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3 | (22) |
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1.1 Our Design Philosophy |
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5 | (2) |
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1.2 Insights from Other Fields |
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7 | (2) |
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1.3 How Should You Study? |
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9 | (3) |
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12 | (1) |
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1.5 Some Glimpses of Modeling |
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13 | (5) |
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1.5.1 West Nile Virus Models |
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14 | (1) |
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1.5.2 Simple Brain Models |
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15 | (2) |
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17 | (1) |
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1.6 A Roadmap to the Text |
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18 | (4) |
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22 | (3) |
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22 | (3) |
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Part II Using One Variable |
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25 | (36) |
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2.1 A Basic Evolutionary Model |
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25 | (3) |
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27 | (1) |
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28 | (1) |
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28 | (3) |
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30 | (1) |
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30 | (1) |
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2.3 A Difference Equation |
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31 | (2) |
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32 | (1) |
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33 | (1) |
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2.4 The Functional Form of the Frequency |
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33 | (6) |
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35 | (1) |
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36 | (1) |
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2.4.3 Biology and the Model |
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37 | (2) |
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2.5 A Gentle Introduction to MatLab |
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39 | (12) |
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40 | (3) |
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2.5.2 Graphing a Function |
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43 | (2) |
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2.5.3 A Simple Virus Infection Model |
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45 | (6) |
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2.6 Long Term Consequences |
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51 | (1) |
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2.7 The Domestication of Wheat |
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52 | (9) |
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58 | (2) |
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60 | (1) |
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3 Limits and Basic Smoothness |
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61 | (18) |
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64 | (15) |
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3.1.1 The Humble Square Root |
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64 | (2) |
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3.1.2 A Cool Polynomial Trick |
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66 | (3) |
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3.1.3 Change and More Change! |
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69 | (2) |
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3.1.4 How Many Do We Have? |
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71 | (5) |
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3.1.5 This Function Is Smooth! |
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76 | (3) |
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4 Continuity and Derivatives |
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79 | (22) |
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79 | (6) |
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82 | (2) |
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84 | (1) |
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85 | (4) |
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87 | (1) |
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88 | (1) |
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89 | (4) |
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92 | (1) |
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92 | (1) |
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93 | (4) |
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95 | (1) |
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96 | (1) |
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97 | (4) |
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99 | (1) |
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99 | (2) |
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101 | (12) |
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5.1 Sin, Cos and All That! |
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101 | (5) |
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5.1.1 The Sin and Cos Functions |
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101 | (5) |
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106 | (2) |
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107 | (1) |
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107 | (1) |
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5.3 Derivatives of Complicated Things |
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108 | (5) |
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113 | (8) |
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6.1 Simple Integer Power Antiderivatives |
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113 | (3) |
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115 | (1) |
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116 | (1) |
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6.2 Simple Fractional Power Antiderivatives |
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116 | (3) |
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118 | (1) |
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118 | (1) |
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6.3 Simple Trigonometric Function Antiderivatives |
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119 | (2) |
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119 | (1) |
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120 | (1) |
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121 | (8) |
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7.1 Simple Substitution Polynomials |
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121 | (4) |
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7.2 Substitution for Polynomials Quick and Dirty |
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125 | (2) |
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126 | (1) |
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127 | (2) |
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127 | (1) |
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128 | (1) |
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129 | (36) |
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129 | (5) |
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133 | (1) |
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133 | (1) |
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8.2 Riemann Sums in MatLab |
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134 | (3) |
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135 | (2) |
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8.3 Graphing Riemann Sums |
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137 | (11) |
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8.3.1 Automating Riemann Sums |
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141 | (4) |
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8.3.2 Uniform Partition Riemann Sums |
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145 | (3) |
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148 | (4) |
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8.4.1 The Riemann Integral as a Limit |
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149 | (1) |
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150 | (2) |
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8.5 The Fundamental Theorem of Calculus |
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152 | (3) |
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8.6 The Cauchy Fundamental Theorem of Calculus |
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155 | (3) |
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157 | (1) |
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158 | (1) |
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8.7 Riemann Integration with Substitution |
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158 | (2) |
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159 | (1) |
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8.8 Integration with Jumps |
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160 | (5) |
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8.8.1 Removable Discontinuity |
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160 | (2) |
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162 | (1) |
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163 | (2) |
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9 The Logarithm and Its Inverse |
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165 | (14) |
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9.1 The Natural Logarithm Function |
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165 | (2) |
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167 | (4) |
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9.2.1 Worked Out Examples: Derivatives |
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168 | (1) |
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9.2.2 Homework: Derivatives |
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169 | (1) |
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9.2.3 Worked Out Examples: Integrals |
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170 | (1) |
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9.2.4 Homework: Integrals |
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171 | (1) |
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9.3 The Exponential Function |
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171 | (2) |
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9.4 Exponential Functions |
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173 | (4) |
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9.4.1 Worked Out Examples: Derivatives |
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173 | (1) |
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9.4.2 Homework: Exponential Derivatives |
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174 | (1) |
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9.4.3 Worked Out Examples: Exponential Integrals |
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175 | (1) |
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9.4.4 Homework: Exponential Integrals |
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176 | (1) |
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9.5 Our Antiderivatives So Far |
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177 | (2) |
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10 Exponential and Logarithm Function Properties |
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179 | (26) |
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10.1 Positive Integer Powers of e |
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179 | (3) |
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181 | (1) |
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10.2 Negative Integer Powers of e |
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182 | (3) |
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184 | (1) |
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10.3 Adding Natural Logarithms |
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185 | (6) |
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10.3.1 Adding Logarithms: Both Logarithms are Bigger Than 1 |
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185 | (3) |
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10.3.2 Adding Logarithms: One Logarithm Less Than 1 and One Bigger Than 1 |
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188 | (2) |
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10.3.3 Generalizing These Results |
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190 | (1) |
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10.3.4 Doing Subtracts in General |
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190 | (1) |
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191 | (2) |
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10.5 The Logarithm Function Properties |
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193 | (2) |
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195 | (1) |
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10.6 The Exponential Function Properties |
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195 | (10) |
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10.6.1 Properties of the Exponential Function |
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198 | (6) |
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204 | (1) |
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205 | (24) |
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11.1 Solving a Simple Rate Problem: Indefinite Approach |
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209 | (5) |
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11.1.1 Resolution of the Absolute Value |
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211 | (1) |
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211 | (2) |
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213 | (1) |
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11.2 Solving a Simple Rate Problem: Definite Approach |
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214 | (4) |
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215 | (2) |
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217 | (1) |
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11.3 The Half Life in Exponential Decay Problems |
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218 | (4) |
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11.4 The Carbon Dating Problem |
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222 | (2) |
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11.4.1 A Simple Dating Problem |
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223 | (1) |
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223 | (1) |
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224 | (1) |
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11.5 Simple Rate Problems with Jumps |
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224 | (5) |
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227 | (1) |
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227 | (2) |
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229 | (28) |
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12.1 The Integrating Factor Approach |
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229 | (3) |
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230 | (2) |
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232 | (1) |
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12.2 The Integrating Factor Approach with a Constant on the Right |
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232 | (3) |
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235 | (1) |
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235 | (9) |
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12.3.1 The Underlying Biology |
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237 | (3) |
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12.3.2 Worked Out Examples |
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240 | (3) |
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243 | (1) |
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12.4 The Response Time in Protein Synthesis Problems |
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244 | (3) |
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246 | (1) |
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12.5 Signal On and Off Scenarios |
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247 | (3) |
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248 | (2) |
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12.6 Transcription Error Rates |
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250 | (7) |
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12.6.1 A First Attempt to Explain the Error Rate |
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251 | (2) |
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12.6.2 The Second Attempt: Kinetic Proofreading |
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253 | (4) |
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257 | (22) |
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257 | (9) |
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13.1.1 An Integration Side Trip: Partial Fraction Decompositions |
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258 | (2) |
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260 | (6) |
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13.2 The General Solution Method |
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266 | (8) |
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13.2.1 A Streamlined Solution |
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272 | (2) |
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13.3 Solving a Logistics Model on Paper |
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274 | (5) |
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274 | (3) |
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277 | (2) |
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14 Function Approximation |
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279 | (22) |
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279 | (3) |
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280 | (2) |
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14.2 The Zeroth Order Taylor Polynomial |
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282 | (2) |
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283 | (1) |
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283 | (1) |
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14.3 The First Order Taylor Polynomial |
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284 | (5) |
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286 | (3) |
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289 | (1) |
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14.4 Quadratic Approximations |
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289 | (6) |
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290 | (2) |
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292 | (3) |
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14.5 Exponential Approximations |
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295 | (6) |
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297 | (1) |
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298 | (3) |
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301 | (14) |
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301 | (2) |
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302 | (1) |
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303 | (1) |
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15.2 The Newton Cooling Project |
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303 | (12) |
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305 | (1) |
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15.2.2 Your Newton Cooling Project |
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305 | (3) |
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308 | (1) |
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15.2.4 Some Sample Calculations |
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309 | (6) |
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16 Numerical Methods Order One ODEs |
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315 | (32) |
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315 | (25) |
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16.1.1 Approximating the Solution to First Order Differential Equations |
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317 | (4) |
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16.1.2 Euler Approximates Again |
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321 | (3) |
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16.1.3 Euler Approximates the Last Time |
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324 | (5) |
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329 | (2) |
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16.1.5 Adding Time to Euler's Method |
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331 | (1) |
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16.1.6 Simple MatLab Experiments |
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332 | (3) |
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16.1.7 Matlab Euler Functions |
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335 | (1) |
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336 | (1) |
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16.1.9 The True Versus the Euler Approximate Solution |
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337 | (3) |
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340 | (1) |
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340 | (7) |
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16.2.1 The MatLab Implementation |
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341 | (4) |
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345 | (1) |
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345 | (2) |
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17 Advanced Protein Models |
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347 | (24) |
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17.1 Binding Time Estimates |
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347 | (2) |
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349 | (3) |
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352 | (1) |
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352 | (1) |
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17.3 Transcription Regulation |
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352 | (7) |
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356 | (3) |
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359 | (1) |
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359 | (4) |
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362 | (1) |
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362 | (1) |
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363 | (8) |
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366 | (1) |
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367 | (1) |
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368 | (3) |
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Part III Using Multiple Variables |
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371 | (14) |
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371 | (4) |
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372 | (1) |
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373 | (1) |
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18.1.3 The Identity Matrices |
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373 | (1) |
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18.1.4 The Transpose of a Matrix |
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374 | (1) |
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375 | (1) |
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18.2 Operations on Matrices |
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375 | (3) |
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377 | (1) |
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378 | (1) |
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18.4 Operations on Vectors |
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379 | (1) |
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18.5 The Magnitude of a Vector |
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379 | (4) |
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382 | (1) |
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18.5.2 Some Matrix--Vector Calculations |
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382 | (1) |
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18.6 The Inner Product of Two Column Vectors |
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383 | (2) |
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384 | (1) |
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385 | (14) |
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19.1 Two Allele TSG Models |
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387 | (4) |
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391 | (1) |
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19.3 Solving the Top Pathway Exactly |
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392 | (2) |
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19.3.1 The X0 -- X1 Subsystem |
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392 | (1) |
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393 | (1) |
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19.4 Approximation of the Top Pathway |
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394 | (5) |
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394 | (1) |
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395 | (1) |
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396 | (2) |
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398 | (1) |
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20 First Order Multivariable Calculus |
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399 | (30) |
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20.1 Functions of Two Variables |
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399 | (7) |
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20.1.1 Drawing an Annotated Surface |
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400 | (6) |
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406 | (1) |
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406 | (2) |
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408 | (8) |
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414 | (2) |
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416 | (5) |
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20.4.1 The Tangent Plane to a Surface |
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416 | (2) |
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418 | (1) |
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419 | (1) |
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20.4.4 Computational Results |
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419 | (2) |
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421 | (1) |
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20.5 Derivatives in Two Dimensions! |
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421 | (4) |
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425 | (4) |
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426 | (1) |
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427 | (2) |
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21 Second Order Multivariable Calculus |
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429 | (24) |
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21.1 Tangent Plane Approximation Error |
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429 | (1) |
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21.2 Second Order Error Estimates |
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430 | (2) |
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431 | (1) |
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432 | (1) |
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21.3 Hessian Approximations |
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432 | (5) |
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21.3.1 Ugly Error Estimates! |
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433 | (3) |
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436 | (1) |
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437 | (5) |
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440 | (2) |
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442 | (1) |
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21.5 A Regression to Regression |
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442 | (7) |
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447 | (1) |
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447 | (2) |
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21.6 Regression and Covariances |
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449 | (4) |
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450 | (1) |
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451 | (1) |
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452 | (1) |
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22 Hamilton's Rule in Evolutionary Biology |
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453 | (26) |
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22.1 How Do We Define Altruism |
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454 | (7) |
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22.1.1 A Shared Common Good Model |
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454 | (3) |
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22.1.2 The Abstract Version |
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457 | (4) |
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461 | (3) |
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464 | (1) |
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464 | (1) |
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464 | (3) |
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22.3.1 Back to Covariance! |
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466 | (1) |
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22.4 Altruism Spread Under Additive Fitness |
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467 | (2) |
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469 | (1) |
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469 | (1) |
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22.5 Altruism Spread Under Additive Genetics |
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469 | (4) |
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472 | (1) |
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473 | (1) |
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22.6 The Optimization Approach |
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473 | (6) |
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474 | (1) |
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474 | (1) |
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475 | (4) |
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Part IV Summing It All Up |
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479 | (4) |
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480 | (3) |
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Part V Advise to the Beginner |
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483 | (4) |
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484 | (3) |
Glossary |
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487 | (12) |
Index |
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499 | |