFD) model is constructed for numerical simulations to analyze the fuel cell power output and the water content in the GDM with different hydrophobicity gradients. Experiments with different hydrophobicity gradients, which are specifically prepared with corresponding concentrations of polytetrafluoroethylene (PTFE) solutions, are conducted for validation of simulation results. It is shown that the positive hydrophobicity gradient of MPL and GDL provides a better capacity for water removal and oxygen transport. The contact angles of MPL and GDL are further optimized as 147.9°-138.6° by genetic algorithm integrated with the CFD simulations.
{"title":"Hydrophobicity gradient optimization of fuel cell gas diffusion media for its application in vehicles","authors":"","doi":"10.1016/j.fmre.2024.01.007","DOIUrl":"10.1016/j.fmre.2024.01.007","url":null,"abstract":"<div><div>During Fuel Cell Vehicle (FCV) operation, the liquid water in gas diffusion media (GDM) prevents the reaction gas from reaching the reaction zone and lead to output power fluctuation and reduce the lifespan of FCV. In the present research, hydrophobicity gradient settings of micro-porous layer (MPL) and gas diffusion layer (GDL) are optimized to improve the water removal ability of GDM. Computational fluid dynamics (CFD) model is constructed for numerical simulations to analyze the fuel cell power output and the water content in the GDM with different hydrophobicity gradients. Experiments with different hydrophobicity gradients, which are specifically prepared with corresponding concentrations of polytetrafluoroethylene (PTFE) solutions, are conducted for validation of simulation results. It is shown that the positive hydrophobicity gradient of MPL and GDL provides a better capacity for water removal and oxygen transport. The contact angles of MPL and GDL are further optimized as 147.9°-138.6° by genetic algorithm integrated with the CFD simulations.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"4 5","pages":"Pages 1036-1046"},"PeriodicalIF":6.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139684681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1016/j.fmre.2023.01.001
Compared with silicon, gallium nitride, silicon carbide, and other traditional semiconductors, gallium oxide (Ga2O3) who possesses, an ultrawide bandgap of approximately 5.0 eV and a higher breakdown field strength of approximately 8 MV/cm has attracted increasing attention from researchers, especially for the potential application in power devices. Moreover, Ga2O3 material has natural ultraviolet detection ability for photodetectors due to its ultrawide bandgap. These future commercial applications put forward an urgent require for high-quality epitaxial Ga2O3 material in an efficient growth method at a lower cost. Although there are some conventional methods for single crystal Ga2O3 film epitaxial growth such as MBE and MOCVD, these methods always need a vacuum growth environment and expensive equipment. As a fast-growing method, Mist-CVD gives the growth of Ga2O3 in a vacuum-free, process-simple, and low-cost method, which will greatly reduce the cost and facilitate the development of Ga2O3. This review has summarizes the Mist-CVD epitaxy growth mechanism of Ga2O3, recent progress in the Ga2O3 film epitaxial growth, and various device properties based on the Mist-CVD method. Our work aims to provide help for the development of Ga2O3 material growth and device applications.
{"title":"Recent progress of Ga2O3 materials and devices based on the low-cost, vacuum-free Mist-CVD epitaxial growth method","authors":"","doi":"10.1016/j.fmre.2023.01.001","DOIUrl":"10.1016/j.fmre.2023.01.001","url":null,"abstract":"<div><div>Compared with silicon, gallium nitride, silicon carbide, and other traditional semiconductors, gallium oxide (Ga<sub>2</sub>O<sub>3</sub>) who possesses, an ultrawide bandgap of approximately 5.0 eV and a higher breakdown field strength of approximately 8 MV/cm has attracted increasing attention from researchers, especially for the potential application in power devices. Moreover, Ga<sub>2</sub>O<sub>3</sub> material has natural ultraviolet detection ability for photodetectors due to its ultrawide bandgap. These future commercial applications put forward an urgent require for high-quality epitaxial Ga<sub>2</sub>O<sub>3</sub> material in an efficient growth method at a lower cost. Although there are some conventional methods for single crystal Ga<sub>2</sub>O<sub>3</sub> film epitaxial growth such as MBE and MOCVD, these methods always need a vacuum growth environment and expensive equipment. As a fast-growing method, Mist-CVD gives the growth of Ga<sub>2</sub>O<sub>3</sub> in a vacuum-free, process-simple, and low-cost method, which will greatly reduce the cost and facilitate the development of Ga<sub>2</sub>O<sub>3</sub>. This review has summarizes the Mist-CVD epitaxy growth mechanism of Ga<sub>2</sub>O<sub>3</sub>, recent progress in the Ga<sub>2</sub>O<sub>3</sub> film epitaxial growth, and various device properties based on the Mist-CVD method. Our work aims to provide help for the development of Ga<sub>2</sub>O<sub>3</sub> material growth and device applications.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"4 5","pages":"Pages 1292-1305"},"PeriodicalIF":6.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42903693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1016/j.fmre.2023.04.013
In recent years, the emergence of numerous applications of artificial intelligence (AI) has sparked a new technological revolution. These applications include facial recognition, autonomous driving, intelligent robotics, and image restoration. However, the data processing and storage procedures in the conventional von Neumann architecture are discrete, which leads to the “memory wall” problem. As a result, such architecture is incompatible with AI requirements for efficient and sustainable processing. Exploring new computing architectures and material bases is therefore imperative. Inspired by neurobiological systems, in-memory and in-sensor computing techniques provide a new means of overcoming the limitations inherent in the von Neumann architecture. The basis of neural morphological computation is a crossbar array of high-density, high-efficiency non-volatile memory devices. Among the numerous candidate memory devices, ferroelectric memory devices with non-volatile polarization states, low power consumption and strong endurance are expected to be ideal candidates for neuromorphic computing. Further research on the complementary metal–oxide–semiconductor (CMOS) compatibility for these devices is underway and has yielded favorable results. Herein, we first introduce the development of ferroelectric materials as well as their mechanisms of polarization reversal and detail the applications of ferroelectric synaptic devices in artificial neural networks. Subsequently, we introduce the latest developments in ferroelectrics-based in-memory and in-sensor computing. Finally, we review recent works on hafnium-based ferroelectric memory devices with CMOS process compatibility and give a perspective for future developments.
{"title":"Ferroelectric materials for neuroinspired computing applications","authors":"","doi":"10.1016/j.fmre.2023.04.013","DOIUrl":"10.1016/j.fmre.2023.04.013","url":null,"abstract":"<div><div>In recent years, the emergence of numerous applications of artificial intelligence (AI) has sparked a new technological revolution. These applications include facial recognition, autonomous driving, intelligent robotics, and image restoration. However, the data processing and storage procedures in the conventional von Neumann architecture are discrete, which leads to the “memory wall” problem. As a result, such architecture is incompatible with AI requirements for efficient and sustainable processing. Exploring new computing architectures and material bases is therefore imperative. Inspired by neurobiological systems, in-memory and in-sensor computing techniques provide a new means of overcoming the limitations inherent in the von Neumann architecture. The basis of neural morphological computation is a crossbar array of high-density, high-efficiency non-volatile memory devices. Among the numerous candidate memory devices, ferroelectric memory devices with non-volatile polarization states, low power consumption and strong endurance are expected to be ideal candidates for neuromorphic computing. Further research on the complementary metal–oxide–semiconductor (CMOS) compatibility for these devices is underway and has yielded favorable results. Herein, we first introduce the development of ferroelectric materials as well as their mechanisms of polarization reversal and detail the applications of ferroelectric synaptic devices in artificial neural networks. Subsequently, we introduce the latest developments in ferroelectrics-based in-memory and in-sensor computing. Finally, we review recent works on hafnium-based ferroelectric memory devices with CMOS process compatibility and give a perspective for future developments.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"4 5","pages":"Pages 1272-1291"},"PeriodicalIF":6.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47150658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1016/j.fmre.2023.02.012
Atmospheric oxidation processes are of central importance in atmospheric climate models. It is often considered that volatile organic molecules are mainly removed by hydroxyl radical; however, the kinetics of some reactions of hydroxyl radical with volatile organic molecules are slow. Here we report rate constants for rapid reactions of formyl fluoride with Criegee intermediates. These rate constants are calculated by dual-level multistructural canonical variational transition state theory with small-curvature tunneling (DL-MS-CVT/SCT). The treatment contains beyond-CCSD(T) electronic structure calculations for transition state theory, and it employs validated density functional input for multistructural canonical variational transition state theory with small-curvature tunneling and for variable-reaction-coordinate variational transition state theory. We find that the M11-L density functional has higher accuracy than CCSD(T)/CBS for the HC(O)F + CH2OO and HC(O)F + anti-CH3CHOO reactions. We find significant negative temperature dependence in the ratios of the rate constants for HC(O)F + CH2OO/anti-CH3CHOO to the rate constant for HC(O)F + OH. We also find that different Criegee intermediates have different rate-determining-steps in their reactions with formyl fluoride, and we find that the dominant gas-phase removal mechanism for HC(O)F in the atmosphere is the reaction with CH2OO and/or anti-CH3CHOO Criegee intermediates.
{"title":"Reactions with Criegee intermediates are the dominant gas-phase sink for formyl fluoride in the atmosphere","authors":"","doi":"10.1016/j.fmre.2023.02.012","DOIUrl":"10.1016/j.fmre.2023.02.012","url":null,"abstract":"<div><div>Atmospheric oxidation processes are of central importance in atmospheric climate models. It is often considered that volatile organic molecules are mainly removed by hydroxyl radical; however, the kinetics of some reactions of hydroxyl radical with volatile organic molecules are slow. Here we report rate constants for rapid reactions of formyl fluoride with Criegee intermediates. These rate constants are calculated by dual-level multistructural canonical variational transition state theory with small-curvature tunneling (DL-MS-CVT/SCT). The treatment contains beyond-CCSD(T) electronic structure calculations for transition state theory, and it employs validated density functional input for multistructural canonical variational transition state theory with small-curvature tunneling and for variable-reaction-coordinate variational transition state theory. We find that the M11-L density functional has higher accuracy than CCSD(T)/CBS for the HC(O)F + CH<sub>2</sub>OO and HC(O)<em>F</em> + <em>anti</em>-CH<sub>3</sub>CHOO reactions. We find significant negative temperature dependence in the ratios of the rate constants for HC(O)F + CH<sub>2</sub>OO/<em>anti</em>-CH<sub>3</sub>CHOO to the rate constant for HC(O)<em>F</em> + OH. We also find that different Criegee intermediates have different rate-determining-steps in their reactions with formyl fluoride, and we find that the dominant gas-phase removal mechanism for HC(O)F in the atmosphere is the reaction with CH<sub>2</sub>OO and/or <em>anti</em>-CH<sub>3</sub>CHOO Criegee intermediates.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"4 5","pages":"Pages 1216-1224"},"PeriodicalIF":6.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42326705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1016/j.fmre.2022.09.010
Tailoring the degree of structural disorder in Ge-Sb-Te alloys is important for the development of non-volatile phase-change memory and neuro-inspired computing. Upon crystallization from the amorphous phase, these alloys form a cubic rocksalt-like structure with a high content of intrinsic vacancies. Further thermal annealing results in a gradual structural transition towards a layered structure and an insulator-to-metal transition. In this work, we elucidate the atomic-level details of the structural transition in crystalline GeSb2Te4 by in situ high-resolution transmission electron microscopy experiments and ab initio density functional theory calculations, providing a comprehensive real-time and real-space view of the vacancy ordering process. We also discuss the impact of vacancy ordering on altering the electronic and optical properties of GeSb2Te4, which is relevant to multilevel storage applications. The phase evolution paths in Ge-Sb-Te alloys and Sb2Te3 are illustrated using a summary diagram, which serves as a guide for designing phase-change memory devices.
{"title":"In situ characterization of vacancy ordering in Ge-Sb-Te phase-change memory alloys","authors":"","doi":"10.1016/j.fmre.2022.09.010","DOIUrl":"10.1016/j.fmre.2022.09.010","url":null,"abstract":"<div><div>Tailoring the degree of structural disorder in Ge-Sb-Te alloys is important for the development of non-volatile phase-change memory and neuro-inspired computing. Upon crystallization from the amorphous phase, these alloys form a cubic rocksalt-like structure with a high content of intrinsic vacancies. Further thermal annealing results in a gradual structural transition towards a layered structure and an insulator-to-metal transition. In this work, we elucidate the atomic-level details of the structural transition in crystalline GeSb<sub>2</sub>Te<sub>4</sub> by <em>in situ</em> high-resolution transmission electron microscopy experiments and <em>ab initio</em> density functional theory calculations, providing a comprehensive real-time and real-space view of the vacancy ordering process. We also discuss the impact of vacancy ordering on altering the electronic and optical properties of GeSb<sub>2</sub>Te<sub>4</sub>, which is relevant to multilevel storage applications. The phase evolution paths in Ge-Sb-Te alloys and Sb<sub>2</sub>Te<sub>3</sub> are illustrated using a summary diagram, which serves as a guide for designing phase-change memory devices.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"4 5","pages":"Pages 1235-1242"},"PeriodicalIF":6.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45753173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1016/j.fmre.2022.07.005
Inorganic CsPbI3 perovskite has exhibited great application potential in perovskite solar cells (PSCs) due to its suitable optical bandgap and high chemical stability. However, the perovskite phases of CsPbI3 are not stable at room temperature, where they transition to non-perovskite phases. Humidity or water has been thought to be the primary factor inducing this phase transition, which should be avoided throughout the procedure of film and device processing. Surprisingly, the present study indicates that preparing a precursor solution in humid air is beneficial to the growth of high-quality CsPbI3 perovskite to enhance device performance. It is demonstrated that the incorporation of H2O in the precursor solution from humid air or by intentional addition significantly changes the composition of coordination compounds and increases the amount of low iodine coordination complexes. As a result, the crystallization of dimethylammonium lead iodide (DMAPbI3) intermediate is suppressed well, which accelerates its subsequent conversion to CsPbI3 perovskite. Consequently, an oriented CsPbI3 perovskite film with improved crystallinity and lower defect density is obtained. Most importantly, carbon-based PSCs (C-PSCs) based on the CsPbI3 perovskite film achieve an efficiency of 16.05%, a new record for inorganic C-PSCs.
{"title":"Moisture is not always bad: H2O accelerates the conversion of DMAPbI3 intermediate to CsPbI3 for boosting the efficiency of carbon-based perovskite solar cells to over 16%","authors":"","doi":"10.1016/j.fmre.2022.07.005","DOIUrl":"10.1016/j.fmre.2022.07.005","url":null,"abstract":"<div><div>Inorganic CsPbI<sub>3</sub> perovskite has exhibited great application potential in perovskite solar cells (PSCs) due to its suitable optical bandgap and high chemical stability. However, the perovskite phases of CsPbI<sub>3</sub> are not stable at room temperature, where they transition to non-perovskite phases. Humidity or water has been thought to be the primary factor inducing this phase transition, which should be avoided throughout the procedure of film and device processing. Surprisingly, the present study indicates that preparing a precursor solution in humid air is beneficial to the growth of high-quality CsPbI<sub>3</sub> perovskite to enhance device performance. It is demonstrated that the incorporation of H<sub>2</sub>O in the precursor solution from humid air or by intentional addition significantly changes the composition of coordination compounds and increases the amount of low iodine coordination complexes. As a result, the crystallization of dimethylammonium lead iodide (DMAPbI<sub>3</sub>) intermediate is suppressed well, which accelerates its subsequent conversion to CsPbI<sub>3</sub> perovskite. Consequently, an oriented CsPbI<sub>3</sub> perovskite film with improved crystallinity and lower defect density is obtained. Most importantly, carbon-based PSCs (C-PSCs) based on the CsPbI<sub>3</sub> perovskite film achieve an efficiency of 16.05%, a new record for inorganic C-PSCs.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"4 5","pages":"Pages 1110-1117"},"PeriodicalIF":6.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45780908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-01DOI: 10.1016/j.fmre.2022.12.003
Harmful Maillard reaction products (HMRPs) derived from brown fermented milk pose a potential threat to human health, but the conversion mechanism during the manufacturing process remains elusive and urgently needs to be controlled. Acrylamide (FC 2.14, adjusted p-value = 0.041), 5-hydroxymethylfurfural (FC 2.61, adjusted p-value = 0.026) and methylglyoxal (FC 2.07, adjusted p-value = 0.019) were identified as the significantly increased HMRPs after browning in this study and the analysis of proteomics integrated with untargeted metabolomics demonstrated that the degradation of HMRPs was jointly accomplished by Streptococcus thermophilus and Lactobacillus bulgaricus. The galactose oligosaccharide metabolism in Streptococcus thermophilus was identified as a key biochemical reaction for HMRPs degradation, and the hydrolysates of pectin could be utilized as prebiotics for Streptococcus thermophilus. Eighteen classes of enzymes of L. bulgaricus and Streptococcus thermophilus related to energy metabolism were upregulated in the pectin-added group, indicating that the entry of acrylamide and methylglyoxal into the tricarboxylic acid cycle was accelerated. NAD-aldehyde dehydrogenase and alanine dehydrogenase are enzymes belonging to Streptococcus thermophilus, and their downregulation accelerated the efflux of acetate, which was beneficial for the proliferation of L. bulgaricus and prevented the conversion of pyruvate to l-alanine, thus facilitating the energy metabolism. The recoveries and relative standard deviations of the intraday and interday precision experiments were 89.1%-112.5%, 1.3%-8.4% and 2.1%-9.4%, respectively, indicating that the developed approach was credible. Sensory evaluation results revealed that the brown fermented milk added with pectin had a better flavor, which was due to the fact that the supplement of polysaccharide promoted the fatty acid metabolism of lactic acid bacteria and increased the aroma substances including octoic acid and valeric acid. This study provided an insight into the formation and degradation mechanism of HMRPs in brown fermented milk, aiming to reduce the intake of advanced glycation end products in the diet.
从棕色发酵乳中提取的有害马氏反应产物（HMRPs）对人类健康构成潜在威胁，但生产过程中的转化机制仍难以确定，亟需加以控制。丙烯酰胺（FC 2.14，调整后 p 值 = 0.041）、5-羟甲基糠醛（FC 2.61，调整后 p 值 = 0.026）和甲基乙二醛（FC 2.07，调整后 p 值 = 0.蛋白质组学与非靶向代谢组学相结合的分析表明，嗜热链球菌和保加利亚乳杆菌共同完成了对 HMRPs 的降解。嗜热链球菌的半乳糖寡糖代谢被认为是降解 HMRPs 的关键生化反应，果胶的水解产物可作为嗜热链球菌的益生元。添加果胶组中保加利亚鹅膏菌和嗜热链球菌的 18 类与能量代谢有关的酶被上调，表明丙烯酰胺和甲基乙二醛进入三羧酸循环的速度加快。NAD-醛脱氢酶和丙氨酸脱氢酶属于嗜热链球菌的酶，它们的下调加速了醋酸的外流，有利于保加利亚鹅膏菌的增殖，并阻止丙酮酸转化为丙氨酸，从而促进了能量代谢。日内和日间精密度实验的回收率和相对标准偏差分别为 89.1%-112.5%、1.3%-8.4% 和 2.1%-9.4%，表明所开发的方法是可信的。感官评价结果表明，添加果胶的棕色发酵乳风味更好，这是由于多糖的补充促进了乳酸菌的脂肪酸代谢，增加了辛酸和戊酸等香味物质。这项研究有助于深入了解棕色发酵乳中 HMRP 的形成和降解机制，从而减少膳食中高级糖化终产物的摄入量。
{"title":"Complex pectin metabolism by Lactobacillus and Streptococcus suggests an effective control approach for Maillard harmful products in brown fermented milk","authors":"","doi":"10.1016/j.fmre.2022.12.003","DOIUrl":"10.1016/j.fmre.2022.12.003","url":null,"abstract":"<div><div>Harmful Maillard reaction products (HMRPs) derived from brown fermented milk pose a potential threat to human health, but the conversion mechanism during the manufacturing process remains elusive and urgently needs to be controlled. Acrylamide (FC 2.14, adjusted <em>p</em>-value = 0.041), 5-hydroxymethylfurfural (FC 2.61, adjusted <em>p</em>-value = 0.026) and methylglyoxal (FC 2.07, adjusted <em>p</em>-value = 0.019) were identified as the significantly increased HMRPs after browning in this study and the analysis of proteomics integrated with untargeted metabolomics demonstrated that the degradation of HMRPs was jointly accomplished by <em>Streptococcus thermophilus</em> and <em>Lactobacillus bulgaricus</em>. The galactose oligosaccharide metabolism in <em>Streptococcus thermophilus</em> was identified as a key biochemical reaction for HMRPs degradation, and the hydrolysates of pectin could be utilized as prebiotics for <em>Streptococcus thermophilus</em>. Eighteen classes of enzymes of <em>L. bulgaricus</em> and <em>Streptococcus thermophilus</em> related to energy metabolism were upregulated in the pectin-added group, indicating that the entry of acrylamide and methylglyoxal into the tricarboxylic acid cycle was accelerated. NAD-aldehyde dehydrogenase and alanine dehydrogenase are enzymes belonging to <em>Streptococcus thermophilus,</em> and their downregulation accelerated the efflux of acetate, which was beneficial for the proliferation of <em>L. bulgaricus</em> and prevented the conversion of pyruvate to <span>l</span>-alanine, thus facilitating the energy metabolism. The recoveries and relative standard deviations of the intraday and interday precision experiments were 89.1%-112.5%, 1.3%-8.4% and 2.1%-9.4%, respectively, indicating that the developed approach was credible. Sensory evaluation results revealed that the brown fermented milk added with pectin had a better flavor, which was due to the fact that the supplement of polysaccharide promoted the fatty acid metabolism of lactic acid bacteria and increased the aroma substances including octoic acid and valeric acid. This study provided an insight into the formation and degradation mechanism of HMRPs in brown fermented milk, aiming to reduce the intake of advanced glycation end products in the diet.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"4 5","pages":"Pages 1171-1184"},"PeriodicalIF":6.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48274793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01DOI: 10.1016/j.fmre.2024.04.014
DNA barcodes, short and unique DNA sequences, play a crucial role in sample identification when processing many samples simultaneously, which helps reduce experimental costs. Nevertheless, the low quality of long-read sequencing makes it difficult to identify barcodes accurately, which poses significant challenges for the design of barcodes for large numbers of samples in a single sequencing run. Here, we present a comprehensive study of the generation of barcodes and develop a tool, PRO, that can be used for selecting optimal barcode sets and demultiplexing. We formulate the barcode design problem as a combinatorial problem and prove that finding the optimal largest barcode set in a given DNA sequence space in which all sequences have the same length is theoretically NP-complete. For practical applications, we developed the novel method PRO by introducing the probability divergence between two DNA sequences to expand the capacity of barcode kits while ensuring demultiplexing accuracy. Specifically, the maximum size of the barcode kits designed by PRO is 2,292, which keeps the length of barcodes the same as that of the official ones used by Oxford Nanopore Technologies (ONT). We validated the performance of PRO on a simulated nanopore dataset with high error rates. The demultiplexing accuracy of PRO reached 98.29% for a barcode kit of size 2,922, 4.31% higher than that of Guppy, the official demultiplexing tool. When the size of the barcode kit generated by PRO is the same as the official size provided by ONT, both tools show superior and comparable demultiplexing accuracy.
DNA 条形码是一种简短而独特的 DNA 序列，在同时处理许多样本时对样本识别起着至关重要的作用，有助于降低实验成本。然而，由于长读程测序的质量较低，很难准确识别条形码，这给在一次测序中为大量样本设计条形码带来了巨大挑战。在此，我们对条形码的生成进行了全面研究，并开发了一种可用于选择最佳条形码集和解复用的工具 PRO。我们将条形码设计问题表述为一个组合问题，并证明在所有序列长度相同的给定 DNA 序列空间中寻找最优的最大条形码集在理论上是 NP-完全的。在实际应用中，我们开发了新方法 PRO，通过引入两个 DNA 序列之间的概率发散，在确保解复用精度的同时扩大了条形码套件的容量。具体来说，PRO 所设计的条形码试剂盒的最大尺寸为 2292，与牛津纳米孔技术公司（ONT）正式使用的条形码长度相同。我们在误差率较高的模拟纳米孔数据集上验证了 PRO 的性能。在条形码大小为 2,922 的情况下，PRO 的解复用准确率达到 98.29%，比官方解复用工具 Guppy 高出 4.31%。当 PRO 生成的条形码工具包大小与 ONT 提供的官方大小相同时，两种工具的解复用准确率都很高，不相上下。
{"title":"Generating barcodes for nanopore sequencing data with PRO","authors":"","doi":"10.1016/j.fmre.2024.04.014","DOIUrl":"10.1016/j.fmre.2024.04.014","url":null,"abstract":"<div><p>DNA barcodes, short and unique DNA sequences, play a crucial role in sample identification when processing many samples simultaneously, which helps reduce experimental costs. Nevertheless, the low quality of long-read sequencing makes it difficult to identify barcodes accurately, which poses significant challenges for the design of barcodes for large numbers of samples in a single sequencing run. Here, we present a comprehensive study of the generation of barcodes and develop a tool, PRO, that can be used for selecting optimal barcode sets and demultiplexing. We formulate the barcode design problem as a combinatorial problem and prove that finding the optimal largest barcode set in a given DNA sequence space in which all sequences have the same length is theoretically NP-complete. For practical applications, we developed the novel method PRO by introducing the probability divergence between two DNA sequences to expand the capacity of barcode kits while ensuring demultiplexing accuracy. Specifically, the maximum size of the barcode kits designed by PRO is 2,292, which keeps the length of barcodes the same as that of the official ones used by Oxford Nanopore Technologies (ONT). We validated the performance of PRO on a simulated nanopore dataset with high error rates. The demultiplexing accuracy of PRO reached 98.29% for a barcode kit of size 2,922, 4.31% higher than that of Guppy, the official demultiplexing tool. When the size of the barcode kit generated by PRO is the same as the official size provided by ONT, both tools show superior and comparable demultiplexing accuracy.</p></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"4 4","pages":"Pages 785-794"},"PeriodicalIF":6.2,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667325824001924/pdfft?md5=ff23f335fd4d810b3e30973aca3b4f7d&pid=1-s2.0-S2667325824001924-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140791015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01DOI: 10.1016/j.fmre.2022.06.001
Tingting Hu , Zhan Zhou , Jiajia Zha , Gareth R. Williams , Zhikang Wu , Wei Zhao , Weicheng Shen , Hai Li , Xisheng Weng , Ruizheng Liang , Chaoliang Tan
Combining photodynamic therapy (PDT) with chemodynamic therapy (CDT) has been proven to be a promising strategy to improve the treatment efficiency of cancer, because of the synergistic therapeutic effect arising between the two modalities. Herein, we report an inorganic nanoagent based on ternary NiCoTi-layered double hydroxide (NiCoTi-LDH) nanosheets to realize highly efficient photodynamic/chemodynamic synergistic therapy. The NiCoTi-LDH nanosheets exhibit oxygen vacancy-promoted electron-hole separation and photogenerated hole-induced O2-independent reactive oxygen species (ROS) generation under acidic circumstances, realizing in situ pH-responsive PDT. Moreover, due to the effective conversion between Co3+ and Co2+ caused by photogenerated electrons, the NiCoTi-LDH nanosheets catalyze the release of hydroxyl radicals (·OH) from H2O2 through Fenton reactions, resulting in CDT. Laser irradiation enhances the catalyzed ability of the NiCoTi-LDH nanosheets to promote the ROS generation, resulting in a better performance than TiO2 nanoparticles at pH 6.5. In vitro and in vivo experimental results show conclusively that NiCoTi-LDH nanosheets plus irradiation lead to efficient cell apoptosis and significant inhibition of tumor growth. This study reports a new pH-responsive inorganic nanoagent with oxygen vacancy-promoted photodynamic/chemodynamic synergistic performance, offering a potentially appealing clinical strategy for selective tumor elimination.
{"title":"Ternary NiCoTi-layered double hydroxide nanosheets as a pH-responsive nanoagent for photodynamic/chemodynamic synergistic therapy","authors":"Tingting Hu , Zhan Zhou , Jiajia Zha , Gareth R. Williams , Zhikang Wu , Wei Zhao , Weicheng Shen , Hai Li , Xisheng Weng , Ruizheng Liang , Chaoliang Tan","doi":"10.1016/j.fmre.2022.06.001","DOIUrl":"10.1016/j.fmre.2022.06.001","url":null,"abstract":"<div><p>Combining photodynamic therapy (PDT) with chemodynamic therapy (CDT) has been proven to be a promising strategy to improve the treatment efficiency of cancer, because of the synergistic therapeutic effect arising between the two modalities. Herein, we report an inorganic nanoagent based on ternary NiCoTi-layered double hydroxide (NiCoTi-LDH) nanosheets to realize highly efficient photodynamic/chemodynamic synergistic therapy. The NiCoTi-LDH nanosheets exhibit oxygen vacancy-promoted electron-hole separation and photogenerated hole-induced O<sub>2</sub>-independent reactive oxygen species (ROS) generation under acidic circumstances, realizing <em>in situ</em> pH-responsive PDT. Moreover, due to the effective conversion between Co<sup>3+</sup> and Co<sup>2+</sup> caused by photogenerated electrons, the NiCoTi-LDH nanosheets catalyze the release of hydroxyl radicals (·OH) from H<sub>2</sub>O<sub>2</sub> through Fenton reactions, resulting in CDT. Laser irradiation enhances the catalyzed ability of the NiCoTi-LDH nanosheets to promote the ROS generation, resulting in a better performance than TiO<sub>2</sub> nanoparticles at pH 6.5. <em>In vitro</em> and <em>in vivo</em> experimental results show conclusively that NiCoTi-LDH nanosheets plus irradiation lead to efficient cell apoptosis and significant inhibition of tumor growth. This study reports a new pH-responsive inorganic nanoagent with oxygen vacancy-promoted photodynamic/chemodynamic synergistic performance, offering a potentially appealing clinical strategy for selective tumor elimination.</p></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"4 4","pages":"Pages 926-933"},"PeriodicalIF":6.2,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667325822002308/pdfft?md5=c6ca0dafd3572b87f866522e9440ac25&pid=1-s2.0-S2667325822002308-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141951321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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