/******************************************************************************* * McStas, neutron ray-tracing package * Copyright 1997-2003, All rights reserved * Risoe National Laboratory, Roskilde, Denmark * Institut Laue Langevin, Grenoble, France * * Component: SANSNanodiscsWithTags * * %I * Written by: Martin Cramer Pedersen (mcpe@nbi.dk) * Date: October 17, 2012 * Origin: KU-Science * * A sample of monodisperse phospholipid bilayer nanodiscs in solution (water) - with * histidine tag still on the belt proteins. * * %D * A component simulating the scattering from a box-shaped, thin solution (water) * of monodisperse phospholipid bilayer nanodiscs - with histidine tags still * on the belt proteins. * * %P * AxisRatio: [] Axis ratio of the bilayer patch. * NumberOfLipids: [] Number of lipids per nanodisc. * AreaPerLipidHeadgroup: [AA^2] Area per lipid headgroup - default is POPC. * HeightOfMSP: [AA] Height of the belt protein - default is MSP1D1. * RadiusOfGyrationForHisTag: [AA] Radius of gyration for the his-tag. * VolumeOfOneMSP: [AA^3] Volume of one belt protein - default is MSP1D1. * VolumeOfHeadgroup: [AA^3] Volume of one lipid headgroup - default is POPC. * VolumeOfCH2Tail: [AA^3] Volume of the CH2-chains of one lipid - default is POPC. * VolumeOfCH3Tail: [AA^3] Volume of the CH3-tails of one lipid - default is POPC. * VolumeOfOneHisTag: [AA^3] Volume of one his-tag. * ScatteringLengthOfOneMSP: [cm] Scattering length of one belt protein - default is MSP1D1. * ScatteringLengthOfHeadgroup: [cm] Scattering length of one lipid headgroup - default is POPC. * ScatteringLengthOfCH2Tail: [cm] Scattering length of the CH2-chains of one lipid - default is POPC. * ScatteringLengthOfCH3Tail: [cm] Scattering length of the CH3-tails of one lipid - default is POPC. * ScatteringLengthOfOneHisTag: [cm] Scattering length of one his-tag. * Roughness: [] Factor used to smear the interfaces of the nanodisc. * Concentration: [mM] Concentration of sample. * RhoSolvent: [cm/AA^3] Scattering length density of solvent - default is D2O. * AbsorptionCrosssection: [1/m] Absorption cross section of the sample. * xwidth: [m] Dimension of component in the x-direction. * yheight: [m] Dimension of component in the y-direction. * zdepth: [m] Dimension of component in the z-direction. * SampleToDetectorDistance: [m] Distance from sample to detector (for focusing the scattered neutrons). * DetectorRadius: [m] Radius of the detector (for focusing the scattered neutrons). * * %E *******************************************************************************/ DEFINE COMPONENT SANSNanodiscsWithTags SETTING PARAMETERS (AxisRatio = 1.4, NumberOfLipids = 130.0, AreaPerLipidHeadgroup = 65.0, HeightOfMSP = 24.0, RadiusOfGyrationForHisTag = 10.0, VolumeOfOneMSP = 26296.5, VolumeOfHeadgroup = 319.0, VolumeOfCH2Tail = 818.8, VolumeOfCH3Tail = 108.6, VolumeOfOneHisTag = 2987.3, ScatteringLengthOfOneMSP = 8.8E-10, ScatteringLengthOfHeadgroup = 7.05E-12, ScatteringLengthOfCH2Tail = -1.76E-12, ScatteringLengthOfCH3Tail = -9.15E-13,ScatteringLengthOfOneHisTag = 1.10E-10, Roughness = 5.0, Concentration = 0.01, RhoSolvent = 6.4e-14, AbsorptionCrosssection = 0.0, xwidth, yheight, zdepth, SampleToDetectorDistance, DetectorRadius) DEPENDENCY " @GSLFLAGS@ " NOACC SHARE %{ #ifndef NANODISCS #define NANODISCS %include "nanodiscs.h" #endif #ifndef NANODISCS #define NANODISCS #endif %} DECLARE %{ // Declarations double Absorption; double q; double NumberDensity; // Scattering lengths double RhoBelt; double RhoHead; double RhoCH2Tail; double RhoCH3Tail; double RhoTag; double DeltaRhoHead; double DeltaRhoBelt; double DeltaRhoCH2Tail; double DeltaRhoCH3Tail; double DeltaRhoTag; // Geometric properties double MajorSemiAxis; double MinorSemiAxis; double ThicknessOfBelt; double HeightOfBelt; double HeightOfLipids; double HeightOfTails; double HeightOfCH3; %} INITIALIZE %{ // Rescale concentration into number of aggregates per m^3 times 10^-4 NumberDensity = Concentration * 6.02214129e19; // Computations if (!xwidth || !yheight || !zdepth) { printf ("%s: Sample has no volume, check parameters!\n", NAME_CURRENT_COMP); } Absorption = AbsorptionCrosssection; // Scattering properties of different components RhoBelt = ScatteringLengthOfOneMSP / VolumeOfOneMSP; RhoHead = ScatteringLengthOfHeadgroup / VolumeOfHeadgroup; RhoCH2Tail = ScatteringLengthOfCH2Tail / VolumeOfCH2Tail; RhoCH3Tail = ScatteringLengthOfCH3Tail / VolumeOfCH3Tail; RhoTag = ScatteringLengthOfOneHisTag / VolumeOfOneHisTag; DeltaRhoBelt = RhoBelt - RhoSolvent; DeltaRhoHead = RhoHead - RhoSolvent; DeltaRhoCH2Tail = RhoCH2Tail - RhoSolvent; DeltaRhoCH3Tail = RhoCH3Tail - RhoSolvent; DeltaRhoTag = RhoTag - RhoSolvent; // Geometric properties of different components const double AreaOfLipids = NumberOfLipids * AreaPerLipidHeadgroup / 2.0f; MinorSemiAxis = sqrt (AreaOfLipids / (PI * AxisRatio)); MajorSemiAxis = MinorSemiAxis * AxisRatio; HeightOfLipids = 2.0f * (VolumeOfHeadgroup + VolumeOfCH2Tail + VolumeOfCH3Tail) / AreaPerLipidHeadgroup; HeightOfTails = 2.0f * (VolumeOfCH2Tail + VolumeOfCH3Tail) / AreaPerLipidHeadgroup; HeightOfCH3 = 2.0f * VolumeOfCH3Tail / AreaPerLipidHeadgroup; ThicknessOfBelt = sqrt (pow (MinorSemiAxis + MajorSemiAxis, 2) / 4.0 + 2 * VolumeOfOneMSP / (PI * HeightOfMSP)) - (MajorSemiAxis + MinorSemiAxis) / 2.0; %} TRACE %{ // Declarations double t0; double t1; double l_full; double l; double l1; double Intensity; double Weight; double IntensityPart; double SolidAngle; double qx; double qy; double qz; double v; double dt; double vx_i; double vy_i; double vz_i; char Intersect = 0; // Computation Intersect = box_intersect (&t0, &t1, x, y, z, vx, vy, vz, xwidth, yheight, zdepth); if (Intersect) { if (t0 < 0.0) { fprintf (stderr, "Neutron already inside sample %s - absorbing...\n", NAME_CURRENT_COMP); ABSORB; } // Compute properties of neutron v = sqrt (pow (vx, 2) + pow (vy, 2) + pow (vz, 2)); l_full = v * (t1 - t0); dt = rand01 () * (t1 - t0) + t0; PROP_DT (dt); l = v * (dt - t0); // Store properties of incoming neutron vx_i = vx; vy_i = vy; vz_i = vz; // Generate new direction of neutron randvec_target_circle (&vx, &vy, &vz, &SolidAngle, 0, 0, SampleToDetectorDistance, DetectorRadius); NORM (vx, vy, vz); vx *= v; vy *= v; vz *= v; // Compute q qx = V2K * (vx_i - vx); qy = V2K * (vy_i - vy); qz = V2K * (vz_i - vz); q = sqrt (pow (qx, 2) + pow (qy, 2) + pow (qz, 2)); // Compute scattering l1 = v * t1; Intensity = exp (-pow (q * Roughness, 2)) * IntensityOfEmptyNanodiscsWithTags (q, MajorSemiAxis, MinorSemiAxis, ThicknessOfBelt, HeightOfMSP, HeightOfLipids, HeightOfTails, HeightOfCH3, RadiusOfGyrationForHisTag, VolumeOfOneHisTag, DeltaRhoBelt, DeltaRhoHead, DeltaRhoCH2Tail, DeltaRhoCH3Tail, DeltaRhoTag); p *= l_full * SolidAngle / (4.0 * PI) * NumberDensity * Intensity * exp (-Absorption * (l + l1) / v); SCATTER; } %} MCDISPLAY %{ box (0, 0, 0, xwidth, yheight, zdepth, 0, 0, 1, 0); %} END