教学时程
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| 课 | 课程单元 | 重要日期 |
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| 1 | 非共价性生物分子交互作用Noncovalent Biomolecular Interactions 细胞功能之重要性Significance in Cell Function 分子层次之量测、模拟与操作Measure, Model, Manipulate at Molecular Level 键结力（氢键、凡德瓦、静电以及伦敦力)Bonding Forces (HB, VdW, Elec, HE) 溶解以及水所扮演的角色Solvation and the Role of Water 标准态、自由能、 KdStandard States, Free Energy, Kd 亲合力之标准范围，结合以及分离之速率Typical Ranges of Affinity, On and Off Rates 自由能，熵,以及焓Free Energy, Enthalpy, and Entropy 介面特性Characteristics of Interfaces Ala校验和双突变循环Ala Scan and Double Mutant Cycles |
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| 2 | 蛋白质-配位子之结合性平衡Protein-Ligand Binding Equilibria 单价可逆性平衡Monovalent Reversible Equilibria 分析型和假性一级等温反应Analytic and Pseudo - 1st Order Approx Isotherms 固定式蛋白质／配位子交互作用Immobilized Protein/Ligand Interactions 结合平衡之图形表达Graphical Representations of Binding Equilibria 固定式蛋白质结合Immobilized Protein Binding 资料绘图以及分析Data Plotting and Analysis 多重相同配位之统计学Statistics of Multiple Identical Sites |
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| 3 | 多价性结合平衡Multivalent Binding Equilibria 变构性以及协调性Allostery and Cooperativity 反应自由能Interaction Free Energy 亲合力以及有效浓度（Jencks）Avidity and Effective Concentration (Jencks) 受体交联模型Receptor Crosslinking Models |
缴交第一次作业Homework 1 due |
| 4 | 多价性结合平衡（续）Multivalent Binding Equilibria (cont.) 固定式多价型分子（Pluckthun）Immobilized Multivalency (Pluckthun) 可溶性多价型分子以及连结分子长度（Zhou） Soluble Multivalency and Linker Length (Zhou) |
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| 5 | 光谱学以及萤光理论Spectroscopy and Fluorescence 光、物质、散射与吸收间之交互作用Interactions of Light w/Matter, Scatter and Absorb 毕氏定理Beer's Law 萤光理论（能量转移，萤光共振能量转移(FRET)）Fluorescence Theory (Stokes Shift, FRET) 萤光应用（绿萤光蛋白(GFP)、萤光共振能量转移(FRET)、流体细胞测量仪、共聚焦以及双光子显微镜）Fluorescence Applications (GFP, FRET, Flow Cytometry, Confocal and 2 Photon Microscopy) |
缴交第二次作业Homework 2 due |
| 6 | 量测结合平衡Measurement of Binding Equilibria 表面等离子体共振 (SPR)SPR 光谱学Optical Spectroscopy 微盘试验 (Microplate assays)Microplate Assays 细胞表面滴定Cell Surface Titration 热量测量、超高速离心Calorimetry, Ultracentrifugation |
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| 7 | 结合动力学中之扩散限制Diffusion Limits in Association Kinetics Shoup/Szabo与Burg/Purcell表面扩散Shoup/Szabo and Burg/Purcell Surface Diffusion 区域性消耗以及回收Local Depletion and Recapture Smoluchowski扩散限制Smoluchowski Diffusion Limit 方向性依赖型交互作用Orientation-dependent Interactions |
缴交第三次作业Homework 3 due |
| 8 | 结合动力学中温度以及盐分之依存Temperature and Salt Dependence of Association Kinetics Arrhenius依赖性以及过渡态理论Arrhenius Dependence and Transition State Theory 德拜-虎克Debye-Hückel 统计学Statistics 广泛非线性最小平方Global Nonlinear Least Squares 选用参数时之可信赖区间Confidence Intervals on Fit Parameters |
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| 9 | 生物分子反应动力学Biomolecular Interaction Kinetics 分析型以及假性一级溶液反应Analytical and Pseudo 1st - Order Solutions 缓和（弛张）反应（干扰、温度突增）Relaxation (Perturbation, Temperature Jump) 隐藏性动力学之双变因研究方法Double Jump Approach for Hidden Kinetics |
缴交第四次作业Homework 4 due |
| 10 | 生物感应器资料分析Biosensor Data Analysis 实验方法及其设计方式Experimental Method and Design 一惯性检验以及人为误差Consistency Checks and Artifacts 大量传输效应以及模型Mass Transport Effects and Modeling |
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| 11 | 酵素动力学Enzyme Kinetics Michaeli-Menten演算Michaelis-Menten Derivation 可回复性抑制反应Reversible Inhibition 受体讯息传递以及激脢Receptor Signaling and Kinases |
缴交第五次作业Homework 5 due |
| 12 | 复合体反应以及相互作用Complex Reactions and Interactions 学生报告指定研究文献Student Presentations on Assigned Papers |
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| 13 | 蛋白质合成、消减以及定位之动力学Kinetics of Protein Synthesis, Turnover, and Localization 一般原料平衡以及成长调控General Material Balance and Growth Dilution 细胞内蛋白质之稳定态以及动力学Steady-state and Kinetics of Intracellular Proteins 受体之内噬效应以及受体数目之消减Receptor Endocytosis and Downregulation 暂停反应以及追踪配位子Pulse/Chase 内噬以及分泌速率Internalization and Secretion Rates |
缴交第一份模型执行作业Model implementation 1 due |
| 14 | 蛋白质生成循环以及定位Protein Lifecycles and Localization 学生报告指定研究文献Student Presentations on Assigned Papers |
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| 15 | 或然率Probability Poisson计算模式Poisson Processes 推导Poisson分布理论Derivation of Poisson Distribution 指数型等待时间Exponential Waiting Times 白血球移动（滚动）模型Example of Leukocyte Rolling 蒙地卡罗模拟Monte Carlo Simulations 乱数产生法Random Number Generation 模拟Simulations |
缴交第二份模型执行作业Model implementation 2 due |
| 16 | 生物学系统中之杂因子Noise in Biology 学生报告指定研究文献Student Presentations on Assigned Papers |
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| 17 | 细胞生长动力学以及生物反应器Cell Growth Kinetics and Bioreactors 平衡性生长、计量学、马诺(Monod)分类法Balanced Growth, Stoichiometry, Monod 分离以及结构性Classifications, Segregated and Structured 细胞培养系统平衡以及移位Chemostat Balance and Washout |
缴交第三份模型执行作业Model implementation 3 due |
| 18 | 网络以及系统Networks and Systems 细胞移行Chemotaxis 基础控制理论及其弹性Basic Control Theory and Robustness |
缴交第六次作业Homework 6 due |
| 19 | 族群总体Populations 学生报告指定研究文献Student Presentations on Assigned Papers |
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| 20 | 非线性力学基础Fundamentals of Nonlinear Dynamics 一般微分方程之线性系统Linear Systems of ODEs 固定数点之分类Fixed Point Classification 线性化以及区域性稳定Linearization and Local Stability 分歧现象Bifurcations |
缴交第四份模型执行作业Model implementation 4 due |
| 21 | 基因表现－滞候以及转换现象Gene Expression - Hysteresis and Switches 学生报告指定研究文献Student Presentations on Assigned Papers |
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| 22 | 基因表现－震荡现象Gene Expression: Oscillations 学生报告指定研究文献Student Presentations on Assigned Papers |
缴交第五份模型执行作业Model implementation 5 due |
| 23 | 空间型异质性：扩散以及药物动力学Spatial heterogeneity: Diffusion and Pharmacokinetics 学生报告指定研究文献Student Presentations on Assigned Papers |
缴交第六份模型执行作业Model implementation 6 due |
| 24 | 药物动力学Pharmacokinetics 血浆中物质之清除动力效应以及机制Plasma Clearance Kinetics and Mechanisms 单一以及双单位模型One and Two Compartment Models 生理模型Physiological Models 公式化以及生物利用度Formulation and Bioavailability |
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| 25 | 生物分子反应中之输送效应Transport Effects on Biomolecular Interactions 怀兹(Weisz)分析、塞尔(Thiele) 模量、丹克勒(Damkohler)数Weisz Analysis, Thiele Modulus, Damkohler # 核皱缩模型以及肿瘤渗透Shrinking Core Model and Tumor Penetration |
