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  1. Book ; Online: Offloading electromagnetic shower transport to GPUs

    Amadio, G. / Apostolakis, J. / Buncic, P. / Cosmo, G. / Dosaru, D. / Gheata, A. / Hageboeck, S. / Hahnfeld, J. / Hodgkinson, M. / Morgan, B. / Novak, M. / Petre, A. A. / Pokorski, W. / Ribon, A. / Stewart, G. A. / Vila, P. M.

    2022  

    Abstract: Making general particle transport simulation for high-energy physics (HEP) single-instruction-multiple-thread (SIMT) friendly, to take advantage of accelerator hardware, is an important alternative for boosting the throughput of simulation applications. ... ...

    Abstract Making general particle transport simulation for high-energy physics (HEP) single-instruction-multiple-thread (SIMT) friendly, to take advantage of accelerator hardware, is an important alternative for boosting the throughput of simulation applications. To date, this challenge is not yet resolved, due to difficulties in mapping the complexity of Geant4 components and workflow to the massive parallelism features exposed by graphics processing units (GPU). The AdePT project is one of the R\&D initiatives tackling this limitation and exploring GPUs as potential accelerators for offloading some part of the CPU simulation workload. Our main target is to implement a complete electromagnetic shower demonstrator working on the GPU. The project is the first to create a full prototype of a realistic electron, positron, and gamma electromagnetic shower simulation on GPU, implemented as either a standalone application or as an extension of the standard Geant4 CPU workflow. Our prototype currently provides a platform to explore many optimisations and different approaches. We present the most recent results and initial conclusions of our work, using both a standalone GPU performance analysis and a first implementation of a hybrid workflow based on Geant4 on the CPU and AdePT on the GPU.

    Comment: 8 pages, 4 figures, 20th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 2021), to be published in Journal of Physics: Conference Series, editor Andrei Gheata
    Keywords High Energy Physics - Experiment ; I.6.8
    Subject code 621
    Publishing date 2022-09-30
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Predicting interactions between small molecules and RNA

    Apostolakis J / Tietze S

    Chemistry Central Journal, Vol 3, Iss Suppl 1, p P

    2009  Volume 59

    Keywords Chemistry ; QD1-999 ; Science ; Q ; DOAJ:Chemistry (General) ; DOAJ:Chemistry
    Language English
    Publishing date 2009-06-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: Data Mining in Crystallography

    Apostolakis, J / Hofmann, D. W. M

    (Structure and bonding ; 134)

    2010  

    Author's details edited by D. W. M. Hofmann, Liudmila N. Kuleshova. With contrib. by J. Apostolakis
    Series title Structure and bonding ; 134
    Keywords Biochemistry ; Chemistry ; Chemistry, inorganic ; Crystallography
    Language English
    Size Online-Ressource, v.: digital
    Publisher Springer-Verlag Berlin Heidelberg
    Publishing place Berlin, Heidelberg
    Document type Book ; Online
    Note Includes bibliographical references and index
    ISBN 9783642047589 ; 9783642047596 ; 3642047580 ; 3642047599
    DOI 10.1007/978-3-642-04759-6
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  4. Article: Massive intracardiac thrombosis during coronary artery bypass grafting surgery.

    Bhandary, Sujatha P / Papadimos, Thomas J / Essandoh, Michael K / Apostolakis, John

    International journal of critical illness and injury science

    2015  Volume 5, Issue 1, Page(s) 56–58

    Abstract: Thrombosis is a potential life-threatening complication in patients undergoing cardiac surgery. Various clinical and heritable conditions, like cancer, trauma, immobilization, the presence of factor V Leiden or prothrombin 20210A, deficiency of or ... ...

    Abstract Thrombosis is a potential life-threatening complication in patients undergoing cardiac surgery. Various clinical and heritable conditions, like cancer, trauma, immobilization, the presence of factor V Leiden or prothrombin 20210A, deficiency of or resistance to the inhibitor proteins C, S, or antithrombin, elevated levels of coagulation proteins, antiphospholipid antibody syndrome, pregnancy, and the use of exogenous hormones, may contribute to catastrophic thrombosis. Massive thrombi with cerebrovascular and cardiovascular events develop in patients with polycythemia vera (PV). However, thrombus formation in the cardiac chambers is extremely rare. We report a case of massive intracardiac thrombosis in a patient undergoing coronary artery bypass grafting.
    Language English
    Publishing date 2015-02-25
    Publishing country India
    Document type Case Reports
    ZDB-ID 2638865-0
    ISSN 2231-5004 ; 2229-5151
    ISSN (online) 2231-5004
    ISSN 2229-5151
    DOI 10.4103/2229-5151.152347
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Automatic determination of reaction mappings and reaction center information. 1. The imaginary transition state energy approach.

    Körner, Robert / Apostolakis, Joannis

    Journal of chemical information and modeling

    2008  Volume 48, Issue 6, Page(s) 1181–1189

    Abstract: Chemical reactions transform the reactant molecules by deleting existing and forming new bonds. The identification of these so-called reacting bonds is important for studying the reaction mechanism and for applications in metabolomics, e.g. for ... ...

    Abstract Chemical reactions transform the reactant molecules by deleting existing and forming new bonds. The identification of these so-called reacting bonds is important for studying the reaction mechanism and for applications in metabolomics, e.g. for interpreting substrate labeling experiments. Here, we introduce an approach which suggests the simplest possible reaction center at the heavy atom level, with high accuracy. In contrast to current methods the approach is motivated by a simple theoretical model based on a crude approximation of the reaction energetics, and takes the complete reacting system into account. Finally, it recovers all optimal solutions to the problem while removing all symmetry-related, redundant solutions. We apply the method on the complete KEGG database of biochemical reactions, and compare our approach with previous methods. The resulting reaction centers are represented as imaginary transition states, which are molecule-like representations of reaction mechanisms. We provide the statistics of the calculations on the KEGG database and discuss some examples for the different types of alternative solutions found.
    MeSH term(s) Databases, Factual ; Enzymes/chemistry ; Enzymes/metabolism ; Hydrogen/chemistry ; Models, Chemical ; Sensitivity and Specificity ; Thermodynamics
    Chemical Substances Enzymes ; Hydrogen (7YNJ3PO35Z)
    Language English
    Publishing date 2008-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 190019-5
    ISSN 1549-9596 ; 0095-2338
    ISSN 1549-9596 ; 0095-2338
    DOI 10.1021/ci7004324
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Computational ligand design.

    Apostolakis, J / Caflisch, A

    Combinatorial chemistry & high throughput screening

    1999  Volume 2, Issue 2, Page(s) 91–104

    Abstract: A variety of computational tools that are used to assist drug design are reviewed. Particular emphasis is given to the limitations and merits of different methodologies. Recently, a number of general methods have been proposed for clustering compounds in ...

    Abstract A variety of computational tools that are used to assist drug design are reviewed. Particular emphasis is given to the limitations and merits of different methodologies. Recently, a number of general methods have been proposed for clustering compounds in classes of drug-like and non-drug-like molecules. The usefulness of this classification for drug design is discussed. The estimation of (relative) binding affinities is from a theoretical point of view the most challenging part of ligand design. We review three methods for the estimation of binding energies. Firstly, quantitative structure-activity relationships (QSAR) are presented. These have gained significantly from recent developments of experimental techniques for combinatorial synthesis and high-throughput screening as well as the use of powerful computational procedures like genetic algorithms and neural networks for the derivation of models. Secondly, empirical energy functions are shown to lead to more general models than standard QSAR, since they are fitted to a variety of complexes. They have been used recently with considerable success. Thirdly, we briefly outline free energy calculations based on molecular dynamics simulations, the method with the most sound theoretical foundation. Recent developments are reestablishing the interest in this approach. In the last part of this review structure-based ligand design programs are described. These are closely related to docking, with the difference that in design, unlike in most docking procedures, ligands are built on a fragment-by-fragment basis. Finally, a short description of our approach to computational combinatorial ligand design is given.
    MeSH term(s) Drug Design ; Ligands ; Pharmaceutical Preparations/metabolism ; Structure-Activity Relationship
    Chemical Substances Ligands ; Pharmaceutical Preparations
    Language English
    Publishing date 1999-04
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2064785-2
    ISSN 1875-5402 ; 1386-2073
    ISSN (online) 1875-5402
    ISSN 1386-2073
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: On the ease of predicting the thermodynamic properties of beta-cyclodextrin inclusion complexes.

    Steffen, Andreas / Apostolakis, Joannis

    Chemistry Central journal

    2007  Volume 1, Page(s) 29

    Abstract: Background: In this study we investigated the predictability of three thermodynamic quantities related to complex formation. As a model system we chose the host-guest complexes of beta-cyclodextrin (beta-CD) with different guest molecules. A training ... ...

    Abstract Background: In this study we investigated the predictability of three thermodynamic quantities related to complex formation. As a model system we chose the host-guest complexes of beta-cyclodextrin (beta-CD) with different guest molecules. A training dataset comprised of 176 beta-CD guest molecules with experimentally determined thermodynamic quantities was taken from the literature. We compared the performance of three different statistical regression methods - principal component regression (PCR), partial least squares regression (PLSR), and support vector machine regression combined with forward feature selection (SVMR/FSS) - with respect to their ability to generate predictive quantitative structure property relationship (QSPR) models for DeltaG degrees, DeltaH degrees and DeltaS degrees on the basis of computed molecular descriptors.
    Results: We found that SVMR/FFS marginally outperforms PLSR and PCR in the prediction of DeltaG degrees, with PLSR performing slightly better than PCR. PLSR and PCR proved to be more stable in a nested cross-validation protocol. Whereas DeltaG degrees can be predicted in good agreement with experimental values, none of the methods led to comparably good predictive models for DeltaH degrees. In using the methods outlined in this study, we found that DeltaS degrees appears almost unpredictable. In order to understand the differences in the ease of predicting the quantities, we performed a detailed analysis. As a result we can show that free energies are less sensitive (than enthalpy or entropy) to the small structural variations of guest molecules. This property, as well as the lower sensitivity of DeltaG degrees to experimental conditions, are possible explanations for its greater predictability.
    Conclusion: This study shows that the ease of predicting DeltaG degrees cannot be explained by the predictability of either DeltaH degrees or DeltaS degrees. Our analysis suggests that the poor predictability of TDeltaS degrees and, to a lesser extent, DeltaH degrees has to do with a stronger dependence of these quantities on the structural details of the complex and only to a lesser extent on experimental error.
    Language English
    Publishing date 2007-11-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 2272440-0
    ISSN 1752-153X ; 1752-153X
    ISSN (online) 1752-153X
    ISSN 1752-153X
    DOI 10.1186/1752-153X-1-29
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: GlamDock: development and validation of a new docking tool on several thousand protein-ligand complexes.

    Tietze, Simon / Apostolakis, Joannis

    Journal of chemical information and modeling

    2007  Volume 47, Issue 4, Page(s) 1657–1672

    Abstract: In this study, we present GlamDock, a new docking tool for flexible ligand docking. GlamDock (version 1.0) is based on a simple Monte Carlo with minimization procedure. The main features of the method are the energy function, which is a continuously ... ...

    Abstract In this study, we present GlamDock, a new docking tool for flexible ligand docking. GlamDock (version 1.0) is based on a simple Monte Carlo with minimization procedure. The main features of the method are the energy function, which is a continuously differentiable empirical potential, and the definition of the search space, which combines internal coordinates for the conformation of the ligand, with a mapping-based description of the rigid body translation and rotation. First, we validate GlamDock on a standard benchmark, a set of 100 protein-ligand complexes, which allows comparative evaluation to existing docking tools. The results on this benchmark show that GlamDock is at least comparable in efficiency and accuracy to the best existing docking tools. The main focus of this work is the validation on the scPDB database of protein-ligand complexes. The size of this data set allows a thorough analysis of the dependencies of docking accuracy on features of the protein-ligand system. In particular, it allows a two-dimensional analysis of the results, which identifies a number of interesting dependencies that are generally lost or even misinterpreted in the one-dimensional approach. The overall result that GlamDock correctly predicts the complex structure in practically half of the cases in the scPDB is important not only for screening ligands against a particular protein but even more so for inverse screening, that is, the identification of the correct targets for a particular ligand.
    MeSH term(s) Ligands ; Models, Molecular ; Proteins/metabolism ; Thermodynamics
    Chemical Substances Ligands ; Proteins
    Language English
    Publishing date 2007-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Validation Studies
    ZDB-ID 190019-5
    ISSN 1549-9596 ; 0095-2338
    ISSN 1549-9596 ; 0095-2338
    DOI 10.1021/ci7001236
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Thesis: Theoretical studies of flexible docking and conformational transitions of proteins in solution

    Apostolakis, Joannis

    1999  

    Author's details Joannis Apostolakis
    Language English
    Size Getr. Zählung, Ill., graph. Darst
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Univ., Diss.--Zürich, 1999
    Note Enth. 5 Zeitschriftensonderabdrucke ; Zsfassung in dt. Sprache
    Database Former special subject collection: coastal and deep sea fishing

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  10. Book: Data mining in crystallography

    Hofmann, Detlef W. M / Kuleshova, Liudmila N / Apostolakis, J

    (Structure and bonding, ; 134)

    2010  

    Author's details volume editors: Detlef W.M. Hofmann, Liudmila N. Kuleshova ; with contributions by J. Apostolakis ... [et al.]
    Series title Structure and bonding, ; 134
    MeSH term(s) Crystallography ; Data Mining
    Language English
    Size xi, 172 p. :, ill. (some col.) ;, 24 cm.
    Publisher Springer
    Publishing place Heidelberg ; New York
    Document type Book
    ISBN 9783642047589 ; 3642047580 ; 9783642047596 ; 3642047599
    Database Catalogue of the US National Library of Medicine (NLM)

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