Advanced Biochemical Engineering Course

Lesson 1 • Thermodynamics of Biological Systems

Applies Gibbs free energy, enthalpy, and entropy to biochemical reactions. Enables prediction of reaction spontaneity and equilibrium in bioprocesses.

Lesson 2 • Stoichiometry of Cell Growth

Quantifies elemental balances for biomass, substrate, and product formation. Provides the mass-balance framework used throughout all subsequent bioprocess chapters.

Lesson 3 • Units, Scales, and Engineering Notation

Standardizes unit systems, dimensional analysis, and scale conventions used in bioprocess engineering. Prevents calculation errors across all subsequent quantitative work.

Lesson 4 • Transport Phenomena in Bioprocesses

Introduces mass, heat, and momentum transfer as rate-limiting factors in bioreactors. Connects transport theory to oxygen transfer and nutrient delivery.

Lesson 1 • Immobilized Enzyme Systems

Covers immobilization techniques and the effect of diffusion limitations on apparent kinetics. Connects internal effectiveness factor to reactor productivity.

Lesson 2 • Enzyme Stability and Deactivation Kinetics

Models first-order and multi-step enzyme deactivation and its impact on reactor performance. Enables prediction of enzyme replacement schedules and economic optimization.

Lesson 3 • Michaelis-Menten Kinetics

Derives the Michaelis-Menten model from rapid-equilibrium and quasi-steady-state assumptions. Establishes Km and Vmax as the primary design parameters for enzymatic processes.

Lesson 4 • Enzyme Inhibition and Regulation

Classifies competitive, uncompetitive, and mixed inhibition with diagnostic plots. Applies inhibition models to process troubleshooting and inhibitor removal strategies.

Lesson 1 • Population Dynamics and Mixed Cultures

Models competition, mutualism, and predator-prey dynamics in mixed microbial populations. Applies population models to co-culture bioprocesses and contamination risk assessment.

Lesson 2 • Product Formation Kinetics

Classifies growth-associated, non-growth-associated, and mixed product formation using Luedeking-Piret models. Links product kinetics to bioreactor operating strategy selection.

Lesson 3 • Environmental Effects on Growth

Quantifies the impact of temperature, pH, dissolved oxygen, and osmolarity on growth kinetics. Enables specification of optimal operating windows for bioreactor control.

Lesson 4 • Structured and Cybernetic Models

Introduces intracellular compartment models and cybernetic frameworks for metabolic regulation. Improves prediction accuracy for complex fermentation dynamics beyond Monod.

Lesson 1 • Aseptic Technique and Contamination Control

Establishes engineering and procedural controls to prevent contamination during inoculation and sampling. Connects contamination prevention to process economics and batch success rates.

Lesson 2 • Air and Gas Sterilization

Designs depth filtration and membrane filter systems for sterile air supply to bioreactors. Ensures particulate and microbial removal efficiency under process flow conditions.

Lesson 3 • Microbial Death Kinetics

Models first-order thermal inactivation using D-values and z-values for target organisms. Provides the quantitative basis for all sterilization cycle design in this chapter.

Lesson 4 • Batch and Continuous Sterilization

Compares in-situ batch sterilization with continuous high-temperature short-time processes. Selects sterilization mode based on nutrient degradation, throughput, and scale.

Lesson 1 • Bioreactor Instrumentation and Control

Covers sensors for pH, DO, temperature, and biomass and integrates them into feedback control loops. Provides the instrumentation basis for automated bioprocess operation.

Lesson 2 • Non-Ideal Flow and Mixing Analysis

Characterizes mixing time, dead zones, and channeling using tracer experiments and RTD analysis. Corrects non-ideal behavior to restore predicted bioreactor performance.

Lesson 3 • Fed-Batch Bioreactor Strategies

Analyzes constant-rate, exponential, and feedback-controlled feeding strategies for fed-batch cultures. Optimizes feeding profiles to maximize biomass or product titer.

Lesson 4 • Oxygen Transfer and Aeration Design

Quantifies the volumetric oxygen transfer coefficient kLa and its dependence on agitation and aeration. Sizes sparger and impeller systems to meet oxygen demand at scale.

Lesson 5 • Ideal Bioreactor Models

Derives mass balances for ideal batch, CSTR, and plug-flow bioreactors using microbial kinetics. Establishes the design equation framework applied throughout this chapter.

Lesson 1 • Cell Harvest and Disruption

Covers centrifugation, microfiltration, and mechanical disruption for biomass recovery and cell lysis. Establishes the first downstream step that determines all subsequent separation efficiency.

Lesson 2 • Membrane Separation Processes

Applies ultrafiltration, diafiltration, and nanofiltration for concentration and buffer exchange. Sizes membrane area and optimizes transmembrane pressure for target flux.

Lesson 3 • Integrated Purification Train Design

Sequences unit operations into a purification train using yield and purification factor analysis. Balances purity, recovery, and cost across the entire downstream process.

Lesson 4 • Chromatographic Separations

Designs ion exchange, affinity, size exclusion, and hydrophobic interaction chromatography steps. Applies plate theory and resolution equations to column sizing and gradient design.

Lesson 1 • Genetic Tools for Pathway Engineering

Reviews promoter engineering, gene knockouts, overexpression, and CRISPR-based editing for metabolic rewiring. Connects genetic interventions to predicted flux changes.

Lesson 2 • Rational Pathway Design Principles

Applies thermodynamic feasibility, cofactor balancing, and precursor availability to design new biosynthetic routes. Evaluates pathway designs before experimental implementation.

Lesson 3 • Strain Optimization and Adaptive Evolution

Combines rational engineering with directed evolution and adaptive laboratory evolution for strain improvement. Integrates omics data to guide iterative design-build-test cycles.

Lesson 4 • Metabolic Flux Analysis

Formulates stoichiometric network models and solves flux distributions using mass balances and isotope labeling. Identifies rate-limiting steps and carbon routing inefficiencies.

Lesson 1 • Scale-Up Criteria and Dimensionless Numbers

Evaluates constant power-per-volume, tip speed, Reynolds number, and mixing time as competing scale-up criteria. Resolves conflicts between criteria using process-specific prioritization.

Lesson 2 • Technology Transfer Protocols

Structures formal technology transfer packages including process descriptions, analytical methods, and acceptance criteria. Ensures receiving sites reproduce process performance within defined limits.

Lesson 3 • Oxygen Transfer Scale-Up

Scales kLa correlations from bench to pilot and production scale using empirical and mechanistic models. Validates oxygen supply adequacy before committing to large-scale runs.

Lesson 4 • Risk Assessment in Scale-Up

Applies failure mode and effects analysis and risk ranking to identify scale-up failure points. Develops mitigation plans that protect product quality and schedule during scale-up.