swharden / ljpcalc

Liquid Junction Potential Calculator

Scott W Harden, DMD, PhD

• Personal website: https://swharden.com
• How to reach me: [email protected]

ljpcalc's Issues

add glucose to ion table

consider adding a special message indicating the source of mobility for each ion added

Mobility sources

Add link to relevant source code

string parsing and localization

LJPcalc fails when system locale uses non-EN roles for . and , characters. It looks like this problem occurs while reading the ion mobility table.

A similar problem is described in ScottPlot/ScottPlot#108

add option to save/load ion set

this is useful when making large ion sets like this and coming back later to re-run the calculation with different concentrations

Add option to change labels to represent cell membranes

Add an option to display "solution A" and "solution B" as "in" and "out" to make it easier to evaluate for people calculating LJP for electrophysiology experiments (inside vs. outside a cell membrane)

document how to use an Ag/AgCl pellet

the LJPCalcWin manual shows this picture on page 20:

Given the ion table above they calculate the LJP caused by the Ag/AgCl pellet is 16.65 mV. How did they calculate this?

This Python shows the answer:

import math

temperatureC = 20
zeroCinK = 273.15

T = zeroCinK + temperatureC # Temperature in K
Nav = 6.02214076e23 # Avogadro constant
B = 1.38064852e-23 # Boltzmann constant
R = Nav * B # gas constant (R)
e = 1.602176634e-19 # electron charge (C)
F = e * Nav # Faraday constant (C/mol)

concClBath = .145 # moles
ljpBath = -1000*(R*T/F)*math.log(concClBath)
print("Bath Ag/AgCl LJP:", ljpBath, "mV")

concClPipette = .075 # moles
ljpPipette = -1000*(R*T/F)*math.log(concClPipette)
print("Pipette Ag/AgCl LJP:", ljpPipette, "mV")

print("Ag/AgCl LJP:", ljpBath - ljpPipette, "mV")

Bath Ag/AgCl LJP: 48.780893847484634 mV
Pipette Ag/AgCl LJP: 65.43456157367899 mV
Ag/AgCl LJP: -16.653667726194357 mV

add demo ion sets to core library

Right now demos are just in the GUI application. Putting some in the LJPmath module makes them accessible to the console application and tests too.

let user break infinite loop

this ion set has been calculating for too long

improve auto-sort

Notes from Dr. Brogioli,

The image that I have in mind is that "x" and "last" should have different sign (if "x" is a cation, "last" is the most common anion). However, I found no practical case in which this matters.

You [currently] select "last" as the ion with largest cL, with the risk that c0 is very small. I do not know if this is a problem, maybe not. However, I was thinking if it is not better to first select "x", then select "last" among the remaining ions, as the one having the largest c0+cL.

The auto-sort logic lives here:

LJPcalc/src/LJPmath/Calculate.cs

Lines 10 to 43 in 5ffd257

	private static List<Ion> AutoSort(List<Ion> ionList)
	{
	// largest cL should be last
	int indexLargestCl = 0;
	double largestCl = 0;
	for (int i = 0; i < ionList.Count; i++)
	{
	if (ionList[i].cL > largestCl)
	{
	indexLargestCl = i;
	largestCl = ionList[i].cL;
	}
	}
	Ion ionLargestCl = ionList[indexLargestCl];
	ionList.RemoveAt(indexLargestCl);
	// largest diff should be second from last
	int indexLargestCdiff = 0;
	double largestCdiff = 0;
	for (int i = 0; i < ionList.Count; i++)
	{
	if (ionList[i].cDiff > largestCdiff)
	{
	indexLargestCdiff = i;
	largestCdiff = ionList[i].cDiff;
	}
	}
	Ion ionLargestCdiff = ionList[indexLargestCdiff];
	ionList.RemoveAt(indexLargestCdiff);
	ionList.Add(ionLargestCdiff);
	ionList.Add(ionLargestCl);
	return ionList;
	}

when new ion selected reset concentrations to 0

alternatively set concentrations to zero when the add button is pressed

program is unresponsive (for minutes) while slow ion sets calculate

Performed a calculation. Swapped sulfate ion used in calculation and app became unresponsive.

prevent ENTER function during ion name edit

also pressing entering zn and hitting ENTER crashes the program 💀

total concentration must be > 0

disable the "add ion" button if concentration is 0 on both sides

GTP missing from table

Guanosine-5'-triphosphate is currently not listed in the ion table

need icon

trivial... but true

determine how order affects LJP

the final 2 ions in the set meaningfully influence calculated LJP, but how much does the order of all the previous ions influence LJP? Write a program to solve LJP using every permutation of ion set orders and plot the result as a histogram using ScottPlot http://swharden.com/scottplot/cookbooks/4.0.25/readme.md.html#advanced-statistics---histogram

when a name is typed auto-select that item in the list

this will also auto-populate the charge and conductivity

GTP charge

should probably be -2

document ion mobility table sources

Mobilities are here, and the first group of non-cited mobilities comes from JLJP (Marino et al., 2014)

LJPcalc/src/LJPcalc.Core/IonLibrary.cs

Lines 38 to 323 in e27e906

	public static Ion[] GetKnownIons(bool removeDuplicates = true)
	{
	List<Ion> ions = new()
	{
	// Inorganic Cations
	MakeReferenceIon("Ag", +1, 61.9),
	MakeReferenceIon("Al", +3, 61),
	MakeReferenceIon("Ba", +2, 63.9),
	MakeReferenceIon("Be", +2, 45),
	MakeReferenceIon("Ca", +2, 59.5),
	MakeReferenceIon("Cd", +2, 54),
	MakeReferenceIon("Ce", +3, 70),
	MakeReferenceIon("Co", +2, 53),
	MakeReferenceIon("Co(NH3)6", +3, 100),
	MakeReferenceIon("Co(ethylenediamine)3", +3, 74.7),
	MakeReferenceIon("Cr", +3, 67),
	MakeReferenceIon("Cs", +1, 77.3),
	MakeReferenceIon("Cu", +2, 56.6),
	MakeReferenceIon("D", +1, 213.7),
	MakeReferenceIon("Dy", +3, 65.7),
	MakeReferenceIon("Er", +3, 66),
	MakeReferenceIon("Eu", +3, 67.9),
	MakeReferenceIon("FeII", +2, 53.5),
	MakeReferenceIon("FeIII", +3, 69),
	MakeReferenceIon("Gd", +3, 67.4),
	MakeReferenceIon("H", +1, 350.1),
	MakeReferenceIon("Hg2", +2, 68.7),
	MakeReferenceIon("Hg", +2, 63.6),
	MakeReferenceIon("Ho", +3, 66.3),
	MakeReferenceIon("K", +1, 73.5),
	MakeReferenceIon("La", +3, 69.6),
	MakeReferenceIon("Li", +1, 38.69),
	MakeReferenceIon("Mg", +2, 53.06),
	MakeReferenceIon("Mn", +2, 53.5),
	MakeReferenceIon("NH", 4, 73.7),
	MakeReferenceIon("N2H5", +1, 59),
	MakeReferenceIon("Na", +1, 50.11),
	MakeReferenceIon("Nd", +3, 69.6),
	MakeReferenceIon("Ni", +2, 50),
	MakeReferenceIon("Pb", +2, 71),
	MakeReferenceIon("Pr", +3, 69.6),
	MakeReferenceIon("Ra", +2, 66.8),
	MakeReferenceIon("Rb", +1, 77.8),
	MakeReferenceIon("Sc", +3, 64.7),
	MakeReferenceIon("Sm", +3, 68.5),
	MakeReferenceIon("Sr", +2, 59.46),
	MakeReferenceIon("Tl", +1, 74.9),
	MakeReferenceIon("Tm", +3, 65.5),
	MakeReferenceIon("UO2", +2, 32),
	MakeReferenceIon("Y", +3, 62),
	MakeReferenceIon("Yb", +3, 65.2),
	MakeReferenceIon("Zn", +2, 52.8),
	// Inorganic Anions
	MakeReferenceIon("Au(CN)2", -1, 50),
	MakeReferenceIon("Au(CN)4", -1, 36),
	MakeReferenceIon("B(C6H5)4", -1, 21),
	MakeReferenceIon("Br", -1, 78.1),
	MakeReferenceIon("Br3", -1, 43),
	MakeReferenceIon("BrO3", -1, 55.7),
	MakeReferenceIon("Cl", -1, 76.31),
	MakeReferenceIon("ClO2", -1, 52),
	MakeReferenceIon("ClO3", -1, 64.6),
	MakeReferenceIon("ClO4", -1, 67.3),
	MakeReferenceIon("CN", -1, 78),
	MakeReferenceIon("CO3", -2, 69.3),
	MakeReferenceIon("Co(CN)6", -3, 98.9),
	MakeReferenceIon("CrO4", -2, 85),
	MakeReferenceIon("F", -1, 55.4),
	MakeReferenceIon("Fe(CN)6 IIII", -4, 110.4),
	MakeReferenceIon("Fe(CN)6 III", -3, 100.9),
	MakeReferenceIon("H2AsO4", -1, 34),
	MakeReferenceIon("HCO3", -1, 44.5),
	MakeReferenceIon("HF2", -1, 75),
	MakeReferenceIon("HPO4", -2, 33),
	MakeReferenceIon("H2PO4", -1, 33),
	MakeReferenceIon("HS", -1, 65),
	MakeReferenceIon("HSO3", -1, 50),
	MakeReferenceIon("HSO4", -1, 50),
	MakeReferenceIon("H2SbO4", -1, 31),
	MakeReferenceIon("I", -1, 76.9),
	MakeReferenceIon("IO3", -1, 40.5),
	MakeReferenceIon("IO4", -1, 54.5),
	MakeReferenceIon("MnO4", -1, 61.3),
	MakeReferenceIon("MoO4", -2, 74.5),
	MakeReferenceIon("N3", -1, 69.5),
	MakeReferenceIon("N(CN)2", -1, 54.5),
	MakeReferenceIon("NO2", -1, 71.8),
	MakeReferenceIon("NO3", -1, 71.42),
	MakeReferenceIon("NH2SO3 (sulfamate)", -1, 48.6),
	MakeReferenceIon("OCN (cyanate)", -1, 64.6),
	MakeReferenceIon("OH", -1, 198),
	MakeReferenceIon("PF6", -1, 56.9),
	MakeReferenceIon("PO3F", -2, 63.3),
	MakeReferenceIon("PO4", -3, 69),
	MakeReferenceIon("P2O7", -4, 96),
	MakeReferenceIon("P3O9", -3, 83.6),
	MakeReferenceIon("P3O10", -5, 109),
	MakeReferenceIon("ReO4", -1, 54.9),
	MakeReferenceIon("SCN (thiocyanate)", -1, 66.5),
	MakeReferenceIon("SeCN", -1, 64.7),
	MakeReferenceIon("SeO4", -2, 75.7),
	MakeReferenceIon("SO3", -2, 79.9),
	MakeReferenceIon("SO4", -2, 80),
	MakeReferenceIon("S2O3", -2, 85),
	MakeReferenceIon("S2O4", -2, 66.5),
	MakeReferenceIon("S2O6", -2, 93),
	MakeReferenceIon("S2O8", -2, 86),
	MakeReferenceIon("WO4", -2, 69.4),
	// Organic Cations
	MakeReferenceIon("Decylpyridinium", +1, 29.5),
	MakeReferenceIon("Diethylammonium", +1, 42),
	MakeReferenceIon("Dimethylammonium", +1, 51.5),
	MakeReferenceIon("Dipropylammonium", +1, 30.1),
	MakeReferenceIon("Dodecylammonium", +1, 23.8),
	MakeReferenceIon("Ethylammonium", +1, 47.2),
	MakeReferenceIon("Ethyltrimethylammonium", +1, 40.5),
	MakeReferenceIon("Isobutylammonium", +1, 38),
	MakeReferenceIon("Methylammonium", +1, 58.3),
	MakeReferenceIon("Piperidinium", +1, 37.2),
	MakeReferenceIon("Propylammonium", +1, 40.8),
	MakeReferenceIon("Tetrabutylammonium", +1, 19.5),
	MakeReferenceIon("Tetraethylammonium", +1, 32.6),
	MakeReferenceIon("Tetramethylammonium", +1, 44.9),
	MakeReferenceIon("Tetrapropylammonium", +1, 23.5),
	MakeReferenceIon("Triethylsulfonium", +1, 36.1),
	MakeReferenceIon("Trimethylammonium", +1, 47.2),
	MakeReferenceIon("Trimethylsulfonium", +1, 51.4),
	MakeReferenceIon("Tripropylammonium", +1, 26.1),
	// Organic Anions
	MakeReferenceIon("Acetate", -1, 41),
	MakeReferenceIon("Benzoate", -1, 32.4),
	MakeReferenceIon("Bromoacetate", -1, 39.2),
	MakeReferenceIon("Bromobenzoate", -1, 30),
	MakeReferenceIon("Butanoate", -1, 32.6),
	MakeReferenceIon("Chloroacetate", -1, 42.2),
	MakeReferenceIon("m-Chlorobenzoate", -1, 31),
	MakeReferenceIon("o-Chlorobenzoate", -1, 30.5),
	MakeReferenceIon("Citrate", -3, 70.2),
	MakeReferenceIon("Crotonate", -1, 33.2),
	MakeReferenceIon("Cyanoacetate", -1, 43.4),
	MakeReferenceIon("Cyclohexanecarboxylate", -1, 28.7),
	MakeReferenceIon("Cyclopropane-1,3-dicarboxylate2", -1, 53.4),
	MakeReferenceIon("Decylsulfonate", -1, 26),
	MakeReferenceIon("Dichloroacetate", -1, 38.3),
	MakeReferenceIon("Diethylbarbiturate", -2, 26.3),
	MakeReferenceIon("Dihydrogencitrate", -1, 30),
	MakeReferenceIon("Dimethylmalonate", -2, 49.4),
	MakeReferenceIon("3, 5-Dinitrobenzoate", -1, 28.3),
	MakeReferenceIon("Dodecylsulfonate", -1, 24),
	MakeReferenceIon("Ethylmalonate", -1, 49.3),
	MakeReferenceIon("Ethylsulfonate", -1, 39.6),
	MakeReferenceIon("Fluoroacetate", -1, 44.4),
	MakeReferenceIon("Fluorobenzoate", -1, 33),
	MakeReferenceIon("Formate", -1, 54.6),
	MakeReferenceIon("Fumarate", -2, 61.8),
	MakeReferenceIon("Glutarate", -2, 52.6),
	MakeReferenceIon("Hydrogenoxalate", -1, 40.2),
	MakeReferenceIon("Iodoacetate", -1, 40.6),
	MakeReferenceIon("Lactate", -1, 38.8),
	MakeReferenceIon("Malate", -2, 58.8),
	MakeReferenceIon("Malonate", -1, 63.5),
	MakeReferenceIon("3-Methylbutanoate", -1, 32.7),
	MakeReferenceIon("Methylsulfonate", -1, 48.8),
	MakeReferenceIon("Naphthylacetate", -1, 28.4),
	MakeReferenceIon("1, 8-Octanedioate", -2, 36),
	MakeReferenceIon("Octylsulfonate", -1, 29),
	MakeReferenceIon("Oxalate", -2, 74.11),
	MakeReferenceIon("Phenylacetate", -1, 30.6),
	MakeReferenceIon("m-Phthalate", -2, 54.7),
	MakeReferenceIon("o-Phthalate", -2, 52.3),
	MakeReferenceIon("Picrate", -1, 30.37),
	MakeReferenceIon("Propanoate", -1, 35.8),
	MakeReferenceIon("Propylsulfonate", -1, 37.1),
	MakeReferenceIon("Salicylate", -1, 36),
	MakeReferenceIon("Succinate", -2, 58.8),
	MakeReferenceIon("Tartrate", -2, 59.6),
	MakeReferenceIon("Trichloroacetate", -1, 36.6),
	MakeReferenceIon("Trimethylacetate", -1, 31.9),
	// UNSW Medicine
	// https://medicalsciences.med.unsw.edu.au/research/research-services/ies/ionicmobilitytables
	MakeReferenceIonScaledToK("Choline", +1, 0.51),
	MakeReferenceIonScaledToK("Cs", +1, 1.05),
	MakeReferenceIonScaledToK("K", +1, 1),
	MakeReferenceIonScaledToK("Li", +1, 0.526),
	MakeReferenceIonScaledToK("NH4 (Ammonium)", +1, 1.001),
	MakeReferenceIonScaledToK("Na", +1, 0.682),
	MakeReferenceIonScaledToK("Rb", +1, 1.059),
	MakeReferenceIonScaledToK("TEA (TetraethylAmmonium)", +1, 0.444),
	MakeReferenceIonScaledToK("TMA (TetramethylAmmonium)", +1, 0.611),
	MakeReferenceIonScaledToK("Acetate", -1, 0.556),
	MakeReferenceIonScaledToK("Benzoate", -1, 0.441),
	MakeReferenceIonScaledToK("Br", -1, 1.063),
	MakeReferenceIonScaledToK("Cl", -1, 1.0382),
	MakeReferenceIonScaledToK("ClO4 (Perchlorate)", -1, 0.916),
	MakeReferenceIonScaledToK("F", -1, 0.753),
	MakeReferenceIonScaledToK("H2PO", -1, 0.45),
	MakeReferenceIonScaledToK("HCO3", -1, 0.605),
	MakeReferenceIonScaledToK("I", -1, 1.0456),
	MakeReferenceIonScaledToK("NO3 (Nitrate)", -1, 0.972),
	MakeReferenceIonScaledToK("Picrate", -1, 0.411),
	MakeReferenceIonScaledToK("Propionate", -1, 0.487),
	MakeReferenceIonScaledToK("SCN (Thiocyanate)", -1, 0.901),
	MakeReferenceIonScaledToK("Co", +2, 0.367),
	MakeReferenceIonScaledToK("Mg", +2, 0.361),
	MakeReferenceIonScaledToK("HPO4", -1, 0.39),
	MakeReferenceIonScaledToK("SO4", -2, 0.544),
	MakeReferenceIonScaledToK("NMDG", +1, 0.33),
	MakeReferenceIonScaledToK("Tris", +1, 0.4),
	MakeReferenceIonScaledToK("Aspartate", -1, 0.3),
	MakeReferenceIonScaledToK("Gluconate", -1, 0.33),
	MakeReferenceIonScaledToK("Glutamate", -1, 0.26),
	MakeReferenceIonScaledToK("HEPES", -1, 0.3),
	MakeReferenceIonScaledToK("Isethionate", -1, 0.52),
	MakeReferenceIonScaledToK("MES", -1, 0.37),
	MakeReferenceIonScaledToK("MOPS", -1, 0.35),
	MakeReferenceIonScaledToK("EGTA(2-)", -2, 0.24),
	MakeReferenceIonScaledToK("EGTA(3-)", -3, 0.25),
	MakeReferenceIonScaledToK("Thallium", +1, 1.02),
	MakeReferenceIonScaledToK("Butyrate", -1, 0.44),
	MakeReferenceIonScaledToK("Citrate", -3, 0.318),
	MakeReferenceIonScaledToK("2-(Methyl-Amino) Ethanol", +1, 0.49),
	MakeReferenceIonScaledToK("N-Methylethanolamine", +1, 0.49),
	MakeReferenceIonScaledToK("Ag", +1, 0.842),
	MakeReferenceIonScaledToK("Diethylammonium", +1, 0.57),
	MakeReferenceIonScaledToK("Dimethylammonium", +1, 0.705),
	MakeReferenceIonScaledToK("Ethyltrimethylammonium", +1, 0.551),
	MakeReferenceIonScaledToK("H", +1, 4.757),
	MakeReferenceIonScaledToK("Piperidinium", +1, 0.506),
	MakeReferenceIonScaledToK("Tetrabutylammonium", +1, 0.265),
	MakeReferenceIonScaledToK("Tetrapropylammonium", +1, 0.318),
	MakeReferenceIonScaledToK("Triethylammonium", +1, 0.467),
	MakeReferenceIonScaledToK("Trimethylammonium", +1, 0.643),
	MakeReferenceIonScaledToK("Bromoacetate", -1, 0.533),
	MakeReferenceIonScaledToK("Bromobenzoate", -1, 0.41),
	//MakeReferenceIon2("Chloroacetate", -1, 0.541), // different by
	MakeReferenceIonScaledToK("CNO (Cyanate)", -1, 0.879),
	MakeReferenceIonScaledToK("Cyanoacetate", -1, 0.59),
	MakeReferenceIonScaledToK("Dichloroacetate", -1, 0.521),
	MakeReferenceIonScaledToK("Ethylsulfate", -1, 0.539),
	MakeReferenceIonScaledToK("Ethylsulfonate", -1, 0.539),
	MakeReferenceIonScaledToK("Fluoroacetate", -1, 0.604),
	MakeReferenceIonScaledToK("Fluorobenzoate", -1, 0.45),
	MakeReferenceIonScaledToK("Formate", -1, 0.743),
	MakeReferenceIonScaledToK("Iodoacetate", -1, 0.552),
	MakeReferenceIonScaledToK("Lactate", -1, 0.528),
	MakeReferenceIonScaledToK("Methylsulfate", -1, 0.664),
	MakeReferenceIonScaledToK("methanesulfonate", -1, 0.664),
	MakeReferenceIonScaledToK("Methylsulfonate", -1, 0.664),
	MakeReferenceIonScaledToK("OH (hydroxide)", -1, 2.69),
	MakeReferenceIonScaledToK("ReO4 (Rhenate)", -1, 0.747),
	MakeReferenceIonScaledToK("Salicylate", -1, 0.49),
	MakeReferenceIonScaledToK("Trichloroacetate", -1, 0.476),
	MakeReferenceIonScaledToK("Cd", +2, 0.37),
	MakeReferenceIonScaledToK("Cu", +2, 0.365),
	MakeReferenceIonScaledToK("Fe", +2, 0.37),
	MakeReferenceIonScaledToK("Hg", +2, 0.433),
	MakeReferenceIonScaledToK("Mn", +2, 0.364),
	MakeReferenceIonScaledToK("Ni", +2, 0.337),
	MakeReferenceIonScaledToK("Pb", +2, 0.48),
	MakeReferenceIonScaledToK("Malate", -2, 0.4),
	MakeReferenceIonScaledToK("Maleate", -2, 0.421),
	MakeReferenceIonScaledToK("Oxalate", -2, 0.504),
	MakeReferenceIonScaledToK("Succinate", -2, 0.4),
	MakeReferenceIonScaledToK("Gd", +3, 0.305),
	MakeReferenceIonScaledToK("Fe", +3, 0.308),
	MakeReferenceIonScaledToK("La", +3, 0.316),
	MakeReferenceIonScaledToK("Citrate", -3, 0.318),
	MakeReferenceIonScaledToK("ATP (Adenosine 5'-Triphosphate)", -2, 0.15),
	MakeReferenceIonScaledToK("ATP (Adenosine 5'-Triphosphate)", -3, 0.15),
	MakeReferenceIonScaledToK("ATP (Adenosine 5'-Triphosphate)", -4, 0.15),
	MakeReferenceIonScaledToK("2-AP (2-aminopyridine)", +1, 0.45),
	MakeReferenceIonScaledToK("3-AP (3-aminopyridine)", +1, 0.46),
	MakeReferenceIonScaledToK("4-AP (4-aminopyridine)", +2, 0.29),
	// By listing such molecules here we confirm we know they exist,
	// and remind users they are probably not important for caculating LJP.
	MakeReferenceIon("GTP", 1, 0),
	MakeReferenceIon("Glucose", 1, 0),
	MakeReferenceIon("Sucrose", 1, 0),
	MakeReferenceIon("Dextrose", 1, 0),
	MakeReferenceIon("Phosphocreatine", 1, 0),
	};

let user set temperature

let user set temperature for KT math

also provide a "more info" button warning the user that a custom conductivity must be supplied for that different temperature

show error when zero-charge ions are added

molecules without charge (e.g., glucose) do not contribute to LJP. They are included in the ion mobility table though (so people don't think they were forgotten).

When zero-charge molecules are selected, a message should display indicating that they do not need to be added to the ion table because they do not contribute to ATP

searches for ion table in current (not program) directory

if launching LJPcalc.exe with a shortcut it doesn't find the IonTable.md file

Noted by @saglag

accomodate slow calculations

The JLJP screenshot ion set hangs for a long time when small amounts of Mg and Ag are added:

notice the calculation time was 42 seconds!

create "add ion" button

We should also add an "add ion", or "ion table details" button below the ion table in the program (#15). If the user clicks it it will launch the website (IonTable.md).

This way the user is pointed to documentation if they try to add an ion they can't find in the list.

output table doesn't show phi

refactor to make Calculate return LjpResult class which includes input parameters, final LJP, a copy of the original ion set, and the ion set after solving (with phis and new concentrations)