Carnegie Mellon: Departments of Physics and Biological Sciences
Membrane Biological
Physics Web Page
· 2014 Group
· 2009 Group
· 2008 Group
· Older Group Photo
· Summary of
Results for Fully Hydrated Bilayers (ppt file)
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Link to CMU/Biological Physics/Nagle,Tristram-Nagle WEBsite
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.