SwePub
Sök i SwePub databas

  Utökad sökning

Träfflista för sökning "AMNE:(NATURAL SCIENCES Biological Sciences Biophysics) ;pers:(Edholm Olle)"

Sökning: AMNE:(NATURAL SCIENCES Biological Sciences Biophysics) > Edholm Olle

  • Resultat 1-10 av 12
Sortera/gruppera träfflistan
   
NumreringReferensOmslagsbildHitta
1.
  • Brandt, Erik G., et al. (författare)
  • Interpretation of Fluctuation Spectra in Lipid Bilayer Simulations
  • 2011
  • Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 100:9, s. 2104-2111
  • Tidskriftsartikel (refereegranskat)abstract
    • 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.
  •  
2.
  • Braun, Anthony R., et al. (författare)
  • Determination of Electron Density Profiles and Area from Simulations of Undulating Membranes
  • 2011
  • Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 100:9, s. 2112-2120
  • Tidskriftsartikel (refereegranskat)abstract
    • 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.
  •  
3.
  • Håkansson, Pär, et al. (författare)
  • 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
  • 2001
  • Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : RSC Publishing. - 1463-9076 .- 1463-9084. ; 3:23, s. 5311-5319
  • Tidskriftsartikel (refereegranskat)abstract
    • EPR line shapes can be calculated from the stochastic Liouville equation assuming a stochastic model for the reorientation of the spin probe. Here we use instead and for the first time a detailed molecular dynamics (MD) simulation to generate the stochastic input to the Langevin form of the Liouville equation. A 0.1 μs MD simulation at T = 50°C of a small lipid bilayer formed by 64 dipalmitoylphosphatidylcholine (DPPC) molecules at the water content of 23 water molecules per lipid was used. In addition, a 10 ns simulation of a 16 times larger system consisting of 32 DPPC molecules with a nitroxide spin moiety attached at the sixth position of the sn2 chain and 992 ordinary DPPC molecules, was used to investigate the extent of the perturbation caused by the spin probe. Order parameters, reorientational dynamics and the EPR FID curve were calculated for spin probe molecules and ordinary DPPC molecules. The timescale of the electron spin relaxation for a spin-moiety attached at the sixth carbon position of a DPPC lipid molecule is 11.9 × 107 rad s−1 and for an unperturbed DPPC molecule it is 3.5 × 107 rad s−1.
  •  
4.
  • Lundberg, Linnea (författare)
  • Dispersion Corrections at Planar Surfaces
  • 2016
  • Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • When simulating a molecular system, a cutoff distance for interactions is often used to speed up the simulations. This is made at the cost of neglecting some interactions which will lead to inaccurate results for energy, pressure components and surface tension (for systems with surfaces). To compensate for the neglected long-range interactions, continuum corrections can be added to the surface tension, system energies and pressures. For a homogenous isotropic system this is straight-forward but for a system with a surface it is more complicated. In this work we have derived expressions for the corrections to the surface tension, system energies and pressures that are more general than previous results. When these corrections are added to multi-component systems with a surface (or single-component systems with vacuum) they compensate for the change in surface tension, system energy and pressures due to the finite cutoff. When simulating systems with no Coulomb-interactions, the structure of the system may change significantly if the cutoffs are too short. If this is the case then these corrections alone will not be enough. The solution is to add corrections to the force acting on each molecule added during the simulation, which we derive in this work. This solves the structural problem at low cutoffs and makes it possible to calculate an accurate surface tension independent of cutoff. 
  •  
5.
  • Brandt, Erik G., 1982- (författare)
  • Molecular Dynamics Simulations of Fluid Lipid Membranes
  • 2011
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Lipid molecules form thin biological membranes that envelop all living cells, and behave as two-dimensional liquid sheets immersed in bulk water. The interactions of such biomembranes with their environment lay the foundation of a plethora of biological processes rooted in the mesoscopic domain - length scales of 1-1000 nm and time scales of 1-1000 ns. Research in this intermediate regime has for a long time been out of reach for conventional experiments, but breakthroughs in computer simulation methods and scattering experimental techniques have made it possible to directly probe static and dynamic properties of biomembranes on these scales. Biomembranes are soft, with a relatively low energy cost of bending, and are thereby influenced by random, thermal fluctuations of individual molecules. Molecular dynamics simulations show how in-plane (density fluctuations) and out-of-plane (undulations) motions are intertwined in the bilayer in the mesoscopic domain. By novel methods, the fluctuation spectra of lipid bilayers can be calculated withdirect Fourier analysis. The interpretation of the fluctuation spectra reveals a picture where density fluctuations and undulations are most pronounced on different length scales, but coalesce in the mesoscopic regime. This analysis has significant consequences for comparison of simulation data to experiments. These new methods merge the molecular fluctuations on small wavelengths, with continuum fluctuations of the elastic membrane sheet on large wavelengths, allowing electron density profiles (EDP) and area per lipid to be extracted from simulations with high accuracy. Molecular dynamics simulations also provide insight on the small-wavelength dynamics of lipid membranes. Rapidly decaying density fluctuations can be described as propagating sound waves in the framework of linearized hydrodynamics, but there is a slow, dispersive, contribution that needs to be described by a stretched exponential over a broad range of length- and time scales - recent experiments suggest that this behavior can prevail even on micrometer length scales. The origin of this behavior is discussed in the context of fluctuations of the bilayer interface and the molecular structure of the bilayer itself. Connections to recent neutron scattering experiments are highlighted.
  •  
6.
  • Hofsäss, Christofer, et al. (författare)
  • Molecular dynamics simulations of phospholipid bilayers with cholesterol
  • 2003
  • Ingår i: Biophysical Journal. - 0006-3495 .- 1542-0086. ; 84:4, s. 2192-206
  • Tidskriftsartikel (refereegranskat)abstract
    • To investigate the microscopic interactions between cholesterol and lipids in biological membranes, we have performed a series of molecular dynamics simulations of large membranes with different levels of cholesterol content. The simulations extend to 10 ns, and were performed with hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers. The bilayers contain 1024 lipids of which 0-40% were cholesterol and the rest DPPC. The effects of cholesterol on the structure and mesoscopic dynamics of the bilayer were monitored as a function of cholesterol concentration. The main effects observed are a significant ordering of the DPPC chains (as monitored by NMR type order parameters), a reduced fraction of gauche bonds, a reduced surface area per lipid, less undulations--corresponding to an increased bending modulus for the membrane, smaller area fluctuations, and a reduced lateral diffusion of DPPC-lipids as well as cholesterols.
  •  
7.
  •  
8.
  •  
9.
  •  
10.
  • Edholm, Olle (författare)
  • Time and length scales in lipid bilayer simulations
  • 2008
  • Ingår i: Computational Modeling Of Membrane Bilayers. - 9780123738936 ; , s. 91-110
  • Bokkapitel (refereegranskat)abstract
    • Time and length scales for different kinds of local and collective motions in lipid bilayers that may be probed in molecular dynamics simulations are discussed. The possibility to determine parameters in continuum models using simulation techniques is discussed. Agreements and discrepancies between simulations and experimental data are presented and discussed. The chapter covers large scale undulations and peristaltic thickness fluctuations, hydrocarbon chain reorientation motion, lipid lateral diffusion and motion of the entire monolayers with respect to each other and with respect to the water.
  •  
Skapa referenser, mejla, bekava och länka
  • Resultat 1-10 av 12

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

 
pil uppåt Stäng

Kopiera och spara länken för att återkomma till aktuell vy