Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation

Autor: Hao-Bo Guo, Vanessa A. Varaljay, Gary Kedziora, Kimberly Taylor, Sanaz Farajollahi, Nina Lombardo, Eric Harper, Chia Hung, Marie Gross, Alexander Perminov, Patrick Dennis, Nancy Kelley-Loughnane, Rajiv Berry

Publikováno v: Scientific Reports, Vol 13, Iss 1, Pp 1-11 (2023)

Abstract Despite the success of AlphaFold2 (AF2), it is unclear how AF2 models accommodate for ligand binding. Here, we start with a protein sequence from Acidimicrobiaceae TMED77 (T7RdhA) with potential for catalyzing the degradation of per- and pol

Externí odkaz: https://doaj.org/article/431950e19a134e218e73e62dcc282d68

AlphaFold2 models indicate that protein sequence determines both structure and dynamics

Autor: Hao-Bo Guo, Alexander Perminov, Selemon Bekele, Gary Kedziora, Sanaz Farajollahi, Vanessa Varaljay, Kevin Hinkle, Valeria Molinero, Konrad Meister, Chia Hung, Patrick Dennis, Nancy Kelley-Loughnane, Rajiv Berry

Publikováno v: Scientific Reports, Vol 12, Iss 1, Pp 1-15 (2022)

Abstract AlphaFold 2 (AF2) has placed Molecular Biology in a new era where we can visualize, analyze and interpret the structures and functions of all proteins solely from their primary sequences. We performed AF2 structure predictions for various pr

Externí odkaz: https://doaj.org/article/4a27d885751d48129fa8912d727ea523

Demonstrating dynamic surface codes

Autor: Eickbusch, Alec, McEwen, Matt, Sivak, Volodymyr, Bourassa, Alexandre, Atalaya, Juan, Claes, Jahan, Kafri, Dvir, Gidney, Craig, Warren, Christopher W., Gross, Jonathan, Opremcak, Alex, Miao, Nicholas Zobrist Kevin C., Roberts, Gabrielle, Satzinger, Kevin J., Bengtsson, Andreas, Neeley, Matthew, Livingston, William P., Greene, Alex, Rajeev, Acharya, Beni, Laleh Aghababaie, Aigeldinger, Georg, Alcaraz, Ross, Andersen, Trond I., Ansmann, Markus, Frank, Arute, Arya, Kunal, Asfaw, Abraham, Babbush, Ryan, Ballard, Brian, Bardin, Joseph C., Bilmes, Alexander, Jenna, Bovaird, Bowers, Dylan, Brill, Leon, Broughton, Michael, Browne, David A., Buchea, Brett, Buckley, Bob B., Tim, Burger, Burkett, Brian, Bushnell, Nicholas, Cabrera, Anthony, Campero, Juan, Chang, Hung-Shen, Chiaro, Ben, Chih, Liang-Ying, Cleland, Agnetta Y., Cogan, Josh, Collins, Roberto, Conner, Paul, Courtney, William, Alexander, Crook, L., Curtin, Ben, Das, Sayan, Barba, Alexander Del Toro, Demura, Sean, De Lorenzo, Laura, Di Paolo, Agustin, Donohoe, Paul, Drozdov, Ilya K., Dunsworth, Andrew, Elbag, Aviv Moshe, Elzouka, Mahmoud, Erickson, Catherine, Ferreira, Vinicius S., Burgos, Leslie Flores, Forati, Ebrahim, Fowler, Austin G., Foxen, Brooks, Ganjam, Suhas, Gonzalo, Garcia, Gasca, Robert, Genois, Élie, Giang, William, Gilboa, Dar, Gosula, Raja, Dau, Alejandro Grajales, Dietrich, Graumann, Ha, Tan, Habegger, Steve, Hansen, Monica, Harrigan, Matthew P., Harrington, Sean D., Heslin, Stephen, Heu, Paula, Higgott, Oscar, Hiltermann, Reno, Hilton, Jeremy, Huang, Hsin-Yuan, Huff, Ashley, Huggins, William J., Jeffrey, Evan, Jiang, Zhang, Jin, Xiaoxuan, Jones, Cody, Joshi, Chaitali, Juhas, Pavol, Kabel, Andreas, Kang, Hui, Amir, Karamlou, H., Kechedzhi, Kostyantyn, Khaire, Trupti, Khattar, Tanuj, Khezri, Mostafa, Kim, Seon, Kobrin, Bryce, Korotkov, Alexander N., Kostritsa, Fedor, Kreikebaum, John Mark, Kurilovich, Vladislav D., Landhuis, David, Tiano, Lange-Dei, Langley, Brandon W., Lau, Kim-Ming, Ledford, Justin, Lee, Kenny, Lester, Brian J., Guevel, Loïck Le, Wing, Li, Yan, Lill, Alexander T., Locharla, Aditya, Lucero, Erik, Lundahl, Daniel, Lunt, Aaron, Madhuk, Sid, Maloney, Ashley, Mandrà, Salvatore, Martin, Leigh S., Martin, Orion, Maxfield, Cameron, McClean, Jarrod R., Meeks, Seneca, Anthony, Megrant, Molavi, Reza, Molina, Sebastian, Montazeri, Shirin, Movassagh, Ramis, Newman, Michael, Nguyen, Anthony, Nguyen, Murray, Ni, Chia-Hung, Oas, Logan, Orosco, Raymond, Ottosson, Kristoffer, Pizzuto, Alex, Potter, Rebecca, Pritchard, Orion, Quintana, Chris, Ramachandran, Ganesh, Reagor, Matthew J., Rhodes, David M., Rosenberg, Eliott, Rossi, Elizabeth, Sankaragomathi, Kannan, Schurkus, Henry F., Shearn, Michael J., Shorter, Aaron, Shutty, Noah, Shvarts, Vladimir, Small, Spencer, Smith, W. Clarke, Springer, Sofia, Sterling, George, Suchard, Jordan, Szasz, Aaron, Sztein, Alex, Thor, Douglas, Tomita, Eifu, Torres, Alfredo, Torunbalci, M. Mert, Vaishnav, Abeer, Vargas, Justin, Sergey, Vdovichev, Vidal, Guifre, Heidweiller, Catherine Vollgraff, Waltman, Steven, Waltz, Jonathan, Wang, Shannon X., Ware, Brayden, Weidel, Travis, White, Theodore, Wong, Kristi, Woo, Bryan W. K., Woodson, Maddy, Xing, Cheng, Yao, Z. Jamie, Yeh, Ping, Ying, Bicheng, Yoo, Juhwan, Yosri, Noureldin, Young, Grayson, Zalcman, Adam, Yaxing, Zhang, Zhu, Ningfeng, Boixo, Sergio, Kelly, Julian, Smelyanskiy, Vadim, Neven, Hartmut, Bacon, Dave, Chen, Zijun, Klimov, Paul V., Roushan, Pedram, Neill, Charles, Chen, Yu, Morvan, Alexis

A remarkable characteristic of quantum computing is the potential for reliable computation despite faulty qubits. This can be achieved through quantum error correction, which is typically implemented by repeatedly applying static syndrome checks, per

Externí odkaz: http://arxiv.org/abs/2412.14360

Observation of disorder-free localization and efficient disorder averaging on a quantum processor

Autor: Gyawali, Gaurav, Cochran, Tyler, Lensky, Yuri, Rosenberg, Eliott, Karamlou, Amir H., Kechedzhi, Kostyantyn, Berndtsson, Julia, Westerhout, Tom, Asfaw, Abraham, Abanin, Dmitry, Acharya, Rajeev, Beni, Laleh Aghababaie, Andersen, Trond I., Ansmann, Markus, Arute, Frank, Arya, Kunal, Astrakhantsev, Nikita, Atalaya, Juan, Babbush, Ryan, Ballard, Brian, Bardin, Joseph C., Bengtsson, Andreas, Bilmes, Alexander, Bortoli, Gina, Bourassa, Alexandre, Bovaird, Jenna, Brill, Leon, Broughton, Michael, Browne, David A., Buchea, Brett, Buckley, Bob B., Buell, David A., Burger, Tim, Burkett, Brian, Bushnell, Nicholas, Cabrera, Anthony, Campero, Juan, Chang, Hung-Shen, Chen, Zijun, Chiaro, Ben, Claes, Jahan, Cleland, Agnetta Y., Cogan, Josh, Collins, Roberto, Conner, Paul, Courtney, William, Crook, Alexander L., Das, Sayan, Debroy, Dripto M., De Lorenzo, Laura, Barba, Alexander Del Toro, Demura, Sean, Di Paolo, Agustin, Donohoe, Paul, Drozdov, Ilya, Dunsworth, Andrew, Earle, Clint, Eickbusch, Alec, Elbag, Aviv Moshe, Elzouka, Mahmoud, Erickson, Catherine, Faoro, Lara, Fatemi, Reza, Ferreira, Vinicius S., Burgos, Leslie Flores, Forati, Ebrahim, Fowler, Austin G., Foxen, Brooks, Ganjam, Suhas, Gasca, Robert, Giang, William, Gidney, Craig, Gilboa, Dar, Gosula, Raja, Dau, Alejandro Grajales, Graumann, Dietrich, Greene, Alex, Gross, Jonathan A., Habegger, Steve, Hamilton, Michael C., Hansen, Monica, Harrigan, Matthew P., Harrington, Sean D., Heslin, Stephen, Heu, Paula, Hill, Gordon, Hilton, Jeremy, Hoffmann, Markus R., Huang, Hsin-Yuan, Huff, Ashley, Huggins, William J., Ioffe, Lev B., Isakov, Sergei V., Jeffrey, Evan, Jiang, Zhang, Jones, Cody, Jordan, Stephen, Joshi, Chaitali, Juhas, Pavol, Kafri, Dvir, Kang, Hui, Khaire, Trupti, Khattar, Tanuj, Khezri, Mostafa, Kieferová, Mária, Kim, Seon, Klimov, Paul V., Klots, Andrey R., Kobrin, Bryce, Korotkov, Alexander N., Kostritsa, Fedor, Kreikebaum, John Mark, Kurilovich, Vladislav D., Landhuis, David, Lange-Dei, Tiano, Langley, Brandon W., Laptev, Pavel, Lau, Kim-Ming, Guevel, Loïck Le, Ledford, Justin, Lee, Joonho, Lee, Kenny, Lester, Brian J., Li, Wing Yan, Lill, Alexander T., Liu, Wayne, Livingston, William P., Locharla, Aditya, Lundahl, Daniel, Lunt, Aaron, Madhuk, Sid, Maloney, Ashley, Mandrà, Salvatore, Martin, Leigh S., Martin, Steven, Martin, Orion, Maxfield, Cameron, McClean, Jarrod R., McEwen, Matt, Meeks, Seneca, Megrant, Anthony, Mi, Xiao, Miao, Kevin C., Mieszala, Amanda, Molina, Sebastian, Montazeri, Shirin, Morvan, Alexis, Movassagh, Ramis, Neill, Charles, Nersisyan, Ani, Newman, Michael, Nguyen, Anthony, Nguyen, Murray, Ni, Chia-Hung, Niu, Murphy Yuezhen, Oliver, William D., Ottosson, Kristoffer, Pizzuto, Alex, Potter, Rebecca, Pritchard, Orion, Pryadko, Leonid P., Quintana, Chris, Reagor, Matthew J., Rhodes, David M., Roberts, Gabrielle, Rocque, Charles, Rubin, Nicholas C., Saei, Negar, Sankaragomathi, Kannan, Satzinger, Kevin J., Schurkus, Henry F., Schuster, Christopher, Shearn, Michael J., Shorter, Aaron, Shutty, Noah, Shvarts, Vladimir, Sivak, Volodymyr, Skruzny, Jindra, Small, Spencer, Smith, W. Clarke, Springer, Sofia, Sterling, George, Suchard, Jordan, Szalay, Marco, Szasz, Aaron, Sztein, Alex, Thor, Douglas, Torunbalci, M. Mert, Vaishnav, Abeer, Vdovichev, Sergey, Vidal, Guifré, Heidweiller, Catherine Vollgraff, Waltman, Steven, Wang, Shannon X., White, Theodore, Wong, Kristi, Woo, Bryan W. K., Xing, Cheng, Yao, Z. Jamie, Yeh, Ping, Ying, Bicheng, Yoo, Juhwan, Yosri, Noureldin, Young, Grayson, Zalcman, Adam, Zhang, Yaxing, Zhu, Ningfeng, Zobrist, Nicholas, Boixo, Sergio, Kelly, Julian, Lucero, Erik, Chen, Yu, Smelyanskiy, Vadim, Neven, Hartmut, Kovrizhin, Dmitry, Knolle, Johannes, Halimeh, Jad C., Aleiner, Igor, Moessner, Roderich, Roushan, Pedram

One of the most challenging problems in the computational study of localization in quantum manybody systems is to capture the effects of rare events, which requires sampling over exponentially many disorder realizations. We implement an efficient pro

Externí odkaz: http://arxiv.org/abs/2410.06557

Quantum error correction below the surface code threshold

Autor: Acharya, Rajeev, Aghababaie-Beni, Laleh, Aleiner, Igor, Andersen, Trond I., Ansmann, Markus, Arute, Frank, Arya, Kunal, Asfaw, Abraham, Astrakhantsev, Nikita, Atalaya, Juan, Babbush, Ryan, Bacon, Dave, Ballard, Brian, Bardin, Joseph C., Bausch, Johannes, Bengtsson, Andreas, Bilmes, Alexander, Blackwell, Sam, Boixo, Sergio, Bortoli, Gina, Bourassa, Alexandre, Bovaird, Jenna, Brill, Leon, Broughton, Michael, Browne, David A., Buchea, Brett, Buckley, Bob B., Buell, David A., Burger, Tim, Burkett, Brian, Bushnell, Nicholas, Cabrera, Anthony, Campero, Juan, Chang, Hung-Shen, Chen, Yu, Chen, Zijun, Chiaro, Ben, Chik, Desmond, Chou, Charina, Claes, Jahan, Cleland, Agnetta Y., Cogan, Josh, Collins, Roberto, Conner, Paul, Courtney, William, Crook, Alexander L., Curtin, Ben, Das, Sayan, Davies, Alex, De Lorenzo, Laura, Debroy, Dripto M., Demura, Sean, Devoret, Michel, Di Paolo, Agustin, Donohoe, Paul, Drozdov, Ilya, Dunsworth, Andrew, Earle, Clint, Edlich, Thomas, Eickbusch, Alec, Elbag, Aviv Moshe, Elzouka, Mahmoud, Erickson, Catherine, Faoro, Lara, Farhi, Edward, Ferreira, Vinicius S., Burgos, Leslie Flores, Forati, Ebrahim, Fowler, Austin G., Foxen, Brooks, Ganjam, Suhas, Garcia, Gonzalo, Gasca, Robert, Genois, Élie, Giang, William, Gidney, Craig, Gilboa, Dar, Gosula, Raja, Dau, Alejandro Grajales, Graumann, Dietrich, Greene, Alex, Gross, Jonathan A., Habegger, Steve, Hall, John, Hamilton, Michael C., Hansen, Monica, Harrigan, Matthew P., Harrington, Sean D., Heras, Francisco J. H., Heslin, Stephen, Heu, Paula, Higgott, Oscar, Hill, Gordon, Hilton, Jeremy, Holland, George, Hong, Sabrina, Huang, Hsin-Yuan, Huff, Ashley, Huggins, William J., Ioffe, Lev B., Isakov, Sergei V., Iveland, Justin, Jeffrey, Evan, Jiang, Zhang, Jones, Cody, Jordan, Stephen, Joshi, Chaitali, Juhas, Pavol, Kafri, Dvir, Kang, Hui, Karamlou, Amir H., Kechedzhi, Kostyantyn, Kelly, Julian, Khaire, Trupti, Khattar, Tanuj, Khezri, Mostafa, Kim, Seon, Klimov, Paul V., Klots, Andrey R., Kobrin, Bryce, Kohli, Pushmeet, Korotkov, Alexander N., Kostritsa, Fedor, Kothari, Robin, Kozlovskii, Borislav, Kreikebaum, John Mark, Kurilovich, Vladislav D., Lacroix, Nathan, Landhuis, David, Lange-Dei, Tiano, Langley, Brandon W., Laptev, Pavel, Lau, Kim-Ming, Guevel, Loïck Le, Ledford, Justin, Lee, Kenny, Lensky, Yuri D., Leon, Shannon, Lester, Brian J., Li, Wing Yan, Li, Yin, Lill, Alexander T., Liu, Wayne, Livingston, William P., Locharla, Aditya, Lucero, Erik, Lundahl, Daniel, Lunt, Aaron, Madhuk, Sid, Malone, Fionn D., Maloney, Ashley, Mandrá, Salvatore, Martin, Leigh S., Martin, Steven, Martin, Orion, Maxfield, Cameron, McClean, Jarrod R., McEwen, Matt, Meeks, Seneca, Megrant, Anthony, Mi, Xiao, Miao, Kevin C., Mieszala, Amanda, Molavi, Reza, Molina, Sebastian, Montazeri, Shirin, Morvan, Alexis, Movassagh, Ramis, Mruczkiewicz, Wojciech, Naaman, Ofer, Neeley, Matthew, Neill, Charles, Nersisyan, Ani, Neven, Hartmut, Newman, Michael, Ng, Jiun How, Nguyen, Anthony, Nguyen, Murray, Ni, Chia-Hung, O'Brien, Thomas E., Oliver, William D., Opremcak, Alex, Ottosson, Kristoffer, Petukhov, Andre, Pizzuto, Alex, Platt, John, Potter, Rebecca, Pritchard, Orion, Pryadko, Leonid P., Quintana, Chris, Ramachandran, Ganesh, Reagor, Matthew J., Rhodes, David M., Roberts, Gabrielle, Rosenberg, Eliott, Rosenfeld, Emma, Roushan, Pedram, Rubin, Nicholas C., Saei, Negar, Sank, Daniel, Sankaragomathi, Kannan, Satzinger, Kevin J., Schurkus, Henry F., Schuster, Christopher, Senior, Andrew W., Shearn, Michael J., Shorter, Aaron, Shutty, Noah, Shvarts, Vladimir, Singh, Shraddha, Sivak, Volodymyr, Skruzny, Jindra, Small, Spencer, Smelyanskiy, Vadim, Smith, W. Clarke, Somma, Rolando D., Springer, Sofia, Sterling, George, Strain, Doug, Suchard, Jordan, Szasz, Aaron, Sztein, Alex, Thor, Douglas, Torres, Alfredo, Torunbalci, M. Mert, Vaishnav, Abeer, Vargas, Justin, Vdovichev, Sergey, Vidal, Guifre, Villalonga, Benjamin, Heidweiller, Catherine Vollgraff, Waltman, Steven, Wang, Shannon X., Ware, Brayden, Weber, Kate, White, Theodore, Wong, Kristi, Woo, Bryan W. K., Xing, Cheng, Yao, Z. Jamie, Yeh, Ping, Ying, Bicheng, Yoo, Juhwan, Yosri, Noureldin, Young, Grayson, Zalcman, Adam, Zhang, Yaxing, Zhu, Ningfeng, Zobrist, Nicholas

Quantum error correction provides a path to reach practical quantum computing by combining multiple physical qubits into a logical qubit, where the logical error rate is suppressed exponentially as more qubits are added. However, this exponential sup

Externí odkaz: http://arxiv.org/abs/2408.13687