forked from albr7/ITC-draft
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.html
2710 lines (2139 loc) · 148 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
<!DOCTYPE html>
<html ng-app='ITC'>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<title>Oxford Chemistry - ITC Experimental Design Strategy Puzzle</title>
<meta property="og:url" content="https://learntech.imsu.ox.ac.uk/SPR/" />
<meta property="og:type" content="website" />
<meta property="og:title" content="Experimental Design Strategy Puzzle (SPR) - Oxford Biochemistry" />
<meta property="og:description" content="Learn experimental design through playing with a simulation of surface plasmon resonance. Created by Oxford Biochemistry Department." />
<meta property="og:image" content="http://www.your-domain.com/path/image.jpg" /
<!-- Angular Libraries & Credits -->
<script type="text/javascript" src="libraries/angular/angular.js"></script>
<script src="https://ajax.googleapis.com/ajax/libs/angularjs/1.4.8/angular-route.js"></script>
<script type="text/javascript" src="libraries/angular/angular-cookies.min.js"></script>
<!-- jQuery Libraries & Credits, load before Bootstrap & Flot since they requires it -->
<script type="text/javascript" src="libraries/jquery/jquery-1.11.3.min.js"></script>
<!-- Bootstrap Libraries -->
<link rel="stylesheet" href="libraries/bootstrap/bootstrap.min.css">
<link rel="stylesheet" href="libraries/bootstrap/bootstrap-theme.min.css">
<script type="text/javascript" src="libraries/bootstrap/bootstrap.min.js"></script>
<!-- Angular Flot Chart Libraries & Credits -->
<script type="text/javascript" src="libraries/flot/jquery.flot.js"></script>
<script type="text/javascript" src="libraries/flot/angular-flot.js"></script>
<script type="text/javascript" src="libraries/flot/jquery.flot.tooltip.min.js"></script>
<script type="text/javascript" src="libraries/flot/jquery.flot.axislabels.js"></script>
<script type="text/javascript" src="libraries/flot/jquery.flot.selection.js"></script>
<script type="text/javascript" src="scripts/services/chart-config.js"></script>
<!-- Ui-grid Libraries & Credits -->
<link rel="stylesheet" href="libraries/ui-grid/ui-grid.min.css">
<script type="text/javascript" src="libraries/ui-grid/ui-grid.min.js"></script>
<script type="text/javascript" src="libraries/ui-grid/exporter.js"></script>
<script type="text/javascript" src="libraries/ui-grid/selection.js"></script>
<script type="text/javascript" src="libraries/random.js"></script>
<script type='text/javascript' src='libraries/pdfmake/pdfmake.min.js'></script>
<script type='text/javascript' src='libraries/pdfmake/vfs_fonts.js'></script>
<script type="text/javascript" src="scripts/services/table-config.js"></script>
<script type='text/javascript' src='libraries/localstorage/angular-local-storage.min.js'></script>
<!-- Google Fonts Web Font Embedding & Credits
<link rel='stylesheet' type='text/css' href='https://fonts.googleapis.com/css?family=PT+Sans:700'>
<link rel='stylesheet' type='text/css' href='https://fonts.googleapis.com/css?family=Work+Sans:300,500'>-->
<!-- Personal libraries, load last since these files will be referencing to those previous libraries too -->
<script type="text/javascript" src="scripts/index_modules.js"></script>
<script type="text/javascript" src="scripts/services/system_model.js"></script>
<script type="text/javascript" src="scripts/services/experiment_status.js"></script>
<script type="text/javascript" src="scripts/services/output_model.js"></script>
<script type="text/javascript" src="scripts/filters/time_filter.js"></script>
<script type="text/javascript" src="scripts/filters/keylength.js"></script>
<!-- <script type="text/javascript" src="scripts/filters/mw_filter.js"></script>
<script type="text/javascript" src="scripts/filters/uM_filter.js"></script> -->
<script type="text/javascript" src="scripts/index_controller.js"></script>
<link rel="stylesheet" href="styles/main.css">
<title>ITC SIMULATION</title>
</head>
<body ng-controller="viewControl as view">
<!-- Distinguishing content for small device size media query -->
<div class="smallDevice">
<h1 class="smallDevice-heading">Oh No!</h1><br>
<h4 class="smallDevice-message">We know you are excited to start the practical</h4>
<h4 class="smallDevice-message">However, for the best experience</h4>
<h4 class="smallDevice-message">we would suggest switching to a device with larger screen size <br><font color="red">(at least an iPad viewing in landscape)</font></h4>
<h4 class="smallDevice-message">See you there!</h4>
</div>
<!-- Distinguishing content for large device size media query -->
<div class="largeDevice" style="min-height: 100%; padding-bottom: 150px; position:relative;">
<!-- 1. Navigation Bar -->
<nav id="oxonHeaderFooter" class="navbar navbar-fixed-top navbar-custom">
<div class="navbar-menu">
<!--a href="" class="navbar-text navbar-link">HOME</a>
<a href="" class="navbar-text navbar-link">OBJECTIVES</a>
<a href="" class="navbar-text navbar-link">SPR</a>
<a href="" class="navbar-text navbar-link">EXPERIMENT DESIGN</a>
<a href="" class="navbar-text navbar-link">CRITIQUE</a>
<div class="navbar-text navbar-clicked">SIMULATION</div>
<a href="" class="navbar-text navbar-link">SUMMARY</a>
<a href="" class="navbar-text navbar-link">CONTACT</a-->
<div id="navbar-placeholder">Goal: Complete the tutorial to teach yourself Isothermal Titration Calorimetry and practice experimental design skills.</div>
</div>
</nav>
<!--MODALS-->
<!-- ANSWERS MODAL -->
<div id="answers_modal" class="modal fade" tabindex="-1" role="dialog">
<div class="modal-dialog modal-lg" role="document">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span class="modal-cross" aria-hidden="true">×</span></button>
<h4 class="modal-title" id="modalLabel">Answers</h4>
</div>
<div class="modal-body">
When you have completed the practical, export your answer to PDF for the instructor to look at. For this feature to work, you must change the settings of the Chrome browser to open PDFs in the default viewer. <br><br>
Navigate to settings -> Privacy -> Content Settings -> PDF Documents -> Enable 'Open PDF files in default viewer'<br><br>
<div id="answer-table">
<div class="answer-grid" ui-grid="view.table.answerOptions" ui-grid-selection ui-grid-exporter></div>
</div><br>
</div>
</div>
</div>
</div>
<!-- RUNS MODAL -->
<div id="runs_modal" class="modal fade" tabindex="-1" role="dialog">
<div class="modal-dialog modal-lg" role="document">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span class="modal-cross" aria-hidden="true">×</span></button>
<h4 class="modal-title" id="modalLabel">Completed Runs</h4>
</div>
<div class="modal-body">
<div id="answer-table">
<div class="answer-grid" ui-grid="view.table.runOptions" ui-grid-selection ui-grid-exporter ui-grid-auto-resize></div>
</div><br>
</div>
</div>
</div>
</div>
<div id="calculating_modal" class="modal fade" tabindex="-1" role="dialog">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<h4 class="modal-title" id="modalLabel">Calculating...</h4>
</div>
</div>
</div>
</div>
<!-- INITIALIZATION MODAL -->
<div id="initialising_modal" class="modal fade in" tabindex="-1" role="dialog">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<!--button type="button" class="close" data-dismiss="modal" aria-label="Close"><span class="modal-cross" aria-hidden="true">×</span></button-->
<h4 class="modal-title" id="modalLabel">Welcome to ITClab!</h4>
</div>
<div class="modal-body">
Welcolme to the Isothermal Titration Calorimetry Laboratory - ITClab<br><br>
The aim of the lab is to teach you to characterise a reversible association reaction by designing an ITC experiment. This software is designed to mimic an ITC machine, allowing you to control the independent variables and have access to the results.<br><br>
However, before you plan and run an investigation to practice your experimental design skills, we want to teach you the theory and practice behind the technique. By reading the informaion available here, integrating it with your prior knowledge, and answering questions you will have a strong grounding in ITC. <br><br>
<font color="#51A7F9">Hence this lab is broken into 2 parts:</font><br>
<font color="#c5b552">(1) Interactive Tutorial:</font> You explore the software and answer questions on the presented material. Answering some questions will unlock other questions and information while answering other questions will unlock aspects of the software.<br>
<font color="#c5b552">(2) Investigation:</font> : You use the knowlege you gained in exploration to design, run and analyse an ITC investigation into reactions of your choice. The investigation becomes avaialable on completion of the interactive tutorial <br><br>
First, we will show you how the questions work...<br><br>
<font color="#51A7F9">QUESTION MECHANICS</font><br>
In order to unlock the investigation part of this tutorial, you must answer all questions correctly. Most questions are presented in multiple choice format, some are written answers, and some are both. If you get the question wrong at first then there are are a few options as to what happens:<br>
(1) You are prompted to answer the question again, but the second time round you are given a hint, or asked to answer the question in written form.<br>
(2) The software will ask you to talk to a demonstrator, who will explain the answer. When the demonstrator has finished, they will enter a code which lets the software know you have spoken to them.
<br><br>
This example shows you how it works - just select an answer and hit confirm. You can try both ways if you want - refresh the page in between and click restart.
</div>
<div class=question-box ng-show='view.experiment.questions[0].IsCorrect==null'>
<div class='modal-question-question'>Example Question</div>
<div class=modal-question-content>
{{view.experiment.questions[0].question}}<br><br>
{{view.experiment.questions[0][1]}}<br>
{{view.experiment.questions[0][2]}}<br>
{{view.experiment.questions[0][3]}}<br>
{{view.experiment.questions[0][4]}}<br>
</div>
<div class='modal-question-footer'>
<select id='mquestion' class='units_dropdown' ng-model='answer' ng-init="answer=1">
<option ng-value="1">A</option>
<option ng-value="2">B</option>
</select>
<button type='button' class='button clickable2' ng-click="view.mQuestion(answer,0)">CONFIRM</button>
</div>
</div>
<div class=question-box ng-show='view.experiment.questions[0].IsCorrect'>
<div class='modal-question-title-correct'>Correct!</div>
<div class=modal-question-content>
Congratulations, you answered the first question right! It will get harder...<br><br>
An isothermal process is one in which the temperature of the system does not change. This can be achieved by using a large heat sink (such as a constant temperature water bath) surrounding the system. Any heat released/absorbed by the system is absorbed/released by the water bath, keeping the temperature constant.
</div>
<div class='modal-question-footer'></div>
</div>
<div class=question-box ng-show='view.experiment.questions[0].IsCorrect==false'>
<div class='modal-question-title-incorrect'>Incorrect!</div>
<div class=modal-question-content>
Your answer is incorrect! Normally you would have to contact a demonstrator...<br><br>
This time just enter 'ITC' (without quotation marks) in the box below.
</div>
<div class='modal-question-footer'>
<form novalidate name='answer_form'>
<div>
Demonstrator Input:<br>
<input class="form" name="macroConc" ng-model='answer' type="string" required>
<button type="button" class="modal-button clickable2" ng-click="view.releaseFirstQuestion(answer,0)">Answer</button>
</div>
</form>
</div>
</div>
<div class ='modal-body'>
As you progress through the tutorial and you answer questions your answers are made available by clicking the 'Answers' button. In this tab you can export your answers to PDF - you'll have to do this at the end to give them to the demonstrator. Go there now and check it out if you want!<br><br>
As you progress though the tutorial your position is saved, if you accidentally close the browser - don't worry! Just reopen the page and click 'Continue'.<br><br>
Now you have answered the first question, the 'Theory' section has unlocked. Close this tab and navigate ther now.
</div>
<div class='modal-body' id='center_buttons'>
<button type="button" class="modal-button clickable2" data-dismiss="modal" >Continue</button>
</div>
</div>
</div>
</div>
<!-- THEORY MODAL -->
<div id="basics_modal" class="modal fade" tabindex="-1" role="dialog">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span class="modal-cross" aria-hidden="true">×</span></button>
<h4 class="modal-title" id="modalLabel">THEORY</h4>
</div>
<div class="modal-body">
<font color="#51A7F9"><b>WHAT IS THE PURPOSE OF AN ITC EXPERIMENT?</b></font><br><br>
Isothermal Titration Calorimetry (ITC) is a biophysical technique that is used to determine the thermodynamic parameters of association reactions. In just one well designed ITC experiment, the parameters ΔH<sub>R</sub>, K<sub>a</sub> and the stoichiometry (n) can all be determined. From these, ΔG<sub>R</sub> and ΔS<sub>R</sub> can also easily be calculated. <br><br>
This is achieved by measuring the energy change during a binding event across a range of solution compositions.<br><br>
</div>
<!-- CALCULATING THERMO PARAMETERS -->
<!-- question -->
<div class=question-box ng-show='view.experiment.questions[1].IsCorrect==null'>
<div class='modal-question-question'>Calculation</div>
<div class='modal-question-content'>
Given that:<br><br>
ΔH<sub>R</sub> = 11.60kJmol<sup>-1</sup><br>
K<sub>a</sub> = 3.10x10<sup>5</sup><br>
at T = 328K<br><br>
{{view.experiment.questions[1].question}}
</div>
<div class='modal-question-footer'>
<form novalidate name='answer_form'>
<div>
<input class="form" name="macroConc" ng-model='macroConc' type="number" required>
<button type="button" class="modal-button clickable2" ng-click="view.cQuestion(macroConc,1)">Answer</button>
</div>
</form>
</div>
</div>
<!-- correct -->
<div class=question-box ng-show='view.experiment.questions[1].IsCorrect'>
<div class='modal-question-title-correct'>Correct!</div>
<div class=modal-question-content>
Congratulations, you answered the question right! <br><br>
ΔG<sub>R</sub> = -RT ln (K<sub>a</sub>)<br>
ΔG<sub>R</sub> = ΔH<sub>R</sub> - TΔS<sub>R</sub>
</div>
<div class='modal-question-footer'>
</div>
</div>
<!-- WRONG1x try again-->
<div class=question-box ng-show='view.experiment.questions[1].IsCorrect==false && view.experiment.questions[1].beenWrong==1'>
<div class='modal-question-title-incorrect'>Calculation <b>Incorrect</b></div>
<div class='modal-question-content'>
<b>Your answer is wrong - please try again!</b><br><br>
Given that:<br><br>
ΔH<sub>R</sub> = 11.60kJmol<sup>-1</sup><br>
K<sub>a</sub> = 3.10x10<sup>5</sup><br>
at T = 328K<br><br>
{{view.experiment.questions[1].question}}
The calculation is carried out using basic thermodynamic expressions.<br>
</div>
<div class='modal-question-footer'>
<form novalidate name='answer_form'>
<div>
Please try again<br>
<input class="form" name="macroConc" ng-model='macroConc' type="number" required>
<button type="button" class="modal-button clickable2" ng-click="view.cQuestion(macroConc,1)">Answer</button>
</div>
</form>
</div>
</div>
<!-- WRONG 2X try again-->
<div class=question-box ng-show='view.experiment.questions[1].IsCorrect==false && view.experiment.questions[1].beenWrong==2'>
<div class='modal-question-title-incorrect'>Calculation <b>Incorrect</b></div>
<div class=modal-question-content>
Your answer is incorrect for the 2nd time. <br><br>
Given that:<br><br>
ΔH<sub>R</sub> = 11.60kJmol<sup>-1</sup><br>
K<sub>a</sub> = 3.10x10<sup>5</sup><br>
at T = 328K<br><br>
N.B. <br><br>
ΔG<sub>R</sub> = -RT ln (K<sub>a</sub>)<br>
ΔG<sub>R</sub> = ΔH<sub>R</sub> - TΔS<sub>R</sub><br><br>
{{view.experiment.questions[1].question}}<br><br>
Please try again.
</div>
<div class='modal-question-footer'>
<input class="form" name="macroConc" ng-model='macroConc' type="number" required>
<button type="button" class="modal-button clickable2" ng-click="view.cQuestion(macroConc,1)">Answer</button>
</div>
</div>
<!-- Wrong 3x - talk to demonstrator -->
<div class=question-box ng-show='view.experiment.questions[1].IsCorrect==false && view.experiment.questions[1].beenWrong==3'>
<div class='modal-question-title-incorrect'>Calculation <b>Incorrect</b></div>
<div class=modal-question-content>
Your answer is incorrect again. <br><br>
N.B. <br><br>
ΔG<sub>R</sub> = -RT ln (K<sub>a</sub>)<br>
ΔG = ΔH<sub>R</sub> - TΔS<sub>R</sub>
Please talk to the demonstrator.
</div>
<div class='modal-question-footer'>
<form novalidate name='answer_form'>
<div>
Demonstrator Input:<br>
<input class="form" name="macroConc" ng-model='answer' type="number" required>
<button type="button" class="modal-button clickable2" ng-click="view.releaseQuestion(answer,1)">Answer</button>
</div>
</form>
</div>
</div>
<!-- factors affecting thermo parameters questions -->
<div class=question-box ng-show='view.experiment.questions[2].IsCorrect==null'>
<div class='modal-question-question'>Question</div>
<div class=modal-question-content>
ITC is the only biophysical technique where all of ΔH<sub>R</sub>, K<sub>a</sub>, ΔG<sub>R</sub> and ΔS<sub>R</sub>, can be determined simultaneously.
{{view.experiment.questions[2].question}}
</div>
<div class='modal-question-footer'>
<form novalidate name='writtenAnswer'>
<textarea class='answer-form' name='WrittenAnswer' ng-model='WrittenAnswer' type='string' rows='4' placeholder='Written answer here...'></textarea>
<button type='button' class='button clickable2' ng-click="view.wQuestion(null,WrittenAnswer,2)">SUBMIT</button>
</form>
</div>
</div>
<div class=question-box ng-show='view.experiment.questions[2].IsCorrect==true'>
<div class='modal-question-title-correct'>Submitted</div>
<div class=modal-question-content>
Thank you for your answer, it will be checked by the demonstrator at the end of the tutorial.<br><br>
</div>
<div class='modal-question-footer'></div>
</div>
<div class='modal-body'>
<font color="#51A7F9"><b>HOW ARE THE MEASUREMENTS TAKEN?</b></font><br><br>
In a standard ITC machine there are two cells (shown below):<br>
<font color="#c5b552"><b>the sample cell</b></font> (filled with a sample solution) and <br>
<font color="#c5b552"><b>the reference cell</b></font> (filled with buffer solution);<br>
Both are in good thermal contact with a large heat sink (an<font color="#c5b552"><b> adiabatic jacket</b></font>), and a small amount of heat power (a baseline) is applied equally to both cells via separate heaters. The ligand is injected into the sample cell with a very sensitive, programable mechanical<font color="#c5b552"><b> syringe</b></font>. The temperature difference between the two cells is measured continuously and heat power to the sample cell is adjusted via a <font color="#c5b552"><b>feedback loop</b></font> to maintain the cells at exactly equal temperatures. Hence, if the reaction is exothermic the power applied to the <font color="#c5b552"><b>sample cell</b></font> (relative to the baseline power) is reduced, and visa versa for endothermic reactions. This differential power is the direct observable of the experiment and is used to calculate how much heat is released or absorbed during each injection. <br><br>
<img src="images/itcDiagram.png" alt='Diagram of ITC machine' style="width:300px;height:260px;display:block;margin:auto"></img><br><br>
</div>
<!-- EXAMPLE: ONE INJECTION -->
<div class=question-box ng-show='view.experiment.examples[0].isComplete==false || view.experiment.examples[1].isComplete==false'>
<div class='modal-example-title'>EXAMPLE 1!</div>
<div class=modal-question-content>
Its time to run your first ITC experiment!<br><br>
In this example we want you to get used to how the machine works by running two double injection experiments with different equilibration times (Injection Interval).<br><br>
<font color="#51A7F9"><b>Objectives:</b></font><br>
+ Learn how the inputs of the machine work.<br>
+ Understand the shape of the single injection output and how it relates to the injection interval.<br>
+ Understand if an output is exothermic or endothermic.<br><br>
Here are the parameters we want you to enter to the input fields on the right (all stay constant apart from injection interval):<br><br>
Number of Injections: 1,<br>
Volume of injections: 10μl,<br>
[ligand]: 300μM<br>
[macromolecule]: 30μM<br>
Injection interval: 100s and 500s<br><br>
<i>When you 'Process' the results the software integrates each individual injection peak and plots it against the molar ratio of ligand to sample. It outputs these data to the 'Results Table' below the Console. These data can be exported by clicking the menu item on the table and then clicking 'export to .csv'.<br><br>
You do not need to export the data from this experiment. </i>
</div>
<div class='modal-question-footer'>
<button type="button" class="modal-button clickable2" data-dismiss="modal" ng-click="view.runExample([0,1])">Start Example</button>
</div>
</div>
<div class=question-box ng-show='view.experiment.examples[0].isComplete==true && view.experiment.examples[1].isComplete==true'>
<div class='modal-example-title'>EXAMPLE 1 COMPLETE!</div>
<div class=modal-question-content>
Well Done!<br><br>
That was an example with just two injections. The power profile is defined by a sharp change, followed by a return to equilibrium value. Initially when the ligand is injected the net rate (forwards vs reverse) is at its highest, hence the large heat output. As the mixture comes closer to equilibrium, the net rate gets closer and closer to 0 (forwards rate ≈ backwards rate) and less and less heat is released.<br><br>
During ITC, it is very important that the cell is allowed to equilibrate between injections. Equilibration time changes is due to kinetic factors - a lower rate results in longer equilibration time. It may be useful to check using a similar two injection experiment whether the time between injections is long enough to achieve equilibration. <b>Do not just use an unneccessarily long equillibration time because the experiment will take much longer than it should!</b>
</div>
</div>
<!-- QUESTION: TWO INJECTIONS -->
<div class=question-box ng-show='view.experiment.questions[3].IsCorrect==null && view.experiment.examples[0].isComplete==true && view.experiment.examples[1].isComplete==true'>
<div class='modal-question-question'>Question</div>
<div class=modal-question-content>
{{view.experiment.questions[3].question}}<br><br>
{{view.experiment.questions[3][1]}}<br>
{{view.experiment.questions[3][2]}}<br>
{{view.experiment.questions[3][3]}}<br>
{{view.experiment.questions[3][4]}}<br>
</div>
<div class='modal-question-footer'>
<select id='mquestion' class='units_dropdown' ng-model='answer' ng-init="answer=1">
<option ng-value="1">A</option>
<option ng-value="2">B</option>
</select>
<button type='button' class='button clickable2' ng-click="view.mQuestion(answer,3)">SUBMIT</button>
</div>
</div>
<div class=question-box ng-show='view.experiment.questions[3].IsCorrect'>
<div class='modal-question-title-correct'>Correct</div>
<div class=modal-question-content>
Congratulations, you answered the question right! <br><br>
{{view.experiment.questions[3].ifCorrect}}
</div>
<div class='modal-question-footer'></div>
</div>
<div class=question-box ng-show='view.experiment.questions[3].IsCorrect==false && view.experiment.questions[3].beenWrong==1 '>
<div class='modal-question-title-incorrect'>Incorrect</div>
<div class=modal-question-content>
Remember that the calorimeter works by power compenstation. That is, if the heat of the cell increases then the power supplied to the cell decreases to keep the difference in temperature between the two cells as low as possible.<br><br>
So an increase in power corresponds to an endothermic reaction.<br><br>
{{view.experiment.questions[3].question}}<br><br>
{{view.experiment.questions[3][1]}}<br>
{{view.experiment.questions[3][2]}}<br>
{{view.experiment.questions[3][3]}}<br>
{{view.experiment.questions[3][4]}}<br>
</div>
<div class='modal-question-footer'>
<form novalidate name='answer_form'>
<div>
Demonstrator Input:<br>
<input class="form" name="macroConc" ng-model='answer' type="number" required>
<button type="button" class="modal-button clickable2" ng-click="view.releaseQuestion(answer,3)">Answer</button>
</div>
</form>
</div>
</div>
<div class="modal-body">
<font color="#51A7F9"><b>WHAT DO THE RESULTS OF AN ITC EXPERIMENT LOOK LIKE AND WHY?</b></font><br><br>
An ITC experiment consists of not just one or two injections but a series of injections (25-30 is normal). The molar ratio of titrant to titrand (ligand:sample) increases stepwise over the course of the experiment and importantly, the saturation of the sample is higher with each injection. The heat change is therfore not constant for each injection due to the increasing saturation of the sample. If the experiment is well designed then the set of injections will produce very varied heats of injection over the molar ratio range. <br><br>
Lets consider why the total heat produced per injection varies over the course of the experiment (an exothermic example): on the first few injections, almost all of the ligand associates with the sample. With subsequent injections, the sample already has more ligand associated to it, and hence less of the injected ligand will bind, producing less heat per injection. The sample passes through an equivalence point and into the late stages of the experiment and less and less ligand binds to a more saturated sample, until the sample is fully saturated and no heat is released upon injection.<br><br>
The resulting graph takes a sigmoidal shape with the inflection point of the graph representing the stoichiometry of the reaction. A typical ITC experimental output is seen below. The graph on top is the raw data output. By integrating each peak, you get a total heat output per injection, which is plotted in the lower half of the figure below. It is possible to change the x-axis to molar ratio for convienience. <br><br>
The thermodynamic parameters can be extracted from this graph, either using an computer based iterative method, or a manual method. <br><br>
<img src="images/itcOutput.png" style='width:300px;height:360px;display:block;margin:auto'>
<font color="#51A7F9"><b>ANALYSIS</b></font><br><br>
The thermodynamic parameters can be extracted from this graph, either using an computer based iterative method, or a less robust manual method. Both will breifly be discussed here: <br><br>
The stoichiometry (n) is easy: it is represented by the position of the infection point. For instance, if the inflection point is located at a molar ratio of 1, then n=1. If it is at 3, then n = 3.<br><br>
<font color="#51A7F9"><u>(1) Iterative Method</u></font><br>
The method solves for ΔH<sub>R</sub> and K<sub>a</sub> simultaneously by starting from an approximate K<sub>a</sub> and then calculating hypothetical ΔH<sub>R</sub> for each addition of titrant. Based on the variation between these enthalpy figures, the approximate K<sub>a</sub> value is adjusted, and the enthalpies recalculated. Over a large number of iterations, the variation between the individual ΔH<sub>R</sub> is minimised, to yield the values of K<sub>a</sub> and ΔH<sub>R</sub>.<br><br>
<font color="#51A7F9"><u>(2) Asymptote Method</u></font>
First, ΔH<sub>R</sub> is calculated from a non-zero asymptote of the sigmoidal curve binding isotherm. The complete reaction of a vanishingly small addition of titrant can be assumed (the relative extent of reaction approaches unity as the concentration approaches zero). In other words, we assume that all of the ligand binds in the first injection, and calcuate ΔH<sub>R</sub> from that <br><br>
Once the figure for ΔH<sub>R</sub> is known, the true extent of reaction for each injection can be calculated (from total heat evolved through to that addition relative to the total moles of titrant added through that same point) and hence values for K<sub>a</sub> can be found for each injection (from total amounts of product formed and reactant remaining based on each total extent of reaction). Importantly, the value of K<sub>a</sub> is calculated with the least error in the inflection region of the experiment. For the earliest or latest points in the titration, there is very high relative error resulting from very little product formed or very little reactant remaining, hence the lowest-uncertainty association constant results will come from the middle part of the titration curve.<br><br>
Do not worry if you do not undertstand this fully - the analysis using the asymptote method will be covered in detail later in the tutorial, when you will create a spreadsheet that will allow you to complete many sets of data analysis. The most important thing to know for now is that you want the shape of the graph to be sigmoidal.
</div>
<div class=question-box ng-show='view.experiment.questions[4].IsCorrect==null'>
<div class='modal-question-question'>Question</div>
<div class=modal-question-content>
{{view.experiment.questions[4].question}}<br><br>
{{view.experiment.questions[4][1]}}<br>
{{view.experiment.questions[4][2]}}<br>
{{view.experiment.questions[4][3]}}<br>
{{view.experiment.questions[4][4]}}<br>
</div>
<div class='modal-question-footer'>
<select id='mquestion' class='units_dropdown' ng-model='answer' ng-init="answer=1">
<option ng-value="1">A</option>
<option ng-value="2">B</option>
<option ng-value="3">C</option>
</select>
<button type='button' class='button clickable2' ng-click="view.mQuestion(answer,4)">CONFIRM ANSWER</button>
</div>
</div>
<div class=question-box ng-show='view.experiment.questions[4].IsCorrect'>
<div class='modal-question-title-correct'>Correct!</div>
<div class=modal-question-content>
Congratulations, you answered the question right! <br><br>
This tyoe of equilibrium constant is known as a concentration equilibrium constant. Normally, the units of K<sub>a</sub> would be unitless, but in thies case, we use units of mol<sup>-1</sup>dm<sup>3</sup>.
</div>
<div class='modal-question-footer'></div>
</div>
<div class=question-box ng-show='view.experiment.questions[4].IsCorrect==false && view.experiment.questions[4].beenWrong==1'>
<div class='modal-question-title-incorrect'>Incorrect</div>
<div class=modal-question-content>
Your answer is incorrect. <br><br>
<b>Contact the demonstrator now if you are having problems. If you are incorrect again the demonstrator will help you before you can continue.</b><br><br>
{{view.experiment.questions[4].question}}<br><br>
{{view.experiment.questions[4][1]}}<br>
{{view.experiment.questions[4][2]}}<br>
{{view.experiment.questions[4][3]}}<br>
{{view.experiment.questions[4][4]}}<br>
</div>
<div class='modal-question-footer'>
<select id='mquestion' class='units_dropdown' ng-model='answer' ng-init="answer=A" >
<option ng-value="1">A</option>
<option ng-value="2">B</option>
<option ng-value="3">C</option>
</select>
<button type='button' class='button clickable2' ng-click="view.mQuestion(answer,4)">CONFIRM</button>
</form>
</div>
</div>
<div class=question-box ng-show='view.experiment.questions[4].IsCorrect==false && view.experiment.questions[4].beenWrong==2'>
<div class='modal-question-title-incorrect'>Incorrect!</div>
<div class=modal-question-content>
Your answer is incorrect for the 2nd time, please contact a demonstrator to discuss.
</div>
<div class='modal-question-footer'>
<form novalidate name='answer_form'>
<div>
Demonstrator Input:<br>
<input class="form" name="macroConc" ng-model='answer' type="number" required>
<button type="button" class="modal-button clickable2" ng-click="view.releaseQuestion(answer,4)">Answer</button>
</div>
</form>
</div>
</div>
</div>
</div>
</div>
<!-- EXPERIMENTAL OVERVIEW MODAL -->
<div id="overview1_modal" class="modal fade" tabindex="-1" role="dialog">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span class="modal-cross" aria-hidden="true">×</span></button>
<h4 class="modal-title" id="modalLabel">Experimental Overview</h4>
</div>
<div class="modal-body">
The basics steps that make up an ITC experiment are laid out below:<br><br>
+ <b>Planning</b><br>
Select: concentrations, volume of injection, number of injections, time between injections<br><br>
</div>
<div class="modal-body" ng-show="expression">
</div>
<div class="modal-body">
+ <b>Solution Preparation</b><br>
Do: make solutions, ?test solutions for concenrations<br><br>
</div>
<div class="modal-body" ng-show="expression">
</div>
<div class="modal-body">
+ <b>Collect Raw Data</b><br>
Run the experiment<br><br>
</div>
<div class="modal-body" ng-show="expression">
</div>
<div class="modal-body">
+ <b>Correct Raw Data</b><br>
Determine other contributions to heat release and adjust raw data<br><br>
</div>
<div class="modal-body" ng-show="expression">
</div>
<div class="modal-body">
+ <b>Process and Analyse Data</b><br>
Determine if hypothesis has been tested and/or disproved/proved<br><br>
</div>
<div class="modal-body" ng-show="expression">
</div>
<div class="modal-body">
+ <b>Repeat</b><br>
If results are inconclusive, adjust parameters/hypothesis accordingly and re-run experiment.<br><br>
</div>
<div class="modal-body" ng-show="expression">
</div>
</div>
</div>
</div>
<!-- PLANNING MODAL -->
<div id="planning_modal" class="modal fade" tabindex="-1" role="dialog">
<div class="modal-dialog" role="document">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal" aria-label="Close"><span class="modal-cross" aria-hidden="true">×</span></button>
<h4 class="modal-title" id="modalLabel">PLANNING</h4>
</div>
<div class="modal-body">
<i>Before you try to design a good experiment, you need to first understand the technique you are using and what you are expecting. Review your knowledge on ITC in the Theory Tab, or ask a demonstrator if you need any help.</i><br><br>
<font color="#51A7F9">Planning of an ITC experiment is very important.</font> Being able to determine ΔH<sub>R</sub> and K<sub>a</sub> relies on choosing the correct concentrations of ligand and sample macromolecule because:<br><br>
<font color="#c5b552">+ finding ΔH<sub>R</sub> </font> is constrained by the sensitivity of the instrument - if not enough heat is produced per injection because concentrations are too low (signal to noise ratio is to low) then you cannot find ΔH<sub>R</sub>.<br><br>
<font color="#c5b552">+ finding K<sub>a</sub></font> depends on the heat change varying between injections to produce a smooth sigmoid that was discussed in 'Theory'. The shape of the curve is a function of K<sub>a</sub> and the concentration of macromolecule in the sample cell. <br><br>
<font color="#51A7F9"><b>How is the shape affected by changing K<sub>a</sub> and [Macromolecule]? Lets find out!</font></b><br><br>
Brandt's experimental parameter (c) is defined by:<br><br>
<font color="#ED621D"><div style='text-align: center'><b><i>c = K<sub>a</sub> x [Macromolecule] x n</i></b> </div></font> <br><br>
For the sigmoidal curve to be the correct shape to achieve characterisation, <font color="#ED621D">c should lie between 10 and 1000</font>, with best results found in the middle of the range.<font color="#c5b552"> Hence, in order to plan an ITC experiment, you need to have a rough idea of K<sub>a</sub>,</font> so that you can choose a concentration of macromolecule which brings c into the acceptable range. <br><br>
<font color="#ED621D"><div style='text-align: center'><b><i>10 < c < 1000</i></b> </div></font> <br><br>
It seems counterintuitive that in order to design a good experiment and determine K<sub>a</sub> you need to have a rough estimate of that parameter! Normally when attempting to run an ITC, data will be gathered to find a rough estimate of them beforehand. Techniques that are used to find estimates of K<sub>a</sub> include:<br>
<font color="#c5b552">+ Fluorescence spectroscopy</font><br>
<font color="#c5b552">+ Surface plasmon resonance</font><br><br>
ITC is then used to determine a much more accurate value of K<sub>a</sub> and additionally ΔH<sub>R</sub>.<br><br>
So [Macromolecule] is chosen to keep c within the acceptable range based on an estimate of K<sub>a</sub>. <font color="#51A7F9">How then, do you select the [ligand]?</font> Consider the stoichiometry. We want the equivalence point of the reaction to occur halfway though the experiment, so select the concentrations that will achieve this based on the stoichiometry, injection volume and number of injections. You will get some practice determining these concentrations shortly.<br><br>
When researchers were looking into the effect of c on the shape of the ITC curve, they simulated many ITC runs to work out exactly the acceptable range. Lets run a range of experiments to show the effect directly. From the results, we can discuss how best to select c values, and the specific limitations of high and low K<sub>a</sub> values.<br><br>
But first, we need to be sure that we can calculate the concentrations of ligand and macromolecule required based on the Brandt's c parameter...
</div>
<!-- WORKED EXAMPLE 1 -->
<div class=question-box ng-show='view.experiment.worked[0].stage==1'>
<div class='modal-example-title-'>Worked Example 1</div>
<div class=modal-question-content>
N.B. In this ITC machine the following is true:<br>
Volume sample cell = 0.000994l (994μl)<br>
Volume syringe = 0.000250l (250μl)<br><br>
In this example:<br>
K<sub>a</sub> ≈ 4.0 x 10<sup>6</sup><br>
ΔH<sub>R</sub> ≈ -10 kJ/mol<br><br>
<font color="#51A7F9">1) Calculate a suitable concentration for the macromolecule solution.</font><br>
<font color="#c5b552">2) Calculate a suitable concentration for the ligand solution.</font><br><br>
<font color="#51A7F9">1) Recall that ideal conditions are 10<c<1000, where c = K<sub>a</sub> x [Macromolecule] x n</i>. We select c = 50.<br><br>
c = 50 = (4.0 x 10<sup>6</sup>) x [macromolecule],<br>
[macromolecule] = 50/(4.0 x 10<sup>6</sup>) = 12.5μM<br><br></font>
<font color="#c5b552">2) We want the equivalence point to occur halfway through the titration, so moles of titrant should be twice the moles of ligand n<sub>macro</sub>=994μl*12.5μM = 12.425nM, thus n<sub>ligand</sub>=24.85nM.<br><br>
Assuming that we use the total volume of the syringe for the titration: [ligand] = 24.85nM/250μl = 99.4μM<br><br></font>
When you are happy with this calculation click continue, you will be asked to complete a similar calculation before we move on.
</div>
<div class='modal-question-footer'>
<button type="button" class="modal-button clickable2" ng-click="view.experiment.worked[0].stage=2">Continue</button>
</div>
</div>
<!-- CALCULATION QUESTION -->
<!-- QUESITON 1a [macromolecule]-->
<div class=question-box ng-show='view.experiment.worked[0].stage==2 && view.experiment.questions[5].IsCorrect==null'>
<div class='modal-question-question'>Calculation (a)</div>
<div class='modal-question-content'>
N.B. In this ITC machine the following is true:<br>
Volume sample cell = 0.000994l,<br>
Volume syringe = 0.000250l<br><br>
In this example:<br>
K<sub>a</sub> ≈ 2.0 x 10<sup>9</sup><br>
ΔH<sub>R</sub> ≈ -21 kJ/mol<br><br>
<b>1) Calculate a suitable concentration for the macromolecule solution.</b><br>
afterwards you will be asked to:<br>
2) Calculate a suitable concentration for the ligand solution.<br><br>
Select c = 50 as previously.<br>
YOUR ANSWER SHOULD BE ENTERED IN MOLAR UNITS
</div>
<div class='modal-question-footer'>
<form novalidate name='answer_form'>
<div>
Macromolecule<br>
<input class="form" name="macroConc" ng-model='macroConc' type="number" required>
<button type="button" class="modal-button clickable2" ng-click="view.cQuestion(macroConc,5)">Answer</button>
</div>
</form>
</div>
</div>
<!-- CORRECT -->
<div class=question-box ng-show='view.experiment.questions[5].IsCorrect && view.experiment.worked[0].stage==2'>
<div class='modal-question-title-correct'>Correct!</div>
<div class=modal-question-content>
Congratulations, you answered the question right! <br><br>
</div>
<div class='modal-question-footer'>
<button type="button" class="modal-button clickable2" ng-click="view.experiment.worked[0].stage=3">Continue</button>
</div>
</div>
<!-- WRONG -->
<div class=question-box ng-show='view.experiment.worked[0].stage==2 && view.experiment.questions[5].IsCorrect==false && view.experiment.questions[5].beenWrong==1'>
<div class='modal-question-title-incorrect'>Calculation (a) <b>Incorrect</b></div>
<div class='modal-question-content'>
<b>Your answer is wrong - please try again!</b><br><br>
N.B. In this ITC machine the following is true:<br>
Volume sample cell = 0.000994l,<br>
Volume syringe = 0.000250l<br><br>
In this example:<br>
K<sub>a</sub> ≈ 2.0 x 10<sup>9</sup><br>
ΔH<sub>R</sub> ≈ -21 kJ/mol<br><br>
<b>1) Calculate a suitable concentration for the macromolecule solution.</b></b><br>
afterwards you will be asked to:<br>
2) Calculate a suitable concentration for the ligand solution.<br><br>
Select c = 50 as previously.<br>
YOUR ANSWER SHOULD BE ENTERED IN MOLAR UNITS
</div>
<div class='modal-question-footer'>
<form novalidate name='answer_form'>
<div>
Please try again - Macromolecule<br>
<input class="form" name="macroConc" ng-model='macroConc' type="number" required>
<button type="button" class="modal-button clickable2" ng-click="view.mQuestion(macroConc,5)">Answer</button>
</div>
</form>
</div>
</div>
<!-- WRONG 2X -->
<div class=question-box ng-show='view.experiment.questions[5].IsCorrect==false && view.experiment.questions[5].beenWrong==2'>
<div class='modal-question-title-incorrect'>Incorrect!</div>
<div class=modal-question-content>
Your answer is incorrect for the 2nd time. The worked example can be found below:<br><br>
c = 50 = (2.0 x 10⁹) x [macromolecule],<br>
[macromolecule] = 50/(2.0 x 1⁹) = 25nM<br><br>
<i>You will have to perfrom this calculation multiple times from here on. </i>
</div>
<div class='modal-question-footer'>
<button type="button" class="modal-button clickable2" ng-click="view.experiment.worked[0].stage=3;view.experiment.questions[5].IsCorrect=true">Continue</button>
</div>
</div>
<!-- QUESTION 1B [ligand]-->
<div class=question-box ng-show='view.experiment.worked[0].stage==3 && view.experiment.questions[6].IsCorrect==null'>
<div class='modal-question-question'>Calculation (b)</div>
<div class='modal-question-content'>
N.B. In this ITC machine the following is true:<br>
Volume sample cell = 0.000994l,<br>
Volume syringe = 0.000250l<br><br>
In this example:<br>
K<sub>a</sub> ≈ 2.0 x 10<sup>9</sup><br>
ΔH<sub>R</sub> ≈ -21 kJ/mol<br><br>
1) Calculate a suitable concentration for the macromolecule solution.<br>
answer to 1): {{view.experiment.questions[5].answer}}M<br>
<b>2) Calculate a suitable concentration for the ligand solution.</b><br><br>
Select c = 50 as previously.<br>
YOUR ANSWER SHOULD BE ENTERED IN MOLAR UNITS
</div>
<div class='modal-question-footer'>
<form novalidate name='answer_form'>
<div>
Ligand Concentration<br>
<input class="form" name="ligandConc" ng-model='ligandConc' type="number" required>
<button type="button" class="modal-button clickable2" ng-click="view.mQuestion(ligandConc,6)">Answer</button>
</div>
</form>
</div>
</div>
<!-- CORRECT -->
<div class=question-box ng-show='view.experiment.questions[6].IsCorrect && view.experiment.worked[0].stage==3'>
<div class='modal-question-title-correct'>Correct!</div>
<div class=modal-question-content>
Congratulations, you answered the question right! <br><br>
</div>
<div class='modal-question-footer'>
<button type="button" class="modal-button clickable2" ng-click="view.experiment.worked[0].stage=4">Continue</button>
</div>
</div>
<!-- WRONG -->
<div class=question-box ng-show='view.experiment.worked[0].stage==3 && view.experiment.questions[6].IsCorrect==false && view.experiment.questions[6].beenWrong==1'>
<div class='modal-question-title-incorrect'>Calculation (b) <b>Incorrect</b></div>
<div class='modal-question-content'>
Your answer is wrong - please try again!<br><br>
N.B. In this ITC machine the following is true:<br>
Volume sample cell = 0.000994l,<br>
Volume syringe = 0.000250l<br><br>
In this example:<br>
K<sub>a</sub> ≈ 2.0 x 10<sup>9</sup><br>
ΔH<sub>R</sub> ≈ -21 kJ/mol<br><br>
1) Calculate a suitable concentration for the macromolecule solution.<br>
answer to 1): {{view.experiment.questions[5].answer}}M<br>
<b>2) Calculate a suitable concentration for the ligand solution.</b><br><br>
Select c = 50 as previously.<br>
YOUR ANSWER SHOULD BE ENTERED IN MOLAR UNITS
</div>
<div class='modal-question-footer'>
<form novalidate name='answer_form'>
<div>
Please try again - Macromolecule<br>
<input class="form" name="macroConc" ng-model='ligandConc' type="number" required>
<button type="button" class="modal-button clickable2" ng-click="view.mQuestion(ligandConc,6)">Answer</button>
</div>
</form>
</div>
</div>
<!-- WRONG 2x -->
<div class=question-box ng-show='view.experiment.questions[6].IsCorrect==false && view.experiment.questions[6].beenWrong==2 && view.experiment.worked[0].stage==3'>
<div class='modal-question-title-incorrect'>Incorrect!</div>
<div class=modal-question-content>
Your answer is incorrect for the 2nd time. The worked example can be found below:<br><br>
We want the equivalence point to occur halfway through the titration, so moles of titrant should be twice the moles of ligand n<sub>macro</sub>=994μl*25nM = 24.85pmol, thus n<sub>ligand</sub>=49.7pmol.<br><br>
Assuming that we use the total volume of the syringe for the titration: [ligand] = 49.9pmol/250μl = 0.1988μM<br><br>
You will have to perfrom this calculation multiple times from here on so please study it.
</div>
<div class='modal-question-footer'>
<button type="button" class="modal-button clickable2" ng-click="view.experiment.worked[0].stage=4; view.experiment.questions[6].IsCorrect=true;view.compileCookieData()">Continue</button>
</div>
</div>
<!-- CALCULATION WITH 3X STOICHIOMETRY -->
<div class=question-box ng-show='view.experiment.worked[0].stage==4 && view.experiment.questions[7].IsCorrect==null'>
<div class='modal-question-question'>Calculation (c)</div>
<div class='modal-question-content'>
N.B. In this ITC machine the following is true:<br>
Volume sample cell = 0.000994l,<br>
Volume syringe = 0.000250l<br><br>
In the previous examples we assumed that the stoichiometry (n) ≈ 1.0. Consider the case with higher n.<br><br>
In this example:<br>
K<sub>a</sub> ≈ 2.0 x 10<sup>9</sup><br>
ΔH<sub>R</sub> ≈ -21 kJ/mol<br>
The stoichiometry (n) ≈ 3.0<br><br>
1) Calculate a suitable concentration for the macromolecule solution.<br>
answer to 1): {{view.experiment.questions[4].answer}}<br>
<b>2) Calculate a suitable concentration for the ligand solution.</b><br><br>
Select c = 50 as previously.<br>
YOUR ANSWER SHOULD BE ENTERED IN MOLAR UNITS
</div>
<div class='modal-question-footer'>
<form novalidate name='answer_form'>
<div>
Ligand Concentration<br>
<input class="form" name="ligandConc" ng-model='ligandConc' type="number" required>
<button type="button" class="modal-button clickable2" ng-click="view.mQuestion(ligandConc,7)">Answer</button>
</div>
</form>
</div>
</div>
<!-- CORRECT -->
<div class=question-box ng-show='view.experiment.questions[7].IsCorrect && view.experiment.worked[0].stage==4'>
<div class='modal-question-title-correct'>Correct!</div>
<div class=modal-question-content>
Congratulations, you answered the question right! <br><br>
</div>
<div class='modal-question-footer'>
<button type="button" class="modal-button clickable2" ng-click="view.experiment.worked[0].stage=5;view.compileCookieData()">Continue</button>
</div>
</div>
<!-- WRONG -->
<div class=question-box ng-show='view.experiment.worked[0].stage==4 && view.experiment.questions[7].IsCorrect==false && view.experiment.questions[7].beenWrong==1'>
<div class='modal-question-title-incorrect'>Calculation (c) <b>Incorrect</b></div>
<div class='modal-question-content'>
Your answer is wrong - please try again!<br><br>
N.B. In this ITC machine the following is true:<br>
Volume sample cell = 0.000994l,<br>
Volume syringe = 0.000250l<br><br>
In the previous examples we assumed that the stoichiometry (n) ≈ 1.0. Consider the case with higher n.<br><br>
In this example:<br>
K<sub>a</sub> ≈ 2.0 x 10<sup>9</sup><br>
ΔH<sub>R</sub> ≈ -21 kJ/mol<br><br>
The stoichiometry (n) ≈ 3.0
1) Calculate a suitable concentration for the macromolecule solution.<br>
afterwards you will be asked to:
<b>2) Calculate a suitable concentration for the ligand solution.</b><br><br>
Select c = 50 as previously.<br>
YOUR ANSWER SHOULD BE ENTERED IN MOLAR UNITS
</div>
<div class='modal-question-footer'>
<form novalidate name='answer_form'>
<div>
Please try again - Macromolecule<br>
<input class="form" name="macroConc" ng-model='ligandConc' type="number" required>
<button type="button" class="modal-button clickable2" ng-click="view.mQuestion(ligandConc,7)">Answer</button>
</div>
</form>
</div>
</div>
<!-- WRONG 2x -->
<div class=question-box ng-show='view.experiment.questions[7].IsCorrect==false && view.experiment.questions[7].beenWrong==2 && view.experiment.worked[0].stage==4'>
<div class='modal-question-title-incorrect'>Incorrect!</div>
<div class=modal-question-content>
Your answer is incorrect for the 2nd time. The worked example can be found below:<br><br>