DLGNet: Hyperedge Classification through Directed Line Graphs for Chemical Reactions

Autor: Fiorini, Stefano, Bovolenta, Giulia M., Coniglio, Stefano, Ciavotta, Michele, Morerio, Pietro, Parrinello, Michele, Del Bue, Alessio

Graphs and hypergraphs provide powerful abstractions for modeling interactions among a set of entities of interest and have been attracting a growing interest in the literature thanks to many successful applications in several fields. In particular,

Externí odkaz: http://arxiv.org/abs/2410.06969

The need to implement FAIR principles in biomolecular simulations

Autor: Amaro, Rommie, Åqvist, Johan, Bahar, Ivet, Battistini, Federica, Bellaiche, Adam, Beltran, Daniel, Biggin, Philip C., Bonomi, Massimiliano, Bowman, Gregory R., Bryce, Richard, Bussi, Giovanni, Carloni, Paolo, Case, David, Cavalli, Andrea, Chang, Chie-En A., Cheatham III, Thomas E., Cheung, Margaret S., Chipot, Cris, Chong, Lillian T., Choudhary, Preeti, Cisneros, Gerardo Andres, Clementi, Cecilia, Collepardo-Guevara, Rosana, Coveney, Peter, Covino, Roberto, Crawford, T. Daniel, Peraro, Matteo Dal, de Groot, Bert, Delemotte, Lucie, De Vivo, Marco, Essex, Jonathan, Fraternali, Franca, Gao, Jiali, Gelpí, Josep Lluís, Gervasio, Francesco Luigi, Gonzalez-Nilo, Fernando Danilo, Grubmüller, Helmut, Guenza, Marina, Guzman, Horacio V., Harris, Sarah, Head-Gordon, Teresa, Hernandez, Rigoberto, Hospital, Adam, Huang, Niu, Huang, Xuhui, Hummer, Gerhard, Iglesias-Fernández, Javier, Jensen, Jan H., Jha, Shantenu, Jiao, Wanting, Jorgensen, William L., Kamerlin, Shina Caroline Lynn, Khalid, Syma, Laughton, Charles, Levitt, Michael, Limongelli, Vittorio, Lindahl, Erik, Lindorff-Larsen, Kresten, Loverde, Sharon, Lundborg, Magnus, Luo, Yun Lyna, Luque, Francisco Javier, Lynch, Charlotte I., MacKerell, Alexander, Magistrato, Alessandra, Marrink, Siewert J., Martin, Hugh, McCammon, J. Andrew, Merz, Kenneth, Moliner, Vicent, Mulholland, Adrian, Murad, Sohail, Naganathan, Athi N., Nangia, Shikha, Noe, Frank, Noy, Agnes, Oláh, Julianna, O'Mara, Megan, Ondrechen, Mary Jo, Onuchic, José N., Onufriev, Alexey, Osuna, Silvia, Panchenko, Anna R., Pantano, Sergio, Parish, Carol, Parrinello, Michele, Perez, Alberto, Perez-Acle, Tomas, Perilla, Juan R., Pettitt, B. Montgomery, Pietropalo, Adriana, Piquemal, Jean-Philip, Poma, Adolfo, Praprotnik, Matej, Ramos, Maria J., Ren, Pengyu, Reuter, Nathalie, Roitberg, Adrian, Rosta, Edina, Rovira, Carme, Roux, Benoit, Röthlisberger, Ursula, Sanbonmatsu, Karissa Y., Schlick, Tamar, Shaytan, Alexey K., Simmerling, Carlos, Smith, Jeremy C., Sugita, Yuji, Świderek, Katarzyna, Taiji, Makoto, Tao, Peng, Tikhonova, Irina G., Tirado-Rives, Julian, Tunón, Inaki, Van Der Kamp, Marc W., Van der Spoel, David, Velankar, Sameer, Voth, Gregory A., Wade, Rebecca, Warshel, Ariel, Welborn, Valerie Vaissier, Wetmore, Stacey, Wong, Chung F., Yang, Lee-Wei, Zacharias, Martin, Orozco, Modesto

This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a data

Externí odkaz: http://arxiv.org/abs/2407.16584

Computing the Committor with the Committor: an Anatomy of the Transition State Ensemble

Autor: Kang, Peilin, Trizio, Enrico, Parrinello, Michele

Determining the kinetic bottlenecks that make transitions between metastable states difficult is key to understanding important physical problems like crystallization, chemical reactions, or protein folding. In all these phenomena, the system spends

Externí odkaz: http://arxiv.org/abs/2401.05279

Effective Data-Driven Collective Variables for Free Energy Calculations from Metadynamics of Paths

Autor: Müllender, Lukas, Rizzi, Andrea, Parrinello, Michele, Carloni, Paolo, Mandelli, Davide

A variety of enhanced sampling methods predict multidimensional free energy landscapes associated with biological and other molecular processes as a function of a few selected collective variables (CVs). The accuracy of these methods is crucially dep

Externí odkaz: http://arxiv.org/abs/2311.05571

Ground observations of a space laser for the assessment of its in-orbit performance

Autor: The Pierre Auger Collaboration, Lux, O., Krisch, I., Reitebuch, O., Huber, D., Wernham, D., Parrinello, T., Halim, A. Abdul, Abreu, P., Aglietta, M., Allekotte, I., Cheminant, K. Almeida, Almela, A., Aloisio, R., Alvarez-Muñiz, J., Yebra, J. Ammerman, Anastasi, G. A., Anchordoqui, L., Andrada, B., Andringa, S., Anukriti, Apollonio, L., Aramo, C., Ferreira, P. R. Araújo, Arnone, E., Velázquez, J. C. Arteaga, Assis, P., Avila, G., Avocone, E., Badescu, A. M., Bakalova, A., Barbato, F., Mocellin, A. Bartz, Bellido, J. A., Berat, C., Bertaina, M. E., Bhatta, G., Bianciotto, M., Biermann, P. L., Binet, V., Bismark, K., Bister, T., Biteau, J., Blazek, J., Bleve, C., Blümer, J., Boháčová, M., Boncioli, D., Bonifazi, C., Arbeletche, L. Bonneau, Borodai, N., Brack, J., Orchera, P. G. Brichetto, Briechle, F. L., Bueno, A., Buitink, S., Buscemi, M., Bwembya, A., Büsken, M., Caballero-Mora, K. S., Cabana-Freire, S., Caccianiga, L., Caruso, R., Castellina, A., Catalani, F., Cataldi, G., Cazon, L., Cerda, M., Cermenati, A., Chinellato, J. A., Chudoba, J., Chytka, L., Clay, R. W., Cerutti, A. C. Cobos, Colalillo, R., Coleman, A., Coluccia, M. R., Conceição, R., Condorelli, A., Consolati, G., Conte, M., Convenga, F., Santos, D. Correia dos, Costa, P. J., Covault, C. E., Cristinziani, M., Sanchez, C. S. Cruz, Dasso, S., Daumiller, K., Dawson, B. R., de Almeida, R. M., de Jesús, J., de Jong, S. J., Neto, J. R. T. de Mello, De Mitri, I., de Oliveira, J., Franco, D. de Oliveira, de Palma, F., de Souza, V., de Errico, B. P. de Souza, De Vito, E., Del Popolo, A., Deligny, O., Denner, N., Deval, L., di Matteo, A., Dobre, M., Dobrigkeit, C., D'Olivo, J. C., Mendes, L. M. Domingues, Dorosti, Q., Anjos, J. C. dos, Anjos, R. C. dos, Ebr, J., Ellwanger, F., Emam, M., Engel, R., Epicoco, I., Erdmann, M., Etchegoyen, A., Evoli, C., Falcke, H., Farmer, J., Farrar, G., Fauth, A. C., Fazzini, N., Feldbusch, F., Fenu, F., Fernandes, A., Fick, B., Figueira, J. M., Filipčič, A., Fitoussi, T., Flaggs, B., Fodran, T., Fujii, T., Fuster, A., Galea, C., Galelli, C., García, B., Gaudu, C., Gemmeke, H., Gesualdi, F., Gherghel-Lascu, A., Ghia, P. L., Giaccari, U., Glombitza, J., Gobbi, F., Gollan, F., Golup, G., Gongora, J. P., González, J. M., González, N., Goos, I., Gorgi, A., Gottowik, M., Grubb, T. D., Guarino, F., Guedes, G. P., Guido, E., Berisso, M. Gómez, Vitale, P. F. Gómez, Góra, D., Gülzow, L., Hahn, S., Hamal, P., Hampel, M. R., Hansen, P., Harari, D., Harvey, V. M., Haungs, A., Hebbeker, T., Hojvat, C., Horvath, P., Hrabovský, M., Huege, T., Hörandel, J. R., Insolia, A., Isar, P. G., Janecek, P., Johnsen, J. A., Jurysek, J., Kampert, K. H., Keilhauer, B., Khakurdikar, A., Covilakam, V. V. Kizakke, Klages, H. O., Kleifges, M., Knapp, F., Kunka, N., Köhler, J., Lago, B. L., Langner, N., de Oliveira, M. A. Leigui, Lema-Capeans, Y., Letessier-Selvon, A., Lhenry-Yvon, I., Lopes, L., Lu, L., Luce, Q., Lundquist, J. P., Payeras, A. Machado, Majercakova, M., Mandat, D., Manning, B. C., Mantsch, P., Marafico, S., Mariani, F. M., Mariazzi, A. G., Mariş, I. C., Marsella, G., Martello, D., Martinelli, S., Martins, M. A., Bravo, O. Martínez, Mathes, H. J., Matthews, J., Matthiae, G., Mayotte, E., Mayotte, S., Mazur, P. O., Medina-Tanco, G., Meinert, J., Melo, D., Menshikov, A., Merx, C., Michal, S., Micheletti, M. I., Miramonti, L., Mollerach, S., Montanet, F., Morejon, L., Morello, C., Mulrey, K., Mussa, R., Namasaka, W. M., Negi, S., Nellen, L., Nguyen, K., Nicora, G., Niechciol, M., Nitz, D., Nosek, D., Novotny, V., Nožka, L., Nucita, A., Núñez, L. A., Oliveira, C., Palatka, M., Pallotta, J., Panja, S., Parente, G., Paulsen, T., Pawlowsky, J., Pech, M., Pelayo, R., Pereira, L. A. S., Martins, E. E. Pereira, Armand, J. Perez, Perrone, L., Petrera, S., Petrucci, C., Pierog, T., Pimenta, M., Platino, M., Pont, B., Pothast, M., Shahvar, M. Pourmohammad, Privitera, P., Prouza, M., Puyleart, A., Bertolli, C. Pérez, Pękala, J., Querchfeld, S., Rautenberg, J., Ravignani, D., Akim, J. V. Reginatto, Reininghaus, M., Ridky, J., Riehn, F., Risse, M., Rizi, V., de Carvalho, W. Rodrigues, Rodriguez, E., Rojo, J. Rodriguez, Roncoroni, M. J., Rossoni, S., Roth, M., Roulet, E., Rovero, A. C., Ruehl, P., Saftoiu, A., Saharan, M., Salamida, F., Salazar, H., Salina, G., Gomez, J. D. Sanabria, Santos, E. M., Santos, E., Sarazin, F., Sarmento, R., Sato, R., Savina, P., Scherini, V., Schieler, H., Schimassek, M., Schimp, M., Schmidt, D., Scholten, O., Schoorlemmer, H., Schovánek, P., Schröder, F. G., Schulte, J., Schulz, T., Schäfer, C. M., Sciutto, S. J., Scornavacche, M., Segreto, A., Sehgal, S., Shivashankara, S. U., Sigl, G., Silli, G., Sima, O., Simkova, K., Simon, F., Smau, R., Šmída, R., Sommers, P., Soriano, J. F., Squartini, R., Stadelmaier, M., Stanič, S., Stasielak, J., Stassi, P., Straub, M., Strähnz, S., Suomijärvi, T., Supanitsky, A. D., Svozilikova, Z., Szadkowski, Z., Sánchez, F., Tairli, F., Tapia, A., Taricco, C., Timmermans, C., Tkachenko, O., Tobiska, P., Peixoto, C. J. Todero, Tomé, B., Torrès, Z., Travaini, A., Travnicek, P., Trimarelli, C., Tueros, M., Unger, M., Vaclavek, L., Vacula, M., Galicia, J. F. Valdés, Valore, L., Varela, E., Veberič, D., Ventura, C., Quispe, I. D. Vergara, Verzi, V., Vicha, J., Vink, J., Vlastimil, J., Vorobiov, S., Vásquez-Ramírez, A., Watanabe, C., Watson, A. A., Weindl, A., Wiencke, L., Wilczyński, H., Wittkowski, D., Wundheiler, B., Yue, B., Yushkov, A., Zapparrata, O., Zas, E., Zavrtanik, D., Zavrtanik, M.

The wind mission Aeolus of the European Space Agency was a groundbreaking achievement for Earth observation. Between 2018 and 2023, the space-borne lidar instrument ALADIN onboard the Aeolus satellite measured atmospheric wind profiles with global co

Externí odkaz: http://arxiv.org/abs/2310.08616