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1. The need to implement FAIR principles in biomolecular simulations

Author

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, and Orozco, Modesto

Subjects
Quantitative Biology - Biomolecules
Abstract

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 database that allows findability, accessibility, interoperability, and reusability of molecular dynamics simulation data. Such a development would democratize the field and significantly improve the impact of MD simulations on life science research. This will transform our working paradigm, pushing the field to a new frontier. We invite you to support our initiative at the MDDB community (https://mddbr.eu/community/)

Published
2024

2. Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

Author

Lawson, Catherine L., Kryshtafovych, Andriy, Pintilie, Grigore D., Burley, Stephen K., Černý, Jiří, Chen, Vincent B., Emsley, Paul, Gobbi, Alberto, Joachimiak, Andrzej, Noreng, Sigrid, Prisant, Michael G., Read, Randy J., Richardson, Jane S., Rohou, Alexis L., Schneider, Bohdan, Sellers, Benjamin D., Shao, Chenghua, Sourial, Elizabeth, Williams, Chris I., Williams, Christopher J., Yang, Ying, Abbaraju, Venkat, Afonine, Pavel V., Baker, Matthew L., Bond, Paul S., Blundell, Tom L., Burnley, Tom, Campbell, Arthur, Cao, Renzhi, Cheng, Jianlin, Chojnowski, Grzegorz, Cowtan, K. D., DiMaio, Frank, Esmaeeli, Reza, Giri, Nabin, Grubmüller, Helmut, Hoh, Soon Wen, Hou, Jie, Hryc, Corey F., Hunte, Carola, Igaev, Maxim, Joseph, Agnel P., Kao, Wei-Chun, Kihara, Daisuke, Kumar, Dilip, Lang, Lijun, Lin, Sean, Maddhuri Venkata Subramaniya, Sai R., Mittal, Sumit, Mondal, Arup, Moriarty, Nigel W., Muenks, Andrew, Murshudov, Garib N., Nicholls, Robert A., Olek, Mateusz, Palmer, Colin M., Perez, Alberto, Pohjolainen, Emmi, Pothula, Karunakar R., Rowley, Christopher N., Sarkar, Daipayan, Schäfer, Luisa U., Schlicksup, Christopher J., Schröder, Gunnar F., Shekhar, Mrinal, Si, Dong, Singharoy, Abhishek, Sobolev, Oleg V., Terashi, Genki, Vaiana, Andrea C., Vedithi, Sundeep C., Verburgt, Jacob, Wang, Xiao, Warshamanage, Rangana, Winn, Martyn D., Weyand, Simone, Yamashita, Keitaro, Zhao, Minglei, Schmid, Michael F., Berman, Helen M., and Chiu, Wah

Published
2024
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6. A Platform for Ultra-fast Proton Probing of Matter in Extreme Conditions

Author

Volpe, Luca, Perez, Alberto, Cebriano, Teresa, Sánchez, Carlos Sánchez, Malko, Sofia, Curcio, Alessandro, and Khetari, Samia

Subjects
Physics - Plasma Physics, High Energy Physics - Experiment
Abstract

Recent development of Ultra short and Intense laser system paved the way for the generation of short and brilliant proton sources that can be used to study plasmas at extreme conditions in the context of High Energy Density physics. Energy selection, focusing and transport of such sources is still a challenge that is not completely solved. here we present a novel and simple design for a isochrone magnetic selector capable of angular and energy selection of proton sources by drastically reducing the temporal spread if compared with the state of the art. The isochrone selector is demanded for studying proton stopping power in Warm Dense Matter close to the Bragg peak (proton energy below 1 MeV) where the reduced investigated masses imply a short plasma stagnation time ($<$ 100 ps). The proposed selector can also be used at higher proton energy by pushing the final time spread at the level of few ps with important implications for the study of coherent energy deposition in biology and medical physics. Analytical estimations and Monte Carlo simulations are presented to validate the proposed configurations., Comment: 9 Pages, 7 figures

Published
2023

10. Analysis and Impact of Training Set Size in Cross-Subject Human Activity Recognition

Author

Matey-Sanz, Miguel, Torres-Sospedra, Joaquín, González-Pérez, Alberto, Casteleyn, Sven, Granell, Carlos, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Vasconcelos, Verónica, editor, Domingues, Inês, editor, and Paredes, Simão, editor

Published
2024
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11. Automated Defect Recognition of Castings defects using Neural Networks

Author

García-Pérez, Alberto, Gómez-Silva, María José, and de la Escalera, Arturo

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Industrial X-ray analysis is common in aerospace, automotive or nuclear industries where structural integrity of some parts needs to be guaranteed. However, the interpretation of radiographic images is sometimes difficult and may lead to two experts disagree on defect classification. The Automated Defect Recognition (ADR) system presented herein will reduce the analysis time and will also help reducing the subjective interpretation of the defects while increasing the reliability of the human inspector. Our Convolutional Neural Network (CNN) model achieves 94.2\% accuracy (mAP@IoU=50\%), which is considered as similar to expected human performance, when applied to an automotive aluminium castings dataset (GDXray), exceeding current state of the art for this dataset. On an industrial environment, its inference time is less than 400 ms per DICOM image, so it can be installed on production facilities with no impact on delivery time. In addition, an ablation study of the main hyper-parameters to optimise model accuracy from the initial baseline result of 75\% mAP up to 94.2\% mAP, was also conducted., Comment: This preprint has not undergone peer review (when applicable) or any post-submission improvements or corrections. The Version of Record of this article is published in Journal of Nondestructive Evaluation, and is available online at https://doi.org/10.1007/s10921-021-00842-1

Published
2022
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18. Author Correction: Predicting the potential for zoonotic transmission and host associations for novel viruses

Author

Pandit, Pranav S., Anthony, Simon J., Goldstein, Tracey, Olival, Kevin J., Doyle, Megan M., Gardner, Nicole R., Bird, Brian, Smith, Woutrina, Wolking, David, Gilardi, Kirsten, Monagin, Corina, Kelly, Terra, Uhart, Marcela M., Epstein, Jonathan H., Machalaba, Catherine, Rostal, Melinda K., Dawson, Patrick, Hagan, Emily, Sullivan, Ava, Li, Hongying, Chmura, Aleksei A., Latinne, Alice, Lange, Christian, O’Rourke, Tammie, Olson, Sarah, Keatts, Lucy, Mendoza, A. Patricia, Perez, Alberto, de Paula, Cátia Dejuste, Zimmerman, Dawn, Valitutto, Marc, LeBreton, Matthew, McIver, David, Islam, Ariful, Duong, Veasna, Mouiche, Moctar, Shi, Zhengli, Mulembakani, Prime, Kumakamba, Charles, Ali, Mohamed, Kebede, Nigatu, Tamoufe, Ubald, Bel-Nono, Samuel, Camara, Alpha, Pamungkas, Joko, Coulibaly, Kalpy J., Abu-Basha, Ehab, Kamau, Joseph, Silithammavong, Soubanh, Desmond, James, Hughes, Tom, Shiilegdamba, Enkhtuvshin, Aung, Ohnmar, Karmacharya, Dibesh, Nziza, Julius, Ndiaye, Daouda, Gbakima, Aiah, sajali, Zikankuba, Wacharapluesadee, Supaporn, Robles, Erika Alandia, Ssebide, Benard, Suzán, Gerardo, Aguirre, Luis F., Solorio, Monica R., Dhole, Tapan N., Nga, Nguyen T. T., Hitchens, Peta L., Joly, Damien O., Saylors, Karen, Fine, Amanda, Murray, Suzan, Karesh, William B., Daszak, Peter, Mazet, Jonna A. K., and Johnson, Christine K.

Published
2023
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19. Numerical analysis of electrohydrodynamic (EHD) instability in dielectric liquid-gas flows subjected to unipolar injection

Author

Liu, Qiang, Pérez, Alberto T., Selvakumar, R. Deepak, Yang, Pengfei, and Wu, Jian

Subjects
Physics - Fluid Dynamics, 76W05 (Primary) 76E25, 76T10 (Secondary)
Abstract

In this work, the electrohydrodynamic (EHD) instability induced by a unipolar charge injection is extended from a single-phase dielectric liquid to a two-phase system that consists of a liquid-air interface. A volume of fluid (VOF) model based two-phase solver was developed with simplified Maxwell equations implemented in the open-source platform OpenFOAM\textsuperscript. The numerically obtained critical value for the linear stability matches well with the theoretical values. To highlight the effect of the slip boundary at interface, the deformation of the interface is ignored. A bifurcation diagram with hysteresis loop linking the linear and finite amplitude criteria, which is Uf = 0.059, was obtained in this situation. It is concluded that the lack of viscous effect at interface leads to a significant increase in the flow intensity, which is the reason for the smaller instability threshold in two-phase system. The presence of interface also changes the flow structure and makes the flow vortices shift closer to the interface., Comment: 14 pages, 14 figures

Published
2021
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23. Predicting the potential for zoonotic transmission and host associations for novel viruses

Author

Pandit, Pranav S, Anthony, Simon J, Goldstein, Tracey, Olival, Kevin J, Doyle, Megan M, Gardner, Nicole R, Bird, Brian, Smith, Woutrina, Wolking, David, Gilardi, Kirsten, Monagin, Corina, Kelly, Terra, Uhart, Marcela M, Epstein, Jonathan H, Machalaba, Catherine, Rostal, Melinda K, Dawson, Patrick, Hagan, Emily, Sullivan, Ava, Li, Hongying, Chmura, Aleksei A, Latinne, Alice, Lange, Christian, O’Rourke, Tammie, Olson, Sarah, Keatts, Lucy, Mendoza, A Patricia, Perez, Alberto, de Paula, Cátia Dejuste, Zimmerman, Dawn, Valitutto, Marc, LeBreton, Matthew, McIver, David, Islam, Ariful, Duong, Veasna, Mouiche, Moctar, Shi, Zhengli, Mulembakani, Prime, Kumakamba, Charles, Ali, Mohamed, Kebede, Nigatu, Tamoufe, Ubald, Bel-Nono, Samuel, Camara, Alpha, Pamungkas, Joko, Coulibaly, Kalpy J, Abu-Basha, Ehab, Kamau, Joseph, Silithammavong, Soubanh, Desmond, James, Hughes, Tom, Shiilegdamba, Enkhtuvshin, Aung, Ohnmar, Karmacharya, Dibesh, Nziza, Julius, Ndiaye, Daouda, Gbakima, Aiah, Sajali, Zikankuba, Wacharapluesadee, Supaporn, Robles, Erika Alandia, Ssebide, Benard, Suzán, Gerardo, Aguirre, Luis F, Solorio, Monica R, Dhole, Tapan N, Nga, Nguyen TT, Hitchens, Peta L, Joly, Damien O, Saylors, Karen, Fine, Amanda, Murray, Suzan, Karesh, William B, Daszak, Peter, Mazet, Jonna AK, and Johnson, Christine K

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Infectious Diseases, Emerging Infectious Diseases, Prevention, 2.1 Biological and endogenous factors, 2.2 Factors relating to the physical environment, Aetiology, Infection, Africa, Animals, Animals, Wild, Host Specificity, Humans, Viruses, Zoonoses, PREDICT Consortium, Biological sciences, Biomedical and clinical sciences
Abstract

Host-virus associations have co-evolved under ecological and evolutionary selection pressures that shape cross-species transmission and spillover to humans. Observed virus-host associations provide relevant context for newly discovered wildlife viruses to assess knowledge gaps in host-range and estimate pathways for potential human infection. Using models to predict virus-host networks, we predicted the likelihood of humans as hosts for 513 newly discovered viruses detected by large-scale wildlife surveillance at high-risk animal-human interfaces in Africa, Asia, and Latin America. Predictions indicated that novel coronaviruses are likely to infect a greater number of host species than viruses from other families. Our models further characterize novel viruses through prioritization scores and directly inform surveillance targets to identify host ranges for newly discovered viruses.

Published
2022

24. Deep Recurrent Neural Network Performing Spectral Recurrence on Hyperspectral Images for Brain Tissue Classification

Author

Cebrián, Pedro L., Martín-Pérez, Alberto, Villa, Manuel, Sancho, Jaime, Rosa, Gonzalo, Vazquez, Guillermo, Sutradhar, Pallab, Martinez de Ternero, Alejandro, Chavarrías, Miguel, Lagares, Alfonso, Juarez, Eduardo, Sanz, César, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Chavarrías, Miguel, editor, and Rodríguez, Alfonso, editor

Published
2023
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25. Brain Blood Vessel Segmentation in Hyperspectral Images Through Linear Operators

Author

Vazquez, Guillermo, Villa, Manuel, Martín-Pérez, Alberto, Sancho, Jaime, Rosa, Gonzalo, Cebrián, Pedro L., Sutradhar, Pallab, Ternero, Alejandro Martinez de, Chavarrías, Miguel, Lagares, Alfonso, Juarez, Eduardo, Sanz, César, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Chavarrías, Miguel, editor, and Rodríguez, Alfonso, editor

Published
2023
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26. CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

Author

Shekhar, Mrinal, Terashi, Genki, Gupta, Chitrak, Sarkar, Daipayan, Debussche, Gaspard, Sisco, Nicholas J, Nguyen, Jonathan, Mondal, Arup, Vant, John, Fromme, Petra, Van Horn, Wade D, Tajkhorshid, Emad, Kihara, Daisuke, Dill, Ken, Perez, Alberto, and Singharoy, Abhishek

Subjects
Macromolecular and Materials Chemistry, Chemical Sciences, Engineering, Materials Engineering, Nanotechnology, Bioengineering, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Aetiology, 1.4 Methodologies and measurements, Underpinning research, Generic health relevance, Macromolecular and materials chemistry, Materials engineering
Abstract

Cryo-electron microscopy (EM) requires molecular modeling to refine structural details from data. Ensemble models arrive at low free-energy molecular structures, but are computationally expensive and limited to resolving only small proteins that cannot be resolved by cryo-EM. Here, we introduce CryoFold - a pipeline of molecular dynamics simulations that determines ensembles of protein structures directly from sequence by integrating density data of varying sparsity at 3-5 Å resolution with coarse-grained topological knowledge of the protein folds. We present six examples showing its broad applicability for folding proteins between 72 to 2000 residues, including large membrane and multi-domain systems, and results from two EMDB competitions. Driven by data from a single state, CryoFold discovers ensembles of common low-energy models together with rare low-probability structures that capture the equilibrium distribution of proteins constrained by the density maps. Many of these conformations, unseen by traditional methods, are experimentally validated and functionally relevant. We arrive at a set of best practices for data-guided protein folding that are controlled using a Python GUI.

Published
2021

29. Faraday waves under perpendicular electric field

Author

Fernández-Mateo, Raúl and Pérez, Alberto T.

Subjects
Physics - Fluid Dynamics
Abstract

The dispersion relation of vertically oscillating fluid surfaces has been a subject extensively studied in the past, as well as surface instabilities produced by electrohydrodynamic (EHD) waves in similar configurations. In the present work it is studied the unification of both effects and its consequences to the instability of the surface. Given the versatility of the electromagnetic fields, a possible application to the phenomenon of walking droplets is suggested., Comment: 12 pages, 3 figures

Published
2020
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31. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.

Author

Lawson, Catherine L, Kryshtafovych, Andriy, Adams, Paul D, Afonine, Pavel V, Baker, Matthew L, Barad, Benjamin A, Bond, Paul, Burnley, Tom, Cao, Renzhi, Cheng, Jianlin, Chojnowski, Grzegorz, Cowtan, Kevin, Dill, Ken A, DiMaio, Frank, Farrell, Daniel P, Fraser, James S, Herzik, Mark A, Hoh, Soon Wen, Hou, Jie, Hung, Li-Wei, Igaev, Maxim, Joseph, Agnel P, Kihara, Daisuke, Kumar, Dilip, Mittal, Sumit, Monastyrskyy, Bohdan, Olek, Mateusz, Palmer, Colin M, Patwardhan, Ardan, Perez, Alberto, Pfab, Jonas, Pintilie, Grigore D, Richardson, Jane S, Rosenthal, Peter B, Sarkar, Daipayan, Schäfer, Luisa U, Schmid, Michael F, Schröder, Gunnar F, Shekhar, Mrinal, Si, Dong, Singharoy, Abishek, Terashi, Genki, Terwilliger, Thomas C, Vaiana, Andrea, Wang, Liguo, Wang, Zhe, Wankowicz, Stephanie A, Williams, Christopher J, Winn, Martyn, Wu, Tianqi, Yu, Xiaodi, Zhang, Kaiming, Berman, Helen M, and Chiu, Wah

Subjects
Developmental Biology, Biological Sciences, Technology, Medical and Health Sciences
Abstract

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively high accuracy and reproducibility of cryo-EM models derived by 13 participating teams from four benchmark maps, including three forming a resolution series (1.8 to 3.1 Å). The results permit specific recommendations to be made about validating near-atomic cryo-EM structures both in the context of individual experiments and structure data archives such as the Protein Data Bank. We recommend the adoption of multiple scoring parameters to provide full and objective annotation and assessment of the model, reflective of the observed cryo-EM map density.

Published
2021

35. THz nonlinear optics in silicon and germanium for third harmonic generation

Author

Perez, Alberto, Murdin, Benedict, and Litvinenko, Konstantin

Abstract

This thesis is concerned with the generation of terahertz (THz) light in the frequency range of 5–15 THz. This range is difficult to produce at high intensities, and no high-power table-top sources exist for it. The reasons for the interest in this frequency range are broad, and include communications, chemical and biomedical spectroscopy, etc. Different applications require highly specific technological characteristics, such as room temperature operation or very high stability, and satisfying all possible requirements in one generation mechanism is difficult. In this study, we sought to develop a solution to the problem of optical pumping of donor impurities in silicon, to control the orbit and spin of the donor electron in quantum computer gates. It is obvious that great advantages would be obtained if this control were possible with a bench-top source, and this is the key to enabling such high efficiency control to spread to the wider community of physicists and engineers working on spin qubits. To achieve this purpose, we explore the possibility of use a cheap material like single doped silicon and germanium to triple THz radiation from 1.7 to 5 THz (which is available from Quantum Cascade Laser diodes). The presence of the dopants modifies substantially the optical properties of the semiconductors, generating large nonlinear coefficients at THz frequencies. Samples of bismuth doped silicon and phosphorus, arsenic and antimony doped germanium has been characterised using frequency-domain and time-domain spectroscopy, and finally the optical nonlinear coefficient of Si:Bi has been measure by a Four Wave Mixing (FWM) experiment. We have found that the nonlinear susceptibility χ⁽³⁾ of Si:Bi at resonance is the highest ever reported for a bulk material.

Published
2020
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37. Ray Tracing Analysis for UAV-assisted Integrated Access and Backhaul Millimeter Wave Networks

Author

Perez, Alberto, Fouda, Abdurrahman, and Ibrahim, Ahmed S.

Subjects
Electrical Engineering and Systems Science - Signal Processing
Abstract

The use of Millimeter-wave (mmWave) spectrum in cellular communications has recently attracted growing interest to support the expected massive increase in traffic demands. However, the high path-loss at mmWave frequencies poses severe challenges. In this paper, we analyze the potential coverage gains of using unmanned aerial vehicles (UAVs), as hovering relays, in integrated access and backhaul (IAB) mmWave cellular scenarios. Specifically, we utilize the WinProp software package, which employs ray tracing methodology, to study the propagation characteristics of outdoor mmWave channels at 30 and 60 GHz frequency bands in a Manhattan-like environment. In doing so, we propose the implementation of amplify-and-forward (AF) and decode-and-forward (DF) relaying mechanisms in the WinProp software. We show how the 3D deployment of UAVs can be defined based on the coverage ray tracing maps at access and backhaul links. Furthermore, we propose an adaptive UAV transmission power for the AF relaying. We demonstrate, with the aid of ray tracing simulations, the performance gains of the proposed relaying modes in terms of downlink coverage, and the received signal to interference and noise ratio (SINR)., Comment: in Proc. IEEE WoWMoM Workshop Wireless Netw. Planning Comput. UAV Swarms, Washington, DC, USA, Jun.2019

Published
2019

39. Additional material to 'Levitation? Yes, it is possible!'

Author

Pérez, Alberto T., García-Sánchez, Pablo, Quintanilla, Miguel A. S., and Fernández-Prieto, Armando

Subjects
Physics - Physics Education
Abstract

This document contains supplementary material for the article with the same title that appeared in American Journal of Physics in 2019

Published
2019

41. Engineering highly thermostable Cas12b via de novo structural analyses for one-pot detection of nucleic acids

Author

Nguyen, Long T., Rananaware, Santosh R., Yang, Lilia G., Macaluso, Nicolas C., Ocana-Ortiz, Julio E., Meister, Katelyn S., Pizzano, Brianna L.M., Sandoval, Luke Samuel W., Hautamaki, Raymond C., Fang, Zoe R., Joseph, Sara M., Shoemaker, Grace M., Carman, Dylan R., Chang, Liwei, Rakestraw, Noah R., Zachary, Jon F., Guerra, Sebastian, Perez, Alberto, and Jain, Piyush K.

Published
2023
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43. Computing Ligands Bound to Proteins Using MELD-Accelerated MD.

Author

Liu, Cong, Brini, Emiliano, Perez, Alberto, and Dill, Ken A

Subjects
Ligands, Molecular Dynamics Simulation, Proteins, Theoretical and Computational Chemistry, Biochemistry and Cell Biology, Computer Software, Chemical Physics
Abstract

Predicting the poses of small-molecule ligands in protein binding sites is often done by virtual screening algorithms such as DOCK. In principle, molecular dynamics (MD) using atomistic force fields could give better free-energy-based pose selection, but MD is computationally expensive. Here, we ask if modeling employing limited data (MELD)-accelerated MD (MELD × MD) can pick out the best DOCK poses taken as input. We study 30 different ligand-protein pairs. MELD × MD finds native poses, based on best free energies, in 23 out of the 30 cases, 20 of which were previously known DOCK failures. We conclude that MELD × MD can add value for predicting accurate poses of small molecules bound to proteins.

Published
2020

44. NMR‐assisted protein structure prediction with MELDxMD

Author

Robertson, James C, Nassar, Roy, Liu, Cong, Brini, Emiliano, Dill, Ken A, and Perez, Alberto

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Algorithms, Computational Biology, Magnetic Resonance Spectroscopy, Molecular Dynamics Simulation, Protein Conformation, Proteins, Reproducibility of Results, CASP13, MELD, NMR, molecular dynamics, protein structure prediction, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Mathematical sciences
Abstract

We describe the performance of MELD-accelerated molecular dynamics (MELDxMD) in determining protein structures in the NMR-data-assisted category in CASP13. Seeded from web server predictions, MELDxMD was found best in the NMR category, over 17 targets, outperforming the next-best groups by a factor of ~4 in z-score. MELDxMD gives ensembles, not single structures; succeeds on a 326-mer, near the current upper limit for NMR structures; and predicts structures that match experimental residual dipolar couplings even though the only NMR-derived data used in the simulations was NOE-based ambiguous atom-atom contacts and backbone dihedrals. MELD can use noisy and ambiguous experimental information to reduce the MD search space. We believe MELDxMD is a promising method for determining protein structures from NMR data.

Published
2019

45. Bilateral Digitally Aided Tooth Autotransplantation: A 2-Year Case Report.

Author

Martín-Díaz, Ana, Favot, Alberto, Navarrete, Natalia, Calcines-Perez, Alberto, and Rubio-Flores, David

Subjects
TOOTH transplantation, DENTAL implants, OPERATIVE dentistry, CORRECTIVE orthodontics, COMPUTER-assisted surgery, THREE-dimensional imaging, DIGITAL technology, MANDIBLE, REGENERATION (Biology), THIRD molars, PERIODONTAL prosthesis, AUTOGRAFTS, ROOT canal treatment, THREE-dimensional printing, COMPUTED tomography
Abstract

Tooth autotransplantation is an effective treatment to replace missing teeth. Digital planning can facilitate successful autotransplantation. Guiding templates are highly recommended when performing cases in healed ridges in the posterior area to reduce excessive bone loss and increase the chances of fitting the donor tooth in the new socket. This case report highlights the use of 3D planning tools and fully guided drilling templates for successful tooth autotransplantation in the posterior area. Two tooth autotransplantations were performed in a 51-year-old patient using mandibular third molars to replace hopeless mandibular first and second molars. Root canal treatments were carried out before the surgeries, and different alveoloplasty techniques were used in each recipient area. The prosthetic phase was carried out after 9 months. Both teeth were asymptomatic, functional, and exhibited no signs of resorption or apical radiolucency and showed complete regeneration of the periodontal apparatus at the 2-year follow-up. [ABSTRACT FROM AUTHOR]

Published
2024
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47. Data-Type Assessment for Real-Time Hyperspectral Classification in Medical Imaging

Author

Villa, Manuel, Sancho, Jaime, Vazquez, Guillermo, Rosa, Gonzalo, Urbanos, Gemma, Martin-Perez, Alberto, Sutradhar, Pallab, Salvador, Rubén, Chavarrías, Miguel, Lagares, Alfonso, Juarez, Eduardo, Sanz, César, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Desnos, Karol, editor, and Pertuz, Sergio, editor

Published
2022
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48. Instrumented Timed Up and Go Test Using Inertial Sensors from Consumer Wearable Devices

Author

Matey-Sanz, Miguel, González-Pérez, Alberto, Casteleyn, Sven, Granell, Carlos, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Michalowski, Martin, editor, Abidi, Syed Sibte Raza, editor, and Abidi, Samina, editor

Published
2022
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