Publications

Journal articles 2004-

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).

A. R. Braun, E. G. Brandt, O. Edholm, J. F. Nagle and J. N. Sachs
Determination of Electron Density Profiles and Area from Simulations of Undulating Membranes.
Biophys. J. 100:2112-2120 (2011).

E. G. Brandt and O. Edholm
Stretched exponential dynamics in lipid bilayer simulations.
J. Chem. Phys. 133:115101 (2010).

R. Tjörnhammar and O. Edholm
Molecular dynamics simulations of Zn2+ coordination in protein binding sites.
J. Chem. Phys. 132:205101 (2010).

Q. Waheed and O. Edholm
Undulation Contributions to the Area Compressibility in Lipid Bilayer Simulations.
Biophys. J. 97:2754-2760 (2009).

E. G. Brandt and O. Edholm
Dynamic structure factors from lipid membrane molecular dynamics simulations.
Biophys. J. 96:1828-1838 (2009).

A. Cordomi, O. Edholm and J. J. Perez
Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers.
J. Chem. Theory and Comp. 5:2125-2134 (2009).

E. G. Brandt, M. Hellgren, T. Brinck, T. Bergman and O. Edholm
Molecular dynamics study of zinc binding to cysteins in a peptide mimic of the alcohol dehydrogenase structural zinc site.
Phys. Chem. Chem. Phys. 11:975-983 (2009).

Arnau Cordomi, Olle Edholm and Juan J. Perez
The effect of ions on a dipalmitoyl phosphatidylcholine bilayer. A molecular dynamics study.
J. Phys. Chem. B. 112:1397-1408 (2008).

Arnau Cordomi, Olle Edholm and Juan J. Perez
Molecular dynamics simulations of rhodopsin embedded in a DPPC bilayer. The effect of different treatment of long-range interactions and sampling conditions.
J. Comp. Chem. 28:1017-1030 (2007).

C. Blomberg
Fluctuations for good and bad: The role of noise in living systems.
Physics of Life reviews 3:133-161 (2006).

P. Århem, G Klement and C. Blomberg
Channel density regulation of firing patterns in a cortical neuron model.
Biophys. J. 90:4392-4404 (2006).

Peter Århem and Clas Blomberg
Ion channel density and threshold dynamics of repetitive firing in a cortical neuron model
Biosystems in press (2006).

J. Wohlert and O. Edholm
Dynamics in atomistic simulations of phospholipid membranes: NMR relaxation rates and lateral diffusion
J. Chem. Phys. 125:204703 (2006).

M. Hellgren, L. Sandberg and O. Edholm
A Comparison between two prokaryotic potassium channels (KirBac1.1 and Kcsa) in a molecular dynamics simulation study
Biophysical Chemistry 120:1-9 (2006).

J. Wohlert, W.K. den Otter, O. Edholm and W.J Briels
Free energy of a trans-membrane pore calculated from atomistic molecular dynamics simulations
J. Chem. Phys. 124:154905 (2006).

O. Edholm and J.F. Nagle
Areas of molecules in membranes consisting of mixtures
Biophys. J. 89:1827-1832 (2005).

Jakob Wohlert, Olle Edholm
The Range and Shielding of Dipole-Dipole interactions in Phospholipid Bilayers
Biophys. J. 87:2433-2445 (2004)

Lehmann, J., Riedo, B., and Dietler, G.
Folding of small RNAs displaying the GNC base-pattern: implications for the self-organization of the genetic system.
J. Theor. Biol. 227, 381-395 (2004)

Conference proceedings, book chapters, etc.

Olle Edholm
Time and length Scales in Lipid Bilayer Simulations
In Current topics in Membranes, Volume 60:91-110, Elsevier 2008

Olle Edholm
Dynamics of lipid bilayers from molecular dynamics simulations.
Biophys. J. 88, (2005)

Olle Edholm
Simulations of lipid bilayers on mesoscopic scales: Issues, answers and challenges.
Biophys. J. 88, (2005)

Jakob Wohlert, Olle Edholm
Electrostatic dipole interactions in phopholipid bilayers
International Conference on Biological Physics ICBP 2004 and
Simu2004 - Bridging the Scales ( PDF )

Lehmann, J.
Genetic Code.
Essay to be published in Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine, Springer-Verlag.
Detlev Ganten and Klaus Ruckpaul, Eds.
http://encref.springer.de/genomics/

Theses

Erik Brandt
Molecular Dynamics Simulations of Fluid Lipid Membranes
Doctoral Thesis, 2011
TRITA-FYS-2011:48 * ISSN 0280-316X * ISRN KTH/FYS/--11:48--SE

Erik Brandt
Interactions and dynamics in biophysical model systems
Licenciate Thesis, 2009
TRITA-FYS-2009:18 * ISSN 0280-316X * ISRN KTH/FYS/--09:18--SE

Jakob Wohlert
Atomistic computer simulations of lipid bilayers
Doctoral Thesis, 2006
TRITA-FYS-2006:82 * ISSN 0280-316X * ISRN KTH/FYS/--06:82--SE

Jakob Wohlert
Electrostatics in lipid membranes: a computer simulation study
Licentiate Thesis, 2004
TRITA-FYS-2004:35 * ISSN 0280-316X * ISRN KTH/FYS/--04:35--SE

Division staff 2000 - 2003 selected publications

2003

K. Åhman, E. Lindahl, O. Edholm, P. Håkansson  and P.O. Westlund
Structure and dynamics of interfacial water in an L-alpha phase lipid bilayer from  molecular dynamics simulations.
Biophys. J. 84(2003), 2192-2206.

C. Hofsäss, E. Lindahl and O. Edholm,
Molecular dynamics simulations of phospholipid bilayers with cholesterol,
Biophys. J. 84(2003), 2192-2206.

2002

L. Sandberg and O. Edholm,
Nonlinear response effect in continuum models of the hydration of ions,
J. Chem. Phys. 116(2002) 2936-2944.

L. Sandberg , R. Casemyr and O. Edholm,
Calculated hydration free energies of small organics molecules using a nonlinear dielectric continuum model,
J. Phys. Chem. B106(2002), 7889-7897. 

2001

C Blomberg, F. Elinder and P. Århem, (2001)
Na channel kinetics: developing models from non-stationary current fluctuations by analytic methods. Biosystems (2001)

P. Håkansson, P.O. Westlund, E. Lindahl and O. Edholm, (2001),
A direct simulation of EPR slow-motion spectra of spin labelled phospholipids in liquid crystalline bilayers based on a molecular dynamics simulation of the lipid dynamics,
Phys. Chem. Chem. Phys. 3(2001) 5311-5319.

E. Lindahl and O. Edholm, (2001),
Molecular dynamics simulations of NMR relaxation rates and slow dynamics in lipid bilayers,
J. of Chem. Phys. 115(2001) 4938-4950.

S.J. Marrink, E. Lindahl, O. Edholm and A. Mark, (2001),
Simulation of the apontanous aggregation of phospholipids into bilayers,
J. Am. Chem. Soc. 123(2001) 8638-8639.

L. Sandberg and O. Edholm, (2001),
Calculates solvation free energies of amino acids in a dipolar approximation
Journal of Physical Chemistry B, 105, 273-281.

C. Blomberg. (2000)
A primer on noise and chaos.
In: "Disorder versus Order in Brain Functioning - Essays in Theoretical Neurophysics", World Scientific Publ. Co.

C. Blomberg, H. Liljenström, and P. Århem. (2000)
Disorder versus Order in Brain Functioning - An Introduction
In: "Disorder versus Order in Brain Functioning - Essays in Theoretical Neurophysics", World Scientific Publ. Co.

O. Edholm and C. Blomberg, (2000),
Stretched exponentials and barrier distributions
Chemical Physics, 252, pp 221-225.

E. Lindahl and O. Edholm, (2000),
Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations
Biophysics Journal, 79, pp 426-433.

E. Lindahl and O. Edholm, (2000),
Spatial and energetic/entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations
Journal of Chemical Physics, 113, pp3882-3893.

L. Sandberg and O. Edholm, (2000),
A fast and simple method to calculate protonation states in proteins. A reply to Mehler and Warshel
Proteins, Structure, Function and Genetics, 40, pp 4-5.

O. Edholm, P. Nordlander, W. Chen, P.I. Ohlsson, M.L. Smith and J. Paul, (2000),
The effect of water on the Fe^3+/Fe^2+ reduction potential of hemeproteins
Biophysics and Biochemistry Research Commmunications, 268, pp 683-687.


Responsible for this page: Olle Edholm <oed@kth.se>