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arXiv 2018年

作者： Malik, R. Luong, T. Cao, X. Han, B. Shah, N. Han, L. Shenoy, V.B. Lelkes, P.I. Cukierman, E. Cancer Biology Program Fox Chase Cancer Center Dept. Bioengineering Temple University Materials Science and Engineering University of Pennsylvania School of Biomedical Engineering Science and Health Systems Drexel University

Pancreatic ductal adenocarcinoma (PDAC) encompasses a fibrous-like tumor-associated stroma, desmoplasia, produced by cancer-associated fibroblasts (CAFs). As desmoplasia plays dual pro- and anti-tumor roles, efforts are being made to induce its anti-tumor functions for therapeutic gain. We conducted biomechanical manipulations, using variations of pathological and physiological substrates in vitro, to culture patient-harvested CAFs and generate desmoplastic CAF-derived extracellular matrices (CDMs) that can restrict PDAC growth and invasion. We posited that extrinsic modulation of the environment, via substrate rigidity, influences CAF's cell-intrinsic forces affecting CDM production. Substrates used were polyacrylamide gels of physiological (~1.5 kPa) or pathological (~7.5 kPa) stiffnesses. Results showed that physiological substrates influenced CAFs to generate CDMs similar to normal/control fibroblasts. We found CDMs to be softer than the corresponding underlying substrates, and CDM fiber anisotropy (i.e., alignment) to be biphasic and informed via substrate-imparted morphological CAF aspect ratios. Further, the biphasic nature of CDM fiber anisotropy was mathematically modeled and postulated a correlation between CAF aspect ratios and CDM alignment;regulated by extrinsic and intrinsic forces to conserve minimal free energy. Biomechanical manipulation of CDMs, generated on physiological stiffness substrates, lead to reduction in nuclear translocation of pERK1/2 in KRAS-driven PDAC. Specifically, ERK2 was essential for CDM-regulated tumor cell invasion. In vitro findings were validated in vivo, where nuclear pERK1/2 was found significantly higher in human PDAC samples compared to matching normal pancreata. The study suggests that altering underlying substrates enables CAFs to remodel CDMs and restricts KRAS-driven PDAC invasion in an ERK2 dependent manner. Copyright © 2018, The Authors. All rights reserved.

关键词： Diseases

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Considering discrepancy when calibrating a mechanistic electrophysiology model

arXiv

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arXiv 2020年

作者： Lei, Chon Lok Ghosh, Sanmitra Whittaker, Dominic G. Aboelkassem, Yasser Beattie, Kylie A. Cantwell, Chris D. Delhaas, Tammo Houston, Charles Novaes, Gustavo Montes Panfilov, Alexander V. Pathmanathan, Pras Riabiz, Marina Weber dos Santos, Rodrigo Worden, Keith Mirams, Gary R. Wilkinson, Richard D. Computational Biology & Health Informatics Dept. of Computer Science University of Oxford United Kingdom MRC Biostatistics Unit University of Cambridge United Kingdom Centre for Mathematical Medicine & Biology School of Mathematical Sciences University of Nottingham United Kingdom Department of Bioengineering University of California San Diego United States Systems Modeling and Translational Biology GlaxoSmithKline R&D Stevenage United Kingdom ElectroCardioMaths Programme Centre for Cardiac Engineering Imperial College London United Kingdom CARIM School for Cardiovascular Diseases Maastricht University Netherlands Graduate Program in Computational Modeling Universidade Federal de Juiz de Fora Brazil Department of Physics and Astronomy Ghent University Belgium Laboratory of Computational Biology and Medicine Ural Federal University Ekaterinburg Russia U.S. Food and Drug Administration Center for Devices and Radiological Health Office of Science and Engineering Laboratories United States Department of Biomedical Engineering King’s College London Alan Turing Institute United Kingdom Dynamics Research Group Department of Mechanical Engineering University of Sheffield United Kingdom School of Mathematics and Statistics University of Sheffield United Kingdom

Uncertainty quantification (UQ) is a vital step in using mathematical models and simulations to take decisions. The field of cardiac simulation has begun to explore and adopt UQ methods to characterise uncertainty in model inputs and how that propagates through to outputs or predictions. In this perspective piece we draw attention to an important and under-addressed source of uncertainty in our predictions — that of uncertainty in the model structure or the equations themselves. The difference between imperfect models and reality is termed model discrepancy, and we are often uncertain as to the size and consequences of this discrepancy. Here we provide two examples of the consequences of discrepancy when calibrating models at the ion channel and action potential scales. Furthermore, we attempt to account for this discrepancy when calibrating and validating an ion channel model using different methods, based on modelling the discrepancy using Gaussian processes (GPs) and autoregressive-moving-average (ARMA) models, then highlight the advantages and shortcomings of each approach. Finally, suggestions and lines of enquiry for future work are provided. Copyright © 2020, The Authors. All rights reserved.

关键词： Uncertainty analysis

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Revealing the Side-Chain-Dependent Ordering Transition of Highly Crystalline Double-Cable Conjugated Polymers

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Angewandte Chemie 2021年第48期133卷

作者： Guitao Feng Wenliang Tan Safakath Karuthedath Cheng Li Xuechen Jiao Amelia C. Y. Liu Hariprasad Venugopal Zheng Tang Long Ye Frédéric Laquai Christopher R. McNeill Weiwei Li Beijing Advanced Innovation Center for Soft Matter Science and Engineering & State Key Laboratory of Organic-Inorganic Composites Beijing University of Chemical Technology Beijing 100029 China Beijing National Laboratory for Molecular Sciences Key Laboratory of Organic Solids Institute of Chemistry Chinese Academy of Sciences Beijing 100190 P. R. China Department of Materials Science and Engineering Monash University Wellington Road Clayton Victoria 3800 Australia King Abdullah University of Science and Technology (KAUST) KAUST Solar Center (KSC) Physical Sciences and Engineering Division (PSE) Material Science and Engineering Program (MSE) Thuwal 23955-6900 Kingdom of Saudi Arabia School of Physics and Astronomy Monash University Wellington Road Clayton Victoria 3800 Australia Ramaciotti Centre for Cryo-Electron Microscopy Monash University Clayton Victoria 3800 Australia Center for Advanced Low-dimension Materials College of Materials Science and Engineering Donghua University Shanghai 201620 P. R. China School of Materials Science and Engineering Tianjin Key Laboratory of Molecular Optoelectronic Science Tianjin University Tianjin 300350 P. R. China

We developed a series of highly crystalline double-cable conjugated polymers for application in single-component organic solar cells (SCOSCs). These polymers contain conjugated backbones as electron donor and pendant perylene bisimide units (PBIs) as electron acceptor. PBIs are connected to the backbone via alkyl units varying from hexyl (C 6 H 12 ) to eicosyl (C 20 H 40 ) as flexible linkers. For double-cable polymers with short linkers, the PBIs tend to stack in a head-to-head fashion, resulting in large d -spacings (e.g. 64 Å for the polymer P12 with C 12 H 24 linker) along the lamellar stacking direction. When the length of the linker groups is longer than a certain length, the PBIs instead adopt a more ordered packing likely via H -aggregation, resulting in short d -spacings (e.g. 50 Å for the polymer P16 with C 16 H 32 linker). This work highlights the importance of linker length on the molecular packing of the acceptor units and the influences on the photovoltaic performance of SCOSCs.

关键词： cryo-transmission electron microscopy double-cable conjugated polymers lamellar stacking single-component organic solar cells

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The control of brain network dynamics across diverse scales of space and time

arXiv

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arXiv 2019年

作者： Tang, Evelyn Baum, Graham L. Roalf, David R. Satterthwaite, Theodore D. Pasqualetti, Fabio Bassett, Danielle S. Department of Bioengineering School of Engineering & Applied Science University of Pennsylvania PA19104 United States Max Planck Institute for Dynamics and Self-Organization Göttingen37079 Germany Neuroscience Graduate Program Perelman School of Medicine University of Pennsylvania PA19104 United States Department of Psychiatry Perelman School of Medicine University of Pennsylvania PA19104 United States Department of Mechanical Engineering University of California Riverside RiversideCA92521 United States Department of Physics & Astronomy College of Arts & Sciences University of Pennsylvania PA19104 United States Department of Electrical & Systems Engineering School of Engineering & Applied Science University of Pennsylvania PA19104 United States Department of Neurology Perelman School of Medicine University of Pennsylvania PA19104 United States

The human brain is composed of distinct regions that are each associated with particular functions and distinct propensities for the control of neural dynamics. However, the relation between these functions and control profiles is poorly understood, as is the variation in this relation across diverse scales of space and time. Here we probe the relation between control and dynamics in brain networks constructed from diffusion tensor imaging data in a large community based sample of young adults. Specifically, we probe the control properties of each brain region and investigate their relationship with dynamics across various spatial scales using the Laplacian eigenspectrum. In addition, through analysis of regional modal controllability and partitioning of modes, we determine whether the associated dynamics are fast or slow, as well as whether they are alternating or monotone. We find that brain regions that facilitate the control of energetically easy transitions are associated with activity on short length scales and slow time scales. Conversely, brain regions that facilitate control of difficult transitions are associated with activity on long length scales and fast time scales. Built on linear dynamical models, our results offer parsimonious explanations for the activity propagation and network control profiles supported by regions of differing neuroanatomical structure. Copyright © 2019, The Authors. All rights reserved.

关键词： Brain

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WE-184. From “irritative zone” to “irritative network”: a novel interictal estimate of the epileptogenic zone using invasive EEG

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Clinical Neurophysiology 2022年 141卷 S86-S86页

作者： Pesce, Matthew Billardello, Roberto Pace, Lavinia Madsen, Joseph Pearl, Phillip Papadelis, Christos Grant, Ellen Tamilia, Eleonora Fetal-Neonatal Neuroimaging and Developmental Science Center Boston Children's Hospital Boston USA Research Unit of Advanced Robotics and Human-Centered Technologies Department of Engineering University Bio-Medico Campus of Rome Rome Italy Epilepsy Surgery Program Department of Neurosurgery Boston Children’s Hospital Boston USA Harvard Medical School Boston USA Division of Epilepsy and Clinical Neurophysiology Department of Neurology Boston Children’s Hospital Boston USA Jane and John Justin Neurosciences Center Cook Children’s Health Care System Fort Worth USA Department of Bioengineering University of Texas at Arlington Arlington USA Fetal-Neonatal Neuroimaging and Developmental Science Center Boston Children’s Hospital Boston USA

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Magnetic Control of Soft Chiral Phonons in PbTe

arXiv

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arXiv 2021年

作者： Baydin, Andrey Hernandez, Felix G.G. Rodriguez-Vega, Martin Okazaki, Anderson K. Tay, Fuyang Timothy Noe, G. Katayama, Ikufumi Takeda, Jun Nojiri, Hiroyuki Rappl, Paulo H.O. Abramof, Eduardo Fiete, Gregory A. Kono, Junichiro Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Smalley-Curl Institute Rice University HoustonTX77005 United States Instituto de Física Universidade de São Paulo SP São Paulo05508-090 Brazil Theoretical Division Los Alamos National Laboratory Los AlamosNM87545 United States Laboratório Associado de Sensores e Materiais Instituto Nacional de Pesquisas Espaciais SP São José dos Campos12201-970 Brazil Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Physics Graduate School of Engineering Science Yokohama National University Yokohama240-8501 Japan Institute for Materials Research Tohoku University Sendai980-8577 Japan Department of Physics Northeastern University BostonMA02115 United States Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics and Astronomy Rice University HoustonTX77005 United States Department of Material Science and NanoEngineering Rice University HoustonTX77005 United States

PbTe crystals have a soft transverse optical phonon mode in the terahertz frequency range, which is known to efficiently decay into heat-carrying acoustic phonons, resulting in anomalously low thermal conductivity. Here, we studied this phonon via polarization-dependent terahertz spectroscopy. We observed softening of this mode with decreasing temperature, indicative of incipient ferroelectricity, which we explain through a model including strong anharmonicity with a quartic displacement term. In magnetic fields up to 25 T, the phonon mode splits into two modes with opposite handedness, exhibiting circular dichroism. Their frequencies display Zeeman splitting together with an overall diamagnetic shift with increasing magnetic field. Using a group-theoretical approach, we demonstrate that these observations are the result of magnetic field-induced morphic changes in the crystal symmetries through the Lorentz force exerted on the lattice ions. Thus, our study reveals a novel process of controlling phonon properties in a soft ionic lattice by a strong magnetic field. Copyright © 2021, The Authors. All rights reserved.

关键词： Magnetic fields

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Lithium-Ion Batteries: Operando Magnetometry Probing the Charge Storage Mechanism of CoO Lithium-Ion Batteries (Adv. Mater. 12/2021)

引用

Advanced materials 2021年第12期33卷

作者： Hongsen Li Zhengqiang Hu Qingtao Xia Hao Zhang Zhaohui Li Huaizhi Wang Xiangkun Li Fengkai Zuo Fengling Zhang Xiaoxiong Wang Wanneng Ye Qinghao Li Yunze Long Qiang Li Shishen Yan Xiaosong Liu Xiaogang Zhang Guihua Yu Guo-Xing Miao College of Physics Center for Marine Observation and Communications Qingdao University Qingdao 266071 China School of Physics State Key Laboratory of Crystal Materials Shandong University Jinan 250100 China State Key Laboratory of Functional Materials for Informatics Shanghai Institute of Microsystem and Information Technology (SIMIT) Chinese Academy of Sciences Shanghai 200050 China College of Material Science and Engineering Nanjing University of Aeronautics and Astronautics Nanjing 210016 China Materials Science and Engineering Program and Department of Mechanical Engineering The University of Texas at Austin Austin TX 78712 USA Department of Electrical and Computer Engineering & Institute for Quantum Computing University of Waterloo Waterloo ON N2L 3G1 Canada

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Neuroprosthetics: Durable and Fatigue-Resistant Soft Peripheral Neuroprosthetics for In Vivo Bidirectional Signaling (Adv. Mater. 20/2021)

引用

Advanced materials 2021年第20期33卷

作者： Hyunseon Seo Sang Ihn Han Kang-Il Song Duhwan Seong Kyungwoo Lee Sun Hong Kim Taesung Park Ja Hoon Koo Mikyung Shin Hyoung Won Baac Ok Kyu Park Soong Ju Oh Hyung-Seop Han Hojeong Jeon Yu-Chan Kim Dae-Hyeong Kim Taeghwan Hyeon Donghee Son School of Medicine Sungkyunkwan University Suwon 16419 Republic of Korea Center for Biomaterials Biomedical Research Institute Korea Institute of Science and Technology Seoul 02792 Republic of Korea Center for Nanoparticle Research Institute of Basic Science (IBS) Seoul 08826 Republic of Korea School of Chemical and Biological Engineering Seoul National University Seoul 08826 Republic of Korea Medical Device Development Center Daegu-Gyeongbuk Medical Innovation Foundation Daegu 41061 Republic of Korea Department of Electrical and Computer Engineering Sungkyunkwan University Suwon 16419 Republic of Korea Department of Electrical and Computer Engineering Inter-University Semiconductor Research Center Seoul National University Seoul 08826 Republic of Korea Department of Materials Science and Engineering Korea University Seoul 02841 Republic of Korea Interdisciplinary Program for Bioengineering Seoul National University Seoul 08826 Republic of Korea Department of Biomedical Engineering SKKU Institute for Convergence Sungkyunkwan University Suwon 16419 Republic of Korea Center for Neuroscience Imaging Research Institute for Basic Science (IBS) Suwon 16419 Republic of Korea Department of Superintelligence Engineering Sungkyunkwan University Suwon 16419 Republic of Korea

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OPTIMADE, an API for exchanging materials data

arXiv

引用

arXiv 2021年

作者： Andersen, Casper W. Armiento, Rickard Blokhin, Evgeny Conduit, Gareth J. Dwaraknath, Shyam Evans, Matthew L. Fekete, Ádám Gopakumar, Abhijith Gražulis, Saulius Merkys, Andrius Mohamed, Fawzi Oses, Corey Pizzi, Giovanni Rignanese, Gian-Marco Scheidgen, Markus Talirz, Leopold Toher, Cormac Winston, Donald Aversa, Rossella Choudhary, Kamal Colinet, Pauline Curtarolo, Stefano Di Stefano, Davide Draxl, Claudia Er, Suleyman Esters, Marco Fornari, Marco Giantomassi, Matteo Govoni, Marco Hautier, Geoffroy Hegde, Vinay Horton, Matthew K. Huck, Patrick Huhs, Georg Hummelshøj, Jens Kariryaa, Ankit Kozinsky, Boris Kumbhar, Snehal Liu, Mohan Marzari, Nicola Morris, Andrew J. Mostofi, Arash A. Persson, Kristin A. Petretto, Guido Purcell, Thomas Ricci, Francesco Rose, Frisco Scheffler, Matthias Speckhard, Daniel Uhrin, Martin Vaitkus, Antanas Villars, Pierre Waroquiers, David Wolverton, Chris Wu, Michael Yang, Xiaoyu École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Materials Design and Informatics Unit Department of Physics Chemistry and Biology Linköping University Sweden Tilde Materials Informatics Straßmannstraße 25 Berlin10249 Germany Materials Platform for Data Science Sepapaja 6 Tallinn15551 Estonia Theory of Condensed Matter Group Cavendish Laboratory 19 J.J. Thomson Avenue CambridgeCB3 0HE United Kingdom Lawrence Berkeley Labs BerkeleyCA United States Chemin des Étoiles 8 Louvain-la-Neuve1348 Belgium Department of Physics King's College London London United Kingdom Department of Materials Science and Engineering Northwestern University EvanstonIL60208 United States Institute of Biotechnology Life Science Center Vilnius University Saulétekio av. 7 VilniusLT-10257 Lithuania Institute of Computer Science Faculty of Mathematics and Informatics Vilnius University Naugarduko g. 24 VilniusLT-03225 Lithuania Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 Berlin14195 Germany Center for Autonomous Materials Design Duke University DurhamNC27708 United States Department of Mechanical Engineering and Materials Science Duke University DurhamNC27708 United States Humboldt-Universität zu Berlin Institut für Physik and IRIS Adlershof Berlin12489 Germany École Polytechnique Fédérale de Lausanne Sion1951 Switzerland Trieste34136 Italy Hermann-von-Helmholtz-Platz 1 Eggenstein-Leopoldshafen76344 Germany Materials Measurement Laboratory National Institute of Standards and Technology GaithersburgMD20899 United States Ansys 300 Rustat House 62 Clifton Rd CambridgeCB1 7EG United Kingdom De Zaale 20 Eindhoven5612 AJ Netherlands Department of Physics and Science of Advanced Materials Program Central Michigan University Mount PleasantMI48859 United States Argonne National Laboratory LemontIL60439 United States Thayer School of Engineering Dartmouth College HanoverNH03755 United States Los AltosCA940

The Open Databases Integration for materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification. © 2021, CC BY.

关键词： Specifications

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First-principles study of the effect of compressive strain on oxygen adsorption in Pd/Ni/Cu-alloy-core@Pd/Ir-alloy-shell catalysts

arXiv

引用

arXiv 2019年

作者： De Lile, Jeffrey Roshan Lee, So Young Kim, Hyoung-Juhn Pak, Chanho Lee, Seung Geol Department of Organic Material Science and Engineering Pusan National University 2 Busandaehak-ro 63beon-gil Geumjeong-gu Busan46241 Korea Republic of Fuel Cell Research Center Korea Institute of Science and Technology Hwarang-ro 14-gil 5 Seongbuk-gu Seoul02792 Korea Republic of Graduate Program of Energy Technology School of Integrated Technology Institute of Integrated Technology Gwangju Institute of Science and technology 123 Cheomdangwagi-ro Buk-gu Gwangju61005 Korea Republic of

A palladium-based (Pd-based) core@shell catalyst can be modified to achieve the desired oxygen adsorption properties by selecting an appropriate core composition, surface alloying, and compressive strain. Herein, we present the effects of compressive strain, core composition, and surface alloying in Pd3Ni@PdIr(111), Pd3CuNi@PdIr(111), and Pd3Cu@PdIr(111) alloy-core@alloy-shell catalysts on dioxygen adsorption. Using experimental lattice parameters for the unstrained catalysts,-1% to-5%, strain was systematically introduced. The calculated dioxygen-adsorption energies for the surface Pd and surface Ir atoms reveal that the Pd3CuNi@PdIr catalyst has the lowest dioxygen-adsorption energy at a given compressive strain. Bader charge calculations show that the Pd3CuNi@PdIr catalyst surface is the most charge depleted. The d-band model displays an intermediate d-band center downshift for the surface Pd atoms, and the highest downshift for the surface Ir atoms. Due to synergism between charge depletion, the d-band center shift, and the surface alloy effect, the Pd3CuNi@PdIr catalyst has the lowest dioxygen-adsorption energy. The relationship between the experimentally obtained catalyst-surface mass activity and the theoretically calculated d-band center of the surface Pd and the surface Ir is volcano shaped, with the Pd3CuNi@PdIr catalyst at the apex of the volcano. The catalytic activities of these catalysts were observed to follow the order: Pd3CuNi@PdIr >Pd3Cu@PdIr >Pd3Ni@PdIr. This work sheds light on the importance of ligand and strain effects, as well as surface alloying for the fine-tuning of alloy-core@alloy-shell-catalysts during the rational design of catalysts from first principles. Copyright © 2019, The Authors. All rights reserved.

关键词： Electronic structure

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