Carnegie Mellon: Departments of Physics and Biological Sciences

Membrane Biological Physics Web Page

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·  Summary of Results for Fully Hydrated Bilayers (ppt file)

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Something completely different - Link to PA congressional districting

Recent Publications:

(Last updated  12/8/2021)

  • John F. Nagle, Measuring the bending modulus of lipid bilayers with cholesterol.   Physical Review E 104, 044405 (2021).    (pdf)
  • John F. Nagle, Evan A. Evans, Patricia Bassereau, Tobias Baumgartner, Stephanie Tristram-Nagle and Rumiana Dimova, A needless but interesting controversy.   PNAS 118, 2025011118 (2021).    (pdf)
  • John F. Nagle and Alec Ramsay, On Measuring Two-Party Partisan Bias in Unbalanced States.   Election Law Journal 20, 116-138 (2021).   (pdf)
  • M. Mert Terzi, Markus Deserno and John F. Nagle, Mechanical properties of lipid bilayers: a note on the Poisson ratio.   Soft Matter 15, 9085-9092 (2019).   (pdf)
  • John F. Nagle, Area Compressibility Moduli of the Monolayer Leaflets of Asymmetric Bilayers from Simulations.   Biophysical Journal 117, 1051-1056 (2019).   (pdf)
  • John F. Nagle, Richard M. Venable, Ezekiel Maroclo-Kemmerling, Stephanie Tristram-Nagle, Paul E. Harper and Richard W. Pastor, Revisiting volumes of lipid components in bilayers.   J. Phys. Chem. B 123, 2697-2709 (2019).   (pdf) SM (pdf)
  • John F Nagle, Pierre Cognet, Fernando G. Dupuy, and Stephanie Tristram-Nagle, Structure of Gel Phase DPPC Determined by X-ray Diffraction.   Chem. Phys. Lipids 218, 168-177 (2019).   (pdf) SM (pdf)
  • John F. Nagle, What criteria should be used for redistricting reform.   Election Law Journal 18, 63-77 (2019).   (pdf) SM (pdf)
  • Zoran Arsov, Emilio J. Gonzalez-Ram\EDrez, Felix M. Goni, Stephanie Tristram-Nagle, John F. Nagle, Phase behavior of palmitoyl and egg sphingomyelin.   Chem. Phys. Lipids 213, 102-110 (2018).   (pdf) SM (pdf)
  • John F. Nagle, X-ray scattering reveals molecular tilt is an order parameter for the main phase transition in a model biomembrane.   Phys. Rev. E 96, 030401 (2017).   (pdf)
  • J. F. Nagle, Experimentally Determined Tilt and Bending Moduli of Single-Component Lipid Bilayers.   Chem. Phys. Lipids 205, 18-24 (2017).   (pdf) SM (doc)
  • John F. Nagle, How competitive should a fair single member districting plan be?   Election Law Journal 16, 196-209 (2017).   (pdf)
  • J. F. Nagle, Mechanical properties of lipid bilayers.  European Pharmaceutical Journal LXIII, 2016 (1-2).    (pdf)
  • J. F. Nagle, M. S. Jablin, and S. Tristram-Nagle, Sugar does not affect the bending and tilt moduli of simple lipid bilayers.  Chem. Phys. Lipids 196, 76-80 (2016).   (pdf) SM (pdf)
  • J. F. Nagle, K. Akabori, B. W. Treece and S. Tristram-Nagle, Determination of mosaicity in oriented stacks of liipd bilayers.  Soft Matter 12, 1884-91 (2016).   (pdf)
  • Lauren O'Neil, Kathryn Andenoro, Isabella Pagano, Laura Carroll, Leah Langer, Zachary Dell, Davina Perera, Bradley W. Treece, Frank Heinrich, Mathias L\F6sche, John F. Nagle, HIV-1 matrix-31 membrane binding peptide interacts differently with membranes containing PS vs. PI(4,5)P2.   Biochimica et Biophysica Acta 1858 (2016) 3071\963081.   (pdf)
  • D. Kopelevich and J. F. Nagle, Correlation between Length and Tilt of Lipid Tails.  J. Chem. Phys. 143, 154702 (2015).   (pdf) SM (pdf)
  • Kollmitzer, B., Heftberger, P., Podgornik, R. Nagle, J. F. and Pabst, G. Bending Rigidities and Interdomain Forces in Membranes with Coexisting Lipid Domains.  Biophys. J. 108, 2833-2842 (2015).   (pdf)
  • John F. Nagle, Measures of Partisan Bias for Legislating Fair Elections.   Election Law Journal 14, 346-360 (2015).   (pdf)
  • Kiyotaka Akabori and John F Nagle Structure of the DMPC lipid bilayer ripple phase.   Soft Matter 11, 918-926 (2015) : http://xlink.rsc.org/?doi=C4SM02335H (pdf) SM (pdf) Thesis (pdf)      
  • Michael S. Jablin, Kiyotaka Akibori and John F. Nagle. Experimental Evidence for Tilt-Dependent Theory of Biomembrane Mechanics, Phys. Rev. Letts. 113, 248102 (2014).  (pdf) Thesis that gives full details (pdf)
  • Kiyotaka Akabori; Kun Huang; Bradley W Treece; Michael S Jablin; Brian B Maranville; Arthur R Woll; John F Nagle; Angel E Garcia; Stephanie A. Tristram-Nagle, HIV-1 Tat membrane interaction probed using X-ray and neutron scattering, CD spectroscopy and MD simulations. Biochim. Biophys. Acta , 1838, 3078-3087 (2014).  (link) SI (pdf) DOI: 10.1016/j.bbamem.2014.08.014
  • J. C. Albert, L. T. Ray and J. F. Nagle, Testing procedures for extracting fluctuation spectra from lipid bilayer simulations J. Chem. Phys. , 141, 064114 (2014).  (link) http://dx.doi.org/10.1063/1.4892422
  • J. F. Nagle, M. S. Jablin, S. Tristram-Nagle and K. Akabori, What are the true values of the bending modulus of simple lipid bilayers? Chem. Phys. Lipids 185, 3-10 (2015).  (link) http://dx.doi.org/10.1016/j.chemphyslip.2014.04.003
  • K. Akabori and J. F. Nagle, Comparing Lipid Membranes in Different Environments. ACSNano 8, 3123-3127 (2014).  (link) http://dx.doi.org/10.1021/nn501499t
  • A. L. Boscia, K. Akabori, Z. Benamram, J. A. Michel, M. S. Jablin, J. D. Steckbeck, R. C. Montelaro, J. F. Nagle and S. Tristram-Nagle, Membrane Structure Correlates to Function of LLP2 on the Cytoplasmic Tail of HIV-1 gp41 Protein. Biophys. J. 105, 657-666 (2013).  (pdf) http://dx.doi.org/10.1016/j.bpj.2013.06.042
  • A. R. Braun, J. N. Sachs and J. F. Nagle, Comparing Simulations of Lipid Bilayers to Scattering Data: The Gromos 43A1-S3 Force Field.  J. Phys. Chem. B 117, 5065-72 (2013).  (pdf) SI(pdf) dx.doi.org/10.1021/jp401718k |
  • J. F. Nagle, Basic quantities in model biomembranes.  Faraday Discussions 161. Faraday Disc.161 (2013), http://xlink.rsc.org/?doi=C2FD20121F (pdf)  Also, comments and exchanges on pages 113-120, 132-133,144,149,150,264,300, 448,453,459,563,576,583,588.
  • Kelsey M. Hallinen, Stephanie Tristram-Nagle, and John F. Nagle, Stability of Lipid Bilayers.   Phys. Chem. Chem. Phys.  14, 15452-15457 (2012). (pdf) .
  • M. Raghunathan, Y. Zubovski, R. M. Venable, R. W. Pastor, J. F. Nagle and S. Tristram-Nagle, Structure and Elasticity of Lipid Membranes with Genistein and Daidzein Bioflavinoids Using X-ray Scattering and MD Simulations. J. Phys. Chem. B 116, 3918-3927 (2012).  (pdf)  SI (pdf)
  • E. G. Brandt, A. R. Braun, J. N. Sachs, J. F. Nagle and O. Edholm, ,Interpretation of Fluctuation Spectra in Lipid Bilayer Simulations.  Biophys. J. 100, 2104-2111 (2011). (pdf)  Supplementary Material (pdf)
  • A. R. Braun, E. G. Brandt, O. Edholm, J. F. Nagle and J. N. Sachs, Determination of Electron Density Pro_les and Area from Molecular Dynamics Simulations of Large Undulating Lipid Bilayers.  Biophys. J. 100, 2112-2120 (2011). (pdf)  SM (pdf)
  • P. Uppamoochikkal, S. Tristram-Nagle and J. F. Nagle.  Orientation of Tie-Lines in the Phase Diagram of DOPC:DPPC:Cholesterol Model Biomembranes. Langmuir 26, 17363-68 (2010). (pdf)
  • S. Tristram-Nagle, R. Chan, E. Kooijman, P. Uppamoochikkal, W. Qiang, D. P. Weliky and J. F. Nagle.  HIV fusion peptide penetrates, disorders and softens T-cell membrane mimics.  J. Mol. Biol. 402, 139-153. (2010). (pdf)
  • S. Tristram-Nagle, D. J. Kim, N. Akhunzada, N. Kucerka, J. C. Mathai, J. Katsaras, M. Zeidel, and J. F. Nagle.  Structure and water permeability of fully hydrated diphytanoylPC.  Chem. Phys. Lipids 163, 630-637 (2010). (pdf)
  • John F. Nagle, X-ray scattering reveals molecular tilt is an order parameter for the main phase transition in a model biomembrane.   Phys. Rev. E 96, 030401 (2017).    (pdf)
  • J. F. Nagle. In Defense of Gibbs and the Traditional Definition of the Entropy of Distinguishable Particles.   Entropy 12, 1936-1945 (2010).     (pdf)
  • N. Kucerka, J. Katsaras, and J. F. Nagle, Comparing Membrane Simulations to Scattering Experiments: Introducing the SIMtoEXP Software.   J. Membrane Biol.  235, 43-50 (2010). (pdf)
  • J.  Pan, S. Tristram-Nagle, and J. F. Nagle, Effect of cholesterol on structural and mechanical properties of membranes depends on lipid chain saturation.  Phys. Rev. E.  80, 021931(1-12) (2009). (pdf)  
  • J. Pan, S. Tristram-Nagle, and J. F. Nagle, Alamethicin aggregation in lipid membranes.  J. Membrane Biol.  231, 11-27 (2009)  (pdf)
  • Jianjun Pan, PhD Thesis 2009.  Supramolecular Organization of the Antimicrobial Peptide Alamethicin in Fluid Membranes.  (pdf)
  • S.  D. Guler, D. D. Ghosh, J. Pan, J. C. Mathai, M. L. Zeidel, J. F. Nagle and S. Tristram-Nagle, Effects of Ether Linkage on Lipid Bilayer Structure and Water Permeability.  Chem. Phys. Lipids 160, 33-44 (2009). (pdf)  
  • J.  Pan, D. P. Tieleman, J. F. Nagle, N. Kucerka, and S. Tristram-Nagle, Alamethicin in Lipid Bilayers: Combined Use of X-ray Scattering and MD Simulations.  Biochim. Biophys. Acta 1788, 1387-1397 (2009). (pdf)   SI (MSword)
  • T.  T. Mills, J. Huang, G. W. Feigenson, and J. F. Nagle, Effects of Cholesterol and Unsaturated DOPC Lipid on Chain Packing of Saturated Gel-Phase DPPC Bilayers.  Gen. Physiol. Biophys.  28, 126-139 (2009). (pdf)   
  • J. Pan, T. T. Mills. Tristram-Nagle and J. F. Nagle, Cholesterol Perturbs Lipid Bilayers Nonuniversally. Phys. Rev. Letts. 100, 198103 (2008). (pdf)  
  • T. T. Mills, G. E. S. Toombes, S. Tristram-Nagle, D.-M. Smielgies, G. W. Feigenson and J. F. Nagle, Order Parameters and Areas in Fluid-Phase Oriented Lipid Membranes Using Wide Angle X-ray Scattering. Biophys. J. 95, 669-681 (2008). (pdf) (Sup-1) (Sup-2) (Sup-3) (Sup-4) (Sup-5) (Sup-6)   
  • T. T. Mills, S. Tristram-Nagle, F. A. Heberle, N. F. Morales, J. Zhao, J. W u, G. E. S. Toombes, J. F. Nagle and G. W. Feigenson, Liquid-Liquid Domains in Bilayers Detected by Wide Angle X-ray Scattering. Biophys. J. 95, 682-690 (2008). (pdf) (Sup-1) (Sup-2) (Sup-3)   
  • N. Kucerka, J. F. Nagle, J. N. Sachs, S. E. Feller, J. Pencer, A. Jackson and J. Katsaras, Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering Data. Biophys. J. 95, 2356-2367 (2008). (pdf) (Suppl)    
  • A. I. Greenwood, J. Pan, T. T. Mills, J. F. Nagle, R. M. Epand, S. Tristram-Nagle, CRAC motif peptide of the HIV-1 gp41 protein thins SOPC membranes and interacts with cholesterol. Biochim. Biophys. Acta 1778, 1120-1130 (2008). (pdf)   
  • J.F. Nagle, J.C. Mathai, M.L.Zeidel and S. Tristram-Nagle, Theory of Passive Permeability through Lipid Bilayers. J. Gen. Physiol. 131, 77-85 (2008). (pdf) (Suppl)    
  • J.C. Mathai, S. Tristram-Nagle, J.F. Nagle and M. L.Zeidel, Structural Determinants of Water Permeability through the Lipid Membrane. J. Gen. Physiol. 131, 69-76 (2008). (pdf)  
  • J. Pan, S. Tristram-Nagle and J. F. Nagle, Temperature Dependence of Structure, Bending Rigidity and Bilayer Interations of DOPC Bilayers. Biophys. J. 94, 117-124 (2008). (pdf)   
  • Stephanie Tristram-Nagle and John F. Nagle, HIV-1 Fusion Peptide Decreases Bending Energy, Promotes Curved Fusion Intermediates. Biophys. J. 93, 2048-2055 (2007). (pdf)   
  • Norbert Kucerka, J. Pencer, J.N. Sachs, J, F. Nagle and J. Katsaras, Curvature Effect on the Structure of Phospholipid Bilayers. Langmuir 23, 1292-99 (2007). (online) or(pdf)   
  • Stephanie Tristram-Nagle, Preparation of Oriented, Fully Hydrated Lipid Samples for Structure Determination Using X-Ray Scattering. in Molecular Biology 400:(Methods in Membrane Lipids):63-75 (2007) (ed. E.Dopico), Humana Press, Totowa, NJ. (pdf)   
  • Norbert Kucerka, Stephanie Tristram-Nagle and John F. Nagle, Closer Look at Structure of Fully Hydrated Fluid Phase DPPC Bilayers. Biophysical Journal: Biophysical Letters 90, L83-85 (2006). (pdf)
  • A. I. Greenwood, S. Tristram-Nagle and J. F. Nagle, Partial Molecular Volumes of Lipids and Cholesterol. Chem. Phys. Lipids 143, 1-10 (2006). (pdf)  
  • J. B. Klauda, N. Kucerka, B. R. Brooks, R. W. Pastor, and John F. Nagle, Simulation-based Methods for Interpreting X-ray Data from Lipid Bilayers. Biophys. J. 90, 2796-2807 (2006). (pdf)  
  • H. I. Petrache, S. Tristram-Nagle, D. Harries, N. Kucerka, J. F. Nagle, and V.A. Parsegian, Swelling of Phospholipids by Monovalent Salt. J. Lipid Res. 47, 302-309 (2006). (pdf)    
  • R. H. Lozier and J. F. Nagle Comment on "An apparent general solution for the kinetic models of the bacteriorhodopsin photocycles". J. Phys. Chem B 110, 15041-15042 (2006). (pdf) and (supplementary material-pdf)    
  • Norbert Kucerka, Stephanie Tristram-Nagle and John F. Nagle, Structure of Fully Hydrated Fluid Phase Lipid Bilayers with Monounsaturated Chains. J. Membrane Biol. 208, 193-202 (2005). (online) or (pdf)   
  • Best structure yet! Norbert Kucerka, Yufeng Liu, Nanjun Chu, Horia I. Petrache, Stephanie Tristram-Nagle and John F. Nagle, Structure of Fully Hydrated Fluid Phase DMPC and DLPC Bilayers Using X-ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles. Biophys. J. 88, 2626-2637 (2005). (pdf)   
  • New results that resolve an old and contentious issue. Nanjun Chu, Norbert Kucerka, Yufeng Liu, Stephanie Tristram-Nagle and John F. Nagle, Anomalous Swelling of Lipid Bilayer Stacks Is Caused by Softening of the Bending Modulus Phys Rev E. 71, 041904 (2005). (pdf)  
  • Olle Edholm and John F. Nagle, Areas of Molecules in Membranes Consisting of Mixtures. Biophys. J. 89, 1827-1832 (2005). (pdf)  
  • S. Tristram-Nagle, R.N.A.H. Lewis, J.W. Blickenstaff, M. DiPrima, B.F. Marques, R.N. McElhaney, J.F. Nagle and J.W. Schneider. Thermodynamic and structural characterization of amino acid-linked dialkyl lipids. Chem. Phys. Lipids 134, 29-39 (2005). (pdf)   
  • A letter about our breakthrough: Yufeng Liu and John F. Nagle, Diffuse Scattering Provides Material Parameters and Electron Density Profiles of Biomembranes. Phys Rev E (Rapid Communications) 69, 040901(R)(2004). (pdf)  
  • Yufeng Liu's thesis that gives the details behind the previous letter: New Method to Obtain Structure of Biomembranes Using Diffuse X-ray Scattering: Application to Fluid Phase DOPC Lipid Bilayers. (pdf)   
  • Norbert Kucerka, John F Nagle, Scott E Feller and Pavol Balgavy, Models to analyze small angle neutron scattering from unilamellar lipid vesicles. Phys Rev E 69, 051903 (2004). (pdf)  
  • A write-up of the presentation for the Avanti Award given by the Biophysical Society. Stephanie Tristram-Nagle and John F. Nagle, Lipid Bilayers: Thermodynamics, Structure, Fluctuations and Interactions. Invited manuscript for Chem. Phys. Lipids 127, 3-14 (2004). (pdf)  
  • Horia I. Petrache, Stephanie Tristram-Nagle, Klaus Gawrisch, Daniel Harries, V. Adrian Parsegian and John F. Nagle, Structure and Fluctuations of Charged Phosphatidylserine Bilayers in the Absence of Salt. Biophys. J. 86, 1574-86 (2004). (pdf)   
  • John F. Nagle, Regarding the Entropy of Distinguishable Particles. J. Stat. Phys. 117, 1047-1062 (2004). (pdf)  
  • N. V. Eldho, S. E. Feller, S. Tristram-Nagle, I. V. Polozov and K. Gawrisch, Polyunsaturated Docosahexaenoic vs Docosapentaenoic Acid-Differences in Lipid Matrix Properties from the Loss of One Double Bond, J. Am. Chem. Soc. 125, 6409-6421 (2003). (pdf)   
  • S. Tristram-Nagle, Y. Liu, J. Legleiter and John F. Nagle, Structure of Gel Phase DMPC Determined by X-ray Diffraction, Biophys. J. (2002) 83:3324-35. (pdf)  
  • Y. Lyatskaya, Y. Liu, S. Tristram-Nagle, J. Katsaras and John F. Nagle, Method for Obtaining Structure and Interactions from Oriented Lipid Bilayers, Phys. Rev. E 63, 011907[1-9] (2001). (pdf)   
  • P. C. Mason, J. F. Nagle, R. M. Epand and J. Katsaras, Anomalous Swelling in Phospholipid Bilayers Is Not Coupled to the Formation of a Ripple Phase, Phys. Rev. E 63, 030902 (2001) (pdf)   
  • A formal review of earlier lipid bilayer research by John F. Nagle and Stephanie Tristram-Nagle, Structure of Lipid Bilayers, Biochim. Biophys. Acta 1469 (2000) 159-195. (pdf)   
  • A briefer review of recent literature on bilayer structure by John F. Nagle and Stephanie Tristram-Nagle, Lipid Bilayer Structure is published in Current Opinions in Structural Biology (2000), 10:474-480.   
  • J. Katsaras, S. Tristram-Nagle, Y. Liu, R. L. Headrick, E. Fontes, P. C. Mason and John F. Nagle, Clarification of the Ripple Phase of Lecithin Bilayers Using Fully Hydrated, Aligned Samples, Phys. Rev. E61, 5668-5677 (2000). (pdf)  
  • A more informal review of much of this group's research: John F. Nagle and Stephanie Tristram-Nagle, Structure and Interactions of Lipid Bilayers: Role of Fluctuations. (PostScript)   
  • J. F. Nagle, Y. Liu, S. Tristram-Nagle, R. M. Epand and Ruth E. Stark, Re-analysis of Magic Angle Spinning NMR Determination of Interlamellar Waters, Biophys. J. 77, 2062-65 (1999) (pdf)   
  • S. Tristram-Nagle, Y. Isaacson, Y. Lyatskaya, Y. Liu, K. Brummond, John Katsaras and John F. Nagle, Polymorphism in MPPC, Chem. Phys. Lipids 100, 101-13 (1999). (pdf)  
  • John F. Nagle and John Kataras, Absence of a Vestigial Vapor Pressure Paradox, Phys. Rev. E, 59, 7018-24 (1999). (pdf)   
  • Horia I. Petrache, Kechuan Tu and John F. Nagle, Analysis of Simulated NMR Order Parameters for Lipid Bilayer Structure Determination, Biophys. J. 76, 2479-87 (1999). (pdf)  
  • John F. Nagle, Horia I. Petrache, N. Gouliaev, S. Tristram-Nagle, Y. Liu, R. M. Suter and K. Gawrisch, Multiple Mechanisms for Critical Behavior in the Biologically Relevant Phase of Lecithin Bilayers, Phys. Rev. E. 58, 7769-7776 (1998). (pdf)  
  • Horia I. Petrache, S. Tristram-Nagle and John F. Nagle, Fluid Phase Structure of EPC and DMPC Bilayers, Chem. Phys. Lipids 95, 83-94 (1998). (pdf)   
  • Nikolai Gouliaev and John F. Nagle, Simulations of Interacting Membranes, Phys. Rev. Letts. 81, 2610 (1998) (pdf)  
  • Stephanie Tristram-Nagle, Horia I. Petrache and John F. Nagle, Structure and Interactions of Fully Hydrated DOPC Bilayers. Biophys. J. 75, 917-928 (1998). (pdf)   
  • Nikolai Gouliaev and John F. Nagle, Simulations of a Single Membrane Between Two Walls Using a New Monte-Carlo Method, Phys. Rev. E 58, 881-888 (1998). (PostScript) (pdf)         
  • Horia I. Petrache, Nikolai Gouliaev, Stephanie Tristram-Nagle, Ruitian Zhang, Robert M. Suter and John F. Nagle, Interbilayer Interactions from High-Resolution X-Ray Scattering, Phys. Rev. E 57, 7014-24 (1998). (pdf)   
  • John F. Nagle, S. Tristram-Nagle, H. Takahashi and I. Hatta, Comment on DPPC Subgel Phase Formation Process, Euro. Phys. J. B1, 399-400 (1998). pdf    
  • Stephanie Tristram-Nagle, Horia I. Petrache, Robert M. Suter, and John F. Nagle, Effect of Substrate Roughness on D Spacing Supports Theoretical Resolution of Vapor Pressure Paradox. Biophys. J. 74, 1421-1427 (1998). (pdf)  
  • Stephanie Tristram-Nagle, Tisha Moore, Horia I. Petrache and John F. Nagle, DMSO Produces a New Subgel Phase in DPPC: DSC and X-Ray Diffraction Study, BBA 1369, 19-33 (1998). (pdf)  
  • For an older informal review of much of this group's research, see John F. Nagle, Critical Role of Fluctuations in Lipid Bilayers, In "Phase Transitions in Complex Fluids" (World Scientific, 1998) Eds. P. Toledano and A.M.F. Neto, pp. 247-269. (PostScript)  
  • Horia I. Petrache, Scott E. Feller and John F. Nagle, Determination of Component Volumes of Lipid Bilayers from Simulations, Biophys. J. 72, 2237-2242 (1997). (pdf)   

Earlier Publications are listed in a (pdf) file.