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Effect of loops on the mean-square displacement of Rouse-model chromatin

Physical Review E 2024年第4期109卷 044502-044502页

作者： Tianyu Yuan Hao Yan Mary Lou P. Bailey Jessica F. Williams Ivan Surovtsev Megan C. King Simon G. J. Mochrie Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Department of Cell Biology Yale School of Medicine New Haven Connecticut 06520 USA Department of Molecular Cell and Developmental Biology Yale University New Haven Connecticut 06511 USA

Chromatin polymer dynamics are commonly described using the classical Rouse model. The subsequent discovery, however, of intermediate-scale chromatin organization known as topologically associating domains (TADs) in experimental Hi-C contact maps for chromosomes across the tree of life, together with the success of loop extrusion factor (LEF) model in explaining TAD formation, motivates efforts to understand the effect of loops and loop extrusion on chromatin dynamics. This paper seeks to fulfill this need by combining LEF-model simulations with extended Rouse-model polymer simulations to investigate the dynamics of chromatin with loops and dynamic loop extrusion. We show that loops significantly suppress the averaged mean-square displacement (MSD) of a gene locus, consistent with recent experiments that track fluorescently labeled chromatin loci. We also find that loops reduce the MSD's stretching exponent from the classical Rouse-model value of 1/2 to a loop-density-dependent value in the 0.45–0.40 range. Remarkably, stretching exponent values in this range have also been observed in recent experiments [Weber et al., Phys. Rev. Lett. 104, 238102 (2010); Bailey et al., Mol. Biol. Cell 34, ar78 (2023)]. We also show that the dynamics of loop extrusion itself negligibly affects chromatin mobility. By studying static “rosette” loop configurations, we also demonstrate that chromatin MSDs and stretching exponents depend on the location of the locus in question relative to the position of the loops and on the local friction environment.

关键词： Chromatin Chromosomes DNA Polymers Brownian dynamics Langevin equation Rouse model

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Monitoring Stress Level Through EDA by Using Convex Optimization 1

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1st International Conference on Electronics, biomedical engineering, and Health Informatics, ICEBEHI 2020

作者： Fajriaty, Nuzula Dwi Rahma, Osmalina Nur Putri, Yang Sa’ada Kamila Ariyansah Putra, Alfian Pramudita Rahmatillah, Akif Ain, Khusnul Biomedical Engineering Study Program Department of Physics Faculty of Science and Technology Universitas Airlangga Surabaya60115 Indonesia Biomedical Signals and Systems Research Group Faculty of Science and Technology Universitas Airlangga Surabaya60115 Indonesia

ISBN: (数字)9789813369269

ISBN: (纸本)9789813369252

This study designed an effective system for monitoring stress levels based on Electrodermal Activity (EDA) sensors by knowing the signal patterns and characteristics using convex optimization decomposition. The EDA sensor considered accurate and sensitive for identifying stress by analyzing the skin conductivity (SC) due to the changes in sympathetic nerve activity. However, the SC signal consists of phasic and tonic components, which needed to decompose to analyze stress levels. The SC signals also followed by the white Gaussian noise, which represents the error value. Hence, deconvolution is a crucial stage for the further process because the quality of the measurement depends on this result. This study aims to deconvolve the SC signal using the convex optimization method (cvxEDA). This model is physiology inspired by EDA based on Bayesian statistics, convex mathematical optimization, and sparsity. This research conducted with 18 subjects through three sessions of measurement. The given stimuli arise in each session to increase the level of stress. The results showed that this method could separate and identify SC. The Phasic component shows an increase in the stimulus of each session, as seen from the number of peaks. In contrast, there were no significant differences in the tonic component. This study shows that the phasic component is closely related to changes in sudomotor nerve activity (SMNA) and response to a stressor, which could be useful to classify stress levels in the future study. © 2021, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Convex optimization

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Super-Mossian Dielectrics for Nanophotonics

Super-Mossian Dielectrics for Nanophotonics

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Conference on Lasers and Electro-Optics (CLEO)

作者： Xielin Wang Chloe F. Doiron Zhichao Li Jacob B. Khurgin Gururaj V. Naik Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston TX Department of Electrical and Computer Engineering Johns Hopkins University Baltimore MD Department of Electrical and Computer Engineering Rice University Houston TX

Searching for high-index dielectrics, we identify materials that break the index upper bound set by Moss’ rule. We highlight the promise of such super-Mossian materials by demonstrating nanophotonic devices made of F... 详细信息

ISBN: (纸本)9781957171258

关键词： Fourier transform infrared spectroscopy Nanophotonics Optical constants Optical materials Refractive index Whispering gallery modes

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Electrodermal Activity-Based Stress Measurement Using Continuous Deconvolution Analysis Method 1

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1st International Conference on Electronics, biomedical engineering, and Health Informatics, ICEBEHI 2020

作者： Putri, Yang Sa’ada Kamila Ariyansah Rahma, Osmalina Nur Fajriaty, Nuzula Dwi Putra, Alfian Pramudita Rahmatillah, Akif Ain, Khusnul Biomedical Engineering Study Program Department of Physics Faculty of Science and Technology Universitas Airlangga Surabaya60115 Indonesia Biomedical Signals and Systems Research Group Faculty of Science and Technology Universitas Airlangga Surabaya60115 Indonesia

ISBN: (数字)9789813369269

ISBN: (纸本)9789813369252

Stress is a psychological response that must be handled properly, or it can affect psychology and trigger other complicated diseases. Nowadays, stress measured by filling out stress-related forms or interviews with a psychologist. This method still requires a willingness from the patient to consult their condition, which is often not giving the best result due to late treatment. Therefore, we need a system to monitor a person’s stress level conditions independently so they could be threatened quickly if their state gets worsen. One of the non-invasive methods that can be used to measure stress is an Electrodermal Activity (EDA) sensor. EDA is known to be associated with sweat gland activity regulated by SudoMotor Nerve Activity (SMNA), which response to a stressor. However, the SMNA need to decompose into the Skin Conductance Response (SCR) before it could represent stress condition. Hence, the decomposition stage is essential in measuring the quality of the stress condition. In this study, the EDA sensor placed in the palm to obtain the skin conductivity signal. Then, the skin conductivity signals were deconvolved using the Continuous Deconvolution Analysis (CDA) method to capture the SCR. CDA was chosen because it could produce a zero-based line SCR driver and could separate two overlapping peaks in SCR. The result, CDA is adequate to extract SCR, which is shown by the zero baseline of the SCR driver line with a clear peak. The clear SCR peaks are essential for identifying the responses related to the stimulus (stressor). © 2021, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Noninvasive medical procedures

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Low Cost Muon Telescope (LOCOMOTE) 38

Low Cost Muon Telescope (LOCOMOTE)

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38th International Cosmic Ray Conference, ICRC 2023

作者： Huang, Nai-Cheng Lin, Guey-Lin Lai, Kwang-Chang Huang, M.A. Liu, T.C. Institute of Physics National Yang Ming Chiao Tung University Hsinchu City Taiwan Center for General Education Chang Gung University Taoyuan City Taiwan Department of Energy Engineering National United University Taiwan Department of Electrophysics National Yang Ming Chiao Tung University Hsinchu City Taiwan Department of applied physics National PingTung university PingTung City Taiwan Undergraduate Degree Program of Systems Engineering and Technology National Yang Ming Chiao Tung University Hsinchu City Taiwan Chung Cheng Institute of Technology National Defense University Taoyuan Taiwan Leung Center for Cosmology and Particle Astrophysics National Taiwan University Taipei Taiwan

Low Cost Muon Telescope (LOCOMOTE) is a low-cost charged particle detector. Each LOCOMOTE unit includes two pieces of BC408 (2"*2"*1") scintillators, silicon photomultipliers (SiPM), and digital logic circuits. The cost of each LOCOMOTE unit is approximately 200 US dollars and is mainly used as a teaching instrument for high school students in cosmic ray education. Each LOCOMOTE unit can be connected to the network, and data from different units can form a ground array to measure high-energy cosmic ray events. In this report, we present the performance verification of the telescope, including the measurement of cosmic muon angular flux and the feasibility of muon tomography using multiple telescopes. © Copyright owned by the author(s) under the terms of the Creative Commons.

关键词： Telescopes

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Mapping primary motor cortex excitability by TMS-EEG/EMG integration

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Brain Stimulation 2025年第1期18卷 216-217页

作者： Elisa Kallioniemi Sara Määttä Laura Säisänen Jelena Hyppönen Päivi Koskenkorva Jukka Saari Negar Namdar Department of Biomedical Engineering New Jersey Institute of Technology New Jersey USA Department of Clinical Neurophysiology Kuopio University Hospital Finland Department of Applied Physics Faculty of Forestry and Natural Sciences University of Eastern Finland Finland Department of Clinical Neurophysiology Clinical Medicine Faculty of Health Sciences University of Eastern Finland Finland Department of Clinical Radiology Kuopio University Hospital Finland

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Technology Roadmap for Flexible Sensors

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ACS NANO 2023年第6期17卷 5211-5295页

作者： Luo, Yifei Abidian, Mohammad Reza Ahn, Jong-Hyun Akinwande, Deji Andrews, Anne M. Antonietti, Markus Bao, Zhenan Berggren, Magnus Berkey, Christopher A. Bettinger, Christopher John Chen, Jun Chen, Peng Cheng, Wenlong Cheng, Xu Choi, Seon-Jin Chortos, Alex Dagdeviren, Canan Dauskardt, Reinhold H. Di, Chong-an Dickey, Michael D. Duan, Xiangfeng Facchetti, Antonio Fan, Zhiyong Fang, Yin Feng, Jianyou Feng, Xue Gao, Huajian Gao, Wei Gong, Xiwen Guo, Chuan Fei Guo, Xiaojun Hartel, Martin C. He, Zihan Ho, John S. Hu, Youfan Huang, Qiyao Huang, Yu Huo, Fengwei Hussain, Muhammad M. Javey, Ali Jeong, Unyong Jiang, Chen Jiang, Xingyu Kang, Jiheong Karnaushenko, Daniil Khademhosseini, Ali Kim, Dae-Hyeong Kim, Il-Doo Kireev, Dmitry Kong, Lingxuan Lee, Chengkuo Lee, Nae-Eung Lee, Pooi See Lee, Tae-Woo Li, Fengyu Li, Jinxing Liang, Cuiyuan Lim, Chwee Teck Lin, Yuanjing Lipomi, Darren J. Liu, Jia Liu, Kai Liu, Nan Liu, Ren Liu, Yuxin Liu, Yuxuan Liu, Zhiyuan Liu, Zhuangjian Loh, Xian Jun Lu, Nanshu Lv, Zhisheng Magdassi, Shlomo Malliaras, George G. Matsuhisa, Naoji Nathan, Arokia Niu, Simiao Pan, Jieming Pang, Changhyun Pei, Qibing Peng, Huisheng Qi, Dianpeng Ren, Huaying Rogers, John A. Rowe, Aaron Schmidt, Oliver G. Sekitani, Tsuyoshi Seo, Dae-Gyo Shen, Guozhen Sheng, Xing Shi, Qiongfeng Someya, Takao Song, Yanlin Stavrinidou, Eleni Su, Meng Sun, Xuemei Takei, Kuniharu Tao, Xiao-Ming Tee, Benjamin C. K. Thean, Aaron Voon-Yew Trung, Tran Quang Wan, Changjin Wang, Huiliang Wang, Joseph Wang, Ming Wang, Sihong Wang, Ting Wang, Zhong Lin Weiss, Paul S. Wen, Hanqi Xu, Sheng Xu, Tailin Yan, Hongping Yan, Xuzhou Yang, Hui Yang, Le Yang, Shuaijian Yin, Lan Yu, Cunjiang Yu, Guihua Yu, Jing Yu, Shu-Hong Yu, Xinge Zamburg, Evgeny Zhang, Haixia Zhang, Xiangyu Zhang, Xiaosheng Zhang, Xueji Zhang, Yihui Zhang, Yu Zhao, Siyuan Zhao, Xuanhe Zheng, Yuanjin Zheng, Yu-Qing Zheng, Zijian Zhou, Tao Zhu, Bowen Zhu, Ming Zhu, Rong Zhu, Yangzhi Zhu, Yong Zou, Guijin Chen, Xiaodong 08-03 Innovis Singapore 138634 Republic of Singapore Innovative Centre for Flexible Devices (iFLEX) School of Materials Science and Engineering Nanyang Technological University Singapore 639798 Singapore Department of Biomedical Engineering University of Houston Houston Texas 77024 United States School of Electrical and Electronic Engineering Yonsei University Seoul 03722 Republic of Korea Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 United States Microelectronics Research Center The University of Texas at Austin Austin Texas 78758 United States Department of Chemistry and Biochemistry California NanoSystems Institute and Department of Psychiatry and Biobehavioral Sciences Semel Institute for Neuroscience and Human Behavior and Hatos Center for Neuropharmacology University of California Los Angeles Los Angeles California 90095 United States Colloid Chemistry Department Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany Department of Chemical Engineering Stanford University Stanford California 94305 United States Laboratory of Organic Electronics Department of Science and Technology Campus Norrköping Linköping University 83 Linköping Sweden Wallenberg Initiative Materials Science for Sustainability (WISE) and Wallenberg Wood Science Center (WWSC) SE-100 44 Stockholm Sweden Department of Materials Science and Engineering Stanford University Stanford California 94301 United States Department of Biomedical Engineering and Department of Materials Science and Engineering Carnegie Mellon University Pittsburgh Pennsylvania 15213 United States Department of Bioengineering University of California Los Angeles Los Angeles California 90095 United States School of Chemistry Chemical Engineering and Biotechnology Nanyang Technological University Singapore 637457 Singapore Nanobionics Group Department of Chemical and Biological Engineering Monash University Clayton Australia 3800 Monash

Humans rely increasingly on sensors to address grand challenges and to improve quality of life in the era of digitalization and big data. For ubiquitous sensing, flexible sensors are developed to overcome the limitations of conventional rigid counterparts. Despite rapid advancement in bench-side research over the last decade, the market adoption of flexible sensors remains limited. To ease and to expedite their deployment, here, we identify bottlenecks hindering the maturation of flexible sensors and propose promising solutions. We first analyze continued...challenges in achieving satisfactory sensing performance for real-world applications and then summarize issues in compatible sensor-biology interfaces, followed by brief discussions on powering and connecting sensor networks. Issues en route to commercialization and for sustainable growth of the sector are also analyzed, highlighting environmental concerns and emphasizing nontechnical issues such as business, regulatory, and ethical considerations. Additionally, we look at future intelligent flexible sensors. In proposing a comprehensive roadmap, we hope to steer research efforts towards common goals and to guide coordinated development strategies from disparate communities. Through such collaborative

关键词： soft materials mechanics engineering flexible electronics conformable sensors bioelectronics human-machine interfaces body area sensor networks technology translation sustainable electronics

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An interdisciplinary approach to high school curriculum development: Swarming Powered by Neuroscience

An interdisciplinary approach to high school curriculum deve...

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IEEE Integrated STEM Education Conference (ISEC)

作者： Elise Buckley Joseph D. Monaco Kevin M. Schultz Robert W. Chalmers Armin Hadzic Kechen Zhang Grace M. Hwang M. Dwight Carr Applied Physics Laboratory (APL) Johns Hopkins University (JHU) Department of Biomedical Engineering School of Medicine JHU JHUAPL Biomedical Engineering School of Medicine JHU JHUAPL and Johns Hopkins University Kavli Neuroscience Discovery Institute STEM Program Management Office JHUAPL

ISBN: (纸本)9781665484305

This article discusses how to create an interactive virtual training program at the intersection of neuroscience, robotics, and computer science for high school students with equity of access. A four-day microseminar, titled Swarming Powered by Neuroscience (SPN), was conducted virtually through a combination of presentations and interactive computer game simulations. The SPN microseminar was delivered by subject matter experts in neuroscience, mathematics, multi-agent swarm robotics, and education. The objective of this research was to determine if taking an interdisciplinary approach to high school education would enhance the students learning experiences in fields such as neuroscience, robotics, or computer science. This study found an improvement in student engagement for neuroscience by 16.6%, while interest in robotics and computer science improved respectively by 2.7% and 1.8%. The majority of students (64%) strongly agreed that they enjoyed learning from an interdisciplinary team of experts and 70% strongly agreed that the microseminar emphasized the need to have instruction teams with diverse disciplinary backgrounds. The curriculum materials, developed for the SPN microseminar, can be used by high school teachers to further evaluate interdisciplinary instructions across life and physical sciences and computer science.

关键词： Computer science Training Video games Neuroscience Computational modeling Swarm robotics Curriculum development

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An Effective Method for Assessing the Thermoelastostatic State of the Cavity Body

An Effective Method for Assessing the Thermoelastostatic Sta...

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International Conference on Control Systems, Mathematical Modelling, Automation and Energy Efficiency (SUMMA)

作者： Viktor Penkov Lyubov Levina Maksim Levin Department of General Mechanics Lipetsk State Technical University Lipetsk Russia Department of Applied Mathematics Lipetsk State Technical University Lipetsk Russia Department of Physics and Biomedical Engineering Lipetsk State Technical University Lipetsk Russia

The formulation of linear static thermoelasticity problems is considered. The system of determining ratios is decomposed into a sequence of tasks of thermostatics and elastostatics. The statement of boundary conditions allows for variants in which the characteristics of the thermal state (temperature, its gradient) can be related by relations with objects of a mechanical nature (displacement, surface forces). In this case, decomposition is not possible. A resource-saving approach is proposed that makes it possible to effectively approximate the volumetric forces from the influence of a temperature field by polynomials of three-dimensional space. This allows us to strictly write out particular solutions for problems of thermostatics and elasticity theory. It becomes possible to form the basis of a separable Hilbert space of internal states of a thermoelastostatic body. The use of the apparatus of the method of boundary states makes it possible to efficiently construct solutions of both unrelated and related problems for a body of arbitrary geometric configuration. The solution of a series of unrelated problems for a single-cavity 3D body is carried out. The influence of temperature factors on the nature of the stress state is estimated.

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Ultra-Sensitive Detection of Cea and Cyfra 21-1 Using Ethanolamine-Functionalized Boron Doped Diamond Biosensor

SSRN

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SSRN 2025年

作者： Joshi, Sowmya Nara, Arunachalam Ramachandra Rao, M.S. Sudhakar, Swati Madras Chennai600036 India Department of Physics Nano Functional Materials Technology Centre and Materials Science Research Centre Indian Institute of Technology Madras Chennai600036 India Department of Applied Mechanics and Biomedical Engineering Indian Institute of Technology Madras Chennai600036 India

Lung cancer is one of the biggest challenges in global health;therefore, there is a huge need for better methods of early detection since this will improve survival rates and outcomes for patients significantly. One way to do it is by monitoring the lung cancer biomarkers (CEA and CYFRA 21-1) before the onset of any clinical symptoms. This paper introduces a new detection method using an Ethanolamine (ETA) modified Boron Doped Diamond (BDD) current sensor. The sensor was characterized at every step of the process for the successful integration of the biosensor with different layers. Scanning electron microscopy (SEM) revealed changes in the surface morphology after each stage of device preparation and testing. Further proof of the amine functional groups on the BDD surface was carried out through X-ray photoelectron photo-electron spectroscopy (XPS) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. After CEA and CYFRA 21-1 immobilization on the diamond sensor, we obtained a yieldable LOD of 83 and 43 fg/mL for CEA and CYFRA 21-1 respectively. The biosensor exhibited remarkable responses of 8.79% to 69.3% and 10.2% to 66.7% for CYFRA 21-1 and CEA, respectively, of concentration ranging from 0.001 to 400ng/mL. Additionally, it presented stable and accurate detection of CEA antigen in human serum samples. The developed ETA-modified BDD sensor has excellent prospects for the early detection of lung cancer biomarkers. © 2025, The Authors. All rights reserved.

关键词： X ray photoelectron spectroscopy

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