Michael Thomas Flanagan's Java Scientific Library

ImmunoChemistry Class:      Some general methods associated with Immunochemistry

      

Last update: 2 April 2012                                                                                                                              PERMISSION TO COPY
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ImmunoChemistry is a class containing a few general methods required by both the ImmunoKinetics class and the ImmunoAssay class.
The calculation methods in this ImmunoChemistry class assume ideal spherical molecules and return approximations that may only be useful in simple modelling and in setting intial estimates for non-linear regression procedures.

This class contains methods for:
import directive: import flanagan.physchem.ImmunoChemistry;

SUMMARY OF CONSTRUCTORS AND METHODS
Constructors public ImmunoChemistry()
Diffusion coefficient public static double diffusionCoefficient(double effectiveRadius, double viscosity, double temperature)
public static double diffusionCoefficient(double molWeight, double specVol, double viscosity, double temperature)
Diffusion controlled reaction rate public static double diffusionControlledRate(double diffCoeffA, double diffCoeffB, double radiusA, double radiusB, double fractA, double fractB)
Planar Diffusion public static double oneDimensionalDiffusion(double diffCoeff, double zeroDistConcn, double distance, double time)
Molecular radius public static double molecularRadius(double molWeight, double specVol)
public static double molecularRadius(double molWeight)
public static double effectiveRadius(double diffusionCoefficient, double viscosity, double temperature)
Surface concentrations Surface molar concentration public static double surfaceMolarConcn(double effectiveRadius)
public static double surfaceMolarConcn(double molWeight, double specVolume)
Surface number concentration public static double surfaceNumberConcn(effectiveRadius)
public static double surfaceNumberConcn(double molWeight, double specVolume)
Equivalent molar volume concentration public static double equivalentVolumeConcn(double effectiveRadius, double area, double volume)
public static double equivalentVolumeConcn(double molWeight, double area, double volume, double specVolume)
public static double convertSurfaceToVolumeConcn(double surfaceConcn, double area, double volume)
Molecular weights IgG1 public static double getMolWeightIgG1()
IgG2 public static double getMolWeightIgG2()
IgG3 public static double getMolWeightIgG3()
IgG4 public static double getMolWeightIgG4()
IgM public static double getMolWeightIgM()
IgA1 public static double getMolWeightIgA1()
IgA2 public static double getMolWeightIgA2()
IgD public static double getMolWeightIgD()
IgE public static double getMolWeightIgE()


CONSTRUCTOR

CONSTRUCTORS
public ImmunoChemistry()
Usage:                      ImmunoChemistry ic = new ImmunoChemistry();
Creates an instance of ImmunoChemistry. Formal instantiation is not required as all the methods in this class are static.


DIFFUSION COEFFICIENT

public static double diffusionCoefficient(double effectiveRadius, double viscosity, double temperature)
public static double diffusionCoefficient(double molWeight, double specVol, double viscosity, double temperature)
Usage:                      diffCoeff = ImmunoChemistry.diffusionCoefficient(effectiveRadius, viscosity, temperature);
This method returns an approximate diffusion coefficient, D,

as square metres per second, where η is the viscosity of the solution [viscosity in Pascal seconds], T is the temperature of the solution [temperature in degrees Celsius], r is the effective radius, e.g. hydrodynamic radius, [effectiveRadius in metres] and kB is Boltzmann's constant. The method assumes a spherical molecule. See Water for methods returning the viscosity of water, Saline for methods returning the viscosity of aqueous saline solutions and Sucrose for methods returning the viscosity of aqueous sucrose solutions.

Usage:                      diffCoeff = ImmunoChemistry.diffusionCoefficient(molWt, specVol, viscosity, temperature);
This method returns an approximate diffusion coefficient, D,

as square metres per second, where η is the viscosity of the solution [viscosity in Pascal seconds], T is the temperature of the solution [temperature in degrees Celsius] and kB is Boltzmann's constant. The approximate radius of the solute, r, is calculated from the molecular weight, molWeight and a specific volume, specVol in metres per kilogram, of the solute. The method assumes a spherical molecule. See Water for methods returning the viscosity of water, Saline for methods returning the viscosity of aqueous saline solutions and Sucrose for methods returning the viscosity of aqueous sucrose solutions.


DIFFUSION CONTROLLED REACTION RATE

public static double diffusionControlledRate(double diffCoeffA, double diffCoeffB, double radiusA, double radiusB, double fractA, double fractB)
Usage:                      rateConstant = ImmunoChemistry.diffusionControlledRate(diffCoeffA, diffCoeffB, radiusA, radiusB, fractA, fractB);
This method returns the diffusion controlled second order rate constant, kgd,

as M-1 s-1, for the collisional reaction
 A + B −> . . .
where DA is the diffusion coefficient of molecule A [diffCoeffA in square metres per second], DB is the diffusion coefficient of molecule B [diffCoeffB in square metres per second], rA is the radius of molecule A [radiusA in metres], rB is the radius of molecule B [radiusB in metres], fA is the fraction of the surface of molecule A that can react with B on collision [fractA], fB is the fraction of the surface of molecule B that can react with A on collision [fractB] and N is Avagadro’s number.


PLANAR DIFFUSION CONCENTRATIONS

public static double oneDimensionalDiffusion(double diffCoeff, double zeroDistConcn, double distance, double time)
Usage:                      concn = ImmunoChemistry.oneDimensionalDiffusion(diffCoeff, zeroDistanceConcn, distance, time);
This method returns the concentration of a molecule at a distance x from an infinite planar boundary [argument distance in metres], after a time t [argument time in seconds], cx,t,

where c0 is the concentration of the molecule at the infinite boundary [argument zeroDistanceConcn] and D is the diffusion coefficient of the molecule [argument diffCoeff in square metres per second].
This calculation assumes:


MOLECULAR RADIUS

public static double molecularRadius(double molWeight, double specVol)
public static double molecularRadius(double molWeight)
public static double effectiveRadius(double diffusionCoefficient, double viscosity, double temperature)
Usage:                      radius = ImmunoChemistry.molecularRadius(molWt, specVol);
This method returns an approximate molecular radius, as metres, of a molecule of molecular weight, molWeight and a specific volume, specVol in metres per kilogram. The method assumes a spherical molecule.

Usage:                      radius = ImmunoChemistry.molecularRadius(molWt);
This method returns an approximate molecular radius, as metres, of a molecule of molecular weight, molWeight. The method assumes a spherical molecule and a specific volume of 0.74E-3 m/kg (0.74 ml/gm).

Usage:                      radius = ImmunoChemistry.effectiveRadius(diffusionCoefficient, viscosity, temperature);
This method returns an effective radius, r,

as metres, where D is the solute diffusion coefficient [diffusionCoefficient in square metres per second], η is the viscosity of the solution [viscosity in Pascal seconds], T is the temperature of the solution [temperature in degrees Celsius] and kB is Boltzmann's constant. The method assumes a spherical molecule. See Water for methods returning the viscosity of water, Saline for methods returning the viscosity of aqueous saline solutions and Sucrose for methods returning the viscosity of aqueous sucrose solutions.


SURFACE CONCENTRATIONS

Surface molar concentration
public static double surfaceMolarConcn(double effectiveRadius)
public static double surfaceMolarConcn(double molWeight, double specVolume)
Usage:                      sconcn = ImmunoChemistry.surfaceMolarConcn(effectiveRadius);
This method returns an approximate surface concentration, as moles per square metre, of a tightly packed surface monolayer of a molecule of an effective radius, e.g. hydrodynamic radius, effectiveRadius, in metres. The method assumes spherical molecules and hexagonal close packing.

Usage:                      sconcn = ImmunoChemistry.surfaceMolarConcn(molWeight, specVolume);
This method returns an approximate surface concentration, as moles per square metre, of a tightly packed surface monolayer of a molecule of molecular weight, molWeight, and specific volume, specVolume, entered as cubic metres per kilogram. The method assumes spherical molecules and hexagonal close packing.

Surface number concentration
public static double surfaceNumberConcn(double effectiveRadius)
public static double surfaceNumberConcn(double molWeight, double specVolume)
Usage:                      sconcn = ImmunoChemistry.surfaceNumberConcn(effectiveRadius);
This method returns an approximate surface concentration, as number of molecues per square metre, of a tightly packed surface monolayer of a molecule of an effective radius, e.g. hydrodynamic radius, effectiveRadius, in metres. The method assumes spherical molecules and hexagonal close packing.

Usage:                      sconcn = ImmunoChemistry.surfaceNumberConcn(molWeight, specVolume);
This method returns an approximate surface concentration, as number of molecues per square metre, of a tightly packed surface monolayer of a molecule of molecular weight, molWeight, and specific volume, specVolume, entered as cubic metres per kilogram. The method assumes spherical molecules and hexagonal close packing.

Equivalent molar volume concentration
public static double equivalentVolumeConcn(double effectiveRadius, double area, double volume)
public static double equivalentVolumeConcn(double molWeight, double area, double volume, double specVolume)
public static double convertSurfaceToVolumeConcn(double surfaceConcn, double area, double volume)
Usage:                      vconcn = ImmunoChemistry.equivalentVolumeConcn(effectiveRadius, area);
This method returns an approximate equivalent volume molar concentration in a volume of liquid, volume entered as cubic metres, above an area, area entered as square metres, of a tightly packed surface monolayer of a molecule of an effective radius, e.g. hydrodynamic radius, effectiveRadius, in metres. The method assumes spherical molecules and hexagonal close packing.

Usage:                      vconcn = ImmunoChemistry.equivalentVolumeConcn(molWeight, area, volume, specVolume);
This method returns an approximate equivalent volume molar concentration in a volume of liquid, volume entered as cubic metres, above an area, area entered as square metres, of a tightly packed surface monolayer of a molecule of molecular weight, molWeight, and specific volume, specVolume, entered as cubic metres per kilogram. The method assumes spherical molecules and hexagonal close packing.

Usage:                      vconcn = ImmunoChemistry.convertSurfaceToVolumeConcn(surfaceConcn, area, volume);
This method converts a surface concentration, surfaceConcn in moles per square metre, to an equivalent molar volume concentration for a molecule immobilised on a surface area, area in square metres, in contact with a volume, volume in cubic metres.


ANTIBODY MOLECULAR WEIGHTS
public static double getMolWeightIgG1()
public static double getMolWeightIgG2()
public static double getMolWeightIgG3()
public static double getMolWeightIgG4()
public static double getMolWeightIgM()
public static double getMolWeightIgA1()
public static double getMolWeightIgA2()
public static double getMolWeightIgD()
public static double getMolWeightIgE()
Usage:                      molwt = ImmunoChemistry.getMolWeightIgG1();
This method returns the molecular weight of IgG1.

Usage:                      molwt = ImmunoChemistry.getMolWeightIgG2();
This method returns the molecular weight of IgG2.

Usage:                      molwt = ImmunoChemistry.getMolWeightIgG3();
This method returns the molecular weight of IgG3.

Usage:                      molwt = ImmunoChemistry.getMolWeightIgG4();
This method returns the molecular weight of IgG4.

Usage:                      molwt = ImmunoChemistry.getMolWeightIgM();
This method returns the molecular weight of IgM.

Usage:                      molwt = ImmunoChemistry.getMolWeightIgA1();
This method returns the molecular weight of IgA1.

Usage:                      molwt = ImmunoChemistry.getMolWeightIgA2();
This method returns the molecular weight of IgA2.

Usage:                      molwt = ImmunoChemistry.getMolWeightIgD();
This method returns the molecular weight of IgD.

Usage:                      molwt = ImmunoChemistry.getMolWeightIgE();
This method returns the molecular weight of IgE.


OTHER CLASSES USED BY THIS CLASS

 This class uses the following classes in this library:

PERMISSION TO COPY

Permission to use, copy and modify this software and its documentation for NON-COMMERCIAL purposes is granted, without fee, provided that an acknowledgement to the author, Dr Michael Thomas Flanagan at www.ee.ucl.ac.uk/~mflanaga, appears in all copies and associated documentation or publications. Dr Michael Thomas Flanagan makes no representations about the suitability or fitness of the software for any or for a particular purpose. Dr Michael Thomas Flanagan shall not be liable for any damages suffered as a result of using, modifying or distributing this software or its derivatives.

Redistributions of the source code of this class, or parts of the source codes, must retain the copyright notice, this list of conditions and the following disclaimer (all at the top of the source code) and requires written permission from the Michael Thomas Flanagan:

Redistribution in binary form of all or parts of this class must reproduce the copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution and requires written permission from the Michael Thomas Flanagan.


This page was prepared by Dr Michael Thomas Flanagan