Faculty of Arts and Sciences
Permanent URI for this communityhttps://dash.harvard.edu/handle/1/1
This community provides open access to material created by faculty, staff, and students of the Faculty of Arts and Sciences. All material in the repository is also harvested by search engines (such as Google Scholar) and Open Archives Initiative data harvesters.
Browse
4181 results
Search Results
Publication Identification of more than 40 gravitationally magnified stars in a galaxy at redshift 0.725(Springer Science and Business Media LLC, 2025-01-06) Fudamoto, Yoshinobu; Sun, Fengwu; Diego, Jose M.; Dai, Liang; Oguri, Masamune; Zitrin, Adi; Zackrisson, Erik; Jauzac, Mathilde; Lagattuta, David J.; Egami, Eiichi; Iani, Edoardo; Windhorst, Rogier A.; Abe, Katsuya T.; Bauer, Franz Erik; Bian, Fuyan; Bhatawdekar, Rachana; Broadhurst, Thomas J.; Cai, Zheng; Chen, Chian-Chou; Chen, Wenlei; Cohen, Seth H.; Conselice, Christopher J.; Espada, Daniel; Foo, Nicholas; Frye, Brenda L.; Fujimoto, Seiji; Furtak, Lukas J.; Golubchik, Miriam; Hsiao, Tiger Yu-Yang; Jolly, Jean-Baptiste; Kawai, Hiroki; Kelly, Patrick L.; Koekemoer, Anton M.; Kohno, Kotaro; Kokorev, Vasily; Li, Mingyu; Li, Zihao; Lin, Xiaojing; Magdis, Georgios E.; Meena, Ashish K.; Niemiec, Anna; Nabizadeh, Armin; Richard, Johan; Steinhardt, Charles L.; Wu, Yunjing; Zhu, Yongda; Zou, Siwei; fudamoto, yoshinobuStrong gravitational magnifications enable to detect faint background sources, resolve their internal structures, and even identify individual stars in distant galaxies. Highly magnified individual stars allow various appli- cations, including studies of stellar populations in dis- tant galaxies and constraining dark matter structures in the lensing plane. However, these applications have been hampered by the small number of individual stars observed, as typically one or a few stars are identified from each distant galaxy. Here, we report the discovery of more than 40 microlensed stars in a single galaxy be- hind Abell 370 at redshift of 0.725 when the Universe was half of its current age (dubbed “the Dragon arc”), using James Webb Space Telescope (JWST) observations with the time-domain technique. These events are found near the expected lensing critical curves, suggesting that these are magnified stars that appear as transients from intr- acluster stellar microlenses. Through multi-wavelength photometry, we constrain stellar types and find that many of them are consistent with red giants/supergiants magnified by factors of hundreds. This finding reveals an unprecedented high occurrence of microlensing events in the Dragon arc, and proves that JWST’s time-domain observations open up the possibility of conducting statistical studies of high-redshift stars.Publication Opportunities in nanoscale probing of laser-driven phase transitions(Springer Science and Business Media LLC, 2024-08-28) Yannai, Michael; Haller, Matan; Ruimy, Ron; Gorlach, Alexey; Rivera, Nicholas; Basov, Dmitri N.; Kaminer, IdoPublication Thermalization and criticality on an analogue–digital quantum simulator(Springer Science and Business Media LLC, 2025-2-5) Andersen, T. I.; Astrakhantsev, N.; Karamlou, A. H.; Berndtsson, J.; Motruk, J.; Szasz, A.; Gross, J. A.; Schuckert, A.; Westerhout, T.; Zhang, Y.; Forati, E.; Rossi, D.; Kobrin, B.; Paolo, A. Di; Klots, A. R.; Drozdov, I.; Kurilovich, V.; Petukhov, A.; Ioffe, L. B.; Elben, A.; Rath, A.; Vitale, V.; Vermersch, B.; Acharya, R.; Beni, L. A.; Anderson, K.; Ansmann, M.; Arute, F.; Arya, K.; Asfaw, A.; Atalaya, J.; Ballard, B.; Bardin, J. C.; Bengtsson, A.; Bilmes, A.; Bortoli, G.; Bourassa, A.; Bovaird, J.; Brill, L.; Broughton, M.; Browne, D. A.; Buchea, B.; Buckley, B. B.; Buell, D. A.; Burger, T.; Burkett, B.; Bushnell, N.; Cabrera, A.; Campero, J.; Chang, H.-S.; Chen, Z.; Chiaro, B.; Claes, J.; Cleland, A. Y.; Cogan, J.; Collins, R.; Conner, P.; Courtney, W.; Crook, A. L.; Das, S.; Debroy, D. M.; Lorenzo, L. De; Barba, A. Del Toro; Demura, S.; Donohoe, P.; Dunsworth, A.; Earle, C.; Eickbusch, A.; Elbag, A. M.; Elzouka, M.; Erickson, C.; Faoro, L.; Fatemi, R.; Ferreira, V. S.; Burgos, L. Flores; Fowler, A. G.; Foxen, B.; Ganjam, S.; Gasca, R.; Giang, W.; Gidney, C.; Gilboa, D.; Giustina, M.; Gosula, R.; Dau, A. Grajales; Graumann, D.; Greene, A.; Habegger, S.; Hamilton, M. C.; Hansen, M.; Harrigan, M. P.; Harrington, S. D.; Heslin, S.; Heu, P.; Hill, G.; Hoffmann, M. R.; Huang, H.-Y.; Huang, T.; Huff, A.; Huggins, W. J.; Isakov, S. V.; Jeffrey, E.; Jiang, Z.; Jones, C.; Jordan, S.; Joshi, C.; Juhas, P.; Kafri, D.; Kang, H.; Kechedzhi, K.; Khaire, T.; Khattar, T.; Khezri, M.; Kieferová, M.; Kim, S.; Kitaev, A.; Klimov, P.; Korotkov, A. N.; Kostritsa, F.; Kreikebaum, J. M.; Landhuis, D.; Langley, B. W.; Laptev, P.; Lau, K.-M.; Guevel, L. Le; Ledford, J.; Lee, J.; Lee, K. W.; Lensky, Y. D.; Lester, B. J.; Li, W. Y.; Lill, A. T.; Liu, W.; Livingston, W. P.; Locharla, A.; Lundahl, D.; Lunt, A.; Madhuk, S.; Maloney, A.; Mandrà, S.; Martin, L. S.; Martin, O.; Martin, S.; Maxfield, C.; McClean, J. R.; McEwen, M.; Meeks, S.; Miao, K. C.; Mieszala, A.; Molina, S.; Montazeri, S.; Morvan, A.; Movassagh, R.; Neill, C.; Nersisyan, A.; Newman, M.; Nguyen, A.; Nguyen, M.; Ni, C.-H.; Niu, M. Y.; Oliver, W. D.; Ottosson, K.; Pizzuto, A.; Potter, R.; Pritchard, O.; Pryadko, L. P.; Quintana, C.; Reagor, M. J.; Rhodes, D. M.; Roberts, G.; Rocque, C.; Rosenberg, E.; Rubin, N. C.; Saei, N.; Sankaragomathi, K.; Satzinger, K. J.; Schurkus, H. F.; Schuster, C.; Shearn, M. J.; Shorter, A.; Shutty, N.; Shvarts, V.; Sivak, V.; Skruzny, J.; Small, S.; Smith, W. Clarke; Springer, S.; Sterling, G.; Suchard, J.; Szalay, M.; Sztein, A.; Thor, D.; Torres, A.; Torunbalci, M. M.; Vaishnav, A.; Vdovichev, S.; Villalonga, B.; Heidweiller, C. Vollgraff; Waltman, S.; Wang, S. X.; White, T.; Wong, K.; Woo, B. W. K.; Xing, C.; Yao, Z. Jamie; Yeh, P.; Ying, B.; Yoo, J.; Yosri, N.; Young, G.; Zalcman, A.; Zhu, N.; Zobrist, N.; Neven, H.; Babbush, R.; Boixo, S.; Hilton, J.; Lucero, E.; Megrant, A.; Kelly, J.; Chen, Y.; Smelyanskiy, V.; Vidal, G.; Roushan, P.; Läuchli, A. M.; Abanin, D. A.; Mi, X.Abstract Understanding how interacting particles approach thermal equilibrium is a major challenge of quantum simulators1,2. Unlocking the full potential of such systems towards this goal requires flexible initial state preparation, precise time evolution and extensive probes for final state characterization. Here we present a quantum simulator comprising 69 superconducting qubits that supports both universal quantum gates and high-fidelity analogue evolution, with performance beyond the reach of classical simulation in cross-entropy benchmarking experiments. This hybrid platform features more versatile measurement capabilities compared with analogue-only simulators, which we leverage here to reveal a coarsening-induced breakdown of Kibble–Zurek scaling predictions3 in the XY model, as well as signatures of the classical Kosterlitz–Thouless phase transition4. Moreover, the digital gates enable precise energy control, allowing us to study the effects of the eigenstate thermalization hypothesis5–7 in targeted parts of the eigenspectrum. We also demonstrate digital preparation of pairwise-entangled dimer states, and image the transport of energy and vorticity during subsequent thermalization in analogue evolution. These results establish the efficacy of superconducting analogue–digital quantum processors for preparing states across many-body spectra and unveiling their thermalization dynamics.Publication In Situ Techniques for Quinone-Mediated Electrochemical Carbon Capture and Release in Aqueous Environments(American Chemical Society (ACS), 2024-01-31) Amini, Kiana; Cochard, Thomas; Jing, Yan; Sosa, Jordan D.; Xi, Dawei; Alberts, Maia; Emanuel, Michael S.; Kerr, Emily F.; Gordon, Roy G.; Aziz, MichaelWe present two novel experimental techniques designed to quantify the contributions of nucleophilicity-swing and pH-swing mechanisms to carbon capture in the electrochemical aqueous quinone-based CO2 capture process. Through thermodynamic analysis, we elucidate the intricate interplay between these two mechanisms, and emphasize the critical role of understanding this interplay in the material discovery cycle for carbon capture applications. This insight prompts the development of two innovative in situ techniques. The first technique capitalizes on discernible voltage signature differences between quinone, and quinone-CO2 adducts. By incorporating a reference electrode into the carbon capture cell setup, we apply this method to investigate bis[3-(trimethylammonio)propyl]-anthraquinones (BTMAPAQs). Our findings reveal the isolated contributions of nucleophilicity-swing and pH-swing mechanisms to overall carbon capture capacity under varying wait times and CO2 partial pressures. The second method is developed based on our finding that the adduct form of the quinone exhibits a fluorescence emission from an incident light at wavelengths distinct from the fluorescence of the reduced form, enabling differentiation through optical band-pass filtering at each unique fluorescent signature. Thus, we introduce a non-invasive, in situ approach using fluorescence microscopy, providing the unique capability to distinguish between oxidized, reduced, and adduct species with sub-second time resolution at single digit micrometer resolution. This powerful technique holds significant promise for studying such systems, representing an advancement in our ability to understand carbon capture processes.Publication EvoAI enables extreme compression and reconstruction of the protein sequence space(Springer Science and Business Media LLC, 2024-02-23) Zhang, Shuyi; Ma, Ziyuan; Li, Wenjie; Shen, Yunhao; Xu, Yunxin; Liu, Gengjiang; Chang, Jiamin; Li, Zeju; Qin, Hong; Tian, Boxue; Gong, Haipeng; Liu, David; Thuronyi, B; Voigt, ChristopherDesigning proteins with improved functions requires a deep understanding of how sequence and function are related, a vast space that is hard to explore. The ability to efficiently compress this space by identifying functionally important features is extremely valuable. Here, we first establish a method called EvoScan to comprehensively segment and scan the high-fitness sequence space to obtain anchor points that capture its essential features, especially in high dimensions. Our approach is compatible with any biomolecular function that can be coupled to a transcriptional output. We then develop deep learning and large language models to accurately reconstruct the space from these anchors, allowing computational prediction of novel, highly fit sequences without prior homology-derived or structural information. We apply this hybrid experimental-computational method, which we call EvoAI, to a repressor protein and find that only 82 anchors are sufficient to compress the high-fitness sequence space with a compression ratio of 1048. The extreme compressibility of the space informs both applied biomolecular design and understanding of natural evolution.Publication Synaptic connectivity mapping among thousands of neurons via parallelized intracellular recording with a microhole electrode array(Springer Science and Business Media LLC, 2025-02-11) Wang, Jun; Jung, Woo-Bin; Gertner, Rona; Park, Hongkun; Ham, DonheeMassive parallelization of neuronal intracellular recording, which can measure synaptic signals across a network and thus can enable the mapping and characterization of synaptic connections, is a challenge still open in neuroscience, with the state-of-the-art limited to a mapping of ~300 synaptic connections. Here, we report a 4,096 platinum/platinum-black microhole electrode array fabricated on a complementary metal-oxide semiconductor electronic chip that substantially advances parallel intracellular recording and synaptic connectivity mapping. The microhole-neuron interface, together with current-clamp electronics in the underlying semiconductor chip, allows 90% average intracellular coupling rate with rat neuronal cultures, generating network-wide intracellular recording data that abound with synaptic signals. From these data we extract 70,000+ plausible synaptic connections amongst 2,000+ neurons, and catalogue them into inhibitory, weak/uneventful excitatory, and strong/eventful excitatory chemical synaptic connections, and electrical synaptic connections, with an estimated overall error rate of around 5%. The reported scale of synaptic connection mapping, with the ability to characterize synaptic connections, provides a step toward functional connectivity mapping of a large-scale neuronal network.Publication Quantum States and Spectra of Small Cylindrical and Toroidal Lattices(IOP Publishing, 2024-09-16) Brooks, Caelan; Das, Kunal K.We examine the spectrum and quantum states of small lattices with cylindrical and toroidal topology subject to a scalar gauge potential that introduces a position dependent phase in the inter-site coupling. Equivalency of gauges assumed in infinite lattices is generally lost due to the periodic boundary conditions, and conditions that restore it are identified. We trace the impact of various system parameters including gauge choice, boundary conditions and inter-site coupling strengths, and an additional axial field. We find gauge dependent appearance of avoided crossings and persistent degeneracies, and we show their impact on the associated eigenstates. Smaller lattices develop prominent gaps in spectral lines associated with edge states, which are suppressed in the thermodynamic limit. Toroidal lattices have counterparts of most of the features observed in cylindrical lattices, but notably they display a transition from localization to delocalization determined by the relation between the field parameter and the number of lattice sites.Publication Recording of Network-Wide Intracellular Activity and Mapping of Synaptic Connections Using Microhole Electrode Arrays(Springer Nature, 2025-02-11) Wang, Jun; Jung, Woo-Bin; Gertner, Rona; Park, Hongkun; Ham, DonheeNetwork-wide parallelization of neuronal intracellular recording and quantification of synaptic connections and their strengths is a challenge still open in neuroscience, with a mapping limit of ~300 connections. Here, we report a 4,096 microhole electrode array on a semiconductor chip for parallel intracellular recording and synaptic connectivity mapping of rat neuronal cultures using electroporation. The microholes are etched from a complementary metal-oxide semiconductor chip, and the final surface is coated with platinum black to increase roughness and the neuronal interface. The microhole array allows up to 90% average intracellular coupling rate with high coupling fidelity, generating network-wide intracellular recording data containing synaptic signals, and allows regaining intracellular coupling on the same neurons. We extract 70,000+ plausible synaptic connections amongst 2,000+ neurons, and catalogue them into inhibitory, weak/uneventful excitatory, strong/eventful excitatory chemical synaptic connections, and electrical synaptic connections, with an estimated overall error rate of around 5%. The reported scale of chemical and electrical synaptic mapping combines the advantages of patch clamp and extracellular multi-electrode array recordings, providing valuable insights into large-scale neural connectivity.Publication Transcript-specific enrichment enables profiling rare cell states via scRNA-seq(Nature, 2024-03-27) Abay, Tsion; Stickels, Robert R; Takizawa, Meril T; Nalbant, Benan N; Hsieh, Yu-Hsin; Hwang, Sidney; Snopkowski, Catherine; Hei Yu, Kenny Kwok; Abou-Mrad, Zaki; Tabar, Viviane; Ludwig, Leif S; Chaligne, Ronan; Satpathy, Ansuman T; Lareau, Caleb ASingle-cell genomics technologies have accelerated our understanding of cell-state heterogeneity in diverse contexts. Although single-cell RNA sequencing (scRNA-seq) identifies many rare populations of interest that express specific marker transcript combinations, traditional flow sorting limits our ability to enrich these populations for further profiling, including requiring cell surface markers with high-fidelity antibodies. Additionally, many single-cell studies require the isolation of nuclei from tissue, eliminating the ability to enrich learned rare cell states based on extranuclear protein markers. To address these limitations, we describe Programmable Enrichment via RNA Flow-FISH by sequencing (PERFF-seq), a scalable assay that enables scRNA-seq profiling of subpopulations from complex cellular mixtures defined by the presence or absence of specific RNA transcripts. Across immune populations (n = 141,227 cells) and fresh-frozen and formalin-fixed paraffin-embedded brain tissue (n = 29,522 nuclei), we demonstrate the sorting logic that can be used to enrich for cell populations via RNA-based cytometry followed by high-throughput scRNA-seq. Our approach provides a rational, programmable method for studying rare populations identified by one or more marker transcripts.Publication The genetic origin of the Indo-Europeans(Springer Science and Business Media LLC, 2025-02-05) Lazaridis, Iosif; Olalde, Iñigo; Khokhlov, Alexander A.; Kitov, Egor P.; Shishlina, Natalia I.; Ailincăi, Sorin C.; Agapov, Danila S.; Agapov, Sergey A.; Batieva, Elena; Bauyrzhan, Baitanayev; Bereczki, Zsolt; Buzhilova, Alexandra; Changmai, Piya; Chizhevsky, Andrey A.; Ciobanu, Ion; Constantinescu, Mihai; Csányi, Marietta; Dani, János; Dashkovskiy, Peter K.; Évinger, Sándor; Faifert, Anatoly; Flegontov, Pavel; Frînculeasa, Alin; Frînculeasa, Mădălina N.; Hajdu, Tamás; Higham, Tom; Jarosz, Paweł; Jelínek, Pavol; Khartanovich, Valeri I.; Kirginekov, Eduard N.; Kiss, Viktória; Kitova, Alexandera; Kiyashko, Alexeiy V.; Koledin, Jovan; Korolev, Arkady; Kosintsev, Pavel; Kulcsár, Gabriella; Kuznetsov, Pavel; Magomedov, Rabadan; Mamedov, Aslan M.; Melis, Eszter; Moiseyev, Vyacheslav; Molnár, Erika; Monge, Janet; Negrea, Octav; Nikolaeva, Nadezhda A.; Novak, Mario; Ochir-Goryaeva, Maria; Pálfi, György; Popovici, Sergiu; Rykun, Marina P.; Savenkova, Tatyana M.; Semibratov, Vladimir P.; Seregin, Nikolai N.; Šefčáková, Alena; Mussayeva, Raikhan S.; Shingiray, Irina; Shirokov, Vladimir N.; Simalcsik, Angela; Sirak, Kendra; Solodovnikov, Konstantin N.; Tárnoki, Judit; Tishkin, Alexey A.; Trifonov, Viktor; Vasilyev, Sergey; Candilio, Francesca; Cheronet, Olivia; Flegontova, Olga; Keating, Denise; Lawson, Ann Marie; Oppenheimer, Jonas; Qiu, Lijun; Workman, J. Noah; Zalzala, Fatma; Szécsényi-Nagy, Anna; Palamara, Pier Francesco; Mallick, Swapan; Rohland, Nadin; Pinhasi, Ron; Anthony, David; Vyazov, Leonid; Fournier, Romain; Ringbauer, Harald; Akbari, Ali; Brielle, Esther; Callan, Kimberly; Curtis, Elizabeth; Iliev, Lora; Kearns, Aisling; Mah, Matthew; Micco, Adam; Michel, Megan; Reich, DavidThe Yamnaya archaeological complex appeared around 3300 BCE across the steppes north of the Black and Caspian Seas, and by 3000 BCE reached its maximal extent from Hungary in the west to Kazakhstan in the east. To localize Yamnaya origins among preceding Eneolithic people, we assembled ancient DNA from 428 individuals, demonstrating three genetic clines. A “Caucasus-Lower Volga” (CLV) Cline suffused with Caucasus hunter-gatherer1 ancestry extended between a Caucasus Neolithic southern end, and a northern end at Berezhnovka along the Lower Volga river. Bidirectional gene flow created intermediate populations, such as north Caucasus Maikop people, and those at Remontnoye on the steppe. The “Volga Cline” was formed as CLV people mixed with upriver populations of Eastern hunter-gatherer2 ancestry, creating hyper-variable groups as at Khvalynsk. The “Dnipro Cline” was formed as CLV people moved west, mixing with Ukraine Neolithic hunter-gatherers3 along the Dnipro river to establish Serednii Stih groups from whom Yamnaya ancestors formed around 4000 BCE and grew explosively after 3750-3350 BCE. CLV people contributed four-fifths of the ancestry of the Yamnaya, and, entering Anatolia likely from the east, at least a tenth of the ancestry of Bronze Age Central Anatolians, where Hittite was spoken4,5. We thus propose that the final unity of the speakers of “Proto-Indo-Anatolian”, the language ancestral to both Anatolian and Indo-European, was among CLV people sometime between 4400-4000 BCE.