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11,388 results on '"Doni A"'

107. Automatic Multi-Objective Optimization of Coarse-Grained Lipid Force Fields Using SwarmCG

Author

Empereur-mot, Charly, Capelli, Riccardo, Perrone, Mattia, Caruso, Cristina, Doni, Giovanni, and Pavan, Giovanni M.

Subjects
Condensed Matter - Soft Condensed Matter, Physics - Chemical Physics
Abstract

The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning of parameters in order to have the approximated CG models behaving correctly and consistently with, e.g., available higher-resolution simulation data and/or experimental observables. Automatic data-driven approaches are increasingly used to develop accurate models for molecular dynamics simulations. But the parameters obtained via such automatic methods often make use of specifically-designed interaction potentials, and are typically poorly transferable to molecular systems or conditions other than those used for training them. Using a multi-objective approach in combination with an automatic optimization engine (SwarmCG), here we show that it is possible to optimize CG models that are also transferable, obtaining optimized CG force fields (FFs). As a proof of concept, here we use lipids, for which we can avail of reference experimental data (area per lipid, bilayer thickness) and reliable atomistic simulations to guide the optimization. Once the resolution of the CG models (mapping) is set as an input, SwarmCG optimizes the parameters of the CG lipid models iteratively and simultaneously against higher-resolution simulations (bottom-up) and experimental data (top-down references). Including different types of lipid bilayers in the training set in a parallel optimization guarantees the transferability of the optimized lipid FF parameters. We demonstrate that SwarmCG can reach satisfactory agreement with experimental data for different resolution CG FFs. We also obtain stimulating insights on the precision-resolution balance of the FFs. The approach is general and can be effectively used to develop new FFs, as well as to improve existing ones., Comment: This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in J. Chem. Phys. 156, 024801 (2022) and may be found at https://aip.scitation.org/doi/10.1063/5.0079044

Published
2021
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117. Optimizing Plastic Waste Management Through PT Kilang Pertamina Internasional Unit VI Balongan CSR/TJSL Program 'Wiralodra Waste Bank in Balongan Village'

Author

Purnomo, Andromedo Cahyo, Zulkifli, Mohamad, Anis, Muhamad, Irawan, Krisna, Nurdiyanto, Doni, Nugroho, Wisnu Wisi, Saputra, Cahya Eka, Sulastriyana, Sri, Wibowo, Nanda Tri, Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Azizah, Amiril, editor, Fahmi, Nurul, editor, and Dwi Ariyani, Emma, editor

Published
2023
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119. The Role of Song in Developing the Attitude of Responsibility of the Church in the Era of Disruption

Author

Prasetio, Doni, Phangrestu, Poulina, Gunawan, Yehuda Indra, Sabdono, Erastus, Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Zaluchu, Sonny Eli, editor, Siahaan, Harls Evan R., editor, Novalina, Martina, editor, Rouw, Randy Frank, editor, Simanjuntak, Fredy, editor, and Wijaya, Hengki, editor

Published
2023
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120. Semiotics in Gastrodiplomacy of Nusa Gastronomi Restaurant in Jakarta, Indonesia

Author

Wulan, Saptarining, Rachman, Arief F., Muhardiansyah, Doni, Maulana, Alifatqul, Appolloni, Andrea, Series Editor, Caracciolo, Francesco, Series Editor, Ding, Zhuoqi, Series Editor, Gogas, Periklis, Series Editor, Huang, Gordon, Series Editor, Nartea, Gilbert, Series Editor, Ngo, Thanh, Series Editor, Striełkowski, Wadim, Series Editor, Rahmanita, Myrza, editor, Suprina, Rina, editor, and Arafah, Willy, editor

Published
2023
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121. King III Report and CSR

Author

Martini, Silvio Bianchi, Corvino, Antonio, Doni, Federica, Intenza, Marika, Jeronen, Eila, Section editor, Idowu, Samuel O., editor, Schmidpeter, René, editor, Capaldi, Nicholas, editor, Zu, Liangrong, editor, Del Baldo, Mara, editor, and Abreu, Rute, editor

Published
2023
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122. Gorontalo and Arabic Morphology: A Contrastive Analysis to Ease Language Learning and Translation

Author

Pakaya, Nurul Aini N., Hula, Ibnu Rawandhy N., Doni, Chaterina Puteri, Saleh, Sriwahyuningsih R., Husain, Dahlia, Lagalo, Anggraeni M. S., Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Warmansyah, Jhoni, editor, Nesa Chandra, Artha, editor, Haviz, M., editor, Nurmai Yenti, Isra, editor, Safrizal, Safrizal, editor, and Idrus, Hadiyati, editor

Published
2023
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126. Android Learning Design to Increase Interest in Learning Music

Author

Sirait, Erlando Doni, Irfansyah, Puput, Risdiana, Aan, Lee, Chuan-Pei, Series Editor, Weimin, Huang, Series Editor, Doyan, Aris, editor, Hadisaputra, Saprizal, editor, Kechik, Mohd Mustafa Awang, editor, Bilad, Muhammad Roil, editor, Wei, Ching-Ming, editor, and Susilawati, editor

Published
2023
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129. Technology Pedagogical Content Knowledge (TPACK): An Analysis of Ability of Elementary School Teacher

Author

Annazar, M. Fikra Yusuf, Firdaus, Rangga, Andra, Doni, Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Perdana, Ryzal, editor, Sunyono, editor, Putrawan, Gede Eka, editor, Septiawan, Trio Yuda, editor, and Saputra, Bayu, editor

Published
2023
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130. Visual Language: A Literature Review for Bridging Linguistics and Visual Communication Design

Author

Setyawan, Harits, Gunawan, Wawan, Alfaruqy, Doni, Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Perdana, Ryzal, editor, Sunyono, editor, Putrawan, Gede Eka, editor, Septiawan, Trio Yuda, editor, and Saputra, Bayu, editor

Published
2023
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131. A Systematic Review of Project-Based Blended Learning as an Innovative Teaching Model

Author

Suana, Wayan, Andra, Doni, Permadi, Dimas, Putri, Ni Made Anggi A., Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Perdana, Ryzal, editor, Sunyono, editor, Putrawan, Gede Eka, editor, Septiawan, Trio Yuda, editor, and Saputra, Bayu, editor

Published
2023
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132. Preventing Illegal Online Loan Crimes

Author

Awaludin, Arif, Rusito, Rusito, Supriyo, Doni Adi, Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Endah Kusumaningrum, Anggraeni, editor, Indriasti Wardani, Widyorini, editor, Pranoto, Edi, editor, and Pujiyanto, Rohmad, editor

Published
2023
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133. Ownership, Usage, and Maintenance LLINs Behavior in Six Endemic Malaria Areas Post Distribution in Indonesia 2019–2020

Author

Marina, Rina, Lasut, Doni, Shinta, Shinta, Ariati, Yusniar, Widawati, Mutiara, Soehadi, Hariyanto, Nurlaila, Ika, editor, Ulfa, Yunefit, editor, Anastasia, Hayani, editor, Putro, Gurendro, editor, Rachmalina, Rika, editor, Ika Agustiya, Rozana, editor, Sari Dewi Panjaitan, Novaria, editor, Sarassari, Rosantia, editor, Lystia Poetranto, Anna, editor, and Septima Mariya, Sela, editor

Published
2023
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134. Groundwater Recharge Estimation Using Chloride Mass Balance (CMB) : Case Study: an Old Residential Area and a New Residential Area of Yogyakarta, Indonesia

Author

Buana, Lalu Aliyya Tirang ga Aji, Putra, Doni Prakasa Eka, Handini, Esti, Ma, Wanshu, Series Editor, Saputro, Arifin Dwi, editor, Sutiarso, Lilik, editor, Evi Masithoh, Rudiati, editor, Leong, Jik Chang, editor, Keiblinger, Katharina, editor, Borompichaichartkul, Chaleeda, editor, Toker, Omer Said, editor, and Shamsudin, Rosnah, editor

Published
2023
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135. Characteristics and Potential of Confined Aquifers in Genuk and Surrounding Area, Semarang City, Central Java Province

Author

Aghnia, Sokhwatul, Hendrayana, Heru, Putra, Doni Prakasa Eka, Ma, Wanshu, Series Editor, Saputro, Arifin Dwi, editor, Sutiarso, Lilik, editor, Evi Masithoh, Rudiati, editor, Leong, Jik Chang, editor, Keiblinger, Katharina, editor, Borompichaichartkul, Chaleeda, editor, Toker, Omer Said, editor, and Shamsudin, Rosnah, editor

Published
2023
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136. Groundwater Vulnerability Assessment Using Simple Vertical Vulnerability Method : In Wonosari, Gunungkidul, Yogyakarta, Indonesia

Author

Rachman, Moch Hasmannoor, Wilopo, Wahyu, Putra, Doni Prakasa Eka, Ma, Wanshu, Series Editor, Saputro, Arifin Dwi, editor, Sutiarso, Lilik, editor, Evi Masithoh, Rudiati, editor, Leong, Jik Chang, editor, Keiblinger, Katharina, editor, Borompichaichartkul, Chaleeda, editor, Toker, Omer Said, editor, and Shamsudin, Rosnah, editor

Published
2023
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139. Hydrogeochemistry of springwater in Leuwisari subdistrict and surrounding, Tasikmalaya, West Java, Indonesia

Author

Fadillah, Sofia, Budianta, Wawan, Putra, Doni Prakasa Eka, Kuncoro, Dwi Agus, Priandani, Fabian, Ma, Wanshu, Series Editor, Saputro, Arifin Dwi, editor, Sutiarso, Lilik, editor, Evi Masithoh, Rudiati, editor, Leong, Jik Chang, editor, Keiblinger, Katharina, editor, Borompichaichartkul, Chaleeda, editor, Toker, Omer Said, editor, and Shamsudin, Rosnah, editor

Published
2023
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140. Online Teaching and Learning Platform at Vocational Education in Semarang-Indonesia

Author

Hadromi, Hadromi, Widjanarko, Dwi, Kurniawan, Adhetya, Budiman, Febrian Arif, Amron, Husni, Irawan, Doni Yudi, Surya, Muhamad Zulfikar Adi, Gendroyono, R. Ambar Kuntoro Mursit, Striełkowski, Wadim, Editor-in-Chief, Black, Jessica M., Series Editor, Butterfield, Stephen A., Series Editor, Chang, Chi-Cheng, Series Editor, Cheng, Jiuqing, Series Editor, Dumanig, Francisco Perlas, Series Editor, Al-Mabuk, Radhi, Series Editor, Scheper-Hughes, Nancy, Series Editor, Urban, Mathias, Series Editor, Webb, Stephen, Series Editor, Kusumastuti, Adhi, editor, Anis, Samsudin, editor, Hidayanto, Achmad Nizar, editor, Nurmasitah, Sita, editor, Atika, Atika, editor, Apriyani, Delta, editor, Achmadi, Taofan Ali, editor, and Sudiyono, Sudiyono, editor

Published
2023
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147. Erdafitinib versus pembrolizumab in pretreated patients with advanced or metastatic urothelial cancer with select FGFR alterations: cohort 2 of the randomized phase III THOR trial

Author

Bastick, Patricia, Sewak, Sanjeev, Tran, Ben, Pichler, Martin, Shariat, Shahrokh, Rottey, Sylvie, Schatteman, Peter, Schrijvers, Dirk, Verschaeve, Vincent, Vulsteke, Christof, Barros Leite Ferreira, Luiza Aleixo, de Santana Gomes Andrea Juliana, Pereira, Junior, Joao Antonio, Azevedo, Sergio, Bastos, Diogo, Borges, Giuliano, Dettino, Aldo, Antonio, Pires Luis, Luz, Murilo, Martins, Suelen, Mota, Jose Mauricio, Toledo, Joseane, Eigl, Bernhard, Finch, Daygen, Gingerich, Joel, Dong, Haiying, Huang, Jian, Jin, Jie, Pan, Hongming, Sun, Zhongquan, Tian, Ye, Wan, Ben, Wu, Bin, Xu, Ting, Xue, Wei, Zhou, Fangjian, Barthelemy, Philippe, Borchiellini, Delphine, Calcagno, Fabien, Carnot, Aurelien, Cornillon, Pierre, Delva, Remy, Emambux, Sheik, Houede, Nadine, Laguerre, Brigitte, Lauridant, Géraldine, Loriot, Yohann, Mahammedi, Hakim, Maillet, Denis, Pouessel, Damien, Roubaud, Guilhem, Schlurmann-Constans, Friederike, Tosi, Diego, Zanetta, Sylvie, Banek, Severine, Feyerabend, Susan, Kramer, Mario, Niegisch, Guenther, Nuhn, Philipp, Schnabel, Marco, Wuelfing, Christian, Baka, Sofia, Bamias, Aristotelis, Fountzilas, George, Kalofonos, Harabolos, Karalis, Konstantinos, Kotsakis, Athanasios, Timotheadou, Eleni, Landherr, Laszlo, Mangel, Laszlo, Pe’er, Avivit, Levratovsky, Meital, Basso, Umberto, Battelli, Nicola, Cavo, Alessia, De Giorgi, Ugo, Doni, Laura, Galli, Luca, Gigante, Maria Olga, Guadalupi, Valentina, Maio, Michele, Milesi, Laura, Nolè, Franco, Scagliotti, Giorgio, Tortora, Giampaolo, Fukasawa, Satoshi, Harabayashi, Toru, Kamiya, Naoto, Kawahara, Takashi, Kawakita, Mutsushi, Matsubara, Nobunaki, Matsumoto, Kazumasa, Nishimura, Kazuo, Rikiya, Taoka, Shimizu, Nobuaki, Tagaki, Toshio, Kang, Taek Won, Kim, Jwa Hoon, Kim, SeHyun, Lee, Hyo Jin, Lee, Yun-Gyoo, Rha, Sun Young, Seo, Ho Kyung, Los, Maartje, Zurawski, Bogdan, Cortes, Paulo, Faustino, Catia, Vau, Nuno Sineiro, da Luz, Ricardo, Atduev, Vagif, Kirtbaya, Dmitry, Kopyltsov, Evgeny, Lykov, Aleksandr, Marat, Urmantsev, Orlov, Sergey, Penkov, Konstantin, Pirmagomedov, Albert, Semenov, Andrey, Varlamov, Sergey, Anguera, Georgia, Domenech, Montserrat, Girones, Regina, Gonzalez del Alba, Aranzazu, Milagro, Nuria Lainez, Luque, Raquel, Ortega, Esther Martínez, Mellado, Begoña, Méndez Vidal, María Jose, Fernandez, Esteban Nogales, Valderrama, Begoña Perez, Marín, Alvaro Pinto, Santander, Carmen, Huang, Yi-Hsiu, Su, Wen-Pin, Wu, Hung-Chan, Wu, WenJeng, Yu, Kai-Jie, Bilici, Ahmet, Goker, Erdem, Gumus, Mahmut, Karaoglu, Aziz, Kefeli, Umut, Köse, Fatih, Ozguroglu, Mustafa, Tural, Deniz, Turk, Haci, Yalcin, Suayib, Bondarenko, Igor, Khareba, Gennadii, Kidik, Yana, Lychkovskyy, Oleksandr, Sakalo, Valerii, Shevnia, Serghii, Stakhovskyy, Eduard, Bahl, Amit, Crabb, Simon, Powles, Thomas, Sankey, Peter, Sarwar, Mohammad, Benedetto, Pasquale, Burgess, Earle, Dawson, Nancy, Doshi, Gurjyot, Fleming, Mark, Maly, Joseph, Parikh, Mamta, Waterhouse, David, Siefker-Radtke, A.O., Matsubara, N., Park, S.H., Huddart, R.A., Burgess, E.F., Özgüroğlu, M., Valderrama, B.P., Laguerre, B., Basso, U., Triantos, S., Akapame, S., Kean, Y., Deprince, K., Mukhopadhyay, S., and Loriot, Y.

Published
2024
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150. A Collaborative Filtering Approach for the Automatic Tuning of Compiler Optimisations

Author

Cereda, Stefano, Palermo, Gianluca, Cremonesi, Paolo, and Doni, Stefano

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Performance
Abstract

Selecting the right compiler optimisations has a severe impact on programs' performance. Still, the available optimisations keep increasing, and their effect depends on the specific program, making the task human intractable. Researchers proposed several techniques to search in the space of compiler optimisations. Some approaches focus on finding better search algorithms, while others try to speed up the search by leveraging previously collected knowledge. The possibility to effectively reuse previous compilation results inspired us toward the investigation of techniques derived from the Recommender Systems field. The proposed approach exploits previously collected knowledge and improves its characterisation over time. Differently from current state-of-the-art solutions, our approach is not based on performance counters but relies on Reaction Matching, an algorithm able to characterise programs looking at how they react to different optimisation sets. The proposed approach has been validated using two widely used benchmark suites, cBench and PolyBench, including 54 different programs. Our solution, on average, extracted 90% of the available performance improvement 10 iterations before current state-of-the-art solutions, which corresponds to 40% fewer compilations and performance tests to perform., Comment: To be published in the 21st ACM SIGPLAN/SIGBED International Conference on Languages, Compilers, and Tools for Embedded Systems (LCTES 2020) PolyBench dataset available at: https://github.com/stefanocereda/polybench_data cBench dataset available at: https://github.com/amirjamez/COBAYN

Published
2020
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