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Atomistic computer simulations of lipid bilayers
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.ORCID iD: 0000-0001-6732-2571
2006 (English)Doctoral thesis, comprehensive summary (Other scientific)
Abstract [en]

Computer simulation has become an important tool for the study of biomolecular systems. This thesis deals with molecular dynamics simulations of one-component lipid bilayers, which may serve as models for biological membranes.

The main scientific contributions are:

• It is possible to analyze the electrostatic contribution to the surface tension at a lipid-water interface in terms of dipole-dipole interactions between lipid headgroup shielded by a dielectric medium (water). The interaction can be divided into two parts. The in-plane components of the dipoles give rise to a positive, i.e. contractive

contribution to the surface tension, albeit rather short ranged due to them being fluctuating dipoles. The normal components give rise to a negative, i.e. expansive contribution that will dominate the interaction at large distances.

• Simulated membrane areas are extremely sensitive to details, especially the treatment of long-range electrostatic interactions. When cut-offs are used for the electrostatics, the exact definition of charge groups play an important role. Furthermore, using Ewald summation for the long-range interactions seems to have an overall stabilizing effect, and the area becomes less sensitive to other factors, such as system size and hydration.

• Using atomistic simulations it is possible to study formation and evolution of a hydrophilic trans-membrane pore in detail. Free energy of pore nucleation and expansion can be calculated using potentials of mean constraint force. The resulting free energy profile shows no local maximum between the intact and pre-pore states, contrary to what is suggested by experiments.

• The present force field reproduces even the slowest dynamics in the lipid chains, as reflected in NMR relaxation rates. Furthermore, since the simulated system was relatively small, the experimentally observed variation of relaxation rates with Larmor frequency cannot be explained by large scale collective dynamics, or it would not have shown up in the simulation.

• Lipid lateral diffusion can be studied in detail on all relevant time scales by molecular dynamics. Using simple assumptions, the different diffusion coefficients measured on short and long times respectively can be connected in an analytic expression that fit calculated mean square displacements on timescales ranging from picoseconds to hundreds of nanoseconds.

Place, publisher, year, edition, pages
Stockholm: KTH , 2006. , vi, 61 p.
Series
Trita-FYS, ISSN 0280-316X ; 2006:82
National Category
Physical Sciences
Identifiers
URN: urn:nbn:se:kth:diva-4264ISBN: 978-91-7178-551-0 (print)OAI: oai:DiVA.org:kth-4264DiVA: diva2:11523
Public defence
2007-01-17, FA 32, AlbaNova, Roslagstullsbacken 21, Stockholm, 10:15
Opponent
Supervisors
Note
QC 20100927Available from: 2007-01-10 Created: 2007-01-10 Last updated: 2011-12-08Bibliographically approved
List of papers
1. The Range and Shielding of Dipole-Dipole Interactions in Phospholipid Bilay
Open this publication in new window or tab >>The Range and Shielding of Dipole-Dipole Interactions in Phospholipid Bilay
2004 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 87, 2433- p.Article in journal (Refereed) Published
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-6728 (URN)
Note
QC 20100927Available from: 2007-01-10 Created: 2007-01-10 Last updated: 2010-09-27Bibliographically approved
2. Free energy of a trans-membrane pore calculated from atomistic molecular dynamics simulations
Open this publication in new window or tab >>Free energy of a trans-membrane pore calculated from atomistic molecular dynamics simulations
2006 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 124, 154905- p.Article in journal (Refereed) Published
Abstract [en]

Atomistic molecular dynamics simulations of a lipid bilayer were performed to calculate the free energy of a trans-membrane pore as a function of its radius. The free energy was calculated as a function of a reaction coordinate using a potential of mean constraint force. The pore radius was then calculated from the reaction coordinate using Monte Carlo particle insertions. The main characteristics of the free energy that comes out of the simulations are a quadratic shape for a radius less than about 0.3 nm, a linear shape for larger radii than this, and a rather abrupt change without local minima or maxima between the two regions. In the outer region, a line tension can be calculated, which is consistent with the experimentally measured values. Further, this line tension can be rationalized and understood in terms of the energetic cost for deforming a part of the lipid bilayer into a hydrophilic pore. The region with small radii can be described and understood in terms of statistical mechanics of density fluctuations. In the region of crossover between a quadratic and linear free energy there was some hysteresis associated with filling and evacuation of the pore with water. The metastable prepore state hypothesized to interpret the experiments was not observed in this region.

Keyword
lipid-bilayers, reaction coordinate, stabilized pores, surface-tension, fluid bilayer, line tension, constraints, vesicles, electroporation, biomembranes
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-6729 (URN)10.1063/1.2171965 (DOI)000236969500053 ()2-s2.0-34547649222 (Scopus ID)
Note
QC 20100927Available from: 2007-01-10 Created: 2007-01-10 Last updated: 2010-09-27Bibliographically approved
3. Dynamics in atomistic simulations of phospholipid membranes: Nuclear magnetic resonance relaxation rates and lateral diffusion
Open this publication in new window or tab >>Dynamics in atomistic simulations of phospholipid membranes: Nuclear magnetic resonance relaxation rates and lateral diffusion
2006 (English)In: Journal of chemical physics, ISSN 0021-9606, Vol. 125, 204703- p.Article in journal (Refereed) Published
Abstract [en]

It is shown that a long, near microsecond, atomistic simulation can shed some light upon the dynamical processes occurring in a lipid bilayer. The analysis focuses on reorientational dynamics of the chains and lateral diffusion of lipids. It is shown that the reorientational correlation functions exhibits an algebraic decay (rather than exponential) for several orders of magnitude in time. The calculated nuclear magnetic resonance relaxation rates agree with experiments for carbons at the C7 position while there are some differences for C3. Lateral diffusion can be divided into two stages. In a first stage occurring at short times, t < 5 ns, the center of mass of the lipid moves due to conformational changes of the chains while the headgroup position remains relatively fixed. In this stage, the center of mass can move up to similar to 0.8 nm. The fitted short-time diffusion coefficient is D-1=13x10(-7) cm(2) s(-1) On a longer time scale, the diffusion coefficient becomes D-2=0.79x10(-7) cm(2) s(-1).

Keyword
elastic neutron-scattering, particle mesh ewald, molecular-dynamics, lipid-bilayers, nmr relaxation, h-2, distributions, spectroscopy, temperature, length
National Category
Physical Sciences
Identifiers
urn:nbn:se:kth:diva-6730 (URN)10.1063/1.2393240 (DOI)000242408100040 ()2-s2.0-33751556346 (Scopus ID)
Note
QC 20100927Available from: 2007-01-10 Created: 2007-01-10 Last updated: 2010-09-27Bibliographically approved

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