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Computationally designed proteins mimic antibody immune evasion in viral evolution

Immunity 2025年第6期58卷 1411-1421.e6页

作者： Youssef, Noor Gurev, Sarah Ghantous, Fadi Brock, Kelly P. Jaimes, Javier A. Thadani, Nicole N. Dauphin, Ann Sherman, Amy C. Yurkovetskiy, Leonid Soto, Daria Estanboulieh, Ralph Kotzen, Ben Notin, Pascal Kollasch, Aaron W. Cohen, Alexander A. Dross, Sandra E. Erasmus, Jesse Fuller, Deborah H. Bjorkman, Pamela J. Lemieux, Jacob E. Luban, Jeremy Seaman, Michael S. Marks, Debora S. Department of Systems Biology Harvard Medical School Boston 02115 MA United States Broad Institute of Harvard and MIT Cambridge 02139 MA United States Department of Electrical Engineering and Computer Science MIT Cambridge 02139 MA United States Center for Virology and Vaccine Research Beth Israel Deaconess Medical Center Boston 02215 MA United States Program in Molecular Medicine University of Massachusetts Chan Medical School Worcester 01655 MA United States Division of Infectious Diseases Department of Medicine Brigham and Women's Hospital Boston 02115 MA United States Massachusetts General Hospital Boston 02114 MA United States Division of Biology and Biological Engineering California Institute of Technology Pasadena 91125 CA United States Department of Microbiology University of Washington Seattle 98195 WA United States National Primate Research Center Seattle 98109 WA United States HDT Bio Seattle 98109 WA United States Massachusetts Consortium on Pathogen Readiness Boston 02115 MA United States Ragon Institute of MGH MIT and Harvard Cambridge 02139 MA United States

Recurrent waves of viral infection necessitate vaccines and therapeutics that remain effective against emerging viruses. Our ability to evaluate interventions is currently limited to assessments against past or circulating variants, which likely differ in their immune escape potential compared with future variants. To address this, we developed EVE-Vax, a computational method for designing antigens that foreshadow immune escape observed in future viral variants. We designed 83 SARS-CoV-2 spike proteins that transduced ACE2-positive cells and displayed neutralization resistance comparable to variants that emerged up to 12 months later in the COVID-19 pandemic. Designed spikes foretold antibody escape from B.1-BA.4/5 bivalent booster sera seen in later variants. The designed constructs also highlighted the increased neutralization breadth elicited by nanoparticle-based, compared with mRNA-based, boosters in non-human primates. Our approach offers targeted panels of synthetic proteins that map the immune landscape for early vaccine and therapeutic evaluation against future viral strains. © 2025 The Authors

关键词： antibody escape generative protein models immune landscape machine learning protein design vaccine evaluation viral evolution

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Technical Specifications of the Submarine Fiber Optic Channel Bandwidth/Capacity in Optical Fiber Transmission Systems

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Journal of Optical Communications 2019年第s1期45卷 s85-s90页

作者： Amiri, I.S. Rashed, Ahmed Nabih Zaki Jahan, Sohely Paul, Bikash Kumar Ahmed, Kawsar Yupapin, P. Computational Optics Research Group Advanced Institute of Materials Science Ton Duc Thang University Ho Chi Minh City Viet Nam Faculty of Applied Sciences Ton Duc Thang University Ho Chi Minh City Viet Nam Electronics and Electrical Communications Engineering Department Faculty of Electronic Engineering Menoufia University Menouf Menoufia32951 Egypt Department of Computer Science and Engineering University of Barisal Barisal Kornokathi8200 Bangladesh Department of Software Engineering Daffodil International University Dhaka Sukrabad Dhanmondi1207 Bangladesh Group of Bio-photomatiχ MawlanaBhashani Science and Technology University Tangail Santosh1902 Bangladesh Department of Information and Communication Technology MawlanaBhashani Science and Technology University Tangail Santosh1902 Bangladesh

This work outlines technical specifications of the undersea fiber optic communication channel bandwidth, capacity with taken into account the maximum and minimum extended fiber cost in the presence of amplifiers stations. The number of amplifiers in the amplification stage are addressed based on the amplifier distance to strength the light signal in water depth after 5 km distance. The fiber channel capacity is estimated at different water depth and at the surface of the water. Minimum input signal power and required detectable received power are adjusted to ensure the high data rates in submarine cable systems under the best and worst conditions of the seawater pressure. The study emphasizes the high data rates transmission can be achieved at a distance of 10 km depth. © 2019 Walter de Gruyter GmbH, Berlin/Boston 2019.

关键词： Submarines

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Chiral plasmons with twisted atomic bilayers

arXiv

引用

arXiv 2020年

作者： Lin, Xiao Liu, Zifei Stauber, Tobias Gómez-Santos, Guillermo Gao, Fei Chen, Hongsheng Zhang, Baile Low, Tony Interdisciplinary Center for Quantum Information State Key Laboratory of Modern Optical Instrumentation ZJU-Hangzhou Global Science and Technology Innovation Center College of Information Science and Electronic Engineering Zhejiang University Hangzhou310027 China Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University Singapore637371 Singapore Materials Science Factory Instituto de Ciencia de Materiales de Madrid CSIC MadridE-28049 Spain Institute for Theoretical Physics University of Regensburg RegensburgD-93040 Germany Universidad Autónoma de Madrid MadridE-28049 Spain Centre for Disruptive Photonic Technologies NTU Singapore637371 Singapore Department of Electrical and Computer Engineering University of Minnesota MinneapolisMN55455 United States

Van der Waals heterostructures of atomically thin layers with rotational misalignments, such as twisted bilayer graphene, feature interesting structural moirésuperlattices. Due to the quantum coupling between the twisted atomic layers, light-matter interaction is inherently chiral;as such, they provide a promising platform for chiral plasmons in the extreme nanoscale. However, while the interlayer quantum coupling can be significant, its influence on chiral plasmons still remains elusive. Here we present the general solutions from full Maxwell equations of chiral plasmons in twisted atomic bilayers, with the consideration of interlayer quantum coupling. We find twisted atomic bilayers have a direct correspondence to the chiral metasurface, which simultaneously possesses chiral and magnetic surface conductivities, besides the common electric surface conductivity. In other words, the interlayer quantum coupling in twisted van der Waals heterostructures may facilitate the construction of various (e.g., bi-anisotropic) atomically-thin metasurfaces. Moreover, the chiral surface conductivity, determined by the interlayer quantum coupling, determines the existence of chiral plasmons and leads to a unique phase relationship (i.e., ±π/2 phase difference) between their TE and TM wave components. Importantly, such a unique phase relationship for chiral plasmons can be exploited to construct the missing longitudinal spin of plasmons, besides the common transverse spin of plasmons. Copyright © 2020, The Authors. All rights reserved.

关键词： Plasmons

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Direct evidence for Cooper pairing without a spectral gap in a disordered superconductor above Tc

arXiv

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arXiv 2021年

作者： Bastiaans, Koen M. Chatzopoulos, Damianos Ge, Jian-Feng Cho, Doohee Tromp, Willem O. van Ruitenbeek, Jan M. Fischer, Mark H. de Visser, Pieter J. Thoen, David J. Driessen, Eduard F.C. Klapwijk, Teunis M. Allan, Milan P. Leiden Institute of Physics Leiden University Niels Bohrweg 2 Leiden2333 CA Netherlands Department of Physics Yonsei University Seoul03722 Korea Republic of Department of Physics University of Zurich Winterthurersstrasse 190 Zurich8057 Switzerland SRON Netherlands Institute for Space Research Sorbonnelaan 2 Utrecht3584 CA Netherlands Kavli Institute of Nanoscience Delft University of Technology Lorentzweg 1 Delft2628 CJ Netherlands Faculty of Electrical Engineering Mathematics and Computer Science Delft University of Technology Mekelweg 4 Delft2628 CD Netherlands Grenoble 300 Rue de la Piscine Saint-Martin-d'Hères38400 France Institute of Topological Materials Julius-Maximilian-Universität Würzburg Sanderring 2 Würzburg97070 Germany Physics Department Moscow State University of Education 1/1 Malaya Pirogovskaya Str. Moscow119991 Russia

The idea that preformed Cooper pairs could exist in a superconductor above its zero-resistance state has been explored for unconventional, interface, and disordered superconductors, yet direct experimental evidence is lacking. Here, we use scanning tunneling noise spectroscopy to unambiguously show that preformed Cooper pairs exist up to temperatures much higher than the zero-resistance critical temperature Tc in the disordered superconductor titanium nitride, by observing a clear enhancement in the shot noise that is equivalent to a change of the effective charge from 1 to 2 electron charges. We further show that spectroscopic gap fills up rather than closes when increasing temperature. Our results thus demonstrate the existence of a novel state above Tc that, much like an ordinary metal, has no (pseudo)gap, but carries charge via paired electrons. Copyright © 2021, The Authors. All rights reserved.

关键词： Superconducting materials

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Thermal conductance across harmonic-matched epitaxial al-sapphire heterointerfaces

arXiv

引用

arXiv 2019年

作者： Cheng, Zhe Koh, Yee Rui Ahmad, Habib Hu, Renjiu Shi, Jingjing Liao, Michael E. Wang, Yekan Bai, Tingyu Li, Ruiyang Lee, Eungkyu Clinton, Evan A. Matthews, Christopher M. Engel, Zachary Yates, Luke Luo, Tengfei Goorsky, Mark S. Doolittle, William Tian, Zhiting Hopkins, Patrick E. Graham, Samuel George W. Woodruff School of Mechanical Engineering Georgia Institute of Technology AtlantaGA30332 United States Department of Mechanical and Aerospace Engineering University of Virginia CharlottesvilleVA22904 United States School of Electrical and Computer Engineering Georgia Institute of Technology AtlantaGA30332 United States Sibley School of Mechanical and Aerospace Engineering Cornell University IthacaNY14853 United States Materials Science and Engineering University of California Los Angeles Los AngelesCA91355 United States Department of Aerospace and Mechanical Engineering University of Notre Dame Notre DameIN46556 United States University of Notre Dame Notre DameIN46556 United States Department of Materials Science and Engineering University of Virginia CharlottesvilleVA22904 United States Department of Physics University of Virginia CharlottesvilleVA22904 United States School of Materials Science and Engineering Georgia Institute of Technology AtlantaGA30332 United States

A unified fundamental understanding of interfacial thermal transport is missing due to the complicated nature of interfaces which involves complex factors such as interfacial bonding and mixing, surface chemistry, crystal orientation, roughness, and interfacial disorder. This is especially true for metal-nonmetal interfaces which incorporate multiple fundamental heat transport mechanisms such as elastic and inelastic phonon scattering as well as electron-phonon coupling in the metal and across the interface. All these factors jointly affect thermal boundary conductance (TBC). Therefore, the experimentally measured interfaces may not be the same as the ideally modelled, thus obfuscating conclusions drawn from previous experimental and modeling comparisons. This work provides a systematic study of interfacial thermal conductance across well-controlled and ultraclean epitaxial (111) Al || (0001) sapphire interfaces, known as harmonic-matched interface. The measured high TBC is compared with theoretical models of atomistic Green’s function (AGF) and the non-equilibrium Landauer approach, showing that elastic phonon transport dominates the interfacial thermal transport of the Al-sapphire interfaces. By scaling the TBC with the Al heat capacity and sapphire heat capacity with phonon frequency lower than the max Al phonon frequency, a nearly constant transmission coefficient is observed, indicating that the phonons on the Al side limits the Al-sapphire TBC. This confirms that elastic phonon transport dominates interfacial thermal transport of the Al-sapphire interfaces and other mechanisms play negligible roles. Our work enables a quantitative study of TBC to validate theoretical models of thermal transport mechanisms across metal-nonmetal interfaces, and acts as a benchmark when studying how other factors impact TBC. Copyright © 2019, The Authors. All rights reserved.

关键词： Chemical bonds

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2D Metamaterials: Designing Mechanical Metamaterials with Kirigami-Inspired, Hierarchical Constructions for Giant Positive and Negative Thermal Expansion (Adv. Mater. 3/2021)

引用

Advanced materials 2021年第3期33卷

作者： Xiaogang Guo Xiaoyue Ni Jiahong Li Hang Zhang Fan Zhang Huabin Yu Jun Wu Yun Bai Hongshuai Lei Yonggang Huang John A. Rogers Yihui Zhang AML Department of Engineering Mechanics Center for Flexible Electronics Technology Tsinghua University Beijing 100084 China Institute of Advanced Structure Technology Beijing Institute of Technology Beijing 100081 China Center for Bio-Integrated Electronics Northwestern University Evanston IL 60208 USA Department of Materials Science and Engineering Northwestern University Evanston IL 60208 USA Department of Mechanical Engineering Northwestern University Evanston IL 60208 USA Department of Civil and Environmental Engineering Northwestern University Evanston IL 60208 USA Simpson Querrey Institute Northwestern University Chicago IL 60611 USA Department of Biomedical Engineering Northwestern University Evanston IL 60208 USA Department of Chemistry Northwestern University Evanston IL 60208 USA Department of Electrical and Computer Engineering Northwestern University Evanston IL 60208 USA Department of Neurological Surgery Northwestern University Evanston IL 60208 USA

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Structural color 3d printing by shrinking photonic crystals

arXiv

引用

arXiv 2019年

作者： Liu, Yejing Wang, Hao Ho, Jinfa Ng, Ryan C. Ng, Ray J. H. Hall-Chen, Valerian H. Koay, Eleen H. H. Dong, Zhaogang Liu, Hailong Qiu, Cheng-Wei Greer, Julia R. Yang, Joel K. W. Engineering Product Development Singapore University of Technology and Design Singapore487372 Singapore Division of Engineering and Applied Science California Institute of Technology PasadenaCA91125 United States Nanofabrication Department Institute of Materials Research and Engineering Singapore138634 Singapore Rudolf Peierls Centre for Theoretical Physics University of Oxford OxfordOX1 3PU United Kingdom Department of Electrical and Computer Engineering National University of Singapore Singapore117583 Singapore

The rings, spots and stripes found on some butterflies, Pachyrhynchus weevils, and many chameleons are notable examples of natural organisms employing photonic crystals to produce colorful patterns. Despite advances in nanotechnology, we still lack the ability to print arbitrary colors and shapes in all three dimensions at this microscopic length scale. Commercial nanoscale 3D printers based on two-photon polymerization are incapable of patterning photonic crystal structures with the requisite ~300 nm lattice constant to achieve photonic stopbands/bandgaps in the visible spectrum and generate colors. Here, we introduce a means to produce 3D-printed photonic crystals with a 5x reduction in lattice constants (periodicity as small as 280 nm), achieving sub-100-nm features with a full range of colors. The reliability of this process enables us to engineer the bandstructures of woodpile photonic crystals that match experiments, showing that observed colors can be attributed to either slow light modes or stopbands. With these lattice structures as 3D color volumetric elements (voxels), we printed 3D microscopic scale objects, including the first multi-color microscopic model of the Eiffel Tower measuring only 39-ìm tall with a color pixel size of 1.45 ìm. The technology to print 3D structures in color at the microscopic scale promises the direct patterning and integration of spectrally selective devices, such as photonic crystal-based color filters, onto free-form optical elements and curved surfaces. Copyright © 2019, The Authors. All rights reserved.

关键词： 3D printers

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Hydrogen-storing salt NaCl(H2) synthesized at high pressure and high temperature

arXiv

引用

arXiv 2019年

作者： Matsuoka, Takahiro Muraoka, Shu Ishikawa, Takahiro Niwa, Ken Ohta, Kenji Hirao, Naohisa Kawaguchi, Saori Ohishi, Yasuo Shimizu, Katsuya Sasaki, Shigeo Department of Electrical Electronic and Computer Engineering Gifu University Gifu501-1193 Japan Joint Institute for Advanced Materials University of Tennessee TN37996 United States Materials Science and Technology Division Graduate School of Engineering Gifu University Gifu501-1193 Japan Elements Strategy Initiative Center for Magnetic Materials National Institute for Material Science Ibaraki305-0047 Japan Center for Science and Technology under Extreme Conditions Graduate School of Engineering Science Osaka University Osaka560-8531 Japan Department of Materials Physics Nagoya University Nagoya464-8603 Japan Department of Earth and Planetary Sciences Tokyo Institute of Technology Tokyo152-8550 Japan Japan Synchrotron Radiation Research Institute Hyogo679-5198 Japan

X-ray diffraction and Raman scattering measurements, and first-principles calculations are performed to search for the formation of NaCl-hydrogen compound. When NaCl and H2 mixture is laser-heated to above 1500 K at pressures exceeding 40 GPa, we observed the formation of NaClHx with P63/mmc structure which accommodates H2 molecules in the interstitial sites of NaCl lattice forming ABAC stacking. Upon the decrease of pressure at 300 K, NaClHx remains stable down to 17 GPa. Our calculations suggest the observed NaClHx is NaCl(H2). Besides, a hydrogen-richer phase NaCl(H2)4 is predicted to become stable at pressures above 40 GPa. Copyright © 2019, The Authors. All rights reserved.

关键词： Calculations

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An Evaluation of LoRa Communication Range in Urban and Forest Areas: A Case Study in Brazil and Portugal

An Evaluation of LoRa Communication Range in Urban and Fores...

引用

International Conference and Workshop on Computing and Communication (IEMCON)

作者： Mariana Rodrigues Villarim João Vitor Holanda de Luna Douglas de Farias Medeiros Renata Imaculada Soares Pereira Cleonilson Protasio de Souza Orlando Baiocchi Francisco Cipriano da Cunha Martins Postgraduation Program of Electr. Eng. Federal University of Paraíba João Pessoa Brazil Department of Electrical Engineering Federal University of Paraíba João Pessoa Brazil School of Engineering and Technology University of Washington Tacoma Tacoma WA USA Department of Computer Science University of Azores São Miguel Azores Portugal

Due to its particular features, LoRa is gaining more and more attention from industry and academia because it tries to combine long communication range, low-power consumption, and low-data rate application. A very important feature observed on LoRa is that it is highly robust and reliable. Due to this, LoRa is being applied in many IoT solutions in urban environment, but on hard natural environments like dense forest, near river sides, lakes and mangroves, more studies need to be carried out in order to evaluate the its quality. This paper describes experimental studies carried out to measure LoRa communication range and Received Signal Strength Indicator (RSSI), both in natural and urban environments. The experiments took place in two different places of the world, one in the northern hemisphere and another in the southern hemisphere: on the Portuguese archipelago of the Azores (in SãoMiguel Island) and in the city of João Pessoa in Northeast of Brazil, respectively. As a result, we observed that LoRa is very robust in dense urban environments, where it was possible to established long distance connections (approximately 2.1 km). However, the results were inconclusive in forest environments, because in the Azores, the LoRa connection ranged about 800 m thought the forest/lake, while in Brazil it was about 230 m.

关键词： Forestry Lakes Chirp Urban areas Frequency modulation Internet of Things Wireless communication

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Statistically meaningful measure of domain-wall roughness in magnetic thin films

引用

Physical Review B 2020年第18期101卷 184431-184431页

作者： D. Jordán L. J. Albornoz J. Gorchon C. H. Lambert S. Salahuddin J. Bokor J. Curiale S. Bustingorry Instituto Balseiro Universidad Nacional de Cuyo - CNEA Centro Atómico Bariloche (R8402AGP) S. C. de Bariloche Río Negro Argentina Instituto de Nanociencia y Nanotecnología CNEA–CONICET Centro Atómico Bariloche (R8402AGP) S. C. de Bariloche Río Negro Argentina Université de Lorraine CNRS IJL F-54000 Nancy France Department of Electrical Engineering and Computer Science University of California Berkeley California 94720 USA Materials Sciences Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA

Domain walls in magnetic thin films display a complex dynamical response when subject to an external drive. It is claimed that different dynamic regimes are correlated with the domain-wall roughness, i.e., with the fluctuations of domain-wall position due to the inherent disorder in the system. Therefore, key to understanding the dynamics of domain walls is to have a statistically meaningful measure of the domain-wall roughness. Here we present a thorough study of the roughness parameters, i.e., roughness exponent and roughness amplitude, for domain walls in a ferrimagnetic GdFeCo thin film in the creep regime. Histograms of roughness parameters are constructed with more than 40 independent realizations under the same experimental conditions, and the average values and standard deviations are compared in different conditions. We found that the most prominent feature of the obtained distributions is their large standard deviations, which is a signature of large fluctuations. We show that even if the roughness parameters for a particular domain wall are well known, these parameters are not necessarily representative of the underlying physics of the system. In the low field limit, within the creep regime of domain-wall motion, we found the average roughness exponent and roughness amplitude to be around 0.75 and 0.45 μm2, respectively. When an in-plane magnetic field is applied we observed that, even though the distributions are wide, changes in the mean values of roughness parameters can be identified; the roughness exponent decreasing to values around 0.72 while the roughness amplitude increases to 0.65 μm2. Our results call for a careful consideration of statistical averaging over different domains walls when reporting roughness exponents.

关键词： Domain walls Magnetic domains Magnetism Ferrimagnets Thin films Magneto-optical Kerr effect

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