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Unveiling the Conformational dynamics of the Histone Tails Using Markov State Modeling

Journal of Chemical Theory and Computation 2025年第9期21卷 4921-4938页

作者： Patel, Rutika Loverde, Sharon M. Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New York 10016 NY United States Department of Chemistry College of Staten Isl The City University of New York 2800 Victory Boulevard Staten Island 10314 NY United States Ph.D. Program in Chemistry The Graduate Center of the City University of New York New York 10016 NY United States Ph.D. Program in Physics The Graduate Center of the City University of New York New York 10016 NY United States

Biomolecules predominantly exert their function by altering conformational dynamics. The nucleosome core particle (NCP) is the fundamental unit of chromatin. dNA with ∼146 base pairs wraps around the histone octamer to form a nucleosome. The histone octamer is composed of two copies of each histone protein (H3, H4, H2A, and H2B) with a globular core and disordered N-terminal tails. Epigenetic modifications of the histone N-terminal tails play a critical role in regulating the chromatin structure and biological processes such as transcription and dNA repair. Here, we report all-atom molecular dynamics (Md) simulations of the nucleosome at microsecond time scales to construct Markov state models (MSMs) to elucidate distinct conformations of the histone tails. We employ time-lagged independent component analysis (tICA) to capture their essential slow dynamics, with k-means clustering used to discretize the conformational space. MSMs unveil distinct states and transition probabilities to characterize the dynamics and kinetics of the tails. Next, we focus on the H2B tail, which is one of the least studied tails. We show that acetylation increases secondary structure formation with increased transition rates. These findings will aid in understanding the functional implications of tail conformations for nucleosome stability and gene regulation. © 2025 The Authors. Published by American Chemical Society.

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Cytocompatible and antibacterial Fe-, Cu- and Zn-substituted calcium hydroxyapatite materials for skin applications

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Ceramics International 2025年第9期51卷 11286-11296页

作者： Lukaviciute, L. Lukowiak, A. Stankeviciute, Z. Junka, A. Mortimer, M. Zarkov, A. Yang, J.-C. Ganceviciene, R. Kareiva, A. Faculty of Chemistry and Geosciences Vilnius University Naugarduko st. 24 Vilnius03225 Lithuania Institute of Low Temperature and Structure Research Polish Academy of Sciences Okolna 2 Wroclaw50422 Poland Department of Pharmaceutical Microbiology and Parasitology Wroclaw Medical University Borowska 211A Wroclaw50556 Poland Laboratory of Environmental Toxicology National Institute of Chemical Physics and Biophysics Akadeemia tee 23 Tallinn12618 Estonia Graduate Institute of Nanomedicine and Medical Engineering International Ph.D. Program in Biomedical Engineering College of Biomedical Engineering Research Center of Biomedical Device Research Center of Digital Oral Science and Technology Taipei Medical University Taiwan Faculty of Medicine Vilnius University M.K. Ciurlionio st. 21 Vilnius03101 Lithuania

Calcium hydroxyapatite (C10(PO4)6(OH)2;CHAp) and metal-substituted samples (Fe:CHAp, Cu:CHAp, and Zn:CHAp) were synthesized using a recently developed method. This method involved the wet precipitation of amorphous calcium phosphate (ACP), followed by solid-state reaction synthesis of α-tricalcium phosphate (α-TCP), and finally hydrothermal synthesis of CHAp. The effect of Fe3+, Cu2+, and Zn2+ substitution on the phase purity and antimicrobial properties of CHAp are summarized in this study. Notably, it highlights the phase purity of CHAp and Zn:CHAp (in the presence of Fe3+ and Cu2+ ions, the α- and β-TCP phases have formed) as well as the antimicrobial activity of Zn:CHAp and Cu:CHAp against Staphylococcus aureus and Candida albicans. The synthesized nanosized CHAp, Fe:CHAp, Cu:CHAp, and Zn:CHAp samples were used as additives in the preparation of skin creams. In vitro biological studies of the resulting skin creams demonstrated their antimicrobial activity against Pseudomonas aeruginosa, and showed a reduction in osteoblasts cells viability of in the range of 20–40 %. The addition of zinc enhances antimicrobial efficacy but reduces biocompatibility, while copper maintains both high antimicrobial activity and biocompatibility, making it more suitable for the development of medical or cosmetic materials. dermal creams containing CHAp with copper and iron ions also show significant antimicrobial activity while preserving good cell viability. These results highlight the importance of optimizing the balance between antimicrobial effectiveness and biocompatibility in these materials. © 2024

关键词： Biocompatibility

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Surface Interface Engineered and Sulfur Source Inspired Carbon Nanofiber Mediated Growth of NSMO directly on Nickel Foam for Ultra-High Energy density Aqueous Asymmetric Supercapacitors

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Advanced Sustainable Systems 2025年

作者： Tamilselvan, Arun Karuppanan, Aravinth Bhargav, Pamula Balaji Govindasamy, Mani Department of Physics SSN Research Centre Sri Sivasubramaniya Nadar College of Engineering Tamilnadu Kalavakam 603110 India International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices Ming Chi University of Technology New Taipei 243303 Taiwan Research Center for Intelligence Medical Devices Ming Chi University of Technology New Taipei 243303 Taiwan

To advance energy storage technologies, the development of high-performance supercapacitor electrodes is paramount. This study presents a novel, binder-free electrode constructed from earth-abundant materials. A surface interfaced nanocomposite comprising Ni₃S₂ and MnO₂ hierarchical nanostructure (NSMO) is directly grown on carbon nanofibers (CNF) using hydrothermal method. This approach offers scalability and cost-effectiveness for large-scale applications. The electrode's exceptional electrochemical performance arises from the synergistic interactions between the mixed oxidation states and composite structure. It exhibits a maximum specific capacitance of 1470 F g⁻¹ at 1 A g⁻¹, coupled with remarkable stability, retaining 78.94% of its capacitance and delivering a Columbic efficiency of 99.5% after 15,000 cycles. When integrated into an asymmetric supercapacitor (ASC), the electrode demonstrated a specific capacitance of 215.7 F g⁻¹ at 1 A g⁻¹, an energy density of 67 Wh kg⁻¹ at a power density of 750 W kg⁻¹, and excellent cycle life. These results highlight the potential of the binder-free hybrid CNF@NSMO hierarchical nanostructure electrode as a sustainable and high-performance candidate for next-generation supercapacitor applications. © 2025 Wiley-VCH GmbH.

关键词： binder free CNF high energy density ASC MnO2 Ni3S2 supercapacitor

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Graphene quantum dot-decorated TiO2 nanowires/nanotubes: enhanced photocatalysis for methylene blue and pesticide degradation

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Applied physics A: Materials Science and Processing 2025年第4期131卷

作者： Uyen, Ngo Ngoc Tu, Ly Anh Le, phuoc Huu Faculty of Applied Science Ho Chi Minh City University of Technology-VNUHCM 268 Ly Thuong Kiet Street District 10 Ho Chi Minh70000 Viet Nam Center for Plasma and Thin Film Technologies and International Ph.D. Program in Plasma and Thin Film Technology Ming Chi University of Technology New Taipei243303 Taiwan Department of Physics and Biophysics Faculty of Basic Sciences Can Tho University of Medicine and Pharmacy 179 Nguyen Van Cu Street Can Tho94000 Viet Nam

In this study, TiO2 nanowires/nanotubes (TiO2 WT) and graphene quantum dots-decorated TiO2 WT (GQds/TiO2 WT) were fabricated using a combination of anodic oxidation and hydrothermal methods. Both TiO2 WT and GQds/TiO2 WT exhibited anatase phase with preferred orientations along the (101), (004), (112), (200), and (105) planes. The TiO2 WT displayed a well-defined, uniform structure comprising nanotube arrays with an average diameter of ~ 100 nm and a length of ~ 4.8 μm, covered by nanowires with lengths of 2.5–3.5 μm. Amorphous GQds were successfully decorated onto TiO2 WT at various loading levels, as confirmed by XRd, SEM, HRTEM, EdS, Raman spectroscopy, and XPS. GQds/TiO2 WT demonstrated photocatalytic activity approximately twice as high as TiO2 WT for degrading methylene blue (MB) and pesticides, including methiocarb (MTC), carbofuran (CBF), and dimethoate (dMT). The photodegradation rates achieved for GQds-2/TiO2 WT were 1.336 × 10⁻2 min− 1 for MB, 20.3 × 10⁻2 min− 1 for CBF, 121 × 10⁻2 min− 1 for MTC, and 21.8 × 10⁻2 min− 1 for dMT. The enhanced performance was attributed to the synergistic effects of improved photogenerated electron-hole separation and extended light absorption compared to bare TiO2. Stability tests over four cycles of MB degradation showed ~ 80% retention of photocatalytic efficiency, indicating excellent reusability and structural stability. These results highlight the potential of GQds/TiO2 WT as a robust and efficient photocatalyst for environmental remediation, particularly for degrading organic pollutants and pesticides under UV-Vis illumination. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2025.

关键词： Nanowires

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Achieving high surface bioactivity and adhesion in Ti-6Al-4V alloy via anodic oxidation and electrophoretic deposition

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Ceramics International 2025年

作者： Wu, Yu-Jie Wang, Chi-Yun Mana-ay, Haidee Tu, Chi-Shun Lai, Po-Liang Chen, Pin-Yi International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices Ming Chi University of Technology New Taipei City24301 Taiwan Research Center for Intelligent Medical Devices Ming Chi University of Technology New Taipei City24301 Taiwan Department of Physics Fu Jen Catholic University New Taipei City24205 Taiwan Bone and Joint Research Center Department of Orthopedic Surgery Chang Gung Memorial Hospital Taoyuan City33305 Taiwan Department of Mechanical Engineering Chang Gung University Taoyuan City33302 Taiwan Department of Physics Silliman University Dumaguete City6200 Philippines

This study combines 3d printing, anodic oxidation (AO), and electrophoretic deposition (Ed) technologies to develop Ti-6Al-4V alloy (abbreviated as Ti64) with high hydrophilicity, adhesion, and bioactivity. Titanium oxide nanotubes formed by AO treatment on the Ti64 surface exhibited reduced contact angles from 53 ° to 10 °. The adhesion of the calcium (Ca) layer through the integrated technology of the AO and Ed treatments (herein abbreviated as AEd) displays an optimal adhesive force of over 30 N on the Ti64 surface, which is attributed to the stable chemical bond due to the formation of OH− ions on the substrate after the AO treatment and the subsequent oxidation reaction of the Ca2+ ions to form a predominantly Ca(OH)2 layer after the Ed treatment. Moreover, the AEd treatment forms tiny needle-like structures that can effectively promote osteogenic differentiation. The expressions of the osteocyte marker genes (i.e., OCN, OPN, and dMP1) were improved after the AEd treatment, showing increased osteogenic differentiation into mature bone tissue. This work presents the AEd treatment as a valuable surface modification technique to boost the surface bioactivity of Ti64 for clinical orthopedic applications. © 2025

关键词： Anodic oxidation

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Microwave dielectric and structural characteristics in Li2O-B2O3-SiO2 glass ceramics

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Ceramics International 2025年

作者： Qiu, Jun-Yan Tu, Chi-Shun Huang, Szu-Ting Li, Yongxiang Chen, Pin-Yi Chen, Cheng-Sao Montecillo, Rhys Feng, Kuei-Chih International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices Ming Chi University of Technology New Taipei City Taiwan Department of Physics Fu Jen Catholic University New Taipei City Taiwan Department of Mechanical Engineering Ming Chi University of Technology New Taipei City Taiwan School of Engineering RMIT University MelbourneVIC3000 Australia Research Center for Intelligent Medical Devices Ming Chi University of Technology New Taipei City Taiwan Department of Mechanical Engineering Hwa Hsia University of Technology New Taipei City Taiwan

Advancements in high-frequency communication devices have emphasized miniaturization and low energy consumption. This work focuses on developing microwave dielectric materials characterized by an ultra-low dielectric constant and low dielectric loss coefficient. In this study, B2O3 and Li2O were added into the SiO2 matrix to form the LBS glass-ceramics. The B2O3-added SiO2 shows a formation of α-cristobalite phase, and the Li2O additive in the B2O3-SiO2 glass-ceramics sintered at 900 °C reveal a primary quartz phase with a secondary phase Li2Si2O5, that partially transformed into Li2SiO3 in the specimen sintered at 950 °C. The LBS12 (x = 12 wt%) show stronger Raman peaks of Li2Si2O5 and Li2SiO3, indicating increase of highly-crystallized Si-O network. As the quartz phase diminishes, Li2Si2O5 and Li2SiO3 begin to develop in the glass-ceramic matrix. dense microstructures and well-formed crystalline grains were observed in the LBS glass-ceramics. The quality factors were primarily affected by grain size and density. The Li2Si2O5 additive in the LBS glass-ceramics can reduce dielectric permittivity (Εr) and increase Q × f, particularly at higher frequencies. A low Εr of 4.7–5, a high Q × f of 2600 GHz, and a hardness of 249 MHV were achieved in the LBS12 sintered at 900 °C. These LBS glass-ceramics exhibit potential for use in low-temperature co-fired ceramic (LTCC) applications in high-frequency communication devices. © 2025

关键词： Sintering

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Investigation of Short-Circuit Current density in Non-Fullerene-Based Ternary Organic Solar Cells by Incorporating Machine Learning Algorithms with Effective descriptors

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Solar RRL 2025年第10期9卷

作者： Lee, Min-Hsuan Chen, Ying-Chun Chang, Yi-Ming Hou, Bo Ph.D. Program in Biomedical Artificial Intelligence National Tsing Hua University Hsinchu Taiwan Institute of Environmental and Occupational Health Sciences School of Medicine National Yang-Ming Chiao Tung University Taipei Taiwan Institute of Environmental Engineering National Yang-Ming Chiao Tung University Hsinchu Taiwan Department of Mechanical Engineering National Taiwan University of Science and Technology Taipei Taiwan Raynergy Tek Incorporation Hsinchu Taiwan School of Physics and Astronomy Cardiff University Cardiff United Kingdom

Non-fullerene acceptor (NFA)-based ternary organic solar cells (OSCs) are emerging as promising devices for converting sunlight into electricity, contributing to environmental solutions. However, selecting the third component remains a significant challenge, as it plays a critical role in achieving high short-circuit current density (Jsc) in NFA-based ternary OSCs (comprising donors, acceptors, and the third component). Traditional trial-and-error experimental methods face substantial limitations, including high energy consumption, cost, and time demands, which may not be sufficient for investigating the quantitative relationships between material properties and Jsc in ternary OSCs. In this study, we examine the effects of the highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO–LUMO) energy gap (ΔHOMO and ΔLUMO) between different organic materials, considering these as effective molecular descriptors, on the primary photovoltaic parameter (Jsc) in NFA-based ternary OSCs. The eXtreme Gradient Boosting (XGBoost) algorithm yields reasonable predictions, with an R2 value of 0.76. Additionally, three NFA-based ternary OSCs are fabricated and characterized experimentally to validate the predictions made by the proposed model. Using three different NFA-based ternary OSCs as inputs, the model demonstrates good predictive accuracy for Jsc values. The proposed interpretable model and effective molecular descriptors offer a practical machine-learning approach for accelerating the development of NFA-based ternary OSCs with targeted Jsc values and can also be extended to other organic electronic applications. © 2025 Wiley-VCH GmbH.

关键词： Learning algorithms

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doping ratio between ZnO/MgO tunes antimicrobial, osteogenic, and anti-osteoclast activity of CaO-MgO-ZnO-SiO2 bioactive glass-ceramics

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Ceramics International 2025年

作者： Hung, Guan-Yi Xia, Yun-Ze Chen, Pin-Yi Lai, Po-Liang Feng, Kuei-Chih Tu, Chi-Shun Cheng, I.-C. Wang, Chi-Yun International Ph.D. Program in Innovative Technology of Biomedical Engineering and Medical Devices Ming Chi University of Technology New Taipei City24301 Taiwan Department of Physics Fu Jen Catholic University New Taipei City24205 Taiwan Department of Mechanical Engineering Ming-Chi University of Technology New Taipei City24301 Taiwan Bone and Joint Research Center Department of Orthopaedic Surgery Chang Gung Memorial Hospital Taoyuan City33305 Taiwan College of Medicine Chang Gung University Taoyuan City33305 Taiwan Department of Mechanical Engineering Chang Gung University Taoyuan City33305 Taiwan Research Center for Intelligent Medical Devices Ming Chi University of Technology New Taipei City243303 Taiwan

Limitations such as donor site morbidity hamper autologous bone grafts. On the other hand, allogeneic grafts, sourced from cadavers, pose risks of viral transmission and rejection. While hydroxyapatite is a prevalent synthetic graft material, antibiotic-laden fillers addressing infection face challenges with antibiotic-resistant pathogens, driving the emergence of nonantibiotic materials to combat persistent bone infections. Bioactive glass is a potential bone void filler superior to hydroxyapatite. Thus, to improve the antibacterial efficacy and bioactivity, we adjusted the doping ratio of the novel CaO-(1-x) MgO-(x) ZnO-SiO2 glass-ceramics (x = 0, 0.25, 0.50, 0.75, 1). Using XRd, we found a typical amorphous structure alongside polycrystalline diopside (CaMgSi2O6), hardystonite (Ca2ZnSi2O7), and petedunnite (CaZnSi2O6) formations. Raman spectroscopy revealed the silicate-glass matrix structure in all the Zn(100x) glass-ceramics and confirmed that the Zn ions replaced the Mg ions. Zn-doped glass-ceramics promoted apatite layer formation and had greater antibacterial efficacy against E. coli and S. aureus. Zn25 glass-ceramic were biocompatible with L929 and MC3T3-E1 cells. Furthermore, Zn25 glass-ceramic promoted bone cell mineralization and reduced osteoclast formation without affecting ALP activity. In vivo, the Zn25 glass-ceramic exhibited greater osteointegration ability than the HAP and Zn0 glass-ceramic. Taken together, the present study demonstrated that bioactive glass-ceramics with a doping ratio between ZnO and MgO (25:75) can enhance antibacterial and osteogenic activity while impeding osteoclastogenic activity. © 2025

关键词： Escherichia coli

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PVA-based bioinks for 3d bioprinting: A comprehensive review of their applications in tissue engineering

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Bioprinting 2025年 49卷

作者： Narges Johari Zary Adabavazeh Francesco Baino Materials Engineering Group Golpayegan College of Engineering Isfahan University of Technology Golpayegan Iran Ph.D. Program Graduate Institute of Precision Manufacturing National Chin-Yi University of Technology Taichung Taiwan ROC Institute of Materials Physics and Engineering Department of Applied Science and Technology Politecnico di Torino Torino Italy

3d bioprinting is an innovative approach that overcomes the limitations of traditional methods for creating cell-laden biomaterials and constructs. It allows for the fabrication of complex and biologically active tissue structures. This review aims to provide a comprehensive evaluation of polyvinyl alcohol (PVA)-based bioinks within a 3d bioprinting framework. PVA-based bioinks exhibit remarkable properties, such as biocompatibility, biodegradability, and the ability to enhance cell growth and differentiation. These properties make them appropriate for many tissue engineering applications. The study evaluates the physicochemical and biological properties of PVA bioinks, including how they combine with other materials such as gelatin, chitin, chitosan, alginate, agarose, cellulose, κ-carrageenan, methacrylate, nanoparticles, mineral additives, carbon nanotubes, graphene oxide, and extracellular matrix components. Furthermore, this review evaluates the benefits of market availability and enhanced printing resolution, in addition to the challenges posed by complexity, dependency on support baths, and the risk of contamination. The objective of this review is to draw attention to the capabilities of PVA-based bioinks and provide guidelines for future research to improve the effectiveness of these materials in tissue engineering and regenerative medicine.

关键词： Bioprinting Bioink Polyvinyl alcohol PVA-based bioinks

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CompressedMediQ: Hybrid Quantum Machine Learning Pipeline for High-dimensional Neuroimaging data

CompressedMediQ: Hybrid Quantum Machine Learning Pipeline fo...

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Acoustics, Speech, and Signal Processing Workshops (ICASSPW), IEEE International Conference on

作者： Kuan-Cheng Chen Yi-Tien Li Tai-Yu Li Chen-Yu Liu Po-Heng Henry Lee Cheng-Yu Chen Department of Electrical and Electronic Engineering Imperial College London London UK Centre for Quantum Engineering Science and Technology (QuEST) Imperial College London London UK Translational Imaging Research Center Taipei Medical University Hospital Taipei Taiwan Research Center for Neuroscience Taipei Medical University Taipei Taiwan Ph.D. Program in Medical Neuroscience College of Medical Science and Technology Taipei Medical University Taipei Taiwan National Center for High-Performance Computing NARlabs Hsinchu Taiwan Graduate Institute of Applied Physics National Taiwan University Taipei Taiwan Department of Medical Imaging Taipei Medical University Hospital Taipei Taiwan Department of Radiology National Defense Medical Center Taipei Taiwan Department of Radiology School of Medicine College of Medicine Taipei Taiwan

ISBN: (数字)9798331519315

ISBN: (纸本)9798331519322

This paper introduces CompressedMediQ, a novel hybrid quantum-classical machine learning pipeline specifically developed to address the computational challenges associated with high-dimensional multi-class neuroimaging data analysis. Standard neuroimaging datasets, such as large-scale MRI data from the Alzheimer’s disease Neuroimaging Initiative and Neuroimaging in Frontotemporal dementia, present significant hurdles due to their vast size and complexity. CompressedMediQ integrates classical HPC nodes for advanced MRI pre-processing and Convolutional Neural Network (CNN)-PCA-based feature extraction and reduction, addressing the limited-qubit availability for quantum data encoding in the NISQ era. This is followed by Quantum Support Vector Machine (QSVM) classification. By utilizing quantum kernel methods, the pipeline optimizes feature mapping and classification, enhancing data separability and outperforming traditional neuroimaging analysis techniques. Experimental results highlight the pipeline’s superior accuracy in dementia staging, validating the practical use of quantum machine learning in clinical diagnostics. despite the limitations of NISQ devices, this proof-of-concept demonstrates the transformative potential of quantum-enhanced learning, paving the way for scalable and precise diagnostic tools in healthcare and signal processing.

关键词： Neuroimaging Support vector machines Quantum computing Accuracy Magnetic resonance imaging Pipelines Machine learning Medical services Signal processing Standards

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