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Institution

University of Udine

EducationUdine, Italy
About: University of Udine is a education organization based out in Udine, Italy. It is known for research contribution in the topics: Population & Large Hadron Collider. The organization has 6745 authors who have published 20530 publications receiving 669088 citations. The organization is also known as: Università degli Studi di Udine & Universita degli Studi di Udine.


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Journal ArticleDOI
TL;DR: QUANTUM ESPRESSO as discussed by the authors is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave).
Abstract: QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

19,985 citations

Journal ArticleDOI
S. Agostinelli1, John Allison2, K. Amako3, J. Apostolakis4, Henrique Araujo5, P. Arce4, Makoto Asai6, D. Axen4, S. Banerjee7, G. Barrand, F. Behner4, Lorenzo Bellagamba8, J. Boudreau9, L. Broglia10, A. Brunengo8, H. Burkhardt4, Stephane Chauvie, J. Chuma11, R. Chytracek4, Gene Cooperman12, G. Cosmo4, P. V. Degtyarenko13, Andrea Dell'Acqua4, G. Depaola14, D. Dietrich15, R. Enami, A. Feliciello, C. Ferguson16, H. Fesefeldt4, Gunter Folger4, Franca Foppiano, Alessandra Forti2, S. Garelli, S. Gianì4, R. Giannitrapani17, D. Gibin4, J. J. Gomez Y Cadenas4, I. González4, G. Gracia Abril4, G. Greeniaus18, Walter Greiner15, Vladimir Grichine, A. Grossheim4, Susanna Guatelli, P. Gumplinger11, R. Hamatsu19, K. Hashimoto, H. Hasui, A. Heikkinen20, A. S. Howard5, Vladimir Ivanchenko4, A. Johnson6, F.W. Jones11, J. Kallenbach, Naoko Kanaya4, M. Kawabata, Y. Kawabata, M. Kawaguti, S.R. Kelner21, Paul R. C. Kent22, A. Kimura23, T. Kodama24, R. P. Kokoulin21, M. Kossov13, Hisaya Kurashige25, E. Lamanna26, Tapio Lampén20, V. Lara4, Veronique Lefebure4, F. Lei16, M. Liendl4, W. S. Lockman, Francesco Longo27, S. Magni, M. Maire, E. Medernach4, K. Minamimoto24, P. Mora de Freitas, Yoshiyuki Morita3, K. Murakami3, M. Nagamatu24, R. Nartallo28, Petteri Nieminen28, T. Nishimura, K. Ohtsubo, M. Okamura, S. W. O'Neale29, Y. Oohata19, K. Paech15, J Perl6, Andreas Pfeiffer4, Maria Grazia Pia, F. Ranjard4, A.M. Rybin, S.S Sadilov4, E. Di Salvo8, Giovanni Santin27, Takashi Sasaki3, N. Savvas2, Y. Sawada, Stefan Scherer15, S. Sei24, V. Sirotenko4, David J. Smith6, N. Starkov, H. Stoecker15, J. Sulkimo20, M. Takahata23, Satoshi Tanaka30, E. Tcherniaev4, E. Safai Tehrani6, M. Tropeano1, P. Truscott31, H. Uno24, L. Urbán, P. Urban32, M. Verderi, A. Walkden2, W. Wander33, H. Weber15, J.P. Wellisch4, Torre Wenaus34, D.C. Williams, Douglas Wright6, T. Yamada24, H. Yoshida24, D. Zschiesche15 
TL;DR: The Gelfant 4 toolkit as discussed by the authors is a toolkit for simulating the passage of particles through matter, including a complete range of functionality including tracking, geometry, physics models and hits.
Abstract: G eant 4 is a toolkit for simulating the passage of particles through matter. It includes a complete range of functionality including tracking, geometry, physics models and hits. The physics processes offered cover a comprehensive range, including electromagnetic, hadronic and optical processes, a large set of long-lived particles, materials and elements, over a wide energy range starting, in some cases, from 250 eV and extending in others to the TeV energy range. It has been designed and constructed to expose the physics models utilised, to handle complex geometries, and to enable its easy adaptation for optimal use in different sets of applications. The toolkit is the result of a worldwide collaboration of physicists and software engineers. It has been created exploiting software engineering and object-oriented technology and implemented in the C++ programming language. It has been used in applications in particle physics, nuclear physics, accelerator design, space engineering and medical physics.

18,904 citations

Journal ArticleDOI
Georges Aad1, T. Abajyan2, Brad Abbott3, Jalal Abdallah4  +2964 moreInstitutions (200)
TL;DR: In this article, a search for the Standard Model Higgs boson in proton-proton collisions with the ATLAS detector at the LHC is presented, which has a significance of 5.9 standard deviations, corresponding to a background fluctuation probability of 1.7×10−9.

9,282 citations

Journal ArticleDOI
Daniel J. Klionsky1, Kotb Abdelmohsen2, Akihisa Abe3, Joynal Abedin4  +2519 moreInstitutions (695)
TL;DR: In this paper, the authors present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macro-autophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

5,187 citations

Journal ArticleDOI
TL;DR: These guidelines are presented for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

4,316 citations


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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
202350
2022142
20211,338
20201,388
20191,223
20181,102