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1,002 results on '"Thomas, John C."'

2. Chemo-mechanics in alloy phase stability

Author

Behara, Sesha Sai, Thomas, John C., Puchala, Brian, and Van der Ven, Anton

Subjects
Condensed Matter - Materials Science
Abstract

We describe a first-principles statistical mechanics method to calculate the free energies of crystalline alloys that depend on temperature, composition, and strain. The approach relies on an extension of the alloy cluster expansion to include an explicit dependence on homogeneous strain in addition to site occupation variables that track the degree of chemical ordering. The method is applied to the Si-Ge binary alloy and is used to calculate free energies that describe phase stability under arbitrary epitaxial constraints. We find that while the incoherent phase diagram (in which coexisting phases are not affected by coherency constraints) hosts a miscibility gap, coherent phase equilibrium predicts ordering and negative enthalpies of mixing. Instead of chemical instability, the chemo-mechanical free energy exhibits instabilities along directions that couple the composition of the alloy with a volumetric strain order parameter. This has fundamental implications for phase field models of spinodal decomposition as it indicates the importance of gradient energy coefficients that couple gradients in composition with gradients in strain.

Published
2023

3. CASM Monte Carlo: Calculations of the thermodynamic and kinetic properties of complex multicomponent crystals

Author

Puchala, Brian, Thomas, John C., and Van der Ven, Anton

Subjects
Condensed Matter - Materials Science
Abstract

Monte Carlo techniques play a central role in statistical mechanics approaches for connecting macroscopic thermodynamic and kinetic properties to the electronic structure of a material. This paper describes the implementation of Monte Carlo techniques for the study multicomponent crystalline materials within the Clusters Approach to Statistical Mechanics (CASM) software suite, and demonstrates their use in model systems to calculate free energies and kinetic coefficients, study phase transitions, and construct first-principles based phase diagrams. Many crystal structures are complex, with multiple sublattices occupied by differing sets of chemical species, along with the presence of vacancies or interstitial species. This imposes constraints on concentration variables, the form of thermodynamic potentials, and the values of kinetic transport coefficients. The framework used by CASM to formulate thermodynamic potentials and kinetic transport coefficients accounting for arbitrarily complex crystal structures is presented and demonstrated with examples applying it to crystal systems of increasing complexity. Additionally, a new software package is introduced, casm-flow, which helps automate the setup, submission, management, and analysis of Monte Carlo simulations performed using CASM.

Published
2023

4. A substitutional quantum defect in WS$_2$ discovered by high-throughput computational screening and fabricated by site-selective STM manipulation

Author

Thomas, John C., Chen, Wei, Xiong, Yihuang, Barker, Bradford A., Zhou, Junze, Chen, Weiru, Rossi, Antonio, Kelly, Nolan, Yu, Zhuohang, Zhou, Da, Kumari, Shalini, Barnard, Edward S., Robinson, Joshua A., Terrones, Mauricio, Schwartzberg, Adam, Ogletree, D. Frank, Rotenberg, Eli, Noack, Marcus M., Griffin, Sinéad, Raja, Archana, Strubbe, David A., Rignanese, Gian-Marco, Weber-Bargioni, Alexander, and Hautier, Geoffroy

Subjects
Condensed Matter - Materials Science, Quantum Physics
Abstract

Point defects in two-dimensional materials are of key interest for quantum information science. However, the space of possible defects is immense, making the identification of high-performance quantum defects extremely challenging. Here, we perform high-throughput (HT) first-principles computational screening to search for promising quantum defects within WS$_2$, which present localized levels in the band gap that can lead to bright optical transitions in the visible or telecom regime. Our computed database spans more than 700 charged defects formed through substitution on the tungsten or sulfur site. We found that sulfur substitutions enable the most promising quantum defects. We computationally identify the neutral cobalt substitution to sulfur (Co$_{\rm S}^{0}$) as very promising and fabricate it with scanning tunneling microscopy (STM). The Co$_{\rm S}^{0}$ electronic structure measured by STM agrees with first principles and showcases an attractive new quantum defect. Our work shows how HT computational screening and novel defect synthesis routes can be combined to design new quantum defects., Comment: 38 pages, 19 figures

Published
2023

6. Direct visualization of the charge transfer in Graphene/$\alpha$-RuCl$_3$ heterostructure

Author

Rossi, Antonio, Dettori, Riccardo, Johnson, Cameron, Balgley, Jesse, Thomas, John C., Francaviglia, Luca, Schmid, Andreas K., Watanabe, Kenji, Taniguchi, Takashi, Cothrine, Matthew, Mandrus, David G., Jozwiak, Chris, Bostwick, Aaron, Henriksen, Erik A., Weber-Bargioni, Alexander, and Rotenberg, Eli

Subjects
Condensed Matter - Materials Science
Abstract

We investigate the electronic properties of a graphene and $\alpha$-ruthenium trichloride (hereafter RuCl$_3$) heterostructure, using a combination of experimental and theoretical techniques. RuCl$_3$ is a Mott insulator and a Kitaev material, and its combination with graphene has gained increasing attention due to its potential applicability in novel electronic and optoelectronic devices. By using a combination of spatially resolved photoemission spectroscopy, low energy electron microscopy, and density functional theory (DFT) calculations we are able to provide a first direct visualization of the massive charge transfer from graphene to RuCl$_3$, which can modify the electronic properties of both materials, leading to novel electronic phenomena at their interface. The electronic band structure is compared to DFT calculations that confirm the occurrence of a Mott transition for RuCl$_3$. Finally, a measurement of spatially resolved work function allows for a direct estimate of the interface dipole between graphene and RuCl$_3$. The strong coupling between graphene and RuCl$_3$ could lead to new ways of manipulating electronic properties of two-dimensional lateral heterojunction. Understanding the electronic properties of this structure is pivotal for designing next generation low-power opto-electronics devices.

Published
2023
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7. Near-Field Coupling with a Nanoimprinted Probe for Dark Exciton Nanoimaging in Monolayer WSe2

Author

Zhou, Junze, Thomas, John C, Barre, Elyse, Barnard, Edward S, Raja, Archana, Cabrini, Stefano, Munechika, Keiko, Schwartzberg, Adam, and Weber-Bargioni, Alexander

Subjects
tip-enhanced photoluminescence, gap-mode plasmonic cavity, dark exciton, 2D materials, nanobubble, Nanoscience & Nanotechnology
Abstract

Tip-enhanced photoluminescence (TRPL) is a powerful technique for spatially and spectrally probing local optical properties of 2-dimensional (2D) materials that are modulated by the local heterogeneities, revealing inaccessible dark states due to bright state overlap in conventional far-field microscopy at room temperature. While scattering-type near-field probes have shown the potential to selectively enhance and reveal dark exciton emission, their technical complexity and sensitivity can pose challenges under certain experimental conditions. Here, we present a highly reproducible and easy-to-fabricate near-field probe based on nanoimprint lithography and fiber-optic excitation and collection. The novel near-field measurement configuration provides an ∼3 orders of magnitude out-of-plane Purcell enhancement, diffraction-limited excitation spot, and subdiffraction hyperspectral imaging resolution (below 50 nm) of dark exciton emission. The effectiveness of this high spatial XD mapping technique was then demonstrated through reproducible hyperspectral mapping of oxidized sites and bubble areas.

Published
2023

8. RAD54L2 counters TOP2-DNA adducts to promote genome stability

Author

D’Alessandro, Giuseppina, primary, Morales-Juarez, David A., additional, Richards, Sean L., additional, Nitiss, Karin C., additional, Serrano-Benitez, Almudena, additional, Wang, Juanjuan, additional, Thomas, John C., additional, Gupta, Vipul, additional, Voigt, Andrea, additional, Belotserkovskaya, Rimma, additional, Goh, Chen Gang, additional, Bowden, Anne Ramsay, additional, Galanty, Yaron, additional, Beli, Petra, additional, Nitiss, John L., additional, Zagnoli-Vieira, Guido, additional, and Jackson, Stephen P., additional

Published
2023
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9. WS$_2$ Band Gap Renormalization Induced by Tomonaga Luttinger Liquid Formation in Mirror Twin Boundaries

Author

Rossi, Antonio, Thomas, John C., Küchle, Johannes T., Barré, Elyse, Yu, Zhuohang, Zhou, Da, Kumari, Shalini, Tsai, Hsin-Zon, Wong, Ed, Jozwiak, Chris, Bostwick, Aaron, Robinson, Joshua A., Terrones, Mauricio, Raja, Archana, Schwartzberg, Adam, Ogletree, D. Frank, Neaton, Jeffrey B., Crommie, Michael F., Allegretti, Francesco, Auwärter, Willi, Rotenberg, Eli, and Weber-Bargioni, Alexander

Subjects
Condensed Matter - Materials Science
Abstract

Tomonaga-Luttinger liquid (TLL) behavior in one-dimensional systems has been predicted and shown to occur at semiconductor-to-metal transitions within two-dimensional materials. Reports of mirror twin boundaries (MTBs) hosting a Fermi liquid or a TLL have suggested a dependence on the underlying substrate, however, unveiling the physical details of electronic contributions from the substrate require cross-correlative investigation. Here, we study TLL formation in MTBs within defectively engineered WS$_2$ atop graphene, where band structure and the atomic environment is visualized with nano angle-resolved photoelectron spectroscopy, scanning tunneling microscopy and scanning tunneling spectroscopy, and non-contact atomic force microscopy. Correlations between the local density of states and electronic band dispersion elucidated the electron transfer from graphene into a TLL hosted by MTB defects. We find that MTB defects can be substantially charged at a local level, which drives a band gap shift by $\sim$0.5 eV., Comment: Main text is 13 pages, 4 figures; Supplementary text is 14 pages, 11 figures

Published
2023

11. Direct Visualization of the Charge Transfer in a Graphene/α-RuCl3 Heterostructure via Angle-Resolved Photoemission Spectroscopy

Author

Rossi, Antonio, primary, Johnson, Cameron, additional, Balgley, Jesse, additional, Thomas, John C., additional, Francaviglia, Luca, additional, Dettori, Riccardo, additional, Schmid, Andreas K., additional, Watanabe, Kenji, additional, Taniguchi, Takashi, additional, Cothrine, Matthew, additional, Mandrus, David G., additional, Jozwiak, Chris, additional, Bostwick, Aaron, additional, Henriksen, Erik A., additional, Weber-Bargioni, Alexander, additional, and Rotenberg, Eli, additional

Published
2023
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12. Autonomous Investigations over WS$_2$ and Au{111} with Scanning Probe Microscopy

Author

Thomas, John C., Rossi, Antonio, Smalley, Darian, Francaviglia, Luca, Yu, Zhuohang, Zhang, Tianyi, Kumari, Shalini, Robinson, Joshua A., Terrones, Mauricio, Ishigami, Masahiro, Rotenberg, Eli, Barnard, Edward S., Raja, Archana, Wong, Ed, Ogletree, D. Frank, Noack, Marcus M., and Weber-Bargioni, Alexander

Subjects
Condensed Matter - Materials Science, Physics - Applied Physics
Abstract

Individual atomic defects in 2D materials impact their macroscopic functionality. Correlating the interplay is challenging, however, intelligent hyperspectral scanning tunneling spectroscopy (STS) mapping provides a feasible solution to this technically difficult and time consuming problem. Here, dense spectroscopic volume is collected autonomously via Gaussian process regression, where convolutional neural networks are used in tandem for spectral identification. Acquired data enable defect segmentation, and a workflow is provided for machine-driven decision making during experimentation with capability for user customization. We provide a means towards autonomous experimentation for the benefit of both enhanced reproducibility and user-accessibility. Hyperspectral investigations on WS$_2$ sulfur vacancy sites are explored, which is combined with local density of states confirmation on the Au{111} herringbone reconstruction. Chalcogen vacancies, pristine WS$_2$, Au face-centered cubic, and Au hexagonal close packed regions are examined and detected by machine learning methods to demonstrate the potential of artificial intelligence for hyperspectral STS mapping., Comment: Updates from final journal publication

Published
2021
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14. Autonomous scanning probe microscopy investigations over WS2 and Au{111}

Author

Thomas, John C, Rossi, Antonio, Smalley, Darian, Francaviglia, Luca, Yu, Zhuohang, Zhang, Tianyi, Kumari, Shalini, Robinson, Joshua A, Terrones, Mauricio, Ishigami, Masahiro, Rotenberg, Eli, Barnard, Edward S, Raja, Archana, Wong, Ed, Ogletree, D Frank, Noack, Marcus M, and Weber-Bargioni, Alexander

Subjects
Physical Sciences, Condensed Matter Physics, Theoretical and computational chemistry, Materials engineering, Condensed matter physics
Abstract

Individual atomic defects in 2D materials impact their macroscopic functionality. Correlating the interplay is challenging, however, intelligent hyperspectral scanning tunneling spectroscopy (STS) mapping provides a feasible solution to this technically difficult and time consuming problem. Here, dense spectroscopic volume is collected autonomously via Gaussian process regression, where convolutional neural networks are used in tandem for spectral identification. Acquired data enable defect segmentation, and a workflow is provided for machine-driven decision making during experimentation with capability for user customization. We provide a means towards autonomous experimentation for the benefit of both enhanced reproducibility and user-accessibility. Hyperspectral investigations on WS2 sulfur vacancy sites are explored, which is combined with local density of states confirmation on the Au{111} herringbone reconstruction. Chalcogen vacancies, pristine WS2, Au face-centered cubic, and Au hexagonal close-packed regions are examined and detected by machine learning methods to demonstrate the potential of artificial intelligence for hyperspectral STS mapping.

Published
2022

15. Understanding factors influencing primary treatment with intradetrusor onabotulinumtoxinA versus augmentation cystoplasty in patients with spina bifida

Author

Li, Belinda, primary, Peard, Leslie M., additional, Zhao, Shilin, additional, Graham, M. Kyle, additional, Adams, Cyrus, additional, Taylor, Abby S., additional, Thomas, John C., additional, Pope, John C., additional, Adams, Mark C., additional, Brock, John W., additional, and Clayton, Douglass B., additional

Published
2023
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19. Machine learning the DFT potential energy surface for inorganic halide perovskite CsPbBr$_3$

Author

Thomas, John C., Bechtel, Jonathon S., Natarajan, Anirudh Raju, and Van der Ven, Anton

Subjects
Condensed Matter - Materials Science, Physics - Computational Physics
Abstract

Structural phase transitions as a function of temperature dictate the structure--functionality relationships in many technologically important materials. Harmonic Hamiltonians have proven successful in predicting the vibrational properties of many materials. However, they are inadequate for modeling structural phase transitions in crystals with potential energy surfaces that are either strongly anharmonic or no\ n-convex with respect to collective atomic displacements or homogeneous strains. In this paper we develop a framework to express highly anharmonic first-principles potential energy surfaces as polynomials of collective cluster deformati\ ons. We further adapt the approach to a nonlinear extension of the cluster expansion formalism through the use of an artificial neural net model. The machine learning models are trained on a large database of first-principles calculations and are shown to reproduce the potential energy surface with l\ ow error.

Published
2019
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20. SOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling

Author

Sun, Dawei, primary, Llora Batlle, Oriol, additional, van den Ameele, Jelle, additional, Thomas, John C, additional, He, Peng, additional, Lim, Kyungtae, additional, Tang, Walfred, additional, Xu, Chufan, additional, Meyer, Kerstin B, additional, Teichmann, Sarah A, additional, Marioni, John C, additional, Jackson, Stephen P, additional, Brand, Andrea H, additional, and Rawlins, Emma L, additional

Published
2022
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21. Influence of Terminal Carboxyl Groups on the Structure and Reactivity of Functionalized m-Carboranethiolate Self-Assembled Monolayers

Author

Goronzy, Dominic P, Stanek, Jan, Avery, Erin, Guo, Han, Bastl, Zdenek, Dusek, Michal, Gallup, Nathan M, Gun, Saliha, Kucerakova, Monika, Levandowski, Brian J, Machacek, Jan, Sicha, Vaclav, Thomas, John C, Yavuz, Adem, Houk, KN, Danisman, Mehmet Fatih, Mete, Ersen, Alexandrova, Anastassia N, Base, Tomas, and Weiss, Paul S

Subjects
Chemical Sciences, Engineering, Materials
Published
2020

22. PD02-06 COMPARISON OF LONG TERM ADVERSE EVENTS AND RENAL OUTCOMES BETWEEN ILEOVESICOSTOMY AND CONTINENT BLADDER AUGMENTATIONS AT A SINGLE PEDIATRIC INSTITUTION

Author

Flores, Viktor, primary, Matthew, Mikhael, additional, Chen, Heidi, additional, Abelson, Benjamin, additional, Taylor, Abby S., additional, Tanaka, Stacy T., additional, Adams, Cyrus M., additional, Adams, Mark C., additional, Thomas, John C., additional, Pope, John C., additional, Brock, John W., additional, and Clayton, Douglass B., additional

Published
2022
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24. Adressen der Autoren

Author

Adams, Mark C., primary, Albala, David M., additional, Anger, Jennifer T., additional, Anoia, Elizabeth, additional, Assimos, Dean G., additional, Auge, Brian K., additional, Bagley, Demetrius H., additional, Baker, Linda A., additional, Barocas, Daniel A., additional, Barry, John M., additional, Baskin, Laurence S., additional, Beck, Stephen, additional, Bella, Anthony J., additional, Bishoff, Jay T., additional, Bivalacqua, Trinity J., additional, Blaivas, Jerry G., additional, Blute, Michael L., additional, Boorjian, Stephen Anthony, additional, Borer, Joseph, additional, Borin, James F., additional, Brant, William O., additional, Brock, John W., additional, Broghammer, Joshua A., additional, Brugh, Victor M., additional, Buckley, Jill C., additional, Bullock, Travis L., additional, Burkhard, Fiona C., additional, Burnett, Arthur L., additional, Cadeddu, Jeffrey A., additional, Campbell, Jeffrey B., additional, Canes, David, additional, Cartwright, Patrick C., additional, Castle, Erik P., additional, Champagne, Bradley, additional, Chang, Sam S., additional, Chen, Tony Y., additional, Cheng, Earl Y., additional, Cherullo, Edward, additional, Christie, Alison M., additional, Clark, Peter E., additional, Clayman, Ralph V., additional, Cookson, Michael S., additional, Corbett, Sean T., additional, Costabile, Raymond A., additional, Davis, Rodney, additional, Deane, Leslie A., additional, Dechet, Christopher B., additional, DeLancey, John O.L., additional, DeMarco, Romano T., additional, Denstedt, John D., additional, Desai, Mahesh R., additional, Desai, Mihir M., additional, Desai, Rahul A., additional, Disick, Grant, additional, Dmochowski, Roger R., additional, Elder, Jack S., additional, Elliott, Sean P., additional, Elmajian, Donald A., additional, Fergany, Amr, additional, Flynn, Brian J., additional, Fossett, Lindsay, additional, Foster, Richard, additional, Ganpule, Arvind P., additional, Gargollo, Patricio, additional, Gill, Inderbir S., additional, Gjertson, Carl K., additional, Goldfarb, David A., additional, Goldstein, Marc, additional, Gonzalgo, Mark L., additional, Gormley, E. Ann, additional, Guralnick, Michael, additional, Haber, Georges-Pascal, additional, Haleblian, George E., additional, Hartke, David, additional, Hellstrom, Wayne J.G., additional, Herrell, S. Duke, additional, Hinman, Frank, additional, Holzbeierlein, Jeffrey M., additional, Horowitz, Andrew I., additional, Hulbert, William C., additional, Ihara, Hiroyuki, additional, Inman, Brant, additional, Jarrett, Thomas W., additional, Jordan, Gerald H., additional, Kaplan, Steven A., additional, Kaufman, Melissa R., additional, Kavoussi, Louis R., additional, Kesler, Stuart, additional, Kick, Phillip S., additional, Kirsch, Andrew J., additional, Klein, Frederick A., additional, Kobashi, Kathleen C., additional, Koenig, Philippe, additional, Koh, Chester J., additional, Kokorowski, Paul, additional, Krishnamurthi, Venkatesh, additional, Kropp, Bradley P., additional, Kuo, Ramsay L., additional, Landman, Jaime, additional, Larson, Kindra, additional, Latini, Jerilyn M., additional, Leach, Gary E., additional, Lee, David I., additional, Leng, Wendy W., additional, L’Esperance, James O., additional, Leveillee, Raymond J., additional, Levy, David A., additional, Lingeman, James E., additional, Lue, Tom F., additional, Makari, John H., additional, Marderstein, Eric L., additional, Marguet, Charles G., additional, Martin, Frances M., additional, McAninch, Jack W., additional, McClure, R. Dale, additional, McGuire, Edward J., additional, McVary, Kevin T., additional, Mevorach, Robert A., additional, Middleton, Richard G., additional, Milam, Douglas F., additional, Miller, Elizabeth A., additional, Miller, Nicole, additional, Modder, Joshua K., additional, Moinzadeh, Ali, additional, Monga, Manoj, additional, Montague, Drogo K., additional, Montie, James, additional, Moore, Charles R., additional, Morey, Allen F., additional, Morgan, Daniel M., additional, Morrisroe, Shelby N., additional, Mufarrij, Patrick W., additional, Munver, Ravi, additional, Ng, Christopher S., additional, Nisbet, Alan A., additional, Novick, Andrew C., additional, O’Connor, R. Corey, additional, Okeke, Zeph, additional, Pak, Raymond W., additional, Parekh, Dipen J., additional, Pearle, Margaret S., additional, Perer, Elise, additional, Peterson, Andrew C., additional, Phillips, Courtney K., additional, Pierre, Ketsia, additional, Polascik, Thomas J., additional, Ponsky, Lee, additional, Pope, John, additional, Preminger, Glenn M., additional, Prieto, Juan C., additional, Rabinowitz, Ronald, additional, Rapp, David E., additional, Raz, Shlomo, additional, Redman, John F., additional, Richstone, Lee, additional, Roberts, William W., additional, Rosen, Michael J., additional, Rosenblatt, Gregory S., additional, Rowland, Randall G., additional, Saini, Rajiv, additional, Sampaio, Francisco J.B., additional, Scarpero, Harriette M., additional, Scherr, Douglas S., additional, Schlegel, Peter N., additional, Sherman, Neil D., additional, Shields, John, additional, Shinohara, Katsuto, additional, Siegel, Steven W., additional, Skinner, Eila, additional, Skoog, Steven J., additional, Smith, Arthur D., additional, Smith, Joseph A., additional, Snodgrass, Warren T., additional, Soltanian, Hooman, additional, Sotelo, Rene, additional, Spirnak, J. Patrick, additional, Steers, William D., additional, Stein, John P., additional, Stifelman, Michael D., additional, Studer, Urs E., additional, Sundaram, Chandru P., additional, Sur, Roger L., additional, Sutherland, Richard W., additional, Suzuki, Kazuo, additional, Tan, Yeh Hong, additional, Tanrikut, Cigdem, additional, Thiel, David D., additional, Thomas, John C., additional, Thomas, Raju, additional, Triaca, Veronica, additional, Trunzo, Joseph A., additional, Tsuru, Nobuo, additional, Turek, Paul J., additional, Twiss, Christian O., additional, Vanderbrink, Brian A., additional, Vasavada, Sandip P., additional, Vaughan, E. Darracott, additional, Venable, Dennis D., additional, Vourganti, Srinivas, additional, Wagner, Kristofer R., additional, Walsh, Dena L., additional, Walsh, Thomas J., additional, Wan, Julian, additional, Waters, W. Bedford, additional, Webster, George D., additional, Wessells, Hunter, additional, White, Wesley M., additional, Wiener, John S., additional, Wignall, Geoffrey R., additional, Winfield, Howard N., additional, Wise, Paul E., additional, Wolf, J. Stuart, additional, Wolter, Christopher E., additional, Woods, Michael E., additional, and Zeltser, Ilia S., additional

Published
2017
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26. An organoid CRISPRi screen revealed that SOX9 primes human fetal lung tip progenitors to receive WNT and RTK signals

Author

Sun, Dawei, primary, Batlle, Oriol Llora, additional, van den Ameele, Jelle, additional, Thomas, John C., additional, He, Peng, additional, Lim, Kyungtae, additional, Tang, Walfred, additional, Xu, Chufan, additional, Meyer, Kerstin B., additional, Teichmann, Sarah A., additional, Marioni, John C., additional, Jackson, Stephen P., additional, Brand, Andrea H., additional, and Rawlins, Emma L., additional

Published
2022
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31. Acid–Base Control of Valency within Carboranedithiol Self-Assembled Monolayers: Molecules Do the Can-Can

Author

Thomas, John C, Goronzy, Dominic P, Serino, Andrew C, Auluck, Harsharn S, Irving, Olivia R, Jimenez-Izal, Elisa, Deirmenjian, Jacqueline M, Macháček, Jan, Sautet, Philippe, Alexandrova, Anastassia N, Baše, Tomáš, and Weiss, Paul S

Subjects
Chemical Sciences, Physical Sciences, Condensed Matter Physics, nanoscience, self-assembly, carborane, self-assembled monolayer, dipoles, scanning tunneling microscopy, two-dimensional, molecular switch, Nanoscience & Nanotechnology
Abstract

We use simple acid-base chemistry to control the valency in self-assembled monolayers of two different carboranedithiol isomers on Au{111}. Monolayer formation proceeds via Au-S bonding, where manipulation of pH prior to or during deposition enables the assembly of dithiolate species, monothiol/monothiolate species, or combination. Scanning tunneling microscopy (STM) images identify two distinct binding modes in each unmodified monolayer, where simultaneous spectroscopic imaging confirms different dipole offsets for each binding mode. Density functional theory calculations and STM image simulations yield detailed understanding of molecular chemisorption modes and their relation with the STM images, including inverted contrast with respect to the geometric differences found for one isomer. Deposition conditions are modified with controlled equivalents of either acid or base, where the coordination of the molecules in the monolayers is controlled by protonating or deprotonating the second thiol/thiolate on each molecule. This control can be exercised during deposition to change the valency of the molecules in the monolayers, a process that we affectionately refer to as the "can-can." This control enables us to vary the density of molecule-substrate bonds by a factor of 2 without changing the molecular density of the monolayer.

Published
2018

37. The molecular basis for the biotic degradation of metaldehyde

Author

Thomas, John C., Moir, James, Helgason, Thorunn, and Sinclair, Chris

Subjects
572
Abstract

Metaldehyde is a molluscicide that is used to prevent crop damage by slugs and snails. It is frequently found in drinking water sources at concentrations above the legal maximum, and causes >90% of water quality failures in England. There is currently no economical, widely used treatment to remove metaldehyde pollution from water. Prior to the work presented here, it was known that metaldehyde is degraded biotically in soil, but the nature and identity of organisms responsible was unknown. Two novel metaldehyde degrading bacterial strains were isolated from domestic soil that can utilise metaldehyde as a sole carbon and energy source; Acinetobacter calcoaceticus E1 and Variovorax E3. Evidence that acetaldehyde is the primary metabolite of metaldehyde is presented: the metaldehyde dependent expression of an aldehyde dehydrogenase in A. calcoaceticus E1 was found, and the maximum metabolic flux of acetaldehyde was found to be greater than that of metaldehyde in cells grown using metaldehyde. The genomes of the isolated organisms were acquired. Comparative genomics of the two isolates showed that their novel catalytic ability was not dependent on genes shared between them, despite being isolated from the same soil sample. Comparison of the A. calcoaceticus E1 genome against other Acinetobacter that cannot utilise metaldehyde yielded a strong candidate for the primary metaldehyde degrading enzyme that has characteristics consistent with an enzyme that catalysed ether hydrolysis of isochorismate in its ancestral form and has evolved to hydrolyse ether bonds in metaldehyde.

Published
2016

38. Mapping Buried Hydrogen-Bonding Networks

Author

Thomas, John C, Goronzy, Dominic P, Dragomiretskiy, Konstantin, Zosso, Dominique, Gilles, Jérôme, Osher, Stanley J, Bertozzi, Andrea L, and Weiss, Paul S

Subjects
Inorganic Chemistry, Chemical Sciences, self-assembly, hydrogen bonding, scanning tunneling microscopy, image analysis, two-dimensional variational mode decomposition, segmentation, spectroscopic imaging, self-assembled monolayers, disorder, Nanoscience & Nanotechnology
Abstract

We map buried hydrogen-bonding networks within self-assembled monolayers of 3-mercapto-N-nonylpropionamide on Au{111}. The contributing interactions include the buried S-Au bonds at the substrate surface and the buried plane of linear networks of hydrogen bonds. Both are simultaneously mapped with submolecular resolution, in addition to the exposed interface, to determine the orientations of molecular segments and directional bonding. Two-dimensional mode-decomposition techniques are used to elucidate the directionality of these networks. We find that amide-based hydrogen bonds cross molecular domain boundaries and areas of local disorder.

Published
2016

40. Holey Graphene as a Weed Barrier for Molecules

Author

Gethers, Matthew L, Thomas, John C, Jiang, Shan, Weiss, Nathan O, Duan, Xiangfang, Goddard, William A, and Weiss, Paul S

Subjects
Physical Sciences, Condensed Matter Physics, nanoscience, graphene, mask, chemical patterning, self-assembly, scanning tunneling microscopy, Nanoscience & Nanotechnology
Abstract

We demonstrate the use of "holey" graphene as a mask against molecular adsorption. Prepared porous graphene is transferred onto a Au{111} substrate, annealed, and then exposed to dilute solutions of 1-adamantanethiol. In the pores of the graphene lattice, we find islands of organized, self-assembled molecules. The bare Au in the pores can be regenerated by postdeposition annealing, and new molecules can be self-assembled in the exposed Au region. Graphene can serve as a robust, patternable mask against the deposition of self-assembled monolayers.

Published
2015

41. Bladder Function After Fetal Surgery for Myelomeningocele

Author

Brock, John W, Carr, Michael C, Adzick, N Scott, Burrows, Pamela K, Thomas, John C, Thom, Elizabeth A, Howell, Lori J, Farrell, Jody A, Dabrowiak, Mary E, Farmer, Diana L, Cheng, Earl Y, Kropp, Bradley P, Caldamone, Anthony A, Bulas, Dorothy I, Tolivaisa, Susan, and Baskin, Laurence S

Subjects
Reproductive Medicine, Biomedical and Clinical Sciences, Clinical Sciences, Urologic Diseases, Conditions Affecting the Embryonic and Fetal Periods, Clinical Research, Biomedical Imaging, Pediatric, Evaluation of treatments and therapeutic interventions, 6.4 Surgery, Renal and urogenital, Reproductive health and childbirth, Adult, Female, Fetus, Humans, Kidney, Male, Meningomyelocele, Neurosurgical Procedures, Postoperative Complications, Pregnancy, Time Factors, Treatment Outcome, Ultrasonography, Urinary Bladder, Urinary Catheterization, Urodynamics, MOMS Investigators, Medical and Health Sciences, Psychology and Cognitive Sciences, Pediatrics, Biomedical and clinical sciences, Health sciences, Psychology
Abstract

BackgroundA substudy of the Management of Myelomeningocele Study evaluating urological outcomes was conducted.MethodsPregnant women diagnosed with fetal myelomeningocele were randomly assigned to either prenatal or standard postnatal surgical repair. The substudy included patients randomly assigned after April 18, 2005. The primary outcome was defined in their children as death or the need for clean intermittent catheterization (CIC) by 30 months of age characterized by prespecified criteria. Secondary outcomes included bladder and kidney abnormalities observed by urodynamics and renal/bladder ultrasound at 12 and 30 months, which were analyzed as repeated measures.ResultsOf the 115 women enrolled in the substudy, the primary outcome occurred in 52% of children in the prenatal surgery group and 66% in the postnatal surgery group (relative risk [RR]: 0.78; 95% confidence interval [CI]: 0.57-1.07). Actual rates of CIC use were 38% and 51% in the prenatal and postnatal surgery groups, respectively (RR: 0.74; 95% CI: 0.48-1.12). Prenatal surgery resulted in less trabeculation (RR: 0.39; 95% CI: 0.19-0.79) and fewer cases of open bladder neck on urodynamics (RR: 0.61; 95% CI: 0.40-0.92) after adjustment by child's gender and lesion level. The difference in trabeculation was confirmed by ultrasound.ConclusionsPrenatal surgery did not significantly reduce the need for CIC by 30 months of age but was associated with less bladder trabeculation and open bladder neck. The implications of these findings are unclear now, but support the need for long-term urologic follow-up of patients with myelomeningocele regardless of type of surgical repair.

Published
2015

42. Self-Assembled p‑Carborane Analogue of p‑Mercaptobenzoic Acid on Au{111}

Author

Thomas, John C, Boldog, Ishtvan, Auluck, Harsharn S, Bereciartua, Pablo J, Dušek, Michal, Macháček, Jan, Bastl, Zdeněk, Weiss, Paul S, and Baše, Tomáš

Subjects
Inorganic Chemistry, Chemical Sciences, Engineering, Materials, Chemical sciences
Abstract

The p-carborane cluster analogue of p-mercaptobenzoic acid, 1-HS-12-COOH-1,12-C2B10H10, has been synthesized and characterized using nuclear magnetic resonance spectroscopy, single-crystal X-ray diffraction analysis, quantum-chemical calculations, and scanning tunneling microscopy. The single-crystal structure and selected packing aspects are discussed and presented in comparison with the two-dimensional periodic arrangements. Scanning tunneling micrographs, recorded under ambient conditions, are used to compare pure monolayers of 1-HS-1,12-C2B10H11 to coadsorbed monolayers of both the parental precursor and carboxyl-functionalized p-carboranethiolate on Au{111}. Monolayers of both constituents are further characterized by X-ray photoelectron spectroscopy, which shows good agreement between the stoichiometry of each pure monolayer and the nominal stoichiometries of the respective molecules. Results indicate that most of the molecules of both derivatives adsorb as thiolates but that a small fraction of each adsorbs as thiols, without complete SH bond scission, and consequently are labile relative to desorption. Wetting-angle measurements confirm the hydrophilic character of monolayers containing the carboxylic acid constituents. Mixed self-assembled monolayers with functionalized constituents of high axial symmetry provide a convenient basis for grafting two- and three-dimensional structures. (Figure Presented).

Published
2015

43. Contributors

Author

Andrieu, S., primary, As, Donat J., additional, Avrutin, V., additional, Batool, Zahida, additional, Bensaoula, Abdelhak, additional, Bierwagen, Oliver, additional, Blinov, Victorz, additional, Boney, Chris, additional, Chatterjee, Sangam, additional, Chernikov, Alexej, additional, Chi, J.Y., additional, Colli, Alan, additional, Davidson, Bruce, additional, Doran, Molly, additional, Dumesnil, K., additional, Duzik, Adam, additional, Eckstein, James N., additional, Engel-Herbert, Roman, additional, Franchi, Secondo, additional, Freundlich, Alex, additional, Fritz, Rafael, additional, Gogineni, Chaturvedi, additional, Guina, Mircea, additional, Hanser, Drew, additional, Heiblum, M., additional, Hernández-Calderón, Isaac, additional, Hild, Konstanze, additional, Horikoshi, Yoshiji, additional, Hosea, Thomas J.C., additional, Ignatiev, Alex, additional, Imhof, Sebastian, additional, Kossut, J., additional, Ivanov, S.V., additional, Jäger, Roland, additional, Jiang, Zenan, additional, Jin, Shirong, additional, Johnson, Shane R., additional, Katkov, A.V., additional, Kłopotowski, Ł., additional, Koch, Martin, additional, Koch, Stephan W., additional, Koguchi, Nobuyuki, additional, Kolata, Kolja, additional, Kuze, Naohiro, additional, Lewis, Ryan B., additional, Lischka, Klaus, additional, Lu, Xianfeng, additional, Martelli, Faustino, additional, Masnadi-Shirazi, Mostafa, additional, Matsukura, F., additional, Millunchick, Joanna Mirecki, additional, Mooney, Patricia M., additional, Moreau, E., additional, Morkoç, H., additional, Nikiforov, Alexander, additional, Nishinaga, Jiro, additional, Niu, Gang, additional, O'Steen, Mark, additional, Oe, Kunishige, additional, Oh, Seongshik, additional, Ohno, H., additional, Özgür, Ü., additional, Pchelyakov, Oleg, additional, Pridachin, Dmitry, additional, Readinger, Eric, additional, Riordan, Nathaniel A., additional, Rubel, Oleg, additional, Rubini, Silvia, additional, Saint-Girons, Guillaume, additional, Sanguinetti, Stefano, additional, Schöll, Achim, additional, Schreiber, Frank, additional, Sedova, I.V., additional, Shibasaki, Ichiro, additional, Sokolov, Leonid, additional, Sorokin, S.V., additional, Speck, James S., additional, Springholz, Gunther, additional, Sweeney, Stephen J., additional, Thomas, John C., additional, Thränhardt, Angela, additional, Tiedje, Thomas, additional, Tsai, Min-Ying, additional, Umansky, V., additional, Vignaud, D., additional, Vilquin, Bertrand, additional, Volz, Kerstin, additional, Wang, Shu Min, additional, Wang, Guang, additional, Warusawithana, Maitri, additional, Wasilewski, Z.R., additional, White, Mark E., additional, Wojnar, P., additional, Xue, Qi-Kun, additional, Yoshimoto, Masahiro, additional, Zhai, Xiaofang, additional, and Zheng, Mao, additional

Published
2013
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44. Bismuth-containing III–V semiconductors

Author

Batool, Zahida, primary, Chatterjee, Sangam, additional, Chernikov, Alexej, additional, Duzik, Adam, additional, Fritz, Rafael, additional, Gogineni, Chaturvedi, additional, Hild, Konstanze, additional, Hosea, Thomas J.C., additional, Imhof, Sebastian, additional, Johnson, Shane R., additional, Jiang, Zenan, additional, Jin, Shirong, additional, Koch, Martin, additional, Koch, Stephan W., additional, Kolata, Kolja, additional, Lewis, Ryan B., additional, Lu, Xianfeng, additional, Masnadi-Shirazi, Mostafa, additional, Millunchick, Joanna Mirecki, additional, Mooney, Patricia M., additional, Riordan, Nathaniel A., additional, Rubel, Oleg, additional, Sweeney, Stephen J., additional, Thomas, John C., additional, Thränhardt, Angela, additional, Tiedje, Thomas, additional, and Volz, Kerstin, additional

Published
2013
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45. Revolutionizing DNA repair research and cancer therapy with CRISPR–Cas screens

Author

Awwad, Samah W., Serrano-Benitez, Almudena, Thomas, John C., Gupta, Vipul, and Jackson, Stephen P.

Abstract

All organisms possess molecular mechanisms that govern DNA repair and associated DNA damage response (DDR) processes. Owing to their relevance to human disease, most notably cancer, these mechanisms have been studied extensively, yet new DNA repair and/or DDR factors and functional interactions between them are still being uncovered. The emergence of CRISPR technologies and CRISPR-based genetic screens has enabled genome-scale analyses of gene–gene and gene–drug interactions, thereby providing new insights into cellular processes in distinct DDR-deficiency genetic backgrounds and conditions. In this Review, we discuss the mechanistic basis of CRISPR–Cas genetic screening approaches and describe how they have contributed to our understanding of DNA repair and DDR pathways. We discuss how DNA repair pathways are regulated, and identify and characterize crosstalk between them. We also highlight the impacts of CRISPR-based studies in identifying novel strategies for cancer therapy, and in understanding, overcoming and even exploiting cancer-drug resistance, for example in the contexts of PARP inhibition, homologous recombination deficiencies and/or replication stress. Lastly, we present the DDR CRISPR screen (DDRcs) portal, in which we have collected and reanalysed data from CRISPR screen studies and provide a tool for systematically exploring them.

Published
2024
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50. Contributors

Author

Adams, Mark C., primary, Adibe, Obinna O., additional, Adler, Jeremy, additional, Adzick, N. Scott, additional, Albanese, Craig T., additional, Andrews, Walter S., additional, Applebaum, Harry, additional, Arca, Marjorie J., additional, Aronson, Daniel C., additional, Azizkhan, Richard G., additional, Baird, Robert, additional, Barnett, Sean, additional, Barnhart, Douglas C., additional, Barsness, Katherine A., additional, Bartlett, Robert H., additional, Baskin, Laurence S., additional, Beasley, Spencer W., additional, Bentz, Michael L., additional, Billmire, Deborah F., additional, Boulanger, Scott C., additional, Brandt, Mary L., additional, Brock, John W., additional, Brown, Rebeccah L., additional, Btaiche, Imad F., additional, Busuttil, Ronald W., additional, Caldamone, Anthony A., additional, Caniano, Donna A., additional, Caty, Michael G., additional, Chardot, Christophe, additional, Chung, Dai H., additional, Cilley, Robert E., additional, Colon, Nadja C., additional, Columbani, Paul M., additional, Coran, Arnold G., additional, Cotton, Robin T., additional, Cowles, Robert A., additional, Cox,, Charles S., additional, Dassinger, Melvin S., additional, Davidoff, Andrew M., additional, Davidson, Richard S., additional, Coppi, Paolo De, additional, Dicken, Bryan J., additional, Didelot, William, additional, DiFiore, John W., additional, Dillon, Patrick A., additional, Dillon, Peter W., additional, Donahoe, Patricia K., additional, Duchossois, Gina P., additional, Dunn, James C.Y., additional, Dutta, Sanjeev, additional, Eaton, Simon, additional, Ehrlich, Peter F., additional, Eichelberger, Martin R., additional, Elden, Lisa M., additional, Eliason, Jonathan L., additional, Emil, Sherif, additional, Escobar, Mauricio A., additional, Falcone,, Richard A., additional, Fallat, Mary E., additional, Farmer, Diana L., additional, Farmer, Douglas G., additional, Faro, Albert, additional, Fisher, Michael J., additional, Fishman, Steven J., additional, Fitzgerald, Tamara N., additional, Flake, Alan W., additional, Foglia, Robert P., additional, Ford, Henri R., additional, Franklin, Andrew, additional, Frischer, Jason S., additional, Fuller, Stephanie M.P., additional, Gandhi, Sanjiv K., additional, Garcia, Victor F., additional, Gatti, John M., additional, Gauderer, Michael W.L., additional, Geiger, James D., additional, Georgeson, Keith E., additional, Gingalewski, Cynthia A., additional, Glassberg, Kenneth I., additional, Glick, Philip L., additional, Gonzales, Kelly D., additional, Grikscheit, Tracy C., additional, Grosfeld, Jay L., additional, Groth, Travis W., additional, Gruessner, Angelika C., additional, Gruessner, Rainer W.G., additional, Gutierrez, Ivan M., additional, Guzzetta,, Philip C., additional, J. Hall, Jason, additional, Hamilton, Thomas E., additional, Harmon, Carroll M., additional, Harrison, Michael R., additional, Hayes-Jordan, Andrea, additional, Hays, Stephen R., additional, Healey, John H., additional, Hendren, W. Hardy, additional, Hering, Bernhard J., additional, Herndon, David N., additional, Hirose, Shinjiro, additional, Hirsch, Jennifer C., additional, Hirschl, Ronald B., additional, Hoganson, David M., additional, Holcomb, George W., additional, Höllwarth, Michael E., additional, Horn, B. David, additional, Huddleston, Charles B., additional, Hutchinson, Raymond J., additional, Hutson, John M., additional, Hyun, Grace, additional, Inge, Thomas H., additional, Jaksic, Tom, additional, Jea, Andrew, additional, Kaefer, Martin, additional, Kang, Kuang Horng, additional, Karsanac, Christopher J., additional, Kayes, Kosmas, additional, Kelly, Robert E., additional, Kiely, Edward M., additional, Klein, Michael D., additional, Krasin, Matthew J., additional, Krummel, Thomas M., additional, Kulungowski, Ann M., additional, Laberge, Jean-Martin, additional, Landsman, Ira S., additional, Langer, Jacob C., additional, La Quaglia, Michael P., additional, Laufer, Marc R., additional, Lee, Hanmin, additional, Lelli, Joseph L., additional, Levitt, Marc A., additional, Liau, James Y., additional, Lillehei, Craig, additional, Lindahl, Harry, additional, Liu, Gigi Y., additional, Lorenz, H. Peter, additional, Luerssen, Thomas G., additional, Lukish, Jeffrey R., additional, Lund, Dennis P., additional, Magee, John C., additional, McGahren, Eugene D., additional, McLaughlin, Eamon J., additional, McQuiston, Leslie T., additional, Meyers, Rebecka L., additional, Millar, Alastair J.W., additional, Minevich, Eugene, additional, Miranda, Edward P., additional, Mitchell, Michael E., additional, Mollen, Kevin P., additional, Moss, R. Lawrence, additional, Mouriquand, Pierre, additional, Murase, Noriko, additional, Murphy, J. Patrick, additional, Murphy, Joseph T., additional, Nance, Michael L., additional, Nathan, Saminathan S., additional, Newman, Kurt D., additional, Numanoglu, Alp, additional, Nwomeh, Benedict C., additional, Ohye, Richard G., additional, Oldham, Keith T., additional, O'Neill, James A., additional, Pakarinen, Mikko P., additional, Panait, Nicoleta, additional, Pearl, Richard H., additional, Peña, Alberto, additional, Pieretti, Rafael V., additional, Pierro, Agostino, additional, Piper, Hannah G., additional, Potsic, William P., additional, Pryor, Howard I., additional, Puligandla, Pramod S., additional, Puri, Prem, additional, Qureshi, Faisal G., additional, Rescorla, Frederick J., additional, Révillon, Yann, additional, Reyes, Jorge, additional, Reynolds, Marleta, additional, Rhee, Audrey C., additional, Rich, Barrie S., additional, Ricketts, Richard R., additional, Rink, Richard C., additional, Rintala, Risto J., additional, Rocchini, Albert P., additional, Rodeberg, David A., additional, Sadove, A. Michael, additional, Saggi, Bob H., additional, Scherer, L.R., additional, Schmid, Daniel B., additional, Scholz, Stefan, additional, Schwartz, Marshall Z., additional, Shamberger, Robert C., additional, Shapiro, Nina L., additional, Sheldon, Curtis A., additional, Shochat, Stephen J., additional, Sidell, Douglas, additional, Skinner, Michael A., additional, Smith, Jodi L., additional, Smith, Samuel D., additional, Snyder, Charles L., additional, Speer, Allison L., additional, Spitz, Lewis, additional, Spray, Thomas L., additional, Stanley, James C., additional, Starzl, Thomas E., additional, Stehr, Wolfgang, additional, Stolar, Charles J.H., additional, Storm, Phillip B., additional, Stylianos, Steven, additional, Subramaniam, Ramnath, additional, Superina, Riccardo, additional, Sutherland, David E.R., additional, Sutton, Leslie N., additional, Sydorak, Roman, additional, Sylvester, Karl G., additional, Teitelbaum, Daniel H., additional, Tepas, Joseph J., additional, Thomas, John C., additional, Thompson, Dana Mara, additional, Tovar, Juan A., additional, Upperman, Jeffrey S., additional, Vacanti, Joseph P., additional, van Aalst, John A., additional, Vane, Dennis W., additional, Allmen, Daniel Von, additional, Walkovich, Kelly, additional, Walsh, Danielle S., additional, Warner, Brad W., additional, Weber, Thomas R., additional, Weldon, Christopher B., additional, Wesson, David E., additional, Wetmore, Ralph F., additional, Willging, J. Paul, additional, Wilson, Jay M., additional, Woo, Lynn L., additional, Woo, Russell K., additional, Yerkes, Elizabeth B., additional, Ziegler, Moritz M., additional, and Zimmermann, Arthur, additional

Published
2012
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