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A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters (vol 14, pg 352, 2018)

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NATURE CHEMICAL BIOLOGY 2018年第9期14卷 901-901页

作者： Piatkevich, Kiryl D. Jung, Erica E. Straub, Christoph Linghu, Changyang Park, Demian Suk, Ho-Jun Hochbaum, Daniel R. Goodwin, Daniel Pnevmatikakis, Eftychios Pak, Nikita Kawashima, Takashi Yang, Chao-Tsung Rhoades, Jeffrey L. Shemesh, Or Asano, Shoh Yoon, Young-Gyu Freifeld, Limor Saulnier, Jessica L. Riegler, Clemens Engert, Florian Hughes, Thom Drobizhev, Mikhail Szabo, Balint Ahrens, Misha B. Flavell, Steven W. Sabatini, Bernardo L. Boyden, Edward S. Media Lab Massachusetts Institute of Technology (MIT) Cambridge MA USA Howard Hughes Medical Institute Department of Neurobiology Harvard Medical School Boston MA USA Department of Electrical Engineering and Computer Science MIT Cambridge MA USA Harvard-MIT Division of Health Sciences and Technology MIT Cambridge MA USA Simons Center Data Analysis Simons Foundation New York NY USA Department of Mechanical Engineering MIT Cambridge MA USA Janelia Research Campus Howard Hughes Medical Institute Ashburn Virginia USA Picower Institute for Learning & Memory and Department of Brain & Cognitive Sciences MIT Cambridge MA USA Department of Molecular and Cellular Biology and Center for Brain Science Harvard University Cambridge MA USA Department of Neurobiology Faculty of Life Sciences University of Vienna Wien Austria Department of Cell Biology and Neuroscience Montana State University Bozeman Montana USA Department of Biological Physics Eotvos University Budapest Hungary Department of Biological Engineering MIT Cambridge MA USA MIT Center for Neurobiological Engineering MIT Cambridge MA USA Department of Brain and Cognitive Sciences MIT Cambridge MA USA MIT McGovern Institute for Brain Research MIT Cambridge MA USA

We developed a new way to engineer complex proteins toward multidimensional specifications using a simple, yet scalable, directed evolution strategy. By robotically picking mammalian cells that were identified, under a microscope, as expressing proteins that simultaneously exhibit several specific properties, we can screen hundreds of thousands of proteins in a library in just a few hours, evaluating each along multiple performance axes. To demonstrate the power of this approach, we created a genetically encoded fluorescent voltage indicator, simultaneously optimizing its brightness and membrane localization using our microscopy-guided cell-picking strategy. We produced the high-performance opsin-based fluorescent voltage reporter Archon1 and demonstrated its utility by imaging spiking and millivolt-scale subthreshold and synaptic activity in acute mouse brain slices and in larval zebrafish in vivo. We also measured postsynaptic responses downstream of optogenetically controlled neurons in C. elegans.

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Microwave packaging for superconducting qubits

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arXiv 2019年

作者： Lienhard, Benjamin Braumüller, Jochen Woods, Wayne Rosenberg, Danna Calusine, Greg Weber, Steven Vepsäläinen, Antti O'Brien, Kevin Orlando, Terry P. Gustavsson, Simon Oliver, William D. Department of Electrical Engineering & Computer Science Massachusetts Institute of Technology United States Research Laboratory of Electronics Massachusetts Institute of Technology United States MIT Lincoln Laboratory United States Department of Physics Massachusetts Institute of Technology United States

Over the past two decades, the performance of superconducting quantum circuits has tremendously improved. The progress of superconducting qubits enabled a new industry branch to emerge from global technology enterprises to quantum computing startups. Here, an overview of superconducting quantum circuit microwave control is presented. Furthermore, we discuss one of the persistent engineering challenges in the field—how to control the electromagnetic environment of increasingly complex superconducting circuits such that they are simultaneously protected and efficiently controllable. Copyright © 2019, The Authors. All rights reserved.

关键词： Finite element method

Influence of Magnetic Fields on Electrochemical Reactions of Redox Cofactor Solutions

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Angewandte Chemie 2021年第33期133卷

作者： Jimin Park Florian Koehler Georgios Varnavides Marc-Joseph Antonini Prof. Dr. Polina Anikeeva Department of Materials Science and Engineering Massachusetts Institute of Technology Cambridge MA 02139 USA Research Laboratory of Electronics and McGovern Institute for Brain Research Massachusetts Institute of Technology Cambridge MA 02139 USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA 02139 USA Harvard/MIT Health Science & Technology Graduate Program Cambridge MA 02139 USA Department of Brain and Cognitive Sciences Massachusetts Institute of Technology Cambridge MA 02139 USA

Redox cofactors mediate many enzymatic processes and are increasingly employed in biomedical and energy applications. Exploring the influence of external magnetic fields on redox cofactor chemistry can enhance our understanding of magnetic-field-sensitive biological processes and allow the application of magnetic fields to modulate redox reactions involving cofactors. Through a combination of experiments and modeling, we investigate the influence of magnetic fields on electrochemical reactions in redox cofactor solutions. By employing flavin mononucleotide (FMN) cofactor as a model system, we characterize magnetically induced changes in Faradaic currents. We find that radical pair intermediates have negligible influence on current increases in FMN solution upon application of a magnetic field. The dominant mechanism underlying the observed current increases is the magneto-hydrodynamic effect. We extend our analyses to other diffusion-limited electrochemical reactions of redox cofactor solutions and arrive at similar conclusions, highlighting the opportunity to use this framework in redox cofactor chemistry.

关键词： electrochemistry magnetic field effects magneto-hydrodynamic effect radicals redox cofactors

The bulk van der Waals layered magnet CrSBr is a quasi-1D material

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arXiv 2022年

作者： Klein, Julian Pingault, Benjamin Florian, Matthias Heißenbüttel, Marie-Christin Steinhoff, Alexander Song, Zhigang Torres, Kierstin Dirnberger, Florian Curtis, Jonathan B. Weile, Mads Penn, Aubrey Deilmann, Thorsten Dana, Rami Bushati, Rezlind Quan, Jiamin Luxa, Jan Sofer, Zdenek Alù, Andrea Menon, Vinod M. Wurstbauer, Ursula Rohlfing, Michael Narang, Prineha Lončar, Marko Ross, Frances M. Department of Materials Science and Engineering Massachusetts Institute of Technology CambridgeMA02139 United States John A. Paulson School of Engineering and Applied Sciences Harvard University CambridgeMA02138 United States QuTech Delft University of Technology Delft2600 GA Netherlands Department of Electrical and Computer Engineering Department of Physics University of Michigan Ann ArborMI48109 United States Institut für Festkörpertheorie Westfälische Wilhelms-Universität Münster Münster48149 Germany Institut für Theoretische Physik Universität Bremen P.O. Box 330 440 Bremen28334 Germany Bremen Center for Computational Materials Science University of Bremen Bremen28359 Germany Department of Physics City College of New York New YorkNY10031 United States College of Letters and Science UCLA Los AngelesCA90095 United States Department of Physics Technical University of Denmark Kgs. LyngbyDK-2800 Denmark MIT.nano Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics The Graduate Center City University of New York New YorkNY10016 United States Photonics Initiative CUNY Advanced Science Research Center New YorkNY10031 United States Physics Program Graduate Center City University of New York New YorkNY10026 United States Department of Inorganic Chemistry University of Chemistry and Technology Prague Technická 5 Prague 6166 28 Czech Republic Institute of Physics Center for Nanotechnology University of Münster Münster48149 Germany

Correlated quantum phenomena in one-dimensional (1D) systems that exhibit competing electronic and magnetic order are of strong interest for studying fundamental interactions and excitations, such as Tomonaga-Luttinger liquids and topological orders and defects with properties completely different from the quasiparticles expected in their higher-dimensional counterparts. However, clean 1D electronic systems are difficult to realize experimentally, particularly magnetically ordered systems. Here, we show that the van der Waals layered magnetic semiconductor CrSBr behaves like a quasi-1D material embedded in a magnetically ordered environment. The strong 1D electronic character originates from the Cr-S chains and the combination of weak interlayer hybridization and anisotropy in effective mass and dielectric screening with an effective electron mass ratio of meX/meY ∼ 50. This extreme anisotropy experimentally manifests in strong electron-phonon and exciton-phonon interactions, a Peierls-like structural instability and a Fano resonance from a van Hove singularity of similar strength of metallic carbon nanotubes. Moreover, due to the reduced dimensionality and interlayer coupling, CrSBr hosts spectrally narrow (1 meV) excitons of high binding energy and oscillator strength that inherit the 1D character. Overall, CrSBr is best understood as a stack of weakly hybridized monolayers and appears to be an experimentally attractive candidate for the study of exotic exciton and 1D correlated many-body physics in the presence of magnetic order. Copyright © 2022, The Authors. All rights reserved.

关键词： Excitons

Personalized Healthcare: Expandable Polymer Assisted Wearable Personalized Medicinal Platform (Adv. Mater. Technol. 10/2020)

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Advanced Materials Technologies 2020年第10期5卷

作者： Wedyan Babatain Abdurrahman Gumus Irmandy Wicaksono Ulrich Buttner Nazek El-atab Mutee Ur Rehman Nadeem Qaiser David Conchouso Muhammad Mustafa Hussain Electrical Engineering Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal 23955 6900 Saudi Arabia mmh Labs Electrical Engineering Computer Electrical Mathematical Science and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia Department of Electrical and Electronics Engineering Izmir Institute of Technology Urla Izmir 35430 Turkey MIT Media Lab Massachusetts Institute of Technology Cambridge MA 02139 USA EECS Cory Hall University of California Berkeley Berkeley CA 94720 USA

A compositional object-based approach to learning physical dynamics 5

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A compositional object-based approach to learning physical d...

5th International Conference on Learning Representations, ICLR 2017

作者： Chang, Michael B. Ullman, Tomer Torralba, Antonio Tenenbaum, Joshua B. Department of Electrical Engineering and Computer Science MIT Department of Brain and Cognitive Sciences MIT

We present the Neural Physics Engine (NPE), a framework for learning simulators of intuitive physics that naturally generalize across variable object count and different scene configurations. We propose a factorization of a physical scene into composable object-based representations and a neural network architecture whose compositional structure factorizes object dynamics into pairwise interactions. Like a symbolic physics engine, the NPE is endowed with generic notions of objects and their interactions;realized as a neural network, it can be trained via stochastic gradient descent to adapt to specific object properties and dynamics of different worlds. We evaluate the efficacy of our approach on simple rigid body dynamics in two-dimensional worlds. By comparing to less structured architectures, we show that the NPE's compositional representation of the structure in physical interactions improves its ability to predict movement, generalize across variable object count and different scene configurations, and infer latent properties of objects such as mass. © ICLR 2019 - Conference Track Proceedings. All rights reserved.

关键词： Stochastic systems

Why botnets work: Distributed brute-force attacks need no synchronization

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arXiv 2018年

作者： Salamatian, Salman Huleihel, Wasim Beirami, Ahmad Cohen, Asaf Medard, Muriel Department of Electrical Engineering and Computer Science MIT CambridgeMA United States Department of Electrical Engineering Ben-Gurion University Negev Israel

In September 2017, McAffee Labs quarterly report [1] estimated that brute force attacks represent 20% of total network attacks, making them the most prevalent type of attack ex-aequo with browser based vulnerabilities. These attacks have sometimes catastrophic consequences, and understanding their fundamental limits may play an important role in the risk assessment of password-secured systems, and in the design of better security protocols. While some solutions exist to prevent online brute-force attacks that arise from one single IP address, attacks performed by botnets are more challenging. In this paper, we analyze these distributed attacks by using a simplified model. Our aim is to understand the impact of distribution and asynchronization on the overall computational effort necessary to breach a system. Our result is based on Guesswork, a measure of the number of password queries (guesses) before the correct one is found in an optimal attack, which is a direct surrogate for the time and the computational effort. We model the lack of synchronization by a worst-case optimization in which the queries are received in the worst possible order, resulting in a min-max formulation. We show that even without synchronization and for sequences of growing length, the asymptotic optimal performance is achievable by using randomized guesses drawn from an appropriate distribution. Therefore, randomization is key for distributed asynchronous attacks. In other words, asynchronous guessers can asymptotically perform brute-force attacks as efficiently as synchronized guessers. Copyright © 2018, The Authors. All rights reserved.

关键词： Synchronization

MDS Code Constructions With Small Sub-Packetization and Near-Optimal Repair Bandwidth

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MDS Code Constructions With Small Sub-Packetization and Near...

作者： Rawat, Ankit Singh Tamo, Itzhak Guruswami, Venkatesan Efremenko, Klim Research Laboratory of Electronics MIT CambridgeMA02139 United States Department of Electrical Engineering-Systems Tel Aviv University Ramat Aviv69978 Israel Computer Science Department Carnegie Mellon University PittsburghPA15213 United States Department of Computer Science Ben-Gurion University of the Negev Beersheba84105 Israel

This paper addresses the problem of constructing maximum distance separable (MDS) codes that enable exact reconstruction (repair) of each code block by downloading a small amount of information from the remaining code blocks. The total amount of information flow from the remaining code blocks during this reconstruction process is referred to as repair bandwidth of the underlying code. Existing constructions of exact-repairable MDS codes with optimal repair bandwidth require working with large subpacketization levels, which restrict their applicability in practice. This paper presents two general approaches to construct exact-repairable MDS codes that aim at significantly reducing the required subpacketization level at the cost of slightly suboptimal repair bandwidth. The first approach provides MDS codes that have repair bandwidth at most twice the optimal repair bandwidth. In addition, these codes also have the smallest possible subpacketization level O(r), where r denotes the number of parity blocks. This approach is then generalized to design codes that have their repair bandwidth approaching the optimal repair bandwidth at the cost of graceful increment in the required subpacketization level. The second approach transforms an MDS code with optimal repair bandwidth and large subpacketization level into a longer MDS code with small subpacketization level and near-optimal repair bandwidth. For a given r, the codes constructed using this approach have their subpacketization level scaling logarithmically with the code length. In addition, the obtained codes require field size only linear in the code length and ensure load balancing among the intact code blocks in terms of the information downloaded from these blocks during the exact reconstruction of a code block. © 2018 IEEE.

关键词： Bandwidth

An Overview of CHIME, the Canadian Hydrogen Intensity Mapping Experiment

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arXiv 2022年

作者： Amiri, Mandana Bandura, Kevin Boskovic, Anja Chen, Tianyue Cliche, Jean-François Deng, Meiling Denman, Nolan Dobbs, Matt Fandino, Mateus Foreman, Simon Halpern, Mark Hanna, David Hill, Alex S. Hinshaw, Gary Höfer, Carolin Kania, Joseph Klages, Peter Landecker, T.L. Maceachern, Joshua Masui, Kiyoshi Mena-Parra, Juan Milutinovic, Nikola Mirhosseini, Arash Newburgh, Laura Nitsche, Rick Ordog, Anna Pen, Ue-Li Pinsonneault-Marotte, Tristan Polzin, Ava Reda, Alex Renard, Andre Richard Shaw, J. Siegel, Seth R. Singh, Saurabh Smegal, Rick Tretyakov, Ian van Gassen, Kwinten Vanderlinde, Keith Wang, Haochen Wiebe, Donald V. Willis, James S. Wulf, Dallas Department of Physics and Astronomy University of British Columbia VancouverBC Canada Department of Computer Science and Electrical Engineering West Virginia University MorgantownWV United States Center for Gravitational Waves and Cosmology West Virginia University MorgantownWV United States MIT Kavli Institute for Astrophysics and Space Research Massachusetts Institute of Technology CambridgeMA United States Department of Physics McGill University MontrealQC Canada Dominion Radio Astrophysical Observatory Herzberg Astronomy & Astrophysics Research Centre National Research Council Canada PentictonBC Canada Perimeter Institute for Theoretical Physics WaterlooON Canada David A. Dunlap Department of Astronomy & Astrophysics University of Toronto TorontoON Canada Department of Physical Sciences Thompson Rivers University KamloopsBC Canada Department of Computer Science Math Physics and Statistics University of British Columbia-Okanagan KelownaBC Canada Department of Physics and Astronomy West Virginia University MorgantownWV United States Department of Physics Massachusetts Institute of Technology CambridgeMA United States Department of Physics Yale University New HavenCT United States Canadian Institute for Theoretical Astrophysics TorontoON Canada Dunlap Institute for Astronomy and Astrophysics University of Toronto TorontoON Canada Institute of Astronomy and Astrophysics Academia Sinica Taipei Taiwan Department of Astronomy Yale University New HavenCT United States Raman Research Institute Sadashivanagar Bengaluru India Department of Physics University of Toronto TorontoON Canada

The Canadian Hydrogen Intensity Mapping Experiment (CHIME) is a drift scan radio telescope operating across the 400 MHz to 800 MHz band. CHIME is located at the Dominion Radio Astrophysical Observatory near Penticton, BC Canada. The instrument is designed to map neutral hydrogen over the redshift range 0.8 to 2.5 to constrain the expansion history of the Universe. This goal drives the design features of the instrument. CHIME consists of four parallel cylindrical reflectors, oriented north-south, each 100 m × 20 m and outfitted with a 256 element dual-polarization linear feed array. CHIME observes a two degree wide stripe covering the entire meridian at any given moment, observing 3/4 of the sky every day due to Earth rotation. An FX correlator utilizes FPGAs and GPUs to digitize and correlate the signals, with different correlation products generated for cosmological, fast radio burst, pulsar, VLBI, and 21 cm absorber backends. For the cosmology backend, the Nfeed2 correlation matrix is formed for 1024 frequency channels across the band every 31 ms. A data receiver system applies calibration and flagging and, for our primary cosmological data product, stacks redundant baselines and integrates for 10 s. We present an overview of the instrument, its performance metrics based on the first three years of science data, and we describe the current progress in characterizing CHIME's primary beam response. We also present maps of the sky derived from CHIME data;we are using versions of these maps for a cosmological stacking analysis as well as for investigation of Galactic foregrounds. © 2022, CC BY.

关键词： Interferometers