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537 results on '"Roy, Shantanu"'

2. Can Minkowski tensors of a porous microstructure characterize its permeability?

Author

Nair, Prapanch, Mühlbauer, Sebastian, Roy, Shantanu, and Poeschel, Thorsten

Subjects
Physics - Fluid Dynamics, Physics - Computational Physics
Abstract

We show that the permeability of porous media can be reliably predicted from the Minkowski tensors (MTs) describing the pore microstructure geometry. To this end, we consider a large number of simulations of flow through periodic unit cells containing complex shaped obstacles. The prediction is achieved by training a deep neural network (DNN) using the simulation data with the MT elements as attributes. The obtained predictions allow for the conclusion that MTs of the pore microstructure contain sufficient information to determine the permeability, although the functional relation between the MTs and the permeability could be complex to determine.

Published
2020
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4. HMG-CoA Reductase Inhibitors as Drug Leads against Naegleria fowleri

Author

Hahn, Hye Jee, Abagyan, Ruben, Podust, Larissa M, Roy, Shantanu, Ali, Ibne Karim M, and Debnath, Anjan

Subjects
Biochemistry and Cell Biology, Biological Sciences, Biodefense, Emerging Infectious Diseases, Infectious Diseases, Rare Diseases, Neurosciences, Orphan Drug, 6.1 Pharmaceuticals, 5.1 Pharmaceuticals, Good Health and Well Being, Adult, Australia, Central Nervous System Protozoal Infections, Child, Humans, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Naegleria fowleri, Pharmaceutical Preparations, free-living ameba, drug, primary amebic meningoencephalitis, statins, HMG-CoA reductase, Medicinal and Biomolecular Chemistry, Biochemistry and cell biology, Analytical chemistry, Medicinal and biomolecular chemistry
Abstract

Primary amebic meningoencephalitis (PAM), caused by the free-living ameba Naegleria fowleri, has a fatality rate of over 97%. Treatment of PAM relies on amphotericin B in combination with other drugs, but few patients have survived with the existing drug treatment regimens. Therefore, development of effective drugs is a critical unmet need to avert deaths from PAM. Since ergosterol is one of the major sterols in the membrane of N. fowleri, disruption of isoprenoid and sterol biosynthesis by small-molecule inhibitors may be an effective intervention strategy against N. fowleri. The genome of N. fowleri contains a gene encoding HMG-CoA reductase (HMGR); the catalytic domains of human and N. fowleri HMGR share

Published
2020

12. Stabilized Quasi-Newton Optimization of Noisy Potential Energy Surfaces

Author

Schaefer, Bastian, Ghasemi, S. Alireza, Roy, Shantanu, and Goedecker, Stefan

Subjects
Physics - Computational Physics
Abstract

Optimizations of atomic positions belong to the most commonly performed tasks in electronic structure calculations. Many simulations like global minimum searches or characterizations of chemical reactions require performing hundreds or thousands of minimizations or saddle computations. To automatize these tasks, optimization algorithms must not only be efficient, but also very reliable. Unfortunately computational noise in forces and energies is inherent to electronic structure codes. This computational noise poses a sever problem to the stability of efficient optimization methods like the limited-memory Broyden-Fletcher-Goldfarb-Shanno algorithm. We here present a technique that allows obtaining significant curvature information of noisy potential energy surfaces. We use this technique to construct both, a stabilized quasi-Newton minimization method and a stabilized quasi-Newton saddle finding approach. We demonstrate with the help of benchmarks that both the minimizer and the saddle finding approach are superior to comparable existing methods.

Published
2014
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14. Brainstorm: A case of granulomatous encephalitis.

Author

Benoit, Patrick, Wang, Stephanie, Wang, Catherine, Chakravarti, Arpita, Villalba, Julian A, Ali, Ibne Karim M, Roy, Shantanu, Sapp, Sarah GH, Reagan-Steiner, Sarah, Nelson, Kristoff, Cayrol, Romain, Luong, Me-Linh, Grand'Maison, Sophie, and Desjardins, Michaël

Published
2024
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18. Entamoeba sp. infection in a bearded dragon (Pogona vitticeps)

Author

Schwartz Diana, Ali Ibne Karim M., Roy Shantanu, Pohlman Lisa M., Kastl Brandy, and Eshar David

Subjects
entamoeba, enteritis, liver abscess, pogona vitticeps, reptilia, Veterinary medicine, SF600-1100
Abstract

A 3-year-old, male intact, pet inland bearded dragon (Pogona vitticeps) presented with a history of diarrhea, progressive inappetence and weight loss. A palpable cranial celomic mass was identified on physical examination and confirmed to be hepatic in origin by celomic ultrasonography. Hematologic and biochemical abnormalities were mild and consistent with inflammation, regenerative anemia, and hepatocellular injury. Fine needle aspiration of the liver masses was suggestive of amoebiasis and the patient was humanely euthanized. PCR and Sanger DNA sequencing of liver aspirates were supportive of Entamoeba infection, although definitive speciation was not possible. Pathogenic amoebiasis due to infection by E. invadens has been reported in a wide range of reptiles and is an important cause of morbidity and mortality in these species.

Published
2020
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23. Application of 5G Waveform in Internet of Things (IoT) and Its Impact on BER in Physical Layer

Author

Neog, Pallavi, Paul, Rajat, Roy, Shantanu, Bera, Rabindranath, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Ruediger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Liang, Qilian, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Möller, Sebastian, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zhang, Junjie James, Series Editor, Bera, Rabindranath, editor, Sarkar, Subir Kumar, editor, and Chakraborty, Swastika, editor

Published
2018
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24. Wireless Security Over a Point-to-Point 5G Communication System

Author

Paul, Rajat, Neog, Pallavi, Roy, Shantanu, Bera, Rabindranath, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Ruediger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Hirche, Sandra, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Liang, Qilian, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Möller, Sebastian, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zhang, Junjie James, Series Editor, Bera, Rabindranath, editor, Sarkar, Subir Kumar, editor, and Chakraborty, Swastika, editor

Published
2018
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26. The energy landscape of silicon systems and its description by force fields, tight binding schemes, density functional methods and Quantum Monte Carlo methods

Author

Ghasemi, S. Alireza, Amsler, Maximilian, Hennig, Richard G., Roy, Shantanu, Goedecker, Stefan, Umrigar, C. J., Genovese, Luigi, Lenosky, Thomas J., Morishita, Tetsuya, and Nishio, Kengo

Subjects
Physics - Computational Physics, Physics - Chemical Physics
Abstract

The accuracy of the energy landscape of silicon systems obtained from various density functional methods, a tight binding scheme and force fields is studied. Quantum Monte Carlo results serve as quasi exact reference values. In addition to the well known accuracy of DFT methods for geometric ground states and metastable configurations we find that DFT methods give a similar accuracy for transition states and thus a good overall description of the energy landscape. On the other hand, force fields give a very poor description of the landscape that are in most cases too rugged and contain many fake local minima and saddle points or ones that have the wrong height.

Published
2009

27. The performance of Minima Hopping and Evolutionary Algorithms for cluster structure prediction

Author

Schoenborn, Sandro E., Goedecker, Stefan, Roy, Shantanu, and Oganov, Artem R.

Subjects
Condensed Matter - Other Condensed Matter
Abstract

We compare Evolutionary Algorithms with Minima Hopping for global optimization in the field of cluster structure prediction. We introduce a new {\em average offspring} recombination operator and compare it with previously used operators. Minima Hopping is improved with a {\em softening} method and a stronger feedback mechanism. Test systems are atomic clusters with Lennard-Jones interaction as well as silicon and gold clusters described by force fields. The improved Minima Hopping is found to be well-suited to all these homoatomic problems. The evolutionary algorithm is more efficient for systems with compact and symmetric ground states, including LJ$_{150}$, but it fails for systems with very complex energy landscapes and asymmetric ground states, such as LJ$_{75}$ and silicon clusters with more than 30 atoms. Both successes and failures of the evolutionary algorithm suggest ways for its improvement.

Published
2008
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29. A Bell-Evans-Polanyi principle for molecular dynamics trajectories and its implications for global optimization

Author

Roy, Shantanu, Hellmann, Waldemar, and Goedecker, Stefan

Subjects
Physics - Computational Physics, Physics - Chemical Physics
Abstract

The Bell-Evans-Polanyi principle that is valid for a chemical reaction that proceeds along the reaction coordinate over the transition state is extended to molecular dynamics trajectories that in general do not cross the dividing surface between the initial and the final local minima at the exact transition state. Our molecular dynamics Bell-Evans-Polanyi principle states that low energy molecular dynamics trajectories are more likely to lead into the basin of attraction of a low energy local minimum than high energy trajectories. In the context of global optimization schemes based on molecular dynamics our molecular dynamics Bell-Evans-Polanyi principle implies that using low energy trajectories one needs to visit a smaller number of distinguishable local minima before finding the global minimum than when using high energy trajectories.

Published
2007
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31. The contribution of parent-to-offspring transmission of telomeres to the heritability of telomere length in humans

Author

Delgado, Dayana A., Zhang, Chenan, Gleason, Kevin, Demanelis, Kathryn, Chen, Lin S., Gao, Jianjun, Roy, Shantanu, Shinkle, Justin, Sabarinathan, Mekala, Argos, Maria, Tong, Lin, Ahmed, Alauddin, Islam, Tariqul, Rakibuz-Zaman, Muhammad, Sarwar, Golam, Shahriar, Hasan, Rahman, Mahfuzar, Yunus, Muhammad, Doherty, Jennifer A., Jasmine, Farzana, Kibriya, Muhammad G., Ahsan, Habibul, and Pierce, Brandon L.

Published
2019
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43. Screening for gene–environment (G×E) interaction using omics data from exposed individuals: an application to gene-arsenic interaction

Author

Argos, Maria, Tong, Lin, Roy, Shantanu, Sabarinathan, Mekala, Ahmed, Alauddin, Islam, Md. Tariqul, Islam, Tariqul, Rakibuz-Zaman, Muhammad, Sarwar, Golam, Shahriar, Hasan, Rahman, Mahfuzar, Yunus, Md., Graziano, Joseph H., Jasmine, Farzana, Kibriya, Muhammad G., Zhou, Xiang, Ahsan, Habibul, and Pierce, Brandon L.

Published
2018
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44. Supplementary Methods, Tables 1 - 6 from A Genome-wide Association Study of Early-Onset Breast Cancer Identifies PFKM as a Novel Breast Cancer Gene and Supports a Common Genetic Spectrum for Breast Cancer at Any Age

Author

Ahsan, Habibul, primary, Halpern, Jerry, primary, Kibriya, Muhammad G., primary, Pierce, Brandon L., primary, Tong, Lin, primary, Gamazon, Eric, primary, McGuire, Valerie, primary, Felberg, Anna, primary, Shi, Jianxin, primary, Jasmine, Farzana, primary, Roy, Shantanu, primary, Brutus, Rachelle, primary, Argos, Maria, primary, Melkonian, Stephanie, primary, Chang-Claude, Jenny, primary, Andrulis, Irene, primary, Hopper, John L., primary, John, Esther M., primary, Malone, Kathi, primary, Ursin, Giske, primary, Gammon, Marilie D., primary, Thomas, Duncan C., primary, Seminara, Daniela, primary, Casey, Graham, primary, Knight, Julia A., primary, Southey, Melissa C., primary, Giles, Graham G., primary, Santella, Regina M., primary, Lee, Eunjung, primary, Conti, David, primary, Duggan, David, primary, Gallinger, Steve, primary, Haile, Robert, primary, Jenkins, Mark, primary, Lindor, Noralane M., primary, Newcomb, Polly, primary, Michailidou, Kyriaki, primary, Apicella, Carmel, primary, Park, Daniel J., primary, Peto, Julian, primary, Fletcher, Olivia, primary, dos Santos Silva, Isabel, primary, Lathrop, Mark, primary, Hunter, David J., primary, Chanock, Stephen J., primary, Meindl, Alfons, primary, Schmutzler, Rita K., primary, Müller-Myhsok, Bertram, primary, Lochmann, Magdalena, primary, Beckmann, Lars, primary, Hein, Rebecca, primary, Makalic, Enes, primary, Schmidt, Daniel F., primary, Bui, Quang Minh, primary, Stone, Jennifer, primary, Flesch-Janys, Dieter, primary, Dahmen, Norbert, primary, Nevanlinna, Heli, primary, Aittomäki, Kristiina, primary, Blomqvist, Carl, primary, Hall, Per, primary, Czene, Kamila, primary, Irwanto, Astrid, primary, Liu, Jianjun, primary, Rahman, Nazneen, primary, Turnbull, Clare, primary, Dunning, Alison M., primary, Pharoah, Paul, primary, Waisfisz, Quinten, primary, Meijers-Heijboer, Hanne, primary, Uitterlinden, Andre G., primary, Rivadeneira, Fernando, primary, Nicolae, Dan, primary, Easton, Douglas F., primary, Cox, Nancy J., primary, and Whittemore, Alice S., primary

Published
2023
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45. Data from A Genome-wide Association Study of Early-Onset Breast Cancer Identifies PFKM as a Novel Breast Cancer Gene and Supports a Common Genetic Spectrum for Breast Cancer at Any Age

Author

Ahsan, Habibul, primary, Halpern, Jerry, primary, Kibriya, Muhammad G., primary, Pierce, Brandon L., primary, Tong, Lin, primary, Gamazon, Eric, primary, McGuire, Valerie, primary, Felberg, Anna, primary, Shi, Jianxin, primary, Jasmine, Farzana, primary, Roy, Shantanu, primary, Brutus, Rachelle, primary, Argos, Maria, primary, Melkonian, Stephanie, primary, Chang-Claude, Jenny, primary, Andrulis, Irene, primary, Hopper, John L., primary, John, Esther M., primary, Malone, Kathi, primary, Ursin, Giske, primary, Gammon, Marilie D., primary, Thomas, Duncan C., primary, Seminara, Daniela, primary, Casey, Graham, primary, Knight, Julia A., primary, Southey, Melissa C., primary, Giles, Graham G., primary, Santella, Regina M., primary, Lee, Eunjung, primary, Conti, David, primary, Duggan, David, primary, Gallinger, Steve, primary, Haile, Robert, primary, Jenkins, Mark, primary, Lindor, Noralane M., primary, Newcomb, Polly, primary, Michailidou, Kyriaki, primary, Apicella, Carmel, primary, Park, Daniel J., primary, Peto, Julian, primary, Fletcher, Olivia, primary, dos Santos Silva, Isabel, primary, Lathrop, Mark, primary, Hunter, David J., primary, Chanock, Stephen J., primary, Meindl, Alfons, primary, Schmutzler, Rita K., primary, Müller-Myhsok, Bertram, primary, Lochmann, Magdalena, primary, Beckmann, Lars, primary, Hein, Rebecca, primary, Makalic, Enes, primary, Schmidt, Daniel F., primary, Bui, Quang Minh, primary, Stone, Jennifer, primary, Flesch-Janys, Dieter, primary, Dahmen, Norbert, primary, Nevanlinna, Heli, primary, Aittomäki, Kristiina, primary, Blomqvist, Carl, primary, Hall, Per, primary, Czene, Kamila, primary, Irwanto, Astrid, primary, Liu, Jianjun, primary, Rahman, Nazneen, primary, Turnbull, Clare, primary, Dunning, Alison M., primary, Pharoah, Paul, primary, Waisfisz, Quinten, primary, Meijers-Heijboer, Hanne, primary, Uitterlinden, Andre G., primary, Rivadeneira, Fernando, primary, Nicolae, Dan, primary, Easton, Douglas F., primary, Cox, Nancy J., primary, and Whittemore, Alice S., primary

Published
2023
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46. Case of Primary Amebic Meningoencephalitis Associated with Surfing at an Artificial Surf Venue: Environmental Investigation

Author

Miko, Shanna, primary, Cope, Jennifer R., additional, Hlavsa, Michele C., additional, Ali, Ibne Karim M., additional, Brown, Travis W., additional, Collins, Jennifer P., additional, Greeley, Rebecca D., additional, Kahler, Amy M., additional, Moore, Kathleen O., additional, Roundtree, Alexis V., additional, Roy, Shantanu, additional, Sanders, Lacey L., additional, Shah, Vaidehi, additional, Stuteville, Haylea D., additional, and Mattioli, Mia C., additional

Published
2023
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