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Publications (10 of 41) Show all publications
Tjörnhammar, R. & Edholm, O. (2014). Atomistic Simulations of Gel and Liquid Crystalline Lipid Bilayers. Paper presented at 58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA. Biophysical Journal, 106(2), 403A-403A
Open this publication in new window or tab >>Atomistic Simulations of Gel and Liquid Crystalline Lipid Bilayers
2014 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 403A-403AArticle in journal, Meeting abstract (Other academic) Published
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-147970 (URN)000337000402268 ()
Conference
58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA
Note

QC 20140710

Available from: 2014-07-10 Created: 2014-07-10 Last updated: 2017-12-05Bibliographically approved
Tjörnhammar, R. & Edholm, O. (2014). Reparameterized united atom model for molecular dynamics simulations of gel and fluid phosphatidylcholine bilayers. Journal of Chemical Theory and Computation, 10(12), 5706-5715
Open this publication in new window or tab >>Reparameterized united atom model for molecular dynamics simulations of gel and fluid phosphatidylcholine bilayers
2014 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 12, p. 5706-5715Article in journal (Refereed) Published
Abstract [en]

A new united atom parametrization of diacyl lipids like dipalmitoylphosphatidylcholine (DPPC) and the dimyristoylphosphatidylcholine (DMPC) has been constructed based on ab initio calculations to obtain fractional charges and the dihedral potential of the hydrocarbon chains, while the Lennard-Jones parameters of the acyl chains were fitted to reproduce the properties of liquid hydrocarbons. The results have been validated against published experimental X-ray and neutron scattering data for fluid and gel phase DPPC. The derived charges of the lipid phosphatidylcholine (PC) headgroup are shown to yield dipole components in the range suggested by experiments. The aim has been to construct a new force field that retains and improves the good agreement for the fluid phase and at the same time produces a gel phase at low temperatures, with properties coherent with experimental findings. The gel phase of diacyl-PC lipids forms a regular triangular lattice in the hydrocarbon region. The global bilayer tilt obtains an azimuthal value of 31 degrees and is aligned between lattice vectors in the bilayer plane. We also show that the model yields a correct heat of melting as well as decent heat capacities in the fluid and gel phase of DPPC.

National Category
Physical Sciences
Research subject
Biological Physics
Identifiers
urn:nbn:se:kth:diva-151393 (URN)10.1021/ct500589z (DOI)000346324000052 ()2-s2.0-84916613010 (Scopus ID)
Funder
Swedish Research Council
Note

QC 20150220. Updates from submitted to published. Previous title "A Re-parameterized United Atom Model for Molecular Dynamics Simulations of Gel and Fluid Phosphatidylcholine Bilayers".

Available from: 2014-09-19 Created: 2014-09-19 Last updated: 2017-12-05Bibliographically approved
Edholm, O., Tjörnhammar, R. & Waheed, Q. (2013). Cholesterol/Phospholipid Bilayer Phase Diagrams from Coarse Grained Simulations. Paper presented at 57th Annual Meeting of the Biophysical-Society, FEB 02-06, 2013, Philadelphia, PA. Biophysical Journal, 104(2), 590A-590A
Open this publication in new window or tab >>Cholesterol/Phospholipid Bilayer Phase Diagrams from Coarse Grained Simulations
2013 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, no 2, p. 590A-590AArticle in journal, Meeting abstract (Other academic) Published
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-121493 (URN)000316074305525 ()
Conference
57th Annual Meeting of the Biophysical-Society, FEB 02-06, 2013, Philadelphia, PA
Note

QC 20130506

Available from: 2013-05-06 Created: 2013-04-29 Last updated: 2017-12-06Bibliographically approved
Tjörnhammar, R. & Edholm, O. (2013). The shape and free energy of a lipid bilayer surrounding a membrane inclusion. Chemistry and Physics of Lipids, 169, 2-8
Open this publication in new window or tab >>The shape and free energy of a lipid bilayer surrounding a membrane inclusion
2013 (English)In: Chemistry and Physics of Lipids, ISSN 0009-3084, E-ISSN 1873-2941, Vol. 169, p. 2-8Article in journal (Refereed) Published
Abstract [en]

Membrane inclusion interactions are studied within the scope of continuum theory. We show that the free energy functional for the membrane thickness can be rewritten as a constant times a dimensionless integral. For cylindrical inclusions, the resulting differential equation gives a thickness profile that depends on the radius of the cylinder and one single lipid property, a correlation length that is determined by the ratio of the thickness compressibility and bending moduli. The solutions decay in a non-monotonic fashion with one single observable minimum. A solution for planar geometry may either be explicitly constructed or obtained by letting the radius of the cylinder go to infinity. In dimensionless units the initial derivative of the thickness profile is universal and equal to -1/root 2 In physical units, the derivative depends on the size of the hydrophobic mismatch as well as the membrane correlation length and will usually be fairly small but clearly non-zero. The line tension between the protein inclusion and a fluid phase membrane will depend on the hydrophobic mismatch and be of the order of 10 pN (larger for the gel phase). This results in free energy costs for the inclusion that will be up to tens of kJ/mol (in the fluid phase).

Keywords
Membrane protein interactions, Continuum theory, Line tension, Kelvin functions, Coarse graining, Molecular dynamics
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-124470 (URN)10.1016/j.chemphyslip.2012.12.005 (DOI)000319310800002 ()2-s2.0-84876420080 (Scopus ID)
Note

QC 20130708

Available from: 2013-07-08 Created: 2013-07-05 Last updated: 2017-12-06Bibliographically approved
Waheed, Q., Tjörnhammar, R. & Edholm, O. (2012). Phase Transitions in Coarse-Grained Lipid Bilayers Containing Cholesterol by Molecular Dynamics Simulations. Biophysical Journal, 103(10), 2125-2133
Open this publication in new window or tab >>Phase Transitions in Coarse-Grained Lipid Bilayers Containing Cholesterol by Molecular Dynamics Simulations
2012 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 103, no 10, p. 2125-2133Article in journal (Refereed) Published
Abstract [en]

Coarse-grained simulations of model membranes containing mixtures of phospholipid and cholesterol molecules at different concentrations and temperatures have been performed. A random mixing without tendencies for segregation or formation of domains was observed on spatial scales corresponding to a few thousand lipids and timescales up to several micro-seconds. The gel-to-liquid crystalline phase transition is successively weakened with increasing amounts of cholesterol without disappearing completely even at a concentration of cholesterol as high as 60%. The phase transition temperature increases slightly depending on the cholesterol concentration. The gel phase system undergoes a transition with increasing amounts of cholesterol from a solid-ordered phase into a liquid-ordered one. In the solid phase, the amplitude of the oscillations in the radial distribution function decays algebraically with a prefactor that goes to zero at the solid-liquid transition.

Keywords
particle mesh ewald, liquid water, model, tip4p/2005, spectra, range
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-102277 (URN)10.1016/j.bpj.2012.10.014 (DOI)000311419000011 ()2-s2.0-84869465857 (Scopus ID)
Funder
Swedish Research CouncilSwedish e‐Science Research Center
Note

QC 20130107. Updated from accepted to published.

Available from: 2012-09-12 Created: 2012-09-12 Last updated: 2017-12-07Bibliographically approved
Braun, A. R., Brandt, E., Edholm, O., Nagle, J. F. & Sachs, J. N. (2011). Determination of electron density pro les and area-per-lipid from molecular dynamics simulations of large undulating lipid bilayers. Abstract of Papers of the American Chemical Society, 241
Open this publication in new window or tab >>Determination of electron density pro les and area-per-lipid from molecular dynamics simulations of large undulating lipid bilayers
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2011 (English)In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 241Article in journal (Other academic) Published
National Category
Chemical Sciences
Identifiers
urn:nbn:se:kth:diva-36895 (URN)000291982803542 ()
Funder
Swedish e‐Science Research Center
Note
QC 20110720Available from: 2011-07-20 Created: 2011-07-18 Last updated: 2017-12-08Bibliographically approved
Braun, A. R., Brandt, E. G., Edholm, O., Nagle, J. F. & Sachs, J. N. (2011). Determination of Electron Density Profiles and Area from Simulations of Undulating Membranes. Biophysical Journal, 100(9), 2112-2120
Open this publication in new window or tab >>Determination of Electron Density Profiles and Area from Simulations of Undulating Membranes
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2011 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 100, no 9, p. 2112-2120Article in journal (Refereed) Published
Abstract [en]

The traditional method for extracting electron density and other transmembrane profiles from molecular dynamics simulations of lipid bilayers fails for large bilayer systems, because it assumes a flat reference surface that does not take into account long wavelength undulations. We have developed what we believe to be a novel set of methods to characterize these undulations and extract the underlying profiles in the large systems. Our approach first obtains an undulation reference surface for each frame in the simulation and subsequently isolates the long-wavelength undulations by filtering out the intrinsic short wavelength modes. We then describe two methods to obtain the appropriate profiles from the undulating reference surface. Most combinations of methods give similar results for the electron density profiles of our simulations of 1024 DMPC lipids. From simulations of smaller systems, we also characterize the finite size effect related to the boundary conditions of the simulation box. In addition, we have developed a set of methods that use the undulation reference surface to determine the true area per lipid which, due to undulations, is larger than the projected area commonly reported from simulations.

Keywords
MOLECULAR-DYNAMICS SIMULATIONS; X-RAY-SCATTERING; LIPID-BILAYERS; PHASE DMPC; COMPRESSIBILITY; FLUCTUATIONS
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-33983 (URN)10.1016/j.bpj.2011.03.009 (DOI)000290360000007 ()2-s2.0-79959770281 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note
QC 20110527Available from: 2011-05-27 Created: 2011-05-23 Last updated: 2017-12-11Bibliographically approved
Brandt, E. G., Braun, A. R., Sachs, J. N., Nagle, J. F. & Edholm, O. (2011). Interpretation of Fluctuation Spectra in Lipid Bilayer Simulations. Biophysical Journal, 100(9), 2104-2111
Open this publication in new window or tab >>Interpretation of Fluctuation Spectra in Lipid Bilayer Simulations
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2011 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 100, no 9, p. 2104-2111Article in journal (Refereed) Published
Abstract [en]

Atomic resolution and coarse-grained simulations of dimyristoylphosphatidylcholine lipid bilayers were analyzed for fluctuations perpendicular to the bilayer using a completely Fourier-based method. We find that the fluctuation spectrum of motions perpendicular to the bilayer can be decomposed into just two parts: 1), a pure undulation spectrum proportional to q(-4) that dominates in the small-q regime; and 2), a molecular density structure factor contribution that dominates in the large-q regime. There is no need for a term proportional to q(-2) that has been postulated for protrusion fluctuations and that appeared to have been necessary to fit the spectrum for intermediate q. We suggest that earlier reports of such a term were due to the artifact of binning and smoothing in real space before obtaining the Fourier spectrum. The observability of an intermediate protrusion regime from the fluctuation spectrum is discussed based on measured and calculated material constants.

Keywords
MOLECULAR-DYNAMICS SIMULATIONS; ENTROPY-DRIVEN TENSION; COARSE-GRAINED MODEL; PARTICLE MESH EWALD; THERMAL FLUCTUATIONS; BENDING ELASTICITY; CONSTANT-PRESSURE; MEMBRANES; HYDRATION; SCATTERING
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-33982 (URN)10.1016/j.bpj.2011.03.010 (DOI)000290360000006 ()2-s2.0-79959741351 (Scopus ID)
Funder
Swedish e‐Science Research Center
Note
QC 20110530Available from: 2011-05-30 Created: 2011-05-23 Last updated: 2017-12-11Bibliographically approved
Waheed, Q. & Edholm, O. (2011). Quantum Corrections to Classical Molecular Dynamics Simulations of Water and Ice. Journal of Chemical Theory and Computation, 7(9), 2903-2909
Open this publication in new window or tab >>Quantum Corrections to Classical Molecular Dynamics Simulations of Water and Ice
2011 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 9, p. 2903-2909Article in journal (Refereed) Published
Abstract [en]

Classical simulations of simple water models reproduce many properties of the liquid and ice but overestimate the heat capacity by about 65% at ordinary temperatures and much more for low temperature ice. This is due to the fact that the atomic vibrations are quantum mechanical. The application of harmonic quantum corrections to the molecular motion results in good heat capacities for the liquid and for ice at low temperatures but a successively growing positive deviation from experimental results for ice above 200 K that reaches 15% just below melting. We suggest that this deviation is due to the lack of quantum corrections to the anharmonic motions. For the liquid, the anharmonicities are even larger but also softer and thus in less need of quantum correction. Therefore, harmonic quantum corrections to the classically calculated liquid heat capacities result in agreement with the experimental values. The classical model underestimates the heat of melting by 15%, while the application of quantum corrections produces fair agreement. On the other hand, the heat of vaporization is overestimated by 10% in the harmonically corrected classical model.

Keywords
particle mesh ewald, liquid water, model, tip4p/2005, spectra, range
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-41790 (URN)10.1021/ct2003034 (DOI)000294790400026 ()2-s2.0-80052786849 (Scopus ID)
Funder
Swedish Research CouncilSwedish e‐Science Research Center
Note
QC 20111003Available from: 2011-10-03 Created: 2011-10-03 Last updated: 2017-12-08Bibliographically approved
Waheed, Q. & Edholm, O. (2010). Material Properties of Lipid Membranes from Molecular Dynamics Simulations. Biophysical Journal, 98(3), 490A-490A
Open this publication in new window or tab >>Material Properties of Lipid Membranes from Molecular Dynamics Simulations
2010 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 98, no 3, p. 490A-490AArticle in journal, Meeting abstract (Other academic) Published
National Category
Biophysics
Identifiers
urn:nbn:se:kth:diva-152134 (URN)000208762004467 ()
Note

QC 20140924

Available from: 2014-09-24 Created: 2014-09-23 Last updated: 2017-12-05Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-7448-4664

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