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2020 Frontiers in Optics Conference, FiO 2020

作者： Schnell, Martin Mittal, Shachi Falahkheirkhah, Kianoush Mittal, Anirudh Yeh, Kevin Kenkel, Seth Kadjacsy-Balla, Andre Carney, P. Scott Bhargava, Rohit Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Bioengineering University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Chemical and Biomolecular Engineering University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Mechanical Science and Engineering University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Pathology University of Illinois at Chicago ChicagoIL60612 United States The Institute of Optics University of Rochester 480 Intercampus Drive RochesterNY14620 United States Cancer Center at Illinois Department of Electrical and Computer Engineering Department of Chemistry University of Illinois Urbana-Champaign IL61801 United States

Infrared-Optical Hybrid Microscopy (IR-OH) provides mid-IR imaging on the visible microscope platform based on photothermal expansion. Spectral IR imaging of full tissue slides is demonstrated for automated disease di... 详细信息

ISBN: (纸本)9781943580804

关键词： Infrared imaging

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Publisher Correction: Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks

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Nature chemistry 2022年第11期14卷 1335页

作者： Samuel W Schaffter Kuan-Lin Chen Jackson O'Brien Madeline Noble Arvind Murugan Rebecca Schulman Department of Chemical & Biomolecular Engineering Johns Hopkins University Baltimore MD USA. Department of Physics University of Chicago Chicago IL USA. Department of Chemical & Biomolecular Engineering Johns Hopkins University Baltimore MD USA. rschulm3@jhu.edu. Department of Computer Science Johns Hopkins University Baltimore MD USA. rschulm3@jhu.edu. Department of Chemistry Johns Hopkins University Baltimore MD USA. rschulm3@jhu.edu.

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Periodicity Scoring of Time Series Encodes Dynamical Behavior of the Tumor Suppressor p53 ⁎ ⁎

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IFAC-PapersOnLine 2021年第9期54卷 488-495页

作者： Caroline Moosmüller Christopher J. Tralie Mahdi Kooshkbaghi Zehor Belkhatir Maryam Pouryahya José Reyes Joseph O. Deasy Allen R. Tannenbaum Ioannis G. Kevrekidis C. Moosmüller and C. Tralie contributed equally to this work Department of Mathematics University of California San Diego La Jolla CA 92093 USA Department of Medical Physics Memorial Sloan-Kettering Cancer Center NY USA Department of Chemical and Biomolecular Engineering Johns Hopkins University Baltimore MD 21218 USA Department of Mathematics and Computer Science Ursinus College Collegeville PA USA Program in Applied and Computational Mathematics Princeton University NJ USA School of Engineering and Sustainable Development De Montfort University Leicester UK Cancer Biology and Genetics Program and Computational and Systems Biology Program Memorial Sloan-Kettering Cancer Center New York NY 10065 USA and Department of Systems Biology Harvard Medical School Boston MA 02115 USA Departments of Computer Science and Applied Mathematics & Statistics Stony Brook University NY USA

In this paper we analyze the dynamical behavior of the tumor suppressor protein p53, an essential player in the cellular stress response, which prevents a cell from dividing if severe DNA damage is present. When this response system is malfunctioning, e.g. due to mutations in p53, uncontrolled cell proliferation may lead to the development of cancer. Understanding the behavior of p53 is thus crucial to prevent its failing. It has been shown in various experiments that periodicity of the p53 signal is one of the main descriptors of its dynamics, and that its pulsing behavior (regular vs. spontaneous) indicates the level and type of cellular stress. In the present work, we introduce an algorithm to score the local periodicity of a given time series (such as the p53 signal), which we call Detrended Autocorrelation Periodicity Scoring (DAPS). It applies pitch detection (via autocorrelation) on sliding windows of the entire time series to describe the overall periodicity by a distribution of localized pitch scores. We apply DAPS to the p53 time series obtained from single cell experiments and establish a correlation between the periodicity scoring of a cell’s p53 signal and the number of cell division events. In particular, we show that high periodicity scoring of p53 is correlated to a low number of cell divisions and vice versa. We show similar results with a more computationally intensive state-of-the-art periodicity scoring algorithm based on topology known as Sw1PerS. This correlation has two major implications: It demonstrates that periodicity scoring of the p53 signal is a good descriptor for cellular stress, and it connects the high variability of p53 periodicity observed in cell populations to the variability in the number of cell division events.

关键词： Systems biology cellular systems time series modeling bioinformatics computational biology

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Large-scale generation of functional mRNA-encapsulating exosomes via cellular nanoporation (vol 4, pg 69, 020)

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NATURE BIOMEDICAL engineering 2021年第8期5卷 944-945页

作者： Yang, Zhaogang Shi, Junfeng Xie, Jing Wang, Yifan Sun, Jingyao Liu, Tongzheng Zhao, Yarong Zhao, Xiuting Wang, Xinmei Ma, Yifan Malkoc, Veysi Chiang, Chiling Deng, Weiye Chen, Yuanxin Fu, Yuan Kwak, Kwang J. Fan, Yamin Kang, Chen Yin, Changcheng Rhee, June Bertani, Paul Otero, Jose Lu, Wu Yun, Kyuson Lee, Andrew S. Jiang, Wen Teng, Lesheng Kim, Betty Y. S. Lee, L. James Department of Chemical and Biomolecular Engineering The Ohio State University Columbus OH USA Department of Radiation Oncology University of Texas Southwestern Medical Center Dallas TX USA School of Life Sciences Jilin University Changchun China College of Pharmacy Jinan University Guangzhou China College of Medicine The Ohio State University Columbus OH USA Department of Neurological Surgery Mayo Clinic Jacksonville FL USA Department of Neurosurgery The University of Texas MD Anderson Cancer Center Houston TX USA Carver College of Medicine University of Iowa Iowa City IA USA Department of Biophysics Health Science Center Peking University Beijing China Institute for Stem Cell Biology Stanford University Palo Alto CA USA Institute of Cancer Research Shenzhen Bay Laboratory Shenzhen China Department of Electrical and Computer Engineering The Ohio State University Columbus OH USA Department of Neuroscience The Ohio State University Columbus OH USA Peak Center for Pituitary and Brain Tumor Department of Neurosurgery Houston Methodist Research institute Weill-Cornell Medical College Houston TX USA

A Correction to this paper has been published: https://***/10.1038/s41551-021-00725-w.

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engineering for Inclusion:Empowering Individuals with Physical and Neurological Differences through engineering Invention,Research,and Development

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engineering 2021年第2期7卷 141-143页

作者： Peter T.Cummings Philippe M.Fauchet Michael Goldfarb Martha W.M.Jones Maithilee Kunda Jonathan B.Perlin Nilanjan Sarkar Keivan G.Stassun Zachary E.Warren Karl E.Zelik Department of Chemical and Biomolecular Engineering Vanderbilt UniversityNashvilleTN 37235-1604USA Department of Electrical Engineering and Computer Science Vanderbilt UniversityNashvilleTN 37235-1826USA Department of Mechanical Engineering Vanderbilt UniversityNashvilleTN 37235-1592USA Department of Medicine Healthand SocietyVanderbilt UniversityNashvilleTN 37235-1665USA The Frist Center for Autism and Innovation Vanderbilt UniversityNashvilleTN 37212USA Department of Physics and Astronomy Vanderbilt UniversityNashvilleTN 37235-1807USA Department of Biomedical Engineering Vanderbilt UniversityNashvilleTN 37235-1631USA HCA Healthcare NashvilleTN 37203USA Department of Pediatrics Vanderbilt University Medical CenterNashvilleTN 37232USA Treatment and Research Institute for Autism Spectrum Disorders Vanderbilt Kennedy CenterNashvilleTN 37203USA Department of Physical Medicine and Rehabilitation Vanderbilt University Medical CenterNashvilleTN 37212USA

*** The use of engineering tools,design,research,and thinking to create environments and capabilities whereby individuals who are currently under-employed or unemployed due to a physical disability(e.g.,amputation or spinal cord injury)or neurological difference(e.g.,autism)are enabled to become fully productive and employed members of society has been the implicit goal of decades of research at Vanderbilt University and *** Vanderbilt University,progress in these areas has been greatly facilitated by the proximity of the School of engineering to the world-class Vanderbilt University Medical Center and the resulting close collaboration between engineering and medical researchers.

关键词： has environments power

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Artificial confocal microscopy for deep label-free imaging

arXiv

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arXiv 2021年

作者： Chen, Xi Kandel, Mikhail E. He, Shenghua Hu, Chenfei Lee, Young Jae Sullivan, Kathryn Tracy, Gregory Chung, Hee Jung Kong, Hyun Joon Anastasio, Mark Popescu, Gabriel Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign UrbanaIL United States Department of Computer Science & Engineering Washington University in St. Louis St. LouisMO63130 United States Department of Electrical and Computer Engineering University of Illinois at Urbana-Champaign UrbanaIL United States Neuroscience Program University of Illinois at Urbana-Champaign UrbanaIL United States Department of Bioengineering University of Illinois at Urbana-Champaign UrbanaIL United States Department of Molecular and Integrative Physiology University of Illinois at Urbana-Champaign UrbanaIL United States Chemical and Biomolecular Engineering University of Illinois at Urbana-Champaign UrbanaIL United States Carl Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign UrbanaIL United States

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Comparative Study on in-situ Ellipsometric Monitoring of III-Nitride Film Growth via Plasma-Enhanced Atomic Layer Deposition

Comparative Study on in-situ Ellipsometric Monitoring of III...

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作者： Mohammad, Adnan Shukla, Deepa Ilhom, Saidjafarzoda Willis, Brian Okyay, Ali Kemal Biyikli, Necmi University of Connecticut Department of Electrical and Computer Engineering StorrsCT06269 United States University of Connecticut Department of Materials Science and Engineering StorrsCT06269 United States University of Connecticut Dept. of Chemical and Biomolecular Engineering StorrsCT06269 United States Stanford University Department of Electrical Engineering StanfordCA94305 United States Okyay Technologies Inc. Ankara06374 Turkey

In this paper a comparative in-situ ellipsometric analysis is carried out on plasma-assisted ALD-grown III-nitride (AlN, GaN, and InN) films. The precursors used are TMA, TMG, and TMI for AlN, GaN, and InN respectively, while Ar is used as purge gas. For all of the films N2/H2/Ar plasma was used as the co-reactant. The work includes real-time in-situ monitored saturation curves, unit ALD cycle analysis, and >500 cycle film growth runs. In addition, the films are grown at different substrate temperatures to observe the impact of temperature not only on the growth rate but on how it influenced the precursor chemisorption, ligand removal, and nitrogen incorporation surface reactions. All three nitride films confirm fairly linear growth character. The growth rate per cycle (GPC) for each film is also measured with respect to rf-plasma power to obtain the surface saturation conditions during ALD growth. The real-time in-situ monitoring of the film growth can really be beneficial to understand the atomic layer growth and film formation in each individual ALD cycle. © 2019 World Scientific Publishing Company.

关键词： Atomic layer deposition

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0D Pyramid-intercalated 2D Bimetallic Halides with Tunable Electronic Structures and Enhanced Emission under Pressure

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Angewandte Chemie 2023年第52期135卷

作者： Dr. Yang Liu Jiayuan Liang Dr. Zeyu Deng Dr. Songhao Guo Dr. Xiaoqin Ji Congcong Chen Prof. Dr. Pieremanuele Canepa Prof. Dr. Xujie Lü Prof. Dr. Lingling Mao Department of Chemistry SUSTech Energy Institute for Carbon Neutrality Southern University of Science and Technology Shenzhen Guangdong 518055 P. R. China Center for High Pressure Science and Technology Advanced Research (HPSTAR) Shanghai 201203 P. R. China Department of Materials Science and Engineering National University of Singapore 9 Engineering Drive 1 Singapore 117575 Singapore Singapore-MIT Alliance for Research and Technology 1 CREATE Way 10–01 CREATE Tower Singapore 138602 Singapore Department of Chemical and Biomolecular Engineering National University of Singapore 4 Engineering Drive 4 Singapore 117585 Singapore Department of Electrical and Computer Engineering and Texas Center for Superconductivity University of Houston Houston TX 77204 USA

Hybrid metal halides are emerging semiconductors as promising candidates for optoelectronics. The pursuit of hybridizing various dimensions of metal halides remains a desirable yet highly complex endeavor. By utilizing dimension engineering, a diverse array of new materials with intrinsically different electronic and optical properties has been developed. Here, we report a new family of 2D-0D hybrid bimetallic halides, (C 6 N 2 H 14 ) 2 SbCdCl 9 ⋅ 2H 2 O ( SbCd ) and (C 6 N 2 H 14 ) 2 SbCuCl 9 ⋅ 2H 2 O ( SbCu ). These compounds adopt a new layered structure, consisting of alternating 0D square pyramidal [SbCl 5 ] and 2D inorganic layers sandwiched by organic layers. SbCd and SbCu have optical band gaps of 3.3 and 2.3 eV, respectively. These compounds exhibit weak photoluminescence (PL) at room temperature, and the PL gradually enhances with decreasing temperature. Density functional theory (DFT) calculations reveal that SbCd and SbCu are direct gap semiconductors, where first-principles band gaps follow the experimental trend. Moreover, given the different pressure responses of 0D and 2D components, these materials exhibit highly tunable electronic structures during compression, where a remarkable 11 times enhancement in PL emission is observed for SbCd at 19 GPa. This work opens new avenues for designing new layered bimetallic halides and further manipulating their structures and optoelectronic properties via pressure.

关键词： Electronic Properties Hybrid Metal Halide Perovskite Derivatives Photoluminescence Pressure

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Predicting antimicrobial activity of conjugated oligoelectrolyte molecules via machine learning

arXiv

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arXiv 2021年

作者： Tiihonen, Armi Cox-Vazquez, Sarah J. Liang, Qiaohao Ragab, Mohamed Ren, Zekun Hartono, Noor Titan Putri Liu, Zhe Sun, Shijing Zhou, Cheng Incandela, Nathan C. Limwongyut, Jakkarin Moreland, Alex S. Jayavelu, Senthilnath Bazan, Guillermo C. Buonassisi, Tonio Massachusetts Institute of Technology CambridgeMA02139 United States Departments of Chemistry and Chemical and Biomolecular Engineering National University of Singapore Singapore119077 Singapore School of Computer Science and Engineering Nanyang Technological University 50 Nanyang Avenue Singapore639798 Singapore Singapore MIT Alliance for Research and Technology #05-09 Innovation Wing 1 Create Way Singapore138602 Singapore Center for Polymers and Organic Solids Department of Chemistry and Biochemistry University of California Santa Barbara Santa BarbaraCA93106 United States Institute for Infocomm Research Artificial Intelligence Analytics And Informatics Agency for Science Technology and Research Singapore138632 Singapore Shaanxi Xi'An710072 China

New antibiotics are needed to battle growing antibiotic resistance, but the development process from hit, to lead, and ultimately to a useful drug, takes decades. Although progress in molecular property prediction using machine-learning methods has opened up new pathways for aiding the antibiotics development process, many existing solutions rely on large datasets and finding structural similarities to existing antibiotics. Challenges remain in modelling of unconventional antibiotics classes that are drawing increasing research attention. In response, we developed an antimicrobial activity prediction model for conjugated oligoelectrolyte molecules, a new class of antibiotics that lacks extensive prior structure-activity relationship studies. Our approach enables us to predict minimum inhibitory concentration for E. coli K12, with 21 molecular descriptors selected by recursive elimination from a set of 5,305 descriptors. This predictive model achieves an R2 of 0.65 with no prior knowledge of the underlying mechanism. We find the molecular representation optimum for the domain is the key to good predictions of antimicrobial activity. In the case of conjugated oligoelectrolytes, a representation reflecting the 3-dimensional shape of the molecules is most critical. Although it is demonstrated with a specific example of conjugated oligoelectrolytes, our proposed approach for creating the predictive model can be readily adapted to other novel antibiotic candidate domains. © 2021, CC BY-NC-ND.

关键词： Antibiotics

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Plasmonic bacteria on a nanoporous mirror via hydrodynamic trapping for rapid identification of waterborne pathogens

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Light(science & Applications) 2018年第1期7卷 359-367页

作者： Keumrai Whang Jong-Hwan Lee Yonghee Shin Wooju Lee Young Wan Kim Dongchoul Kim Luke P.Lee Taewook Kang Department of Chemical and Biomolecular Engineering Sogang UniversitySeoul 04107Korea Berkeley Sensor and Actuator Center Departments of BioengineeringElectrical Engineering and Computer ScienceBiophysics Graduate ProgramUniversity of CaliforniaBerkeleyBerkeleyCA 94720USA Department of Mechanical Engineering Sogang UniversitySeoul 04107Korea

A rapid,precise method for identifying waterborne pathogens is critically needed for effective disinfection and better ***,conventional methods,such as culture-based counting,generally suffer from slow detection times and low ***,we developed a rapid detection method for tracing waterborne pathogens by an innovative optofluidic platform,a plasmonic bacteria on a nanoporous mirror,that allows effective hydrodynamic cell trapping,enrichment of pathogens,and optical signal *** designed and simulated the integrated optofluidic platform to maximize the enrichment of the bacteria and to align bacteria on the nanopores and plasmonic mirror via hydrodynamic cell *** nanoparticles are self-assembled to form antenna arrays on the surface of bacteria,such as Escherichia coli and Pseudomonas aeruginosa,by replacing citrate with hydroxylamine hydrochloride in order to amplify the signal of the plasmonic optical *** to the synergistic contributions of focused light via the nanopore geometry,self-assembled nanoplasmonic optical antennas on the surface of bacteria,and plasmonic mirror,we obtain a sensitivity of detecting *** as low as 102 cells/ml via surface-enhanced Raman *** believe that our label-free strategy via an integrated optofluidic platform will pave the way for the rapid,precise identification of various pathogens.

关键词： mirror trapping precise

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