Publications
* - these authors contributed equally. $ - corresponding author
Manuscripts under review/Preprints
138. M. Hur, T. Bartol, P. Rangamani, T. Sejnowski, and E. Mjolsness$: Graph Grammar Biomechanics with Synaptic Spine Head Morphodynamics
137. Emily Kobayashi; Nathaniel J Linden-Santangeli; Nicholas Chan; Christopher B Toomey; Sunder Mudaliar; Marinella Temprosa; Sharon Edelstein; Ravi Goyal; Padmini Rangamani, and Amit Majithia$: Longitudinal metabolic trajectories in Diabetes Prevention Program participants reveal subgroups with varying micro and macrovascular complication risk
136. K. J. McCabe, M. Hernandez Mesa, and P. Rangamani$: Calcium dynamics in small spaces: lessons learned from modeling in dendritic spines
135. K. Stark, M. Bonilla-Quintana, A.M. Sokac, and P. Rangamani: Drosophila embryo cellularization is modulated by the viscoelastic dynamics of cortical-membrane interactions (biorxiv link)
134. C. T. Lee$, K. Venkataraman, I. Budin, and P. Rangamani$: Coupling between membrane undulations and lipid curvature leads to transient local enrichment of cardiolipin in mitochondrial membranes (biorxiv link)
133. F. Catala*, M. Bonilla-Quintana*, N. Sanfeliu-Cerdan, P. Rangamani$, and M. Krieg$: Periodic Obstacles Regulate Membrane Tension Propagation to Enable Localized Mechanotransduction (biorxiv link)
132. N. J. Linden-Santangeli, J. Zhang, B. M. Kramer$, and P. Rangamani$: Increasing certainty in systems biology models using Bayesian multimodel inference (bioRxiv link)
131. K. Zhu*, X. Guo*, A. Chandrasekaran*, X. Miao, P. Rangamani$, W. Zhao$, Y. Miao$: Membrane curvature catalyzes actin nucleation through nano-scale condensation of N-WASP-FBP17 (bioRxiv link)
130. A. Mahapatra, S. A. Malingen, P. Rangamani$: Interplay between cortical adhesion and membrane bending regulates microparticle formation (bioRxiv link)
2025
129. E. A. Francis*, E. Sarikhani*, V. Patel, D. P. Meganathan, Z. Jahed$, and P. Rangamani$: Nanoscale curvature of the plasma membrane regulates mechanoadaptation through nuclear deformation and rupture (biorxiv link). Accepted in Adv. Sci.
128. M. Hernandez Mesa, G. C. Garcia, F. Hoerndli, K. J. McCabe, P. Rangamani$: Spine apparatus modulates Ca2+ in spines through spatial localization of sources and sinks (bioRxiv link). Accepted J. Physiol.
127. K. Xiao and P. Rangamani$: Glycocalyx induced formation of membrane tubes (biorxiv link). Accepted Biophys. J
126. Rangamani, P. Continuum modeling of lipid bilayers for curvature generation. Membrane Shape and Biological Function 78 (2025).
125. T. M. Bartol$,*, M. Ordyan, T. J. Sejnowski, P. Rangamani*, and M. B. Kennedy$,*: A spatial model of autophosphorylation of CaMKII in a glutamatergic spine suggests a network-driven kinetic mechanism for bistable changes in synaptic strength (bioRxiv link). Accepted Frontiers in Synaptic Neuroscience.
124. K. Xiao, S. Park, J. C. Stachowiak$, and P. Rangamani$: Biophysical modeling of membrane curvature generation and curvature sensing by the glycocalyx (biorxiv link). Accepted Proc. Natl. Acad. Sci.
123. M. Hernandez Mesa, K. J. McCabe, and P. Rangamani$: Synaptic cleft geometry modulates NMDAR opening probability by tuning glutamate residence time (biorxiv link). Accepted Biophys J. Highlighted as a New and Notable in Kaytanli and Bacca, Morphological trapping of neurotransmitters in synaptic clefts: A new dimension in neural plasticity, Biophysical Journal, 2025)
122. M. Bonilla-Quintana, A. Ghisleni, N. C. Gauthier$, P. Rangamani$: Dynamic mechanisms for membrane skeleton transitions (bioRxiv link). Accepted J. Cell Sci.
2024
121. C. Walker, A. Chandrasekaran*, D. Mansour*, K. Graham3, A. Torres, L. Wang, E. M. Lafer, P. Rangamani$, and J. C. Stachowiak$: Liquid-like condensates that bind actin drive filament polymerization and bundling (biorxiv link). Accepted Dev. Cell.
120. B. Debnath, B. N. Narasimhan, S. I. Fraley$, and P. Rangamani$: Modeling collagen fibril degradation as a function of matrix microarchitecture. (bioRxiv link) Accepted Soft Matter
119. L. Qiao*, A. Khalilimeybodi*, N. Linden-Santangeli*, and P. Rangamani$: The evolution of systems biology and systems medicine: From mechanistic models to uncertainty quantification (arXiv link). Accepted Annual Reviews of Biomedical Engineering
118. L. Qiao, M. Getz, B. Gross, B. Tenner, J. Zhang$, and P. Rangamani$: Spatiotemporal orchestration of calcium-cAMP oscillations on AKAP/AC nanodomains is governed by an incoherent feedforward loop (bioRxiv link). Accepted PLoS Comp Biol
117. E. A. Francis*, J. G. Laughlin*, J. S. Dokken, H. N. T. Finsberg, C. T. Lee, M. E. Rognes$, and P. Rangamani$: Spatial modeling algorithms for reactions and transport (SMART) in biological cells (biorxiv link). Accepted Nat. Comp. Sci.
116. H. Jafarinia, A. Khalilimeybodi, J. Barrasa-Fano, S.I. Fraley, P. Rangamani$, A. Carlier$: Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction. npj Systems Biology and Applications. 10. Article number 90.
115. E. A. Francis, P. Rangamani$: Computational modeling establishes mechanotransduction as a potent entrainment cue for the mammalian circadian clock (bioRxiv link) Accepted, J. Cell Sci
114. A. Ghisleni, M. Bonilla Quintana, M. Crestani, A. Fukuzawa, P. Rangamani$, N. C. Gauthier$. Mechanically induced topological transition of spectrin regulates its distribution in the mammalian cortex (bioRxiv link). Accepted Nat. Comms
113. J. M. Griswold, M. Bonilla-Quintana*, R. Pepper*, C. T. Lee*, S. Raychaudhuri, S. Ma, Q. Gan, S. Syed, C. Zhu, M. Bell, M. Suga, Y. Yamaguchi, R. Chéreau, U. V. Nägerl, G. Knott, P. Rangamani$, S. Watanabe$: Membrane mechanics dictate axonal morphology and function (bioRxiv link). Accepted Nat. Neurosci.
112. E. A. Francis$ and P. Rangamani$: Particle-based simulations shed light on cytoskeleton-membrane dynamics in phagocytosis. Accepted Biophys J.
111. A. Khalilimeybodi, J. Saucerman, P. Rangamani$: Modeling Cardiomyocyte Signaling and Metabolism Predicts Genotype to Phenotype Mechanisms in Hypertrophic Cardiomyopathy (bioRxiv link) Accepted, Computers in Biology and Medicine.
110. A. Fowler, K. R. Knaus, S. Khuu, A. Khalilimeybodi, S. Schenk, S. Ward, A. C. Fry, P. Rangamani, and A. D. McCulloch$: Network model of skeletal muscle cell signaling predicts differential responses to endurance and resistance exercise training. 2024. Accepted Experimental Physiology
109. C. T. Lee$ and P. Rangamani$: Modeling the mechanochemical feedback for membrane-protein interactions using a continuum mesh model. Methods in Enzymology. Ed. by M. Deserno, T. Baumgart, and D. Marquardt. Vol 2. 2 vols. Biophysical Approaches to Lateral and Transverse Lipid Membrane Heterogeneity. Academic Press 2024. In Press.
108. A. Chandrasekaran, K. Graham, J.C. Stachowiak$, and P. Rangamani$: Kinetic trapping organizes actin filaments within liquid-like protein droplets. Accepted Nat. Comms (bioRxiv link)
107. M. Bonilla Quintana, P.Rangamani$: Biophysical modeling of actin-mediated structural plasticity reveals mechanical adaptation in dendritic spines (bioRxiv link). Accepted, eNeuro
106. C. T. Lee, M. K. Bell, M. Bonilla-Quintana, P. Rangamani$: Biophysical modeling of synaptic plasticity. Annual Reviews of Biophysics 2024
105. K. Graham, A. Chandrasekaran, Liping Wang3, Noel Yang1, Eileen M. Lafer3, P. Rangamani$, and J.C. Stachowiak$: Liquid-like condensates mediate competition between actin branching and bundling (bioRxiv link) Accepted PNAS
2023
104. Y. Chen, D. Saintillan$, and P. Rangamani$: Cell motility modes are selected by the interplay of mechanosensitive adhesion and membrane tension (bioRxiv link) Accepted PRX Life
103. H. Alimohamadi and P. Rangamani$: Effective cell membrane tension protects red blood cells against malaria invasion (bioRxiv link) Accepted PLoS Comp Biol.
102. L. A. Parra-Rivas* , K. Madhivanan* , B. D. Aulston, L. Wang, D. D. Prakashchand, N. P. Boyer, V. M. Saia-Cereda, K. Branes-Guerrero , D. P. Pizzo, P. Bagchi, V.S. Sundar, Y. Tang, U. Das, D. A. Scott, P. Rangamani, Y. Ogawa, and S. Roy$. Serine-129 phosphorylation of α-synuclein is a trigger for physiologic protein-protein interactions and synaptic function (bioRxiv link). Accepted. Neuron
101. J. G. Laughlin, J. S. Dokken, H. N. T. Finsberg, E. A. Francis, C. T. Lee, M. E. Rognes, P. Rangamani$. SMART: Spatial Modeling Algorithms for Reaction and Transport (arXiv link). Journal of Open Source Software, 8(90), 5580, https://doi.org/10.21105/joss.05580
100. K. Venkatraman, C. T. Lee*, G. C. Garcia*, A. Mahapatra*, G. Perkins, K-Y Kim, H. A. Pasolli, S. Phan, J. Lippincott-Schwartz, M. Ellisman, P. Rangamani$, I. Budin$. Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome (bioRxiv link). The EMBO Journal (2023) e114054
99. H. Nakamura$, E. Rho, C. T. Lee, K. Itoh, D. Deng, S. Razavi, H. T. Matsubayashi, C. Zhu, E. Jung, P. Rangamani, S. Watanabe, and T. Inoue$. ActuAtor, a Listeria-inspired molecular tool for generating force in living cells: Controlled deformation of intracellular organizations. Cell Reports, 2023. https://doi.org/10.1016/j.celrep.2023.113089
98. G. C. Garcia., K. Gupta, T. M. Bartol, T. J. Sejnowski, P. Rangamani$: Mitochondrial morphology governs ATP production rate (bioRxiv link). J Gen Physiol (2023) 155 (9): e202213263
97. A. Leung, P.Rangamani$: Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling (bioRxiv link). NPJ Systems Biology and Applications. npj Syst Biol Appl 9, 34 (2023). https://doi.org/10.1038/s41540-023-00295-4
96. F. Yuan, C.T. Lee, J. Houser, A. Sangani, L. Wang, E. Lafer, P. Rangamani$, and J. C. Stachowiak$. The ins and outs of membrane bending by intrinsically disordered proteins (bioRxiv link). Science Advances. 2023 9:27 DOI: 10.1126/sciadv.adg3485
95. A. Mahapatra and P. Rangamani$: Formation of protein-mediated tubes is governed by a snapthrough transition. Soft Matter, 2023, 19, 4345-4359 (bioRxiv link)
94. P. Rangamani$. Active nematic fluid films. J. Fluid. Mech. 2023. 960. doi: 10.1017/jfm.2023.133
93. L. Qiao*, S. Sinha*, A. A. A. El-Hafeez, I-C. Lo, T. Ngo, N. Aznar, I. Lopez-Sanchez, V. Gupta, M. G. Farquhar, P. Rangamani$ and P. Ghosh$: A Circuit for Secretion-coupled Cellular Autonomy in Multicellular Eukaryotic cells (bioRxiv link). Mol. Syst. Biol. 2023. doi: 10.15252/msb.202211127
92. L. Qiao, P. Ghosh$ and P. Rangamani$: Design principles of dose-response alignment in coupled GTPase switches (bioRxiv link). NPJ Systems Biology and Applications. npj Syst Biol Appl 9, 3 (2023). https://doi.org/10.1038/s41540-023-00266-9
91. M. K. Bell and P. Rangamani$: Crosstalk between biochemical signaling network architecture & trafficking governs AMPAR dynamics in synaptic plasticity (bioRxiv link). J Physiol. 2023, 601(15): 3377-3402 https://doi.org/10.1113/JP284029
90. E.P. Campbell, A. A. Abushawish, L. A. Valdez, M.K. Bell, M. Haryono, P. Rangamani, and B.L. Bloodgood$: Electrical signals in the ER are cell type and stimulus specific with extreme spatial compartmentalization in neurons. Cell Reports. doi: 10.1016/j.celrep.2022.111943
89. K.D. Graham, A. Chandrasekaran, L. Wang, A. Ladak, E. M. Lafer, P. Rangamani$, and J. C. Stachowiak$: Liquid-like assembly of VASP drives actin polymerization and bundling (bioRxiv link) Nat. Phys. (2023). https://doi.org/10.1038/s41567-022-01924-1. Discussed in The secret life of the protein VASP by Julie Plastino and Highlighted in Physics Today
88. A. Khalilimeybodi, S.I. Fraley$, and P.Rangamani$: Mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signaling (bioRxiv link) J. Physiol. 601(3): 483-515. DOI: 10.1113/JP283966
87. M. K. Bell, C. T. Lee, and P. Rangamani$: Spatiotemporal modeling reveals geometric dependence of AMPAR dynamics on dendritic spine morphology (bioRxiv link) J Physiol. 2023, 601(15): 3329-3350 DOI: 10.1113/JP283407
2022
86. N. Linden, B. Kramer$, and P. Rangamani$: Bayesian Parameter Estimation for Dynamical Models in Systems Biology (Link). PLoS Comp Biol. 2022 Oct 21;18(10):e1010651. doi: 10.1371/journal.pcbi.1010651.
85. S. A. Malingen and P. Rangamani$: Modeling membrane curvature generation using mechanics and machine learning (bioRxiv link). J Roy. Soc. Int. 2022 Sep;19(194):20220448. doi: 10.1098/rsif.2022.0448
84. M.K. Bell*, M. V. Holst*, C. T. Lee, and P. Rangamani$: Dendritic spine morphology regulates calcium-dependent synaptic weight change (biorxiv link). J. Gen. Physiol. 2022 Aug 1;154(8):e202112980. doi: 10.1085/jgp.202112980
83. C. Zhu, C. T. Lee$, and P. Rangamani$: Mem3DG: Modeling Membrane Mechanochemical Dynamics in 3D using Discrete Differential Geometry (biorxiv link). Biophys. Rep. 2022 Sep 14;2(3):100062. doi: 10.1016/j.bpr.2022.100062
82. M. Hernández Mesa , J. van den Brink , W. E. Louch , K. J. McCabe, and P. Rangamani$: Nanoscale organization of ryanodine receptor distribution and phosphorylation pattern determines the dynamics of calcium sparks (Published). PLoS Comp Biol. 2022 Jun 6;18(6):e1010126. doi: 10.1371/journal.pcbi.1010126.
81. D. Serwas, M. Akamatsu, A. Moayed, K. Vegesna, R. Vasan, J. M. Hill, J. Schoeneberg, K. M. Davies, P. Rangamani, and D. G. Drubin$: Actin force generation in vesicle formation: mechanistic insights from cryo-electron tomography. (biorxiv link); Dev. Cell. 2022 May 9;57(9):1132-1145.e5. doi: 10.1016/j.devcel.2022.04.012
80. M. Bonilla Quintana and P. Rangamani$: Can biophysical models give insight into the synaptic changes associated with addiction? (arxiv); Physical Biology. 2022 Jun 14;19(4). doi: 10.1088/1478-3975/ac6cbe
79. P. Rangamani$: The many faces of membrane tension: challenges across systems and scales. BBA: Biomembranes. 2022 Jul 1;1864(7):183897. doi: 10.1016/j.bbamem.2022.183897
78. R. B. Nowak*, H. Alimohamadi*, K. Personjamasp, P. Rangamani, and V. Fowler$: Nanoscale Dynamics of Actin Filaments in the Red Blood Cell Membrane Skeleton (bioRxiv link). Mol. Biol. Cell. 2022 Mar 1;33(3):ar28. doi: 10.1091/mbc.E21-03-0107
2021
77. D. Auddya*, X. Zhang*, R. Gulati, R. Vasan, K. Garikipati, P. Rangamani, and S. Rudraraju$: Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematics and revealed by a three dimensional computational framework (bioRxiv link). Proc. Roy. Soc. A. 2021 Nov;477(2255):20210246. doi: 10.1098/rspa.2021.0246
76. A. Mahapatra, D. Saintillan$, and P. Rangamani$: Curvature-driven feedback on aggregation-diffusion of proteins in lipid bilayers (biorxiv link). Soft Matter, 2021, DOI: 10.1039/D1SM00502B
75. R. Mendelsohn*, G. C.Garcia*, T. M. Bartol, C.T. Lee, P. Khandelwal, E. Liu, D. J. Spencer, A. Husar, E. A. Bushong, S. Phan, M. H. Ellisman, A. Skupin, T. J. Sejnowksi$, and P. Rangamani$ : Morphological principles of neuronal mitochondria (bioRxiv link). J. Comp. Neurol. 2022 Apr;530(6):886-902. doi: 10.1002/cne.25254
74. H. Alimohamadi, M. Bell, S. Halpain, and P. Rangamani$: Mechanical principles governing the shapes of dendritic spines. 2021, Frontiers in Physiology doi: 10.3389/fphys.2021.657074
73. A. Leung, D. Ohadi, G. Pekkurnaz, and P. Rangamani$: Systems modeling predicts that mitochondria ER contact sites regulate the postsynaptic energy landscape (bioRxiv link). 2021. Accepted, NPJ Syst Biol Appl . 2021 Jun2;7(1):26 https://doi.org/10.1038/s41540-021-00185-7
72. K.E. Scott, S.I. Fraley$, and P. Rangamani$: A spatial model of YAP/TAZ signaling reveals how stiffness, dimensionality, and shape contribute to emergent outcomes (bioRxiv link). 2021. Proc. Natl. Acad. Sci. May 18, 2021 118 (20) e2021571118; https://doi.org/10.1073/pnas.2021571118
71. M. K. Bell and P. Rangamani$: Design decisions for incorporating spatial and mechanical aspects in models of signaling networks. Accepted, Curr. Opin. Syst. Biol. 25: 70-77, doi: 10.1016/j.coisb.2021.03.004
70. F. Yuan, H. Alimohamadi, B. Bakka, A. N. Trementozzi, N. L. Fawzi, P. Rangamani$, and J. C. Stachowiak$: Membrane bending by protein phase - separation. Proc. Natl. Acad. Sci. 2021 Mar 16;118(11):e2017435118. doi: 10.1073/pnas.2017435118.
69. K. R. Stevens$, K. S. Masters, P. I. Imoukhuede, K. A. Haynes, L. A. Setton, E. Cosgriff-Hernandez, M. A. L. Bell, P. Rangamani, S. E. Sakiyama-Elbert, S. D. Finley, R. K. Willits, A. N. Koppes, N. C. Chesler, K. L. Christman, J. B. Allen, J. Y. Wong, H. El-Samad, T. A. Desai, and O. Eniola-Adefeso$. Fund Black Scientists. Cell. 2021. https://doi.org/10.1016/j.cell.2021.01.011
68. L. M. Stolerman, P. Ghosh$, and P. Rangamani$: Stability analysis of a signaling circuit with dual species of GTPase switches. Bull Math. Biol. 2021 Feb 20; 83(4) : 34. doi: 10.1007/s11538-021-00864-w
67. C. T. Lee, M. Akamatsu, and P. Rangamani$: The Value of Models for Membrane Budding in Clathrin-Mediated Endocytosis. Curr. Opin. Cell. Biol. 2021. Volume 71, August 2021, Pages 38-45
66. K. J. McCabe$ and P. Rangamani: Computational modeling approaches to cAMP/PKA signaling in cardiomyocytes. J. Mol. Cell. Cardiol. 2021. 154:32-40. doi: 10.1016/j.yjmcc.2021.01.008
65. A. Mahapatra*, C. Uysalel*, and P. Rangamani$: The mechanics and thermodynamics of tubule formation in biological membranes. J. Membr. Biol. 2021 doi: 10.1007/s00232-020-00164-9. (Cover)
2020
64. R. R. Molina, S. Liese, H. Alimohamadi, P. Rangamani and A. Carlson$.: Diffuso-kinetic membrane budding dynamics. Soft Matter. 2020 https://doi.org/10.1039/D0SM01028F.
63. B. Tenner , M. Getz , B. Ross , D. Ohadi , C. Bohrer , E. Greenwald , S. Mehta , J. Xiao , P. Rangamani$, and J. Zhang$: Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit. eLife. 2020. 9:e55013. doi: 10.7554/eLife.55013
62. R. C. Calizo*, M. K. Bell*, A. Ron, M. Hu, S. Bhattacharya, N. J. Wong, W. G. M. Janssen, G. Perumal, P. Pederson, S. Scarlata, J. Hone, E. U. Azeloglu, P. Rangamani$, and R. Iyengar$: Cell shape regulates subcellular organelle location to control early Ca 2+ signal dynamics in vascular smooth muscle cells. Sci. Rep. 2020 10; Article number 17866.
61. P. K. Kreeger$, A. Brock, H. C. Gibbs, K. J. Grande-Allen, A. H. Huang, K. S. Masters, P. Rangamani, M.R. Reagan, S. L. Servoss: Ten Simple Rules for Women Scientists During a Pandemic. Plos Comp Biol. 2020. https://doi.org/10.1371/journal.pcbi.1008370
60. J. A. Nirody$, I. Budin, and P. Rangamani$: ATP synthase: evolution, energetics, and membrane interactions. J. Gen Physiol. 2020. 152 (11): e201912475 doi: 10.1085/jgp.201912475.
59. J.Z. Zhang, T.-W. Lu , L. M. Stolerman, B.Tenner , J. R. Yang , J.-F. Zhang , M. Falcke, P.Rangamani , S.S. Taylor, S.Mehta, Jin Zhang $: Phase Separation of a PKA Regulatory Subunit Controls cAMP Compartmentation and Oncogenic Signaling. Cell. 2020 Aug 20;S0092-8674(20)30991-0. doi: 10.1016/j.cell.2020.07.043.
58. P. Rangamani$, A. Behzadan, and M. J. Holst. Local sensitivity analysis of the 'Membrane shape equation' derived from the Helfrich energy. Mathematics and Mechanics of Solids. 2020. doi:10.1177/1081286520953888 (arXiv version).
57. A. Mahapatra, D. Saintillan, and P. Rangamani$: Transport Phenomena in Fluid Films with Curvature Elasticity. J. Fluid. Mech. 2020. 905, A8. doi:10.1017/jfm.2020.711.
56. M. Ordyan, T. Bartol, M.B. Kennedy, P. Rangamani$, and T. Sejnowksi$: Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator. PLoS Comp Biol. 2020 doi.org/10.1371/journal.pcbi.1008015
55. H. Alimohamadi, A. Smith, R. Nowak, V. Fowler, and P. Rangamani$: Non-uniform distribution of myosin-mediated forces governs red blood cell curvature through tension modulation. PLoS Comp Biol. 2020 doi.org/10.1371/journal.pcbi.1007890 (bioRxiv version).
54. C. T. Lee*, J. G. Laughlin*, N. Angliviel de La Beaumelle, R. E. Amaro, J. A. McCammon, R. Ramamoorthi, M. J. Holst, and P. Rangamani$: 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS Comp Biol doi: doi.org/10.1371/journal.pcbi.1007756 (arXiv version; bioRxiv version). Link to GAMer2 files.
53. M. Getz, P. Rangamani$, and P. Ghosh$: Regulating cellular cyclic AMP: “Sources”, “Sinks”, and now, “Tunable Valves”. WIREs Systems Biology and Systems Medicine. doi: 10.1002/wsbm.1490.
52. H. Alimohamadi, Ben Ovryn, and P. Rangamani$: Modeling membrane nanotube morphology: the role of heterogeneity in composition and material properties. (bioRxiv version). Scientific Reports. https://www.nature.com/articles/s41598-020-59221-x
51. L. M. Stolerman*, M. Getz*, S. G. Llewellyn Smith, M. Holst, and P. Rangamani$: Stability analysis of a bulk-surface reaction model for membrane-protein clustering. Bull. Math. Biol. 2020 Feb 6;82(2):30. doi: 10.1007/s11538-020-00703-4 (arXiv version; bioRxiv version).
50. M. Akamatsu, R. Vasan, D. Serwas, M. Ferrin, P. Rangamani$, and D. G. Drubin$ : Principles of self-organization and load adaptation by the actin cytoskeleton during clathrin-mediated endocytosis. eLife. https://elifesciences.org/articles/49840
49. R. Vasan, M. Rowan, C.T. Lee, G.R. Johnson, P. Rangamani, and M. Holst$: Applications and Challenges of Machine Learning to Enable Realistic Cellular Simulations. 2020, 7:247, doi:10.3389/fphy.2019.00247. (arxiv version) Editor's Choice, Computational Physics.
48. O. B. Tarun, H.I. Okur, P. Rangamani and S. Roke$: Transient domains of ordered water induced by divalent ions lead to lipid membrane curvature fluctuations. Communications Chemistry. 2020, https://doi.org/10.1038/s42004-020-0263-8
2019
47. R. Vasan, S. Rudraraju, M. Akamatsu, K. Garikipati, and P. Rangamani$: A mechanical model reveals that non-axisymmetric buckling lowers the energy barrier associated with membrane neck constriction. Soft Matter. 2020 Jan 22;16(3):784-797 https://doi.org/10.1039/C9SM01494B
46. C. T. Lee$, J. Laughlin, J.B. Moody, R.E. Amaro, J. A. McCammon, M. Holst, and P. Rangamani$: An Open Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries . Biophys. J. https://doi.org/10.1016/j.bpj.2019.11.3400 (bioRxiv version)
45. K.M. Pearce*, M. Bell*, W. H. Linthicum, Q. Wen, J. Srinivasan, P. Rangamani$, and S. Scarlata$: Gq-mediated calcium dynamics and membrane tension modulate neurite plasticity. Mol. Biol. Cell https://doi.org/10.1091/mbc.E19-09-0536 (bioRxiv version).
44. D. Ohadi, D. Schmitt, B. Calabrese, S. Halpain, J. Zhang, and P. Rangamani$: Computational modeling reveals frequency modulation of calcium-cAMP/PKA pathway in dendritic spines. Biophys. J doi: https://doi.org/10.1016/j.bpj.2019.10.003 (bioRxiv version)
43. D. Ohadi and P. Rangamani$: Geometric control of frequency modulation of cAMP oscillations due to Ca2+-bursts in dendritic spines. Biophys. J doi: https://doi.org/10.1016/j.bpj.2019.10.004 (bioRxiv version)
42. R. Vasan, M.M. Maleckar, C.D. Williams$, and P. Rangamani$: DLITE uses cell-cell interface movement to better infer cell-cell tensions. Biophys. J. doi:https://doi.org/10.1016/j.bpj.2019.09.034 (bioRxiv version) (Code).
41. M. Chabanon and P. Rangamani$: Geometric coupling of helicoidal ramps and curvature-inducing proteins in organelle membranes. J R Soc Interface. 2019 Sep 27;16(158):20190354. doi: 10.1098/rsif.2019.0354. (bioRxiv version).
40. A. Cugno, T. Bartol, T. Sejnowski, R. Iyengar, and P. Rangamani$: Geometric principles of second messenger dynamics in dendritic spines. Sci. Rep. (2019) 9:11676 | https://doi.org/10.1038/s41598-019-48028-0 (bioRxiv version)
39. M. Bell, T. Bartol, T. Sejnowski, and P. Rangamani$: Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium. J. Gen. Physiol. 2019 Aug 5;151(8):1017-1034. See associated Research News article.
38. K.E. Scott*, K. Rychel*, S. Ranamukhaarachchi, P. Rangamani, and S.I. Fraley$: Emerging themes and unifying concepts underlying cell behavior regulation by the pericellular space, Acta Biomater. 2019 Sep 15;96:81-98. doi: 10.1016/j.actbio.2019.06.003.
37. M. C. Getz, L. Swanson, R. Sahoo, P. Ghosh$, and P. Rangamani$: Guanine-nucleotide Exchange Modulator, GIV/Girdin, Serves as a Tunable Valve for Growth Factor-Stimulated cAMP Signal. Mol Biol Cell. 2019 Jun 15;30(13):1621-1633. doi: 10.1091/mbc.E18-10-0630.
36. O. Igoshin, J. Chen, J. Xing, J. Liu, T.C. Elston, M. Grabe, K.S. Kim, J. Nirody, P. Rangamani, S. Sun, and C. Wolgemuth: Biophysics at the coffee shop: lessons learned working with George Oster. Mol Biol Cell. 2019 Jul 22;30(16):1882-1889. doi: 10.1091/mbc.E19-02-0107
35. A. Bour, S. G Kruglik, M. Chabanon, P. Rangamani, N. Puff, and S. Bonneau: Lipid unsaturation properties govern the sensitivity of membranes to photo-induced oxidative stress Biophys J. 2019 Mar 5;116(5):910-920. doi: 10.1016/j.bpj.2019.01.033.
2018
34. H. Alimohamadi and P. Rangamani$: Modeling Membrane Curvature Generation due to Membrane -- Protein Interactions, Biomolecules .2018, 8:4, 120-145 https://doi.org/10.3390/biom8040120
33. H. Alimohamadi*, R. Vasan*, J. Hassinger, J. C. Stachowiak, and P. Rangamani$: The role of traction in membrane curvature generation, Mol. Biol. Cell. 2018, 29 :16, 2024-2035. Special issue on forces on and within cells.
32. R. Vasan, M. S. Akamatsu, J. Schöneberg, and P. Rangamani$ (2018) Intracellular Membrane Trafficking: Modeling Local Movements in Cells. In: Stolarska M., Tarfulea N. (eds) Cell Movement. Modeling and Simulation in Science, Engineering and Technology. Birkhäuser, Cham
31. M. Chabanon$ and P. Rangamani$: Solubilization kinetics determines the pulsatory dynamics of lipid vesicles exposed to surfactant BBA Biomem. doi:10.1016/j.bbamem.2018.03.016
30. M. Chabanon and P. Rangamani$: Gaussian Curvature Directs The Distribution Of Spontaneous Curvature On Bilayer Membrane Necks. Soft Matter 2018, doi:10.1039/C8SM00035B
29. W. Su*, D. Gettel*, M. Chabanon*, P. Rangamani$ and A. Parikh$: Pulsatile Gating of Giant Vesicles Containing Macromolecular Crowding Agents induced by Colligative Non-ideality. J. Am. Chem. Soc., 2018, doi:10.1021/jacs.7b10192
2017
28. M. Getz, J. Nirody, and P. Rangamani$: Stability analysis of spatial modeling of cell signaling. WIREs Systems Biology and Systems Medicine, 2017. doi:10.1002/wsbm.1395 (MATLAB files can be found here).
27. M. Chabanon, J. Ho, B. Liedberg, A. Parikh, and P. Rangamani$: Pulsatile lipid vesicles in osmotic stress. Biophysical J. 2017. 112: 8, 1682-1691 (cover). (MATLAB files)
26. W. T. Snead, C. C. Hayden, A. K. Gadok, C. Zhao, E. M. Lafer, P. Rangamani, J. C. Stachowiak$: Membrane fission by protein crowding. Proc. Natl. Acad. Sci. 2017. 114:16 E3258-E3267 doi: 10.1073/pnas.1616199114 (cover)
25. M. Chabanon, J. C. Stachowiak, and P. Rangamani$: Systems biology of cellular membranes: a convergence with biophysics. WIREs Systems Biology and Systems Medicine. 2017. doi:10.1002/wsbm.1386.
24. P. Ghosh, P. Rangamani, and I. Kufareva: The GAPs, GEFs, GDIs and....now, GEMs: New kids on the heterotrimeric G protein signaling block. Cell Cycle. 2017. doi:10.1080/15384101.2017.1282584.
23. J. E. Hassinger, G. Oster, D. G. Drubin, and P. Rangamani$: Design principles for robust vesiculation in clathrin-mediated endocytosis. Proc. Natl. Acad. Sci., 2017, 114:7 E1118-1127 doi:10.1073/pnas1617705114 (MATLAB files can be found here).
22. S. K. Lim , A. S.W. Wong , H. M. de Hoog , P. Rangamani , A. N. Parikh, M. Nallani, S. Sandin, and B. Liedberg . Spontaneous formation of nanometer scale tubular vesicles in aqueous mixtures of lipid and block copolymer amphiphiles. Soft Matter, 2017,doi:10.1039/C6SM01753C (cover).
2016
21. P. Rangamani$, M. Levy, S. Khan, G. Oster$: Paradoxical signaling regulates structural plasticity in dendritic spines. Proc. Natl. Acad. Sci., 2016, doi:10.1073/pnas.1610391113.
20. K. Sriram*, J. G. Laughlin*, P. Rangamani$, D. M. Tartakovsky$: Shear stress induced NO production in endothelial cells. Biophys. J., 2016, 111:208-221.
19. J. Ho, P. Rangamani, B. Liedberg, and A. Parikh: Mixing Water, Transducing Energy, Shaping Membranes: Autonomously Self-regulating Giant Vesicles, Langmuir, doi:10.1021/acs.langmuir.5b04470 (cover).
2015
18. F. Bahmani, J. Christenson and P. Rangamani$: Analysis of lipid flow on minimal surfaces. Cont. Mech. Thermo. 2015, doi:10.1007/s00161-015-0458-x
17. S. Ray, A. Kassan, A. R. Busija, P. Rangamani, and H. H. Patel: The plasma membrane as a capacitor for energy and metabolism, AJP Cell, doi: 10.1152/ajpcell.00087.2015
2014
16. E. K. Eckhert, P. Rangamani, A. E. Davis, G. Oster and J. Berleman: Dual Biochemical Oscillators May Control Cellular Reversals in Myxococcus xanthus, Biophys. J., 2014, 107:2700-2711
15. K. Oglecka, P. Rangamani, R. Kraut, B. Liedberg and A. N. Parikh: Oscillatory phase separation in giant lipid vesicles induced by transmembrane osmotic differentials, eLife, 2014, 3:03695 (cover)
14. P. Rangamani$ and D. J. Steigmann: Variable tilt in lipid membranes, Proc. Royal Soc. A, 2014, 10.1098/rspa.2014.0463
13. P. Rangamani, K. K. Mandadapu and G. Oster: Protein-induced membrane curvature alters local membrane tension. Biophys. J. 2014, 107:571-562
12. P. Rangamani, A. Benjamini, A. Agrawal, B. Smit, D. Steigmann and G. Oster: Small Scale Membrane Mechanics. Biomech. Modeling. Mechanobiol. 2014, 13:697-711
11. P. Rangamani, G. Y. Xiong and R. Iyengar: Multiscale Modeling of Cell Shape from the Actin Cytoskeleton. Prog. Mol. Biol. Transl. Sci., 2014, 123:143-67
2013
10. P. Rangamani, D. Zhang, G. Oster and A. Shen: Lipid Nanotube Formation Driven by Osmotic Pressure. J. R. Soc. Interface, 6 Nov 2013, 10(88):20130637
9. P. Rangamani , A. Lipshtat, E. U. Azeloglu, R. C. Calizo, M. Hu, S. Ghassemi, J. Hone, S. Scarlata, S. R. Neves and R. Iyengar: Decoding Information in Cell Shape. Cell, 12 Sep 2013, 154(6):1356-69
8. P. Rangamani, A. Agrawal, K. K. Mandadapu, G. Oster and D. J. Steigmann: Interaction between surface shape and intra-surface viscous flow on lipid membranes . Biomechanics and Modeling in Mechanobiology, 2013, 12(4):833-845
2011
7. P. Rangamani, M. Fardin, Y. Xiong, A. L., O. Rossier, M. P. Sheetz and R. Iyengar: Signaling network triggers and membrane physical properties control actin cytoskeleton driven isotropic phase of cell spreading . Biophysical Journal, 2011, 100(4): 845-857
2010
6. M. Fardin*, O. Rossier*, P. Rangamani , P. Avignan, W. Vougenut, A. Mathur, R. Iyengar and M. P. Sheetz: Cell spreading as a hydrodynamic process , Soft Matter, 2010, 6, 4788 - 4799.
5. Y. Xiong*, P. Rangamani*, M. Fardin, B. Dubin-Thaler, A. Lipshtat, M. P. Sheetz and R. Iyengar: Mechanisms controlling cell size and shape during isotropic cell spreading. Biophysical Journal, 2010, 98(10):2136-2146
2008
4. P. Rangamani and R. Iyengar: Modeling cellular signaling networks, Essays Biochem 2008, 45:83-94
3. S. R. Neves, P. Tsokas, A. Sarkar, E. A.Grace, P. Rangamani , J. C. Shcaff, R. D. Blitzer, I. I. Moraru and R. Iyengar: Cell shape and negative links in regulatory loops coordinately regulate the propagation of spatial information within signaling networks Cell 2008, 133(4) 666-680
2007
2. P. Rangamani and R. Iyengar Modeling spatio-temporal interactions in the cell, Journal of Biosciences 2007, 32(1) 157-167
1. P. Rangamani and L. Sirovich Survival and Apoptotic Pathways Initiated by TNF-alpha: Modeling and Predictions , Biotechnology and Bioengineering, 2007, 97(5) 1216-1229