Computer Simulation

Qin, B., C. Fei, B. Wang, H. A. Stone, N. S. Wingreen, and B. L. Bassler. (2021) 2021. “Hierarchical Transitions and Fractal Wrinkling Drive Bacterial Pellicle Morphogenesis”. Proc Natl Acad Sci U S A 118.

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Narla, A. V., D. B. Borenstein, and N. S. Wingreen. (2021) 2021. “A Biophysical Limit for Quorum Sensing in Biofilms”. Proc Natl Acad Sci U S A 118.

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Mukhopadhyay, Ranjan, Eldon Emberly, Chao Tang, and Ned Wingreen. (2003) 2003. “Statistical Mechanics of RNA Folding: Importance of Alphabet Size.”. Phys Rev E Stat Nonlin Soft Matter Phys 68 (4 Pt 1): 041904. doi:10.1103/PhysRevE.68.041904.

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Emberly, Eldon, and Ned Wingreen. (2006) 2006. “Hourglass Model for a Protein-Based Circadian Oscillator.”. Phys Rev Lett 96 (3): 038303. doi:10.1103/PhysRevLett.96.038303.

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Kulkarni, Rahul, Kerwyn Casey Huang, Morten Kloster, and Ned Wingreen. (2004) 2004. “Pattern Formation Within Escherichia Coli: Diffusion, Membrane Attachment, and Self-Interaction of MinD Molecules.”. Phys Rev Lett 93 (22): 228103. doi:10.1103/PhysRevLett.93.228103.

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Huang, Kerwyn Casey, Ranjan Mukhopadhyay, and Ned Wingreen. (2006) 2006. “A Curvature-Mediated Mechanism for Localization of Lipids to Bacterial Poles.”. PLoS Comput Biol 2 (11): e151. doi:10.1371/journal.pcbi.0020151.

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Endres, Robert, Olga Oleksiuk, Clinton Hansen, Yigal Meir, Victor Sourjik, and Ned Wingreen. 2008. “Variable Sizes of Escherichia Coli Chemoreceptor Signaling Teams.”. Mol Syst Biol 4: 211. doi:10.1038/msb.2008.49.

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Mukhopadhyay, Ranjan, Kerwyn Casey Huang, and Ned Wingreen. (2008) 2008. “Lipid Localization in Bacterial Cells through Curvature-Mediated Microphase Separation.”. Biophys J 95 (3): 1034-49. doi:10.1529/biophysj.107.126920.

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Hansen, Clinton, Robert Endres, and Ned Wingreen. (2008) 2008. “Chemotaxis in Escherichia Coli: A Molecular Model for Robust Precise Adaptation.”. PLoS Comput Biol 4 (1): e1. doi:10.1371/journal.pcbi.0040001.

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Vizcarra, Christina, Naigong Zhang, Shannon Marshall, Ned Wingreen, Chen Zeng, and Stephen Mayo. (2008) 2008. “An Improved Pairwise Decomposable Finite-Difference Poisson-Boltzmann Method for Computational Protein Design.”. J Comput Chem 29 (7): 1153-62. doi:10.1002/jcc.20878.

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Endres, Robert, Joseph Falke, and Ned Wingreen. (2007) 2007. “Chemotaxis Receptor Complexes: From Signaling to Assembly.”. PLoS Comput Biol 3 (7): e150. doi:10.1371/journal.pcbi.0030150.

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Mora, Thierry, Howard Yu, Yoshiyuki Sowa, and Ned Wingreen. (2009) 2009. “Steps in the Bacterial Flagellar Motor.”. PLoS Comput Biol 5 (10): e1000540. doi:10.1371/journal.pcbi.1000540.

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Mukhopadhyay, Ranjan, and Ned Wingreen. (2009) 2009. “Curvature and Shape Determination of Growing Bacteria.”. Phys Rev E Stat Nonlin Soft Matter Phys 80 (6 Pt 1): 062901. doi:10.1103/PhysRevE.80.062901.

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Endres, Robert, and Ned Wingreen. (2009) 2009. “Maximum Likelihood and the Single Receptor.”. Phys Rev Lett 103 (15): 158101. doi:10.1103/PhysRevLett.103.158101.

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Daly, Kristopher, Kerwyn Casey Huang, Ned Wingreen, and Ranjan Mukhopadhyay. (2011) 2011. “Mechanics of Membrane Bulging During Cell-Wall Disruption in Gram-Negative Bacteria.”. Phys Rev E Stat Nonlin Soft Matter Phys 83 (4 Pt 1): 041922. doi:10.1103/PhysRevE.83.041922.

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Wyart, Matthieu, David Botstein, and Ned Wingreen. (2010) 2010. “Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data.”. PLoS Comput Biol 6 (11): e1000979. doi:10.1371/journal.pcbi.1000979.

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Banigan, Edward, Michael Gelbart, Zemer Gitai, Ned Wingreen, and Andrea Liu. (2011) 2011. “Filament Depolymerization Can Explain Chromosome Pulling During Bacterial Mitosis.”. PLoS Comput Biol 7 (9): e1002145. doi:10.1371/journal.pcbi.1002145.

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Teeffelen, Sven, Siyuan Wang, Leon Furchtgott, Kerwyn Casey Huang, Ned Wingreen, Joshua Shaevitz, and Zemer Gitai. (2011) 2011. “The Bacterial Actin MreB Rotates, and Rotation Depends on Cell-Wall Assembly.”. Proc Natl Acad Sci U S A 108 (38): 15822-7. doi:10.1073/pnas.1108999108.

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Borenstein, David Bruce, Yigal Meir, Joshua Shaevitz, and Ned Wingreen. 2013. “Non-Local Interaction via Diffusible Resource Prevents Coexistence of Cooperators and Cheaters in a Lattice Model.”. PLoS One 8 (5): e63304. doi:10.1371/journal.pone.0063304.

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Borenstein, David Bruce, Peter Ringel, Marek Basler, and Ned Wingreen. (2015) 2015. “Established Microbial Colonies Can Survive Type VI Secretion Assault.”. PLoS Comput Biol 11 (10): e1004520. doi:10.1371/journal.pcbi.1004520.

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