-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathnotation.html
163 lines (160 loc) · 6.06 KB
/
notation.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
<!DOCTYPE html>
<html>
<head>
<title>Notation</title>
<!--
<link rel="stylesheet" type="text/css" href="styles.css" />
-->
<style type="text/css">
body {
background-color: #CCCC99;
font-family: Verdana, sans-serif;
font-size: 12 px;
}
</style>
<script type="text/x-mathjax-config">
MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}});
</script>
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
TeX: {
equationNumbers: { autoNumber: "AMS" },
extensions: ["AMSmath.js", "AMSsymbols.js"]
}
});
</script>
<script type="text/javascript"
src="https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>
<script type="text/javascript" src="functions.js"></script></head>
<body>
<h2> Notation and Technical Terminology </h2>
<table cellspacing="10">
<tr>
<th style="text-align:left">Symbol or Term</th>
<th style="text-align:left">Definition</th>
</tr>
<tr>
<td>$\Phi$</td>
<td>The electrostatic potential, which generally will vary in space and different cellular compartments.
See <a href="javascript:changeTo('ionsNernst','notation','0')">Ion Gradients</a>.
</td>
</tr>
<tr>
<td>$[\mathrm{X}]$</td>
<td>The concentration of species (or state) $\mathrm{X}$, generally equal to $N_X/V$.
See <a href="javascript:changeTo('statesRates','notation','0')">States & Kinetics</a>,
<a href="javascript:changeTo('equil','notation','0')">Equilibrium</a>.
</td>
</tr>
<tr>
<td>$\langle A \rangle$</td>
<td>
Thermodynamic average of the quantity $A$ (under specified conditions).
See <a href="javascript:changeTo('freeThermo','notation','0')">Free Energy & Work</a>.
</td>
</tr>
<tr>
<td>$F$</td>
<td>Helmholtz free energy, $\langle E \rangle - TS$ .
See <a href="javascript:changeTo('freeThermo','notation','0')">Free Energy & Work</a>.
</td>
</tr>
<tr>
<td>$k_B$</td>
<td>Boltzmann's constant. $k_B \, T \sim R T$ is the natural scale of thermal energy at temperature $T$.
See
<a href="javascript:changeTo('idealGas','notation','0')">The Ideal Gas</a>.
</td>
</tr>
<tr>
<td>$k_{ij}$</td>
<td>Rate constant for transitions from $i$ to $j$. Probability per unit time to transition from $i$ to $j$.
See
<a href="javascript:changeTo('massAction','notation','0')">Mass-Action Kinetics</a>,
<a href="javascript:changeTo('statesRates','notation','0')">States & Kinetics</a>,
<a href="javascript:changeTo('catalysis','notation','0')">Catalysis</a>,
<a href="javascript:changeTo('equil','notation','0')">Equilibrium</a>.
</td>
</tr>
<tr>
<td>$k_{\mathrm{off}}$</td>
<td>Rate constant for unbinding - i.e., for bi-molecular dissociation.
Probability per $s$ for a bi-molecular complex to dissociate.
See
<a href="javascript:changeTo('massAction','notation','0')">Mass-Action Kinetics</a>,
<a href="javascript:changeTo('carriers','notation','0')">Activated Carriers</a>.
</td>
</tr>
<tr>
<td>$k_{\mathrm{on}}$</td>
<td>Rate constant for binding - i.e., for bi-molecular association.
Probability per $s$ for a single molecule to bind one molecule of another species, with the latter at the reference 1M concentration.
See
<a href="javascript:changeTo('massAction','notation','0')">Mass-Action Kinetics</a>,
<a href="javascript:changeTo('carriers','notation','0')">Activated Carriers</a>.
</td>
</tr>
<tr>
<td>$k_X$</td>
<td>Rate constant for a process "X", which might be a chemical reaction, isomerization, or (un)binding process - and should be determined by the context.
See
<a href="javascript:changeTo('massAction','notation','0')">Mass-Action Kinetics</a>,
<a href="javascript:changeTo('statesRates','notation','0')">States & Kinetics</a>,
<a href="javascript:changeTo('catalysis','notation','0')">Catalysis</a>,
<a href="javascript:changeTo('synthesis','notation','0')">Synthesis</a>.
</td>
</tr>
<tr>
<td>$N_i$</td>
<td>Number of systems or molecules in state $i$.
See <a href="javascript:changeTo('statesRates','notation','0')">States & Kinetics</a>,
<a href="javascript:changeTo('equil','notation','0')">Equilibrium</a>.
</td>
</tr>
<tr>
<td>$N_X$</td>
<td>Number of copies of species (e.g., molecule) $\mathrm{X}$.
See <a href="javascript:changeTo('statesRates','notation','0')">States & Kinetics</a>,
<a href="javascript:changeTo('equil','notation','0')">Equilibrium</a>.
</td>
</tr>
<tr>
<td>$p_i$</td>
<td>Probability of state $i$, generally equal to $N_i/N$.
See <a href="javascript:changeTo('statesRates','notation','0')">States & Kinetics</a>,
<a href="javascript:changeTo('equil','notation','0')">Equilibrium</a>.
</td>
</tr>
<tr>
<td>$R$</td>
<td>The gas constant. $k_B \, T = R T$ is the natural scale of thermal energy at temperature $T$.
See
<a href="javascript:changeTo('idealGas','notation','0')">The Ideal Gas</a>.
</td>
</tr>
<tr>
<td>$\mathbf{r}^N$</td>
<td>The configuration of a system of $N$ atoms or molecules, it is short-hand for the full set of Cartesian coordinates: $ \mathbf{r}^N = \{ x_1, y_1, z_1, \, x_2, y_2, z_2, \, \ldots, \, x_N, y_N, z_N \}$.
See
<a href="javascript:changeTo('idealGas','notation','0')">The Ideal Gas</a>,
<a href="javascript:changeTo('freeGradient','notation','0')">Free Energy Storage in a Concentration Gradient</a>.
</td>
</tr>
<tr>
<td>$T$</td>
<td>Absolute temperature, in degrees Kelvin.
See <a href="javascript:changeTo('freeThermo','notation','0')">Free Energy & Work</a>,
<a href="javascript:changeTo('idealGas','notation','0')">The Ideal Gas</a>.
</td>
</tr>
<tr>
<td>$V$</td>
<td>Volume of system.
See <a href="javascript:changeTo('idealGas','notation','0')">The Ideal Gas</a>,
<a href="javascript:changeTo('freeGradient','notation','0')">Free Energy Storage in a Concentration Gradient</a>.
</td>
</tr>
</table>
</body>
</html>