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Recent developments in the computational study of protein structural and vibrational energy dynamics

Biophysical Reviews 2020年第2期12卷 317-322页

作者： Leitner, David M. Yamato, Takahisa Department of Chemistry and Chemical Physics Program University of Nevada Reno 89557 NV United States Graduate School of Science Division of Material Science Nagoya University Furo-cho Chikusa-ku Nagoya 464-8602 Japan

Recent developments in the computational study of energy transport in proteins are reviewed, including advances in both methodology and applications. The concept of energy exchange network (EEN) is discussed, and a recent calculation of EENs for the allosteric protein FixL is reviewed, which illustrates how residues and protein regions involved in the allosteric transition can be identified. Recent work has examined relations between EENs and protein dynamics as well as structure. We review some of the computational studies carried out on several proteins that explore connections between energy conductivity across polar contacts in proteins and between proteins and water and equilibrium dynamics of the contacts, and we discuss some of the recent experimental work that addresses this topic. © 2020, International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature.

关键词： Energy exchange network Energy transport FixL Hemoglobin Proteins

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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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An enzyme-free and ultrafast cell-dissociation technique for cell culture applications using acoustofluidics 24

An enzyme-free and ultrafast cell-dissociation technique for...

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24th International Conference on Miniaturized Systems for Chemistry and Life sciences, MicroTAS 2020

作者： Salari, Alinaghi Appak-Baskoy, Sila Coe, Imogen R. Tsai, Scott S.H. Kolios, Michael C. Canada Biomedical Engineering Graduate Program Ryerson University Canada Department of Chemistry and Biology Ryerson University Canada Molecular Science Graduate Program Ryerson University Canada Department of Mechanical and Industrial Engineering Ryerson University Canada Department of Physics Ryerson University Canada

ISBN: (纸本)9781733419017

Cell-culture techniques are widely used for in-vitro drug screening and biochemical analyses. The classical models for dissociating cell monolayers into single-cell suspensions include enzymatic techniques (e.g., trypsinization). All available enzymatic and non-enzymatic techniques require long treatment duration, typically on the order of minutes (5-10 min). Here, we report a novel, ultrafast, and high-throughput technique, using acoustofluidics, that enables the detachment of adhered cells into suspensions within seconds, while maintaining cellular viability similar to that of the trypsinization method. In our technique, only the adhered cells experience the acoustic waves, minimizing any detrimental effects of the dissociating agent on the detached cells. © 2020 CBMS-0001

关键词： Cells

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High throughput intracellular delivery facilitated by acoustofluidics 24

High throughput intracellular delivery facilitated by acoust...

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24th International Conference on Miniaturized Systems for Chemistry and Life sciences, MicroTAS 2020

作者： Salari, Alinaghi Appak-Baskoy, Sila Coe, Imogen R. Abousawan, John Antonescu, Costin N. Tsai, Scott S.H. Kolios, Michael C. Canada Biomedical Engineering Graduate Program Ryerson University Canada Department of Chemistry and Biology Ryerson University Canada Molecular Science Graduate Program Ryerson University Canada Department of Mechanical and Industrial Engineering Ryerson University Canada Department of Physics Ryerson University Canada

ISBN: (纸本)9781733419017

Many cell-based therapies rely on the successful delivery of cargo materials into cells. Here, we present a novel in vitro strategy for intracellular delivery, which is based on adherent cells exposed to acoustic waves. Strong acoustic waves mediated through a substrate inside a microfluidic channel cause the adherent cells to oscillate. As a result of continuous cell oscillation and cell-induced microstreaming, successful delivery of different size dextrans into MDA-MB-231 cells (with delivery efficiencies of 55-85%) is demonstrated. This novel acoustofluidic method achieves rapid and scalable delivery of cargo materials into cells and thus may be preferred over lipofection, electroporation, or other delivery methods. © 2020 CBMS-0001

关键词： Cells

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Multiplexed Nanoscopy via Buffer Exchange

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ACS Nano 2024年第34期18卷 23445-23456页

作者： Chang, Ting-Jui Ben Yang, T. Tony Department of Electrical Engineering National Taiwan University Taipei10617 Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei10617 Taiwan Department of Physics National Taiwan University Taipei10617 Taiwan Nano Science and Technology Program Taiwan International Graduate Program Academia Sinica and National Taiwan University Taipei10617 Taiwan

Understanding cellular functions, particularly in their intricate complexity, can greatly benefit from the spatial mapping of diverse molecules through multitarget single-molecule localization microscopy (SMLM). Existing methodologies, primarily restricting the encoding dimensions to color and lifetime or requiring cyclic staining, often involve broad chromatic detection, specialized optical configurations, or sophisticated labeling techniques. Here, we propose a simple approach called buffer-exchange stochastic optical reconstruction microscopy (beSTORM), which introduces an additional dimension to differentiate between single molecules irrespective of their spectral properties. This method leverages the distinguishable photoblinking responses to distinct buffer conditions, offering a straightforward yet effective means of fluorophore discrimination. Through buffer exchanges, beSTORM achieves multitarget SMLM imaging with minimal crosstalk. Direct integration with expansion microscopy (ExM) demonstrates its capability to resolve up to six proteins at the molecular level within a single emission color without chromatic aberration. Overall, beSTORM presents a highly compatible imaging platform, promising significant advancements in highly multiplexed nanoscopy for exploring multiple targets in biological systems with nanoscale precision. © 2024 The Authors. Published by American Chemical Society.

关键词： Stochastic systems

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Angle and polarization independent plasmonic infrared band-stop filter with metallic disk on SiO2

Angle and polarization independent plasmonic infrared band-s...

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16th Opto-Electronics and Communications Conference, OECC 2011

作者： Abbas, Mohammed Nadhim Cheng, Cheng-Wen Chang, Yia-Chung Shih, Min-Hsiung Research Center for Applied Sciences Academia Sinica Taipei 11529 Taiwan Institute of Physics and Nano Science and Technology Program Taiwan International Graduate Program Academia Sinica Taipei 115 Taiwan Department of Engineering and System Science NTHU Hsinchu 300 Taiwan

ISBN: (纸本)9781612842882

We demonstrated Ag/SiO2 metallic disk structure can be applied as an efficient narrow stop band filter in the IR region. The absorption spectra of such structure are investigated both theoretically and experimentally. The metallic disk exhibits only one significant localized surface plasmon polariton mode for both TM and TE polarizations simultaneously which can give an ultrahigh immunity to incident angles and polarization direction. © 2011 National Sun Yat-Sen Univ.

关键词： Silica

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Hydrodynamic Modelling of Early Peaks in Type Ibc Supernovae with Shock Cooling Emission from Circumstellar Matter

arXiv

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arXiv 2025年

作者： Chiba, Ryotaro Moriya, Takashi J. Astronomical Science Program Graduate Institute for Advanced Studies SOKENDAI 2-21-1 Osawa Mitaka Tokyo181-8588 Japan National Astronomical Observatory of Japan National Institutes of Natural Sciences 2-21-1 Osawa Mitaka Tokyo181-8588 Japan School of Physics and Astronomy Monash University ClaytonVIC3800 Australia

Recent high-cadence transient surveys have uncovered a rare subclass of Type Ibc supernovae (SNe) that exhibit an early, blue peak lasting a few days before the main, radioactively powered peak. Since progenitors of Type Ibc SNe are typically compact and lack an extended envelope, this early peak is commonly attributed to shock cooling emission from circumstellar matter (CSM) surrounding the progenitor star. As such, these SNe provide a unique opportunity to constrain the pre-explosion activity of Type Ibc SN progenitors. We present the first systematic study of this Type Ibc SN population that uses hydrodynamic modelling. We simulated Type Ibc SNe exploding in a CSM using the multi-group radiation-hydrodynamics code STELLA, exploring a range of SN and CSM properties. By comparing the resulting theoretical multi-band light curves to a sample of seven Type Ibc SNe with early peaks, we constrained their CSM properties. Assuming a wind-like density distribution for the CSM, we found CSM masses of 10−2 −10−1 M☉ and CSM radii of (1−5) ×103 R☉. While the masses were roughly consistent with a previous estimate obtained using an analytical model, the radii were significantly different, likely due to our assumption of spatially spread out CSM. We infer that the progenitors could have created CSM via late-time binary mass transfer or pulsational pair instability. We also estimate that, in the planned ULTRASAT high-cadence survey, ∼ 30 shock cooling peaks from Type Ibc SNe will be observed. © 2025, CC BY-SA.

关键词： Supernovae

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Approaching maximum resolution in structured illumination microscopy via accurate noise modeling

Npj imaging

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Npj imaging 2025年第1期3卷 5页

作者： Ayush Saurabh Peter T Brown J Shepard Bryan Iv Zachary R Fox Rory Kruithoff Cristopher Thompson Comert Kural Douglas P Shepherd Steve Pressé Center for Biological Physics Arizona State University Tempe AZ USA. Department of Physics Arizona State University Tempe AZ USA. Computational Science and Engineering Division Oak Ridge National Laboratory Oak Ridge TN USA. Department of Physics The Ohio State University Columbus OH USA. Interdisciplinary Biophysics Graduate Program The Ohio State University Columbus OH USA. School of Molecular Sciences Arizona State University Tempe AZ USA.

Biological images captured by microscopes are characterized by heterogeneous signal-to-noise ratios (SNRs) due to spatially varying photon emission across the field of view convoluted with camera noise. State-of-the-art unsupervised structured illumination microscopy (SIM) reconstruction methods, commonly implemented in the Fourier domain, often do not accurately model this noise. Such methods therefore suffer from high-frequency artifacts, user-dependent choices of smoothness constraints making assumptions on biological features, and unphysical negative values in the recovered fluorescence intensity map. On the other hand, supervised algorithms rely on large datasets for training, and often require retraining for new sample structures. Consequently, achieving high contrast near the maximum theoretical resolution in an unsupervised, physically principled manner remains an open problem. Here, we propose Bayesian-SIM (B-SIM), a Bayesian framework to quantitatively reconstruct SIM data, rectifying these shortcomings by accurately incorporating known noise sources in the spatial domain. To accelerate the reconstruction process, we use the finite extent of the point-spread-function to devise a parallelized Monte Carlo strategy involving chunking and restitching of the inferred fluorescence intensity. We benchmark our framework on both simulated and experimental images, and demonstrate improved contrast permitting feature recovery at up to 25% shorter length scales over state-of-the-art methods at both high- and low SNR. B-SIM enables unsupervised, quantitative, physically accurate reconstruction without the need for labeled training data, democratizing high-quality SIM reconstruction and expands the capabilities of live-cell SIM to lower SNR, potentially revealing biological features in previously inaccessible regimes.

关键词： Biophysics Image processing Imaging and sensing Super-resolution microscopy

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Emergence of large-scale cell death through ferroptotic trigger waves

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Nature 2024年第8021期631卷 654-662页

作者： Co, Hannah K. C. Wu, Chia-Chou Lee, Yi-Chen Chen, Sheng-Hong Molecular and Cell Biology Taiwan International Graduate Program Academia Sinica and Graduate Institute of Life Science National Defense Medical Center Laboratory for Cell Dynamics Institute of Molecular Biology Academia Sinica National Center for Theoretical Sciences Physics Division Genome and Systems Biology Degree Program Academia Sinica and National Taiwan University

Large-scale cell death is commonly observed during organismal development and in human pathologies1–5. These cell death events extend over great distances to eliminate large populations of cells, raising the question... 详细信息

Large-scale cell death is commonly observed during organismal development and in human pathologies^1–5. These cell death events extend over great distances to eliminate large populations of cells, raising the question of how cell death can be coordinated in space and time. One mechanism that enables long-range signal transmission is trigger waves⁶, but how this mechanism might be used for death events in cell populations remains unclear. Here we demonstrate that ferroptosis, an iron- and lipid-peroxidation-dependent form of cell death, can propagate across human cells over long distances (≥5 mm) at constant speeds (around 5.5 μm min⁻¹) through trigger waves of reactive oxygen species (ROS). Chemical and genetic perturbations indicate a primary role of ROS feedback loops (Fenton reaction, NADPH oxidase signalling and glutathione synthesis) in controlling the progression of ferroptotic trigger waves. We show that introducing ferroptotic stress through suppression of cystine uptake activates these ROS feedback loops, converting cellular redox systems from being monostable to being bistable and thereby priming cell populations to become bistable media over which ROS propagate. Furthermore, we demonstrate that ferroptosis and its propagation accompany the massive, yet spatially restricted, cell death events during muscle remodelling of the embryonic avian limb, substantiating its use as a tissue-sculpting strategy during embryogenesis. Our findings highlight the role of ferroptosis in coordinating global cell death events, providing a paradigm for investigating large-scale cell death in embryonic development and human pathologies. © The Author(s) 2024.

关键词： Cell death Dynamical systems Emergence Multistability Regulatory networks

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Pulmonary Disease Pattern Recognition on X-Ray Radiography Image Using Artificial Neural Network (ANN) Method 3

Pulmonary Disease Pattern Recognition on X-Ray Radiography I...

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3rd Annual Scientific Meeting on Medical physics and Biophysics, PIT-FMB in conjunction with the 17th South-East Asia Congress of Medical physics, SEACOMP 2019

作者： Fitriyah, N. Kurniawati, L.D. Purwanti, E. Astuti, S.D. Department of Physics Faculty of Science and Technology Universitas Airlangga Surabaya60115 Indonesia Biomedical Engineering Study Program Faculty of Science and Technology Universitas Airlangga Surabaya60115 Indonesia Department of Biomedical Engineering Post-Graduate Program Faculty of Science and Technology Universitas Airlangga Surabaya60115 Indonesia

This research aims to recognize the pattern of pulmonary disease on x-ray radiography image using artificial neural network (ANN) method. The images, which were used such as images of healthy pulmonary, pulmonary tuberculosis, and pulmonary tumour. Pattern recognition was using an extraction feature of GLCM (Gray Level Co-occurrence Matrix) and back propagation method. Before being identified, the images were processed by median filter and adaptive histogram equalization. The GLCM features that used were homogeneity, energy, contrast, variance and correlation. The parameters were learning rate and hidden layer. Learning rate was 0.3 and hidden layer was 25. Back propagation training showed 100% accuracy, which all of 44 images were used had been successfully identified. From the result, the healthy pulmonary showed 60% accuracy, 83.3% for pulmonary tuberculosis and 100% for pulmonary tumor. Hence, the overall result showed 81.25% accuracy, which 13 of 16 images had been successfully identified. From these result, extraction feature of GLCM using back propagation method was capable to recognize the pattern of pulmonary disease. However, due to narrow range of the feature, this application may not be used optimally for comparing features in every category of images. Therefore, the further research is needed to determine the best features and parameters of training back propagation. © Published under licence by IOP Publishing Ltd.

关键词： Pattern recognition

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