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15. On the thickness of the double layer in ionic liquids

Author

Ruzanov, Anton, Lembinen, Meeri, Jakovits, Pelle, Srirama, Satish N., Voroshylova, Iuliia V., Cordeiro, M. Natália D. S., Pereira, Carlos M., Rossmeisl, Jan, and Ivaništšev, Vladislav B.

Subjects
Condensed Matter - Soft Condensed Matter
Abstract

In this study, we examined the thickness of the electrical double layer (EDL) in ionic liquids using density functional theory (DFT) calculations and molecular dynamics (MD) simulations. We focused on the BF4- anion adsorption from 1-ethyl-3-methylimidazolium tetrafluoroborate (EMImBF4) ionic liquid on the Au(111) surface. At both DFT and MD levels, we evaluated the capacitance-potential dependence for the Helmholtz model of the interface. Using MD simulations, we also explored a more realistic, multilayer EDL model accounting for the ion layering. Concurrent analysis of the DFT and MD results provides a ground for thinking whether the electrical double layer in ionic liquids is one- or multi-ionic-layer thick.

Published
2017
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16. Perturbation Theory Machine Learning Model for Phenotypic Early Antineoplastic Drug Discovery: Design of Virtual Anti-Lung-Cancer Agents.

Author

Kleandrova, Valeria V., Cordeiro, M. Natália D. S., and Speck-Planche, Alejandro

Subjects
MACHINE learning, DRUG discovery, PERTURBATION theory, MACHINE theory, VIRTUAL design
Abstract

Lung cancer is the most diagnosed malignant neoplasm worldwide and it is associated with great mortality. Currently, developing antineoplastic agents is a challenging, time-consuming, and costly process. Computational methods can speed up the early discovery of anti-lung-cancer chemicals. Here, we report a perturbation theory machine learning model based on a multilayer perceptron (PTML-MLP) model for phenotypic early antineoplastic drug discovery, enabling the rational design and prediction of new molecules as virtual versatile inhibitors of multiple lung cancer cell lines. The PTML-MLP model achieved an accuracy above 80%. We applied the fragment-based topological design (FBTD) approach to physicochemically and structurally interpret the PTML-MLP model. This enabled the extraction of suitable fragments with a positive influence on anti-lung-cancer activity against the different lung cancer cell lines. By following the aforementioned interpretations, we could assemble several suitable fragments to design four novel molecules, which were predicted by the PTML-MLP model as versatile anti-lung-cancer agents. Such predictions of potent multi-cellular anticancer activity against diverse lung cancer cell lines were rigorously confirmed by a well-established virtual screening tool reported in the literature. The present work envisages new opportunities for the application of PTML models to accelerate early antineoplastic discovery from phenotypic assays. [ABSTRACT FROM AUTHOR]

Published
2024
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21. Marlim and Voador Fields Revitalization Project

Author

Paula, M. T., additional, Lage, D. H. M., additional, dos Santos, A. B., additional, Pedrosa, C. A., additional, da Silva, G. B., additional, da Fonseca, L. H., additional, Cordeiro, M. G. R., additional, da Costa, T. C., additional, Pereira, R. M. A., additional, and Miranda, T. A., additional

Published
2024
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26. List of contributors

Author

Abdulhussein, Dalia, primary, Abraham, Abu, additional, Agrahari, Vivek, additional, Amrane, Mourad, additional, Ayyagari, Ananta, additional, Buchholzer, Franz, additional, Chastain, James E., additional, Chen, Chiungkuang, additional, Cheng, Andy K., additional, Chia, Audrey, additional, Cordeiro, M. Francesca, additional, Daull, Philippe, additional, deLong, Mitchell A., additional, Foo, Li Lian, additional, Gudibanda, Pooja, additional, Herwig-Carl, Martina C., additional, Huang, Alex A., additional, Husain, Shahid, additional, Idigo, Chinenye, additional, Koizumi, Schuichi, additional, Kosoko-Lasaki, Sade, additional, Kuhn, Megan S., additional, Kundu, Aishwarya, additional, Lamb, William D.B., additional, Leung, Alex, additional, Li, Yu Meng, additional, Limb, G. Astrid, additional, Loeffler, Karin U., additional, Luthert, Phil, additional, Makley, Leah, additional, Manzar, Haider, additional, McDonnell, Fiona S., additional, McKoy, Marshalyn G., additional, Miyake, Hideki, additional, Mohanty, Samarendra, additional, Mudumba, Sreenivasu, additional, Muili, Fatima, additional, Narcisse, Darryl, additional, Ng, Wei Yan, additional, Ngele, Kalu K., additional, Njie-Mbye, Ya Fatou, additional, Ohia, Sunny E., additional, Ohia-Nwoko, Odochi, additional, Ohnuma, Shin-ichi, additional, Okolie, Anthonia, additional, Opere, Catherine A., additional, Pinchuk, Leonard, additional, Raola, Akash, additional, Sadruddin, Omar, additional, Sharif, Najam A., additional, Shibagaki, Keiichi, additional, Shinozaki, Youichi, additional, Singh, Onkar N., additional, Stamer, W. Daniel, additional, Stradiotto, Allison, additional, Sturdivant, Jill, additional, Toshimori, Masanao, additional, Yacoub, Sam, additional, Yalzadeh, Dariush, additional, Yap, Timothy E., additional, Yerxa, Benjamin R., additional, and Zode, Gulab, additional

Published
2022
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30. Neuroprotection for glaucoma: Requirements for clinical translation

Author

Levin, Leonard A, Crowe, Megan E, Quigley, Harry A, Participants, The Lasker IRRF Initiative on Astrocytes and Glaucomatous Neurodegeneration, Cordeiro, M Francesca, Donoso, Larry A, Liao, Y Joyce, Libby, Richard T, Masland, Richard H, Nickells, Robert W, Sieving, Paul A, and Sommer, Alfred

Subjects
Neurosciences, Eye Disease and Disorders of Vision, Neurodegenerative, Aging, Bioengineering, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Eye, Animals, Astrocytes, Axons, Glaucoma, Humans, Neuroprotection, Neuroprotective Agents, Optic Nerve Diseases, Retinal Ganglion Cells, Translational Research, Biomedical, Lasker/IRRF Initiative on Astrocytes and Glaucomatous Neurodegeneration Participants, Retinal ganglion cells, Medical Biochemistry and Metabolomics, Opthalmology and Optometry, Ophthalmology & Optometry
Abstract

Within the field of glaucoma research, neuroprotection is defined as slowing the functional loss in glaucoma by a mechanism independent of lowering of intraocular pressure. There is currently a great potential for research surrounding neuroprotection as it relates to glaucoma. Anatomical targets for neuroprotection should focus on upstream rather than downstream factors, and could include any part of the retinal ganglion cell, the glia, especially astrocytes or Muller cells, and vasculature. The great number of anatomical targets is exceeded only by the number of possible biochemical pathways and potential treatments. Successful treatment may be accomplished through the targeting of one or even a combination of multiple pathways. Once a treatment is shown effective in vitro, it should be evaluated in vivo with carefully chosen animal models and studied in sufficient numbers to detect statistically and clinically significant effects. Such a drug should have few systemic side effects and its delivery should be optimized so as to encourage compliance. There are still a multitude of possible screens available to test the efficacy of a neuroprotective drug and a single gold standard is ideal for the accurate assessment and comparison of new drugs. Future studies in neuroprotection should investigate the genetic component of the disease, novel pharmaceutical agents for new or known pathways, modulations of scleral biomechanics, and relation to research of other complex disorders of the central nervous system.

Published
2017

43. Mr. Silva and Patient Zero: A Medical Social Network and Data Visualization Information System

Author

Gonçalves, Patrícia C. T., Moura, Ana S., Cordeiro, M. Natália D. S., Campos, Pedro, 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, Weikum, Gerhard, Series Editor, Stoyanov, Danail, editor, Taylor, Zeike, editor, Aylward, Stephen, editor, Tavares, João Manuel R.S., editor, Xiao, Yiming, editor, Simpson, Amber, editor, Martel, Anne, editor, Maier-Hein, Lena, editor, Li, Shuo, editor, Rivaz, Hassan, editor, Reinertsen, Ingerid, editor, Chabanas, Matthieu, editor, and Farahani, Keyvan, editor

Published
2018
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