Atomically Traceable Nanostructure Fabrication von Ballard, Josh B, Dick, Don D, McDonnell, Stephen J, Bischof, Maia, Fu, Joseph, Owen, James H G, Owen, William R, Alexander, Justin D, Jaeger, David L, Namboodiri, Pradeep, Fuchs, Ehud, Chabal, Yves J, Wallace, Robert M, Reidy, Richard, Silver, Richard M, Randall, John N, Von Ehr, James

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Spurious dangling bond formation during atomically precise hydrogen depassivation lithography on Si(100): The role of liberated hydrogen von Ballard, Joshua B., Owen, James H. G., Alexander, Justin D., Owen, William R., Fuchs, Ehud, Randall, John N., Longo, Roberto C., Cho, Kyeongjae

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Atomically Traceable Nanostructure Fabrication von Ballard, Josh B., Dick, Don D., McDonnell, Stephen J., Bischof, Maia, Fu, Joseph, Owen, James H. G., Owen, William R., Alexander, Justin D., Jaeger, David L., Namboodiri, Pradeep, Fuchs, Ehud, Chabal, Yves J., Wallace, Robert M., Reidy, Richard, Silver, Richard M., Randall, John N., Von Ehr, James

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An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications von Lemkul, Justin A, Huang, Jing, Roux, Benoît, MacKerell, Alexander D

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Polarizable force field for RNA based on the classical drude oscillator von Lemkul, Justin A., MacKerell, Alexander D.

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Asparagine Plays a Critical Role in Regulating Cellular Adaptation to Glutamine Depletion von Zhang, Ji, Fan, Jing, Venneti, Sriram, Cross, Justin R., Takagi, Toshimitsu, Bhinder, Bhavneet, Djaballah, Hakim, Kanai, Masayuki, Cheng, Emily H., Judkins, Alexander R., Pawel, Bruce, Baggs, Julie, Cherry, Sara, Rabinowitz, Joshua D., Thompson, Craig B.

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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field von Lee, Jumin, Cheng, Xi, Swails, Jason M, Yeom, Min Sun, Eastman, Peter K, Lemkul, Justin A, Wei, Shuai, Buckner, Joshua, Jeong, Jong Cheol, Qi, Yifei, Jo, Sunhwan, Pande, Vijay S, Case, David A, Brooks, Charles L, MacKerell, Alexander D, Klauda, Jeffery B, Im, Wonpil

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Emerging Roles for Serotonin in Regulating Metabolism: New Implications for an Ancient Molecule von Yabut, Julian M, Crane, Justin D, Green, Alexander E, Keating, Damien J, Khan, Waliul I, Steinberg, Gregory R

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Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions von Soteras Gutiérrez, Ignacio, Lin, Fang-Yu, Vanommeslaeghe, Kenno, Lemkul, Justin A., Armacost, Kira A., Brooks, Charles L., MacKerell, Alexander D.

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Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA von Lemkul, Justin A, MacKerell, Alexander D

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Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics von Lemkul, Justin A, MacKerell, Alexander D

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CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field von Kognole, Abhishek A., Lee, Jumin, Park, Sang‐Jun, Jo, Sunhwan, Chatterjee, Payal, Lemkul, Justin A., Huang, Jing, MacKerell, Alexander D., Im, Wonpil

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Antioxidant and Anti-Tumor Effects of Dietary Vitamins A, C, and E von Didier, Alexander J, Stiene, Jennifer, Fang, Lauren, Watkins, Dean, Dworkin, Lance D, Creeden, Justin F

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Mass spectrometry searches using MASST von Wang, Mingxun, Jarmusch, Alan K., Vargas, Fernando, Aksenov, Alexander A., Gauglitz, Julia M., Weldon, Kelly, Petras, Daniel, da Silva, Ricardo, Quinn, Robert, Melnik, Alexey V., van der Hooft, Justin J. J., Caraballo-Rodríguez, Andrés Mauricio, Nothias, Louis Felix, Aceves, Christine M., Panitchpakdi, Morgan, Brown, Elizabeth, Di Ottavio, Francesca, Sikora, Nicole, Elijah, Emmanuel O., Labarta-Bajo, Lara, Gentry, Emily C., Shalapour, Shabnam, Kyle, Kathleen E., Puckett, Sara P., Watrous, Jeramie D., Carpenter, Carolina S., Bouslimani, Amina, Ernst, Madeleine, Swafford, Austin D., Zúñiga, Elina I., Balunas, Marcy J., Klassen, Jonathan L., Loomba, Rohit, Knight, Rob, Bandeira, Nuno, Dorrestein, Pieter C.

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Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks von Huang, Jing, Lemkul, Justin A., Eastman, Peter K., MacKerell, Alexander D.

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Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life von Hime, Paul M, Lemmon, Alan R, Lemmon, Emily C Moriarty, Prendini, Elizabeth, Brown, Jeremy M, Thomson, Robert C, Kratovil, Justin D, Noonan, Brice P, Pyron, R Alexander, Peloso, Pedro L V, Kortyna, Michelle L, Keogh, J Scott, Donnellan, Stephen C, Mueller, Rachel Lockridge, Raxworthy, Christopher J, Kunte, Krushnamegh, Ron, Santiago R, Das, Sandeep, Gaitonde, Nikhil, Green, David M, Labisko, Jim, Che, Jing, Weisrock, David W

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Hypoxia Induces Production of L-2-Hydroxyglutarate von Intlekofer, Andrew M., Dematteo, Raymond G., Venneti, Sriram, Finley, Lydia W.S., Lu, Chao, Judkins, Alexander R., Rustenburg, Ariën S., Grinaway, Patrick B., Chodera, John D., Cross, Justin R., Thompson, Craig B.

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Adverse childhood experiences, adult depression, and suicidal ideation in rural Uganda: A cross-sectional, population-based study von Satinsky, Emily N., Kakuhikire, Bernard, Baguma, Charles, Rasmussen, Justin D., Ashaba, Scholastic, Cooper-Vince, Christine E., Perkins, Jessica M., Kiconco, Allen, Namara, Elizabeth B., Bangsberg, David R., Tsai, Alexander C.

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Hypertension: Do Inflammation and Immunity Hold the Key to Solving this Epidemic? von Madhur, Meena S., Elijovich, Fernando, Alexander, Matthew R., Pitzer, Ashley, Ishimwe, Jeanne, Van Beusecum, Justin P., Patrick, David M., Smart, Charles D., Kleyman, Thomas R., Kingery, Justin, Peck, Robert N., Laffer, Cheryl L., Kirabo, Annet

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Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model von Lemkul, Justin A., Roux, Benoît, van der Spoel, David, MacKerell Jr, Alexander D.

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