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1. GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research

Author

LeGrand, Scott, Scheinberg, Aaron, Tillack, Andreas F., Thavappiragasam, Mathialakan, Vermaas, Josh V., Agarwal, Rupesh, Larkin, Jeff, Poole, Duncan, Santos-Martins, Diogo, Solis-Vasquez, Leonardo, Koch, Andreas, Forli, Stefano, Hernandez, Oscar, Smith, Jeremy C., and Sedova, Ada

Subjects
Quantitative Biology - Biomolecules, Quantitative Biology - Quantitative Methods, J.3, D.1.3
Abstract

Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability to bind to a given protein receptor within a drug-discovery campaign. Experimental drug screening is expensive and time consuming, and it is desirable to carry out large scale docking calculations in a high-throughput manner to narrow the experimental search space. Few of the existing computational docking tools were designed with high performance computing in mind. Therefore, optimizations to maximize use of high-performance computational resources available at leadership-class computing facilities enables these facilities to be leveraged for drug discovery. Here we present the porting, optimization, and validation of the AutoDock-GPU program for the Summit supercomputer, and its application to initial compound screening efforts to target proteins of the SARS-CoV-2 virus responsible for the current COVID-19 pandemic.

Published
2020
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2. QMCPACK : An open source ab initio Quantum Monte Carlo package for the electronic structure of atoms, molecules, and solids

Author

Kim, Jeongnim, Baczewski, Andrew, Beaudet, Todd D., Benali, Anouar, Bennett, M. Chandler, Berrill, Mark A., Blunt, Nick S., Borda, Edgar Josue Landinez, Casula, Michele, Ceperley, David M., Chiesa, Simone, Clark, Bryan K., Clay III, Raymond C., Delaney, Kris T., Dewing, Mark, Esler, Kenneth P., Hao, Hongxia, Heinonen, Olle, Kent, Paul R. C., Krogel, Jaron T., Kylanpaa, Ilkka, Li, Ying Wai, Lopez, M. Graham, Luo, Ye, Malone, Fionn D., Martin, Richard M., Mathuriya, Amrita, McMinis, Jeremy, Melton, Cody A., Mitas, Lubos, Morales, Miguel A., Neuscamman, Eric, Parker, William D., Flores, Sergio D. Pineda, Romero, Nichols A., Rubenstein, Brenda M., Shea, Jacqueline A. R., Shin, Hyeondeok, Shulenburger, Luke, Tillack, Andreas, Townsend, Joshua P., Tubman, Norm M., Van Der Goetz, Brett, Vincent, Jordan E., Yang, D. ChangMo, Yang, Yubo, Zhang, Shuai, and Zhao, Luning

Subjects
Physics - Computational Physics, Physics - Chemical Physics
Abstract

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org .

Published
2018
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4. Using Compiler Directives for Performance Portability in Scientific Computing: Kernels from Molecular Simulation

Author

Sedova, Ada, Tillack, Andreas F., Tharrington, Arnold, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Chandrasekaran, Sunita, editor, Juckeland, Guido, editor, and Wienke, Sandra, editor

Published
2019
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15. High-throughput virtual laboratory for drug discovery using massive datasets

Author

Glaser, Jens, primary, Vermaas, Josh V, additional, Rogers, David M, additional, Larkin, Jeff, additional, LeGrand, Scott, additional, Boehm, Swen, additional, Baker, Matthew B, additional, Scheinberg, Aaron, additional, Tillack, Andreas F, additional, Thavappiragasam, Mathialakan, additional, Sedova, Ada, additional, and Hernandez, Oscar, additional

Published
2021
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18. GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer

Author

LeGrand, Scott, primary, Scheinberg, Aaron, additional, Tillack, Andreas F., additional, Thavappiragasam, Mathialakan, additional, Vermaas, Josh V., additional, Agarwal, Rupesh, additional, Larkin, Jeff, additional, Poole, Duncan, additional, Santos-Martins, Diogo, additional, Solis-Vasquez, Leonardo, additional, Koch, Andreas, additional, Forli, Stefano, additional, Hernandez, Oscar, additional, Smith, Jeremy C., additional, and Sedova, Ada, additional

Published
2020
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19. Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

Author

Acharya, Atanu, primary, Agarwal, Rupesh, primary, Baker, Matthew, primary, Baudry, Jerome, primary, Bhowmik, Debsindhu, primary, Boehm, Swen, primary, Byler, Kendall, primary, Coates, Leighton, primary, Chen, Sam Yen-Chi, primary, Cooper, ConnorJ., primary, Demerdash, Omar, primary, Daidone, Isabella, primary, Eblen, John, primary, R. Ellingson, Sally, primary, Forli, Stefano, primary, Glaser, Jens, primary, Gumbart, James C., primary, Gunnels, John, primary, Hernandez, Oscar, primary, Irle, Stephan, primary, Larkin, Jeffery, primary, Lawrence, Travis J, primary, LeGrand, Scott, primary, Liu, Shih-Hsien, primary, C. Mitchell, Julie, primary, Park, Gilchan, primary, Parks, Jerry M., primary, Pavlova, Anna, primary, Petridis, Loukas, primary, Poole, Duncan, primary, Pouchard, Line, primary, Ramanathan, Arvind, primary, Rogers, David, primary, Santos-Martins, Diogo, primary, Scheinberg, Aaron, primary, Sedova, Ada, primary, Shen, Shawn, primary, Smith, Jeremy C., primary, Smith, Micholas, primary, Soto, Carlos, primary, Tsaris, Aristides, primary, Thavappiragasam, Mathialakan, primary, Tillack, Andreas F., primary, Vermaas, Josh V, primary, Vuong, Van Quan, primary, Yin, Junqi, primary, Yoo, Shinjae, primary, Zahran, Mai, primary, and Zanetti-Polzi, Laura, primary

Published
2020
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20. Performance evaluation of flexible macrocycle docking in AutoDock.

Author

Holcomb, Matthew, Santos-Martins, Diogo, Tillack, Andreas F., and Forli, Stefano

Subjects
MACROCYCLIC compounds, DRUG design, HYDROGEN bonding, MOLECULAR docking, ANISOTROPY
Abstract

Macrocycles represent an important class of ligands, both in natural products and designed drugs. In drug design, macrocyclizations can impart specific ligand conformations and contribute to passive permeation by encouraging intramolecular H-bonds. AutoDock-GPU and Vina can model macrocyclic ligands flexibly, without requiring the enumeration of macrocyclic conformers before docking. Here, we characterize the performance of the method for handling macrocyclic compounds, which is implemented and the default behaviour for ligand preparation with our ligand preparation pipeline, Meeko. A pseudoatom is used to encode bond geometry and produce an anisotropic closure force for macrocyclic rings. This method is evaluated on a diverse set of small molecule and peptide macrocycles, ranging from 7- to 33-membered rings, showing little accuracy loss compared to rigid redocking of the X-ray macrocycle conformers. This suggests that for conformationally flexible macrocycles with unknown binding modes, this method can be effectively used to predict the macrocycle conformation. [ABSTRACT FROM AUTHOR]

Published
2022
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23. QMCPACK: an open sourceab initioquantum Monte Carlo package for the electronic structure of atoms, molecules and solids

Author

Kim, Jeongnim, primary, Baczewski, Andrew D, additional, Beaudet, Todd D, additional, Benali, Anouar, additional, Bennett, M Chandler, additional, Berrill, Mark A, additional, Blunt, Nick S, additional, Borda, Edgar Josué Landinez, additional, Casula, Michele, additional, Ceperley, David M, additional, Chiesa, Simone, additional, Clark, Bryan K, additional, Clay, Raymond C, additional, Delaney, Kris T, additional, Dewing, Mark, additional, Esler, Kenneth P, additional, Hao, Hongxia, additional, Heinonen, Olle, additional, Kent, Paul R C, additional, Krogel, Jaron T, additional, Kylänpää, Ilkka, additional, Li, Ying Wai, additional, Lopez, M Graham, additional, Luo, Ye, additional, Malone, Fionn D, additional, Martin, Richard M, additional, Mathuriya, Amrita, additional, McMinis, Jeremy, additional, Melton, Cody A, additional, Mitas, Lubos, additional, Morales, Miguel A, additional, Neuscamman, Eric, additional, Parker, William D, additional, Pineda Flores, Sergio D, additional, Romero, Nichols A, additional, Rubenstein, Brenda M, additional, Shea, Jacqueline A R, additional, Shin, Hyeondeok, additional, Shulenburger, Luke, additional, Tillack, Andreas F, additional, Townsend, Joshua P, additional, Tubman, Norm M, additional, Van Der Goetz, Brett, additional, Vincent, Jordan E, additional, Yang, D ChangMo, additional, Yang, Yubo, additional, Zhang, Shuai, additional, and Zhao, Luning, additional

Published
2018
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24. Multi-scale theory-assisted nano-engineering of plasmonic-organic hybrid electro-optic device performance

Author

Dalton, Larry R., primary, Josten, Arne, primary, Ayata, Masafumi, primary, Koch, Ueli, primary, Leuthold, Juerg, primary, Salamin, Yannick, primary, Elder, Delwin L., primary, Johnson, Lewis E., primary, Tillack, Andreas F., primary, Robinson, Bruce H., primary, Haffner, Christian, primary, Heni, Wolfgang, primary, Hoessbacher, Claudia B., primary, Fedoryshyn, Yuriy, primary, and Baeuerle, Benedikt, primary

Published
2018
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27. Silicon–Organic and Plasmonic–Organic Hybrid Photonics

Author

Heni, Wolfgang, primary, Kutuvantavida, Yasar, additional, Haffner, Christian, additional, Zwickel, Heiner, additional, Kieninger, Clemens, additional, Wolf, Stefan, additional, Lauermann, Matthias, additional, Fedoryshyn, Yuriy, additional, Tillack, Andreas F., additional, Johnson, Lewis E., additional, Elder, Delwin L., additional, Robinson, Bruce H., additional, Freude, Wolfgang, additional, Koos, Christian, additional, Leuthold, Juerg, additional, and Dalton, Larry R., additional

Published
2017
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29. Nonlinearities of organic electro-optic materials in nanoscale slots and implications for the optimum modulator design

Author

Heni, Wolfgang, primary, Haffner, Christian, additional, Elder, Delwin L., additional, Tillack, Andreas F., additional, Fedoryshyn, Yuriy, additional, Cottier, Raphael, additional, Salamin, Yannick, additional, Hoessbacher, Claudia, additional, Koch, Ueli, additional, Cheng, Bojun, additional, Robinson, Bruce, additional, Dalton, Larry R., additional, and Leuthold, Juerg, additional

Published
2017
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30. 25 Years of Organic Electro-Optics and Future Prospects.

Author

DALTON, LARRY R., ELDER, DELWIN L., JOHNSON, LEWIS E., TILLACK, ANDREAS F., and ROBINSON, BRUCE H.

Subjects
ELECTROOPTICS, WAVEGUIDES, CHROMOPHORES, POLYMERS, ENERGY consumption, BANDWIDTHS
Abstract

Multi-scale modeling methods are employed to assist in the design of improved organic electro-optic (OEO) materials, including simulating the effects of the interaction of such materials with the electrodes of silicon organic hybrid (SOH) and plasmonic organic hybrid (POH) nanoscopic waveguide devices. Theoretical methods have promoted the evolution of OEO materials from low number density chromophore-polymer guesthost composites and chromophores covalently attached to traditional polymer matrices to custom designed high chromophore number density macromolecular materials with controlled intermolecular interactions and reduced matrix dimensionality. New OEO materials exhibit electrooptic activity of 500-600 pm/V in electrically-poled mm thick films and 90-350 pm/V in nm thick films in SOH and POH devices. The improvement in EO activity together with concentration of RF and optical fields in SOH and POH devices has resulted in a substantial improvement in device performance, including reducing voltage-length performance to 40 V-mm, energy efficiency on the order of a femtojoule/bit, device footprints on the order of 1 mm² and bandwidths of > 170 GHz for POH devices. Significant advances with respect to device insertion loss have also been achieved. [ABSTRACT FROM AUTHOR]

Published
2019

31. Alternative bridging architectures in organic nonlinear optical materials: comparison of π- and χ-type structures

Author

Rawal, Meghana, primary, Garrett, Kerry E., additional, Johnson, Lewis E., additional, Kaminsky, Werner, additional, Jucov, Evgheni, additional, Shelton, David P., additional, Timofeeva, Tatiana, additional, Eichinger, Bruce E., additional, Tillack, Andreas F., additional, Robinson, Bruce H., additional, Elder, Delwin L., additional, and Dalton, Larry R., additional

Published
2016
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37. Multi-scale theory-assisted nano-engineering of plasmonic-organic hybrid electro-optic device performance

Author

Tabor, Christopher E., Kajzar, François, Kaino, Toshikuni, Koike, Yasuhiro, Elder, Delwin L., Johnson, Lewis E., Tillack, Andreas F., Robinson, Bruce H., Haffner, Christian, Heni, Wolfgang, Hoessbacher, Claudia, Fedoryshyn, Yuriy, Salamin, Yannick, Baeuerle, Benedikt, Josten, Arne, Ayata, Masafumi, Koch, Ueli, Leuthold, Juerg, and Dalton, Larry R.

Published
2018
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40. Surface Characterization of Polythiophene:Fullerene Blends on Different Electrodes Using Near Edge X-ray Absorption Fine Structure

Author

Tillack, Andreas F., primary, Noone, Kevin M., additional, MacLeod, Bradley A., additional, Nordlund, Dennis, additional, Nagle, Kenneth P., additional, Bradley, Joseph A., additional, Hau, Steven K., additional, Yip, Hin-Lap, additional, Jen, Alex K.-Y., additional, Seidler, Gerald T., additional, and Ginger, David S., additional

Published
2011
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42. Benzocyclobutene barrier layer for suppressing conductance in nonlinear optical devices during electric field poling.

Author

Wenwei Jin, Johnston, Peter V., Elder, Delwin L., Tillack, Andreas F., Olbricht, Benjamin C., Jinsheng Song, Reid, Philip J., Ruimin Xu, Robinson, Bruce H., and Dalton, Larry R.

Subjects
BENZOCYCLOBUTENE, OPTICAL devices, ELECTRIC fields, THIN film devices, CHROMOPHORES, STRAY currents
Abstract

We measured the electro-optic (EO) coefficients (r33) of thin-film devices made from several monolithic, high number density organic EO chromophores with and without additional charge barrier layers. We found that a cross-linkable benzocyclobutene layer was very effective in suppressing unwanted, leakage current, keeping the effective poling voltage nearly identical to the applied voltage. This barrier layer proved to be superior to a titanium dioxide (TiO2) barrier layer. The suppression of the leakage current in combination with a new chromophore enabled the construction of EO devices that had r33 values in the range of 400-500 pm V-1 with poling fields 85V μm-1. [ABSTRACT FROM AUTHOR]

Published
2014
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45. GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research.

Author

LeGrand S, Scheinberg A, Tillack AF, Thavappiragasam M, Vermaas JV, Agarwal R, Larkin J, Poole D, Santos-Martins D, Solis-Vasquez L, Koch A, Forli S, Hernandez O, Smith JC, and Sedova A

Abstract

Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability to bind to a given protein receptor within a drug-discovery campaign. Experimental drug screening is expensive and time consuming, and it is desirable to carry out large scale docking calculations in a high-throughput manner to narrow the experimental search space. Few of the existing computational docking tools were designed with high performance computing in mind. Therefore, optimizations to maximize use of high-performance computational resources available at leadership-class computing facilities enables these facilities to be leveraged for drug discovery. Here we present the porting, optimization, and validation of the AutoDock-GPU program for the Summit supercomputer, and its application to initial compound screening efforts to target proteins of the SARS-CoV-2 virus responsible for the current COVID-19 pandemic.

Published
2020

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