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Topological carnival: electrically-powered motions of toron crystallites in chiral liquid crystals

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arXiv 2020年

作者： Sohn, Hayley R.O. Smalyukh, Ivan I. Department of Physics and Materials Science and Engineering Program University of Colorado BoulderCO80309 United States Department of Electrical Computer and Energy Engineering and Soft Materials Research Center University of Colorado BoulderCO80309 United States Renewable and Sustainable Energy Institute National Renewable Energy Laboratory University of Colorado BoulderCO80309 United States

Malleability of metals is an example of how dynamics of defects like dislocations induced by external stresses alters material properties and enables technological applications. However, these defects move merely to comply with the mechanical forces applied on macroscopic scales whereas the molecular and atomic building blocks behave like rigid particles. Here we demonstrate how motions of crystallites and defects between them can arise within the soft matter medium in an oscillating electric field applied to a chiral liquid crystal with polycrystalline quasi-hexagonal arrangements of self-assembled topological solitons called "torons". Periodic oscillations of electric field applied perpendicular to the plane of hexagonal lattices prompt repetitive shear-like deformations of the solitons, which synchronize the electrically-powered self-shearing directions. The temporal evolution of deformations upon turning voltage on and off is not invariant upon reversal of time, prompting lateral translations of the crystallites of torons within quasi-hexagonal periodically deformed lattices. We probe how these motions depend on voltage and frequency of oscillating field applied in an experimental geometry resembling that of liquid crystal displays. We study the inter-relations between synchronized deformations of the soft solitonic particles and their arrays and the ensuing dynamics and giant number fluctuations mediated by motions of crystallites, 5-7 defects pairs and grain boundaries in the orderly organizations of solitons. We discuss how our findings may lead to technological and fundamental science applications of dynamic self-assemblies of topologically protected but highly deformable particle-like solitons. Copyright © 2020, The Authors. All rights reserved.

关键词： Self assembly

Extracellular Matrix regulates the morphodynamics of 3D migrating cancer cells

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arXiv 2020年

作者： Eddy, Christopher Z. Raposo, Helena Manchanda, Aayushi Wong, Ryan Li, Fuxin Sun, Bo Department of Physics Oregon State University CorvallisOR97331 United States Department of Chemical Biological and Environmental Engineering Oregon State University CorvallisOR97331 United States Molecular and Cellular Biology Program Oregon State University CorvallisOR97331 United States School of Electrical Engineering and Computer Science Oregon State University CorvallisOR97331 United States

Cell shape is linked to cell function. The significance of cell morphodynamics, namely the temporal fluctuation of cell shape, is much less understood. Here we study the morphodynamics of MDA-MB-231 cells in type I collagen extracellular matrix (ECM). We systematically vary ECM physical properties by tuning collagen concentrations, alignment, and gelation temperatures. We find that morphodynamics of 3D migrating cells are externally controlled by ECM mechanics and internally modulated by Rho/ROCK-signaling. We employ machine learning to classify cell shape into four different morphological phenotypes, each corresponding to a distinct migration mode. As a result, we map cell morphodynamics at mesoscale into the temporal evolution of morphological phenotypes. We characterize the mesoscale dynamics including occurrence probability, dwell time and transition matrix at varying ECM conditions, which demonstrate the complex phenotype landscape and optimal pathways for phenotype transitions. In light of the mesoscale dynamics, we show that 3D cancer cell motility is a hidden Markov process whereby the step size distributions of cell migration are coupled with simultaneous cell morphodynamics. Morphological phenotype transitions also facilitate cancer cells to navigate non-uniform ECM such as traversing the interface between matrices of two distinct microstructures. In conclusion, we demonstrate that 3D migrating cancer cells exhibit rich morphodynamics that is controlled by ECM mechanics, Rho/ROCK-signaling, and regulate cell motility. Our results pave the way to the functional understanding and mechanical programming of cell morphodynamics as a route to predict and control 3D cell motility. Copyright © 2020, The Authors. All rights reserved.

关键词： Cells

Enhanced meta-displays using advanced phase-change materials

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arXiv 2021年

作者： Hemmatyar, Omid Abdollahramezani, Sajjad Zeimpekis, Ioannis Lepeshov, Sergey Krasnok, Alex Khan, Asir Intisar Neilson, Kathryn M. Teichrib, Christian Brown, Tyler Pop, Eric Hewak, Daniel W. Wuttig, Matthias Alù, Andrea Muskens, Otto L. Adibi, Ali School of Electrical and Computer Engineering Georgia Institute of Technology 778 Atlantic Drive NW AtlantaGA30332-0250 United States Zepler Institute Faculty of Engineering and Physical Sciences University of Southampton SouthamptonSO17 1BJ United Kingdom ITMO University St. Petersburg197101 Russia Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States Department of Electrical Engineering Department of Materials Science and Engineering Precourt Institute for Energy Stanford University StanfordCA94305 United States Physikalisches Institut IA RWTH Aachen Sommerfeldstrasse 14 Aachen52074 Germany Physics Program Graduate Center City University of New York New YorkNY10016 United States Physics and Astronomy Faculty of Engineering and Physical Sciences University of Southampton SouthamptonSO17 1BJ United Kingdom

Structural colors generated due to light scattering from static all-dielectric metasurfaces have successfully enabled high-resolution, high-saturation, and wide-gamut color printing applications. Despite recent advances, most demonstrations of these structure-dependent colors lack post-fabrication tunability. This hinders their applicability for front-end dynamic display technologies. Phase-change materials (PCMs), with significant contrast of their optical properties between their amorphous and crystalline states, have demonstrated promising potentials in reconfigurable nanophotonics. Herein, we leverage tunable all-dielectric reflective metasurfaces made of newly emerged classes of low-loss optical PCMs, i.e., antimony trisulphide (Sb2S3) and antimony triselenide (Sb2Se3), with superb characteristics to realize switchable, high-saturation, high-efficiency and high-resolution dynamic meta-pixels. Exploiting polarization-sensitive building blocks, the presented meta-pixel can generate two different colors when illuminated by either one of two orthogonally polarized incident beams. Such degrees of freedom (i.e., material phase and polarization state) enable a single reconfigurable metasurface with fixed geometrical parameters to generate four distinct wide-gamut colors. We experimentally demonstrate, for the first time, an electrically-driven micro-scale display through the integration of phase-change metasurfaces with an on-chip heater formed by transparent conductive oxide. Our experimental findings enable a versatile platform suitable for a wide range of applications, including tunable full-color printing, enhanced dynamic displays, information encryption, and anti-counterfeiting. © 2021, CC BY.

关键词： Light scattering

Elastic colloidal monopoles and reconfigurable self-assembly in liquid crystals

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arXiv 2020年

作者： Yuan, Ye Liu, Qingkun Senyuk, Bohdan Smalyukh, Ivan I. Department of Physics University of Colorado BoulderCO80309 United States Department of Electrical Computer and Energy Engineering Materials Science and Engineering Program and Soft Materials Research Center University of Colorado BoulderCO80309 United States Renewable and Sustainable Energy Institute National Renewable Energy Laboratory University of Colorado BoulderCO80309 United States

Monopole-like electrostatic interactions are ubiquitous in biology1 and condensed matter2-4, but they are often screened by counter-ions and cannot be switched from attractive to repulsive. In colloidal science, where the prime goal is to develop colloidal particles2,3 that mimic and exceed the diversity and length-scales of atomic and molecular assembly, electrostatically charged particles cannot change the sign of their surface charge or transform from monopoles to higher-order multipoles4. In liquid-crystal colloids5-7, elastic interactions between particles arise to minimize the free energy associated with elastic distortions in the long-range alignment of rod-like molecules around the particles5. In dipolar6,8, quadrupolar8-12 and hexadecapolar13 nematic colloids, the symmetries of such elastic distortions mimic both electrostatic multipoles14 and the outmost occupied electron shells of atoms7,15,16. Electric and magnetic switching17,18, spontaneous transformations19 and optical control20 of elastic multipoles, as well as their interactions with topological defects and surface boundary conditions, have been demonstrated in such colloids21-23. However, it has long been understood5,24 that elastic monopoles should relax to uniform or higher-order multipole states because of the elastic torques that they induce5,7. Here we develop nematic colloids with strong elastic monopole moments and with elastic torques balanced by optical torques exerted by ambient light. We demonstrate the monopole-to-quadrupole reconfiguration of these colloidal particles by unstructured light, which resembles the driving of atoms between the ground state and various excited states. We show that the sign of the elastic monopoles can be switched, and that like-charged monopoles attract whereas oppositely charged ones repel, unlike in electrostatics14. We also demonstrate the out-of-equilibrium dynamic assembly of these colloidal particles. This diverse and surprising behaviour is explained

关键词： Electrostatics

Some Remarks on Robust Gene Regulation in a Biomolecular Integral Controller

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Some Remarks on Robust Gene Regulation in a Biomolecular Int...

IEEE Annual Conference on Decision and Control

作者： Deepak K. Agrawal Ryan Marshall M. Ali Al-Radhawi Vincent Noireaux Eduardo D Sontag Department of Bioengineering and Department of Electrical and Computer Engineering Northeastern University Boston MA USA School of Physics and Astronomy University of Minnesota Minneapolis MN USA Laboratory of Systems Pharmacology Program in Therapeutic Science Harvard Medical School Boston MA USA

ISBN: (数字)9781728113982

ISBN: (纸本)9781728113999

Integral feedback can help achieve robust tracking independently of external disturbances. Motivated by this knowledge, biological engineers have proposed various designs of biomolecular integral feedback controllers to regulate biological processes. In this paper, we theoretically analyze the operation of a particular synthetic biomolecular integral controller, which we have recently proposed and implemented experimentally. Using a combination of methods, ranging from linearized analysis to sum-of-squares (SOS) Lyapunov functions, we demonstrate that, when the controller is operated in closed-loop, it is capable of providing integral corrections to the concentration of an output species in such a manner that the output tracks a reference signal linearly over a large dynamic range. We investigate the output dependency on the reaction parameters through sensitivity analysis, and quantify performance using control theory metrics to characterize response properties, thus providing clear selection guidelines for practical applications. We then demonstrate the stable operation of the closed-loop control system by constructing quartic Lyapunov functions using SOS optimization techniques, and establish global stability for a unique equilibrium. Our analysis suggests that by incorporating effective molecular sequestration, a biomolecular closed-loop integral controller that is capable of robustly regulating gene expression is feasible.

关键词： Steady-state Robustness Mathematical model Proteins Gene expression Kinetic theory Production

Rewriting regulatory DNA to dissect and reprogram gene expression

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Cell 2025年第12期188卷 3349-3366.e23,26页

作者： Martyn, Gabriella E. Montgomery, Michael T. Jones, Hank Guo, Katherine Doughty, Benjamin R. Linder, Johannes Bisht, Deepa Xia, Fan Cai, Xiangmeng S. Chen, Ziwei Cochran, Kelly Lawrence, Kathryn A. Munson, Glen Pampari, Anusri Fulco, Charles P. Sahni, Nidhi Kelley, David R. Lander, Eric S. Kundaje, Anshul Engreitz, Jesse M. Department of Genetics Stanford University School of Medicine Stanford 94305 CA United States Basic Science and Engineering Initiative Stanford Children's Health Betty Irene Moore Children's Heart Center Stanford 94305 CA United States Calico Life Sciences LLC South San Francisco 94080 CA United States Department of Genitourinary Medical Oncology Division of Cancer Medicine The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Department of Genomic Medicine The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Houston 77230 TX United States Department of Bioengineering Stanford University Stanford 94305 CA United States Department of Computer Science Stanford University Stanford 94305 CA United States Novo Nordisk Foundation Center for Genomic Mechanisms of Disease Broad Institute of MIT and Harvard Cambridge 02142 MA United States Gene Regulation Observatory Broad Institute of MIT and Harvard Cambridge 02142 MA United States Broad Institute of MIT and Harvard Cambridge 02142 MA United States Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston 77230 TX United States Quantitative and Computational Biosciences Program Baylor College of Medicine Houston 77030 TX United States Department of Biology MIT Cambridge 02139 MA United States Department of Systems Biology Harvard Medical School Boston 02115 MA United States Stanford Cardiovascular Institute Stanford University Stanford 94305 CA United States

Regulatory DNA provides a platform for transcription factor binding to encode cell-type-specific patterns of gene expression. However, the effects and programmability of regulatory DNA sequences remain difficult to map or predict. Here, we develop variant effects from flow-sorting experiments with CRISPR targeting screens (Variant-EFFECTS) to introduce hundreds of designed edits to endogenous regulatory DNA and quantify their effects on gene expression. We systematically dissect and reprogram 3 regulatory elements for 2 genes in 2 cell types. These data reveal endogenous binding sites with effects specific to genomic context, transcription factor motifs with cell-type-specific activities, and limitations of computational models for predicting the effect sizes of variants. We identify small edits that can tune gene expression over a large dynamic range, suggesting new possibilities for prime-editing-based therapeutics targeting regulatory DNA. Variant-EFFECTS provides a generalizable tool to dissect regulatory DNA and to identify genome editing reagents that tune gene expression in an endogenous context. © 2025 Elsevier Inc.

关键词： CRISPR enhancers gene regulation high-throughput screening non-coding variants predictive models prime editing RNA FlowFISH sequence design transcription factors

Emergent Dimer-Model Topological Order and Quasiparticle Excitations in Liquid Crystals: Combinatorial Vortex Lattices

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Physical Review X 2025年第2期15卷 021084-021084页

作者： Cuiling Meng Jin-Sheng Wu Žiga Kos Jörn Dunkel Cristiano Nisoli Ivan I. Smalyukh Department of Physics and Chemical Physics Program University of Colorado Boulder Colorado 80309 USA International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM) Hiroshima University Higashihiroshima Hiroshima Japan Department of Mathematics Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA Faculty of Mathematics and Physics University of Ljubljana Ljubljana Slovenia Department of Condensed Matter Physics Jožef Stefan Institute Ljubljana Slovenia Theoretical Division Physics of Condensed Matter and Complex Systems and Center For Nonlinear Studies Los Alamos National Laboratory Los Alamos New Mexico 87545 USA Department of Electrical Computer and Energy Engineering Materials Science and Engineering Program University of Colorado Boulder Colorado 80309 USA Renewable and Sustainable Energy Institute National Renewable Energy Laboratory University of Colorado Boulder Colorado 80309 USA

Liquid crystals have proven to provide a versatile experimental and theoretical platform for studying topological objects such as vortices, skyrmions, and hopfions. In parallel, in hard condensed matter physics, the concept of topological phases and topological order has been introduced in the context of spin liquids to investigate emergent phenomena like quantum Hall effects and high-temperature superconductivity. Here, we bridge these two seemingly disparate perspectives on topology in physics. Combining experiments and simulations, we show how topological defects in liquid crystals can be used as versatile building blocks to create complex, highly degenerate topological phases, which we refer to as “combinatorial vortex lattices” (CVLs). CVLs exhibit extensive residual entropy and support locally stable quasiparticle excitations in the form of charge-conserving topological monopoles, which can act as mobile information carriers and be linked via Dirac strings. CVLs can be rewritten and reconfigured on demand, endowed with various symmetries, and modified through laser-induced topological surgery—an essential capability for information storage and retrieval. We demonstrate experimentally the realization, stability, and precise optical manipulation of CVLs, thus opening new avenues for understanding and technologically exploiting higher-hierarchy topology in liquid crystals and other ordered media.

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Silica nanocone array as a template for fabricating a plasmon induced hot electron photodetector

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Photonics Research 2019年第3期7卷 294-299页

作者： ZHIQIANG YANG KANG DU FANFAN LU YANG PANG SHIJIA HUA XUETAO GAN WENDING ZHANG SOO JIN CHUA TING MEI Key Laboratory of Space Applied Physics and Chemistry Ministry of Education and Shaanxi Key Laboratory of Optical Information TechnologySchool of Science Northwestern Polytechnical University Department of Electrical and Computer Engineering National University of Singapore LEES Program Singapore-MIT Alliance for Research & Technology (SMART)

Plasmon induced hot electrons have attracted a great deal of interest as a novel route for photodetection and lightenergy harvesting. Herein, we report a hot electron photodetector in which a large array of nanocones deposited sequentially with aluminum, titanium dioxide, and gold films can be integrated functionally with nanophotonics and microelectronics. The device exhibits a strong photoelectric response at around 620 nm with a responsivity of 180 μA/W under short-circuit conditions with a significant increase under 1 V reverse bias to 360 μA/W. The increase in responsivity and a red shift in the peak value with increasing bias voltage indicate that the bias causes an increase in the hot electron tunneling effect. Our approach will be advantageous for the implementation of the proposed architecture on a vast variety of integrated optoelectronic devices.

关键词： Silica nanocone array plasmon induced hot electron photodetector

OpenKBP-Opt: An international and reproducible evaluation of 76 knowledge-based planning pipelines

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arXiv 2022年

作者： Babier, Aaron Mahmood, Rafid Zhang, Binghao Alves, Victor G.L. Barragán-Montero, Ana Maria Beaudry, Joel Cardenas, Carlos E. Chang, Yankui Chen, Zijie Chun, Jaehee Diaz, Kelly Eraso, Harold David Faustmann, Erik Gaj, Sibaji Gay, Skylar Gronberg, Mary Guo, Bingqi He, Junjun Heilemann, Gerd Hira, Sanchit Huang, Yuliang Ji, Fuxin Jiang, Dashan Giraldo, Jean Carlo Jimenez Lee, Hoyeon Lian, Jun Liu, Shuolin Liu, Keng-Chi Marrugo, José Miki, Kentaro Nakamura, Kunio Netherton, Tucker Nguyen, Dan Nourzadeh, Hamidreza Osman, Alexander F.I. Peng, Zhao Muñoz, José Darío Quinto Ramsl, Christian Rhee, Dong Joo Rodriguez, Juan David Shan, Hongming Siebers, Jeffrey V. Soomro, Mumtaz H. Sun, Kay Hoyos, Andrés Usuga Valderrama, Carlos Verbeek, Rob Wang, Enpei Willems, Siri Wu, Qi Xu, Xuanang Yang, Sen Yuan, Lulin Zhu, Simeng Zimmermann, Lukas Moore, Kevin L. Purdie, Thomas G. McNiven, Andrea L. Chan, Timothy C.Y. Department Of Mechanical And Industrial Engineering University Of Toronto TorontoON Canada Vector Institute TorontoON Canada Department Of Radiation Oncology University Of Virginia Health System CharlottesvilleVA United States Department Of Molecular Imaging Radiation Oncology UCLouvain Louvain-la-Neuve Belgium Department Of Radiation Oncology Memorial Sloan Kettering Cancer Center New YorkNY United States Department Of Radiation Oncology The University Of Alabama At Birmingham BirminghamAL United States Department Of Engineering And Applied Physics University Of Science And Technology Of China Hefei China Shenying Medical Technology Co. Ltd. Guangdong Shenzhen China Department Of Radiation Oncology Yonsei University Seoul Korea Republic of Department Of Physics National University Of Colombia Medellín Colombia Atominstitut Vienna University Of Technology Vienna Austria Department Of Biomedical Engineering Cleveland Clinic ClevelandOH United States Department Of Radiation Physics The University Of Texas MD Anderson Cancer Center HoustonTX United States Department Of Biomedical Engineering Shanghai Jiao Tong University Shanghai China Department Of Radiation Oncology Medical University Of Vienna Vienna Austria Department Of Biomedical Engineering Johns Hopkins University BaltimoreMD United States Department Of Radiation Oncology Peking University Cancer Hospital And Institute Beijing China Department Of Electrical Engineering And Automation Anhui University Hefei China Department Of Radiation Oncology Massachusetts General Hospital BostonMA United States Department Of Radiation Oncology University Of North Carolina At Chapel Hill Chapel HillNC United States Department Of Medical Imaging Taiwan AI Labs Taipei Taiwan Department Of Biomedical And Health Sciences Hiroshima University Hiroshima Japan Laboratory Department Of Radiation Oncology The University Of Texas Southwestern Medical Center DallasTX United States Department Of Radiatio

We establish an open framework for developing plan optimization models for knowledge-based planning (KBP) in radiotherapy. Our framework includes reference plans for 100 patients with head-and-neck cancer and high-quality dose predictions from 19 KBP models that were developed by different research groups during the OpenKBP Grand Challenge. The dose predictions were input to four optimization models to form 76 unique KBP pipelines that generated 7600 plans. The predictions and plans were compared to the reference plans via: dose score, which is the average mean absolute voxel-by-voxel difference in dose a model achieved;the deviation in dosevolume histogram (DVH) criterion;and the frequency of clinical planning criteria satisfaction. We also performed a theoretical investigation to justify our dose mimicking models. The range in rank order correlation of the dose score between predictions and their KBP pipelines was 0.50 to 0.62, which indicates that the quality of the predictions is generally positively correlated with the quality of the plans. Additionally, compared to the input predictions, the KBPgenerated plans performed significantly better (P © 2022, CC BY.

关键词： Forecasting