Bioengineering

Bioengineering is a multidisciplinary field that applies the principles and problem-solving techniques of engineering to biology and medicine. It seeks to understand, modify, or control biological systems to develop solutions that can improve human health, agriculture, and environmental sustainability. This broad discipline encompasses a wide range of applications, including the design of medical devices and artificial organs, the development of novel diagnostic tools, tissue engineering to regenerate damaged tissues, the creation of biocompatible materials, and the genetic modification of organisms to produce pharmaceuticals or enhance crop yields.

1. Foundations of Bioengineering
   1. Foundational Biology
      1. Cell Biology
         1. Prokaryotic and Eukaryotic Cells
            1. Structural Differences
            2. Functional Differences
            3. Evolutionary Origins
            4. Comparative Metabolism
         2. Cellular Organelles and Functions
            1. Nucleus
               1. Nuclear Envelope
               2. Chromatin Organization
               3. Nucleolus
            2. Mitochondria
               1. Structure and Cristae
               2. ATP Synthesis
               3. Mitochondrial DNA
            3. Endoplasmic Reticulum
               1. Rough ER
               2. Smooth ER
               3. Protein Folding
            4. Golgi Apparatus
               1. Protein Modification
               2. Vesicle Transport
            5. Lysosomes and Peroxisomes
               1. Lysosomal Enzymes
               2. Autophagy
               3. Peroxisomal Functions
            6. Cytoskeleton
               1. Microfilaments
               2. Microtubules
               3. Intermediate Filaments
               4. Motor Proteins
            7. Plasma Membrane
               1. Membrane Structure
               2. Membrane Proteins
               3. Membrane Fluidity
         3. Cell Cycle and Division
            1. Phases of Cell Cycle
               1. G1 Phase
               2. S Phase
               3. G2 Phase
               4. M Phase
            2. Mitosis
               1. Prophase
               2. Metaphase
               3. Anaphase
               4. Telophase
               5. Cytokinesis
            3. Meiosis
               1. Meiosis I
               2. Meiosis II
               3. Genetic Recombination
            4. Cell Cycle Regulation
               1. Cyclins and CDKs
               2. Checkpoints
               3. Tumor Suppressors
            5. Apoptosis and Cell Death
               1. Apoptotic Pathways
               2. Necrosis
               3. Autophagy
         4. Cell Signaling and Communication
            1. Types of Cell Signaling
               1. Autocrine Signaling
               2. Paracrine Signaling
               3. Endocrine Signaling
               4. Juxtacrine Signaling
            2. Signal Transduction Pathways
               1. G-Protein Coupled Receptors
               2. Receptor Tyrosine Kinases
               3. Ion Channel Receptors
            3. Receptors
               1. Membrane-bound Receptors
               2. Intracellular Receptors
               3. Receptor Binding Kinetics
            4. Second Messengers
               1. cAMP
               2. Calcium
               3. IP3 and DAG
            5. Cellular Responses
               1. Gene Expression Changes
               2. Metabolic Changes
               3. Structural Changes
      2. Molecular Biology
         1. DNA Structure and Replication
            1. DNA Double Helix
               1. Base Pairing
               2. Major and Minor Grooves
               3. DNA Packaging
            2. DNA Replication Mechanisms
               1. DNA Polymerases
               2. Leading and Lagging Strands
               3. Okazaki Fragments
               4. Proofreading
            3. DNA Repair Mechanisms
               1. Base Excision Repair
               2. Nucleotide Excision Repair
               3. Mismatch Repair
               4. Double-Strand Break Repair
         2. RNA and Transcription
            1. Types of RNA
               1. Messenger RNA
               2. Transfer RNA
               3. Ribosomal RNA
               4. MicroRNA
               5. Long Non-coding RNA
            2. Transcription Process
               1. RNA Polymerases
               2. Promoters and Enhancers
               3. Transcription Factors
               4. Elongation and Termination
            3. RNA Processing and Splicing
               1. 5' Capping
               2. 3' Polyadenylation
               3. Splicing Mechanisms
               4. Alternative Splicing
         3. Protein Synthesis and Translation
            1. Genetic Code
               1. Codon Usage
               2. Start and Stop Codons
               3. Degeneracy
            2. Ribosome Structure and Function
               1. Ribosomal Subunits
               2. rRNA Function
               3. Ribosome Binding Sites
            3. Translation Process
               1. Initiation
               2. Elongation
               3. Termination
               4. Polyribosomes
            4. Post-translational Modifications
               1. Phosphorylation
               2. Glycosylation
               3. Ubiquitination
               4. Protein Folding
         4. Gene Regulation and Expression
            1. Operons and Regulatory Elements
               1. Lac Operon
               2. Trp Operon
               3. Promoter Elements
               4. Silencers and Enhancers
            2. Epigenetic Regulation
               1. DNA Methylation
               2. Histone Modifications
               3. Chromatin Remodeling
            3. Transcription Factors
               1. DNA-binding Domains
               2. Activation Domains
               3. Transcriptional Networks
            4. RNA Interference
               1. siRNA
               2. miRNA
               3. RISC Complex
      3. Human Physiology
         1. Organ Systems Overview
            1. Nervous System
               1. Central Nervous System
               2. Peripheral Nervous System
               3. Autonomic Nervous System
            2. Cardiovascular System
               1. Heart
               2. Blood Vessels
               3. Blood Components
            3. Respiratory System
               1. Airways
               2. Alveoli
               3. Gas Exchange
            4. Musculoskeletal System
               1. Skeletal Muscle
               2. Smooth Muscle
               3. Cardiac Muscle
               4. Bone Tissue
            5. Digestive System
               1. Gastrointestinal Tract
               2. Accessory Organs
               3. Nutrient Absorption
            6. Renal System
               1. Kidneys
               2. Ureters and Bladder
               3. Filtration and Excretion
            7. Endocrine System
               1. Hormone-producing Glands
               2. Hormone Types
               3. Feedback Mechanisms
            8. Immune System
               1. Innate Immunity
               2. Adaptive Immunity
               3. Lymphoid Organs
         2. Homeostasis and Feedback Control
            1. Negative Feedback Loops
               1. Temperature Regulation
               2. Blood Glucose Control
               3. Blood Pressure Control
            2. Positive Feedback Loops
               1. Blood Clotting
               2. Childbirth
            3. Set Points and Regulation
               1. Physiological Set Points
               2. Adaptation Mechanisms
         3. Neurophysiology
            1. Neuron Structure and Function
               1. Cell Body
               2. Dendrites
               3. Axon
               4. Synapses
            2. Action Potentials
               1. Resting Potential
               2. Depolarization
               3. Repolarization
               4. Refractory Periods
            3. Synaptic Transmission
               1. Neurotransmitters
               2. Synaptic Vesicles
               3. Postsynaptic Receptors
            4. Sensory and Motor Pathways
               1. Sensory Transduction
               2. Motor Control
               3. Reflex Arcs
         4. Cardiovascular Physiology
            1. Heart Anatomy and Function
               1. Heart Chambers
               2. Heart Valves
               3. Cardiac Muscle Properties
            2. Blood Vessels and Circulation
               1. Arteries
               2. Veins
               3. Capillaries
               4. Systemic and Pulmonary Circulation
            3. Blood Pressure Regulation
               1. Baroreceptors
               2. Renin-Angiotensin System
               3. Vasodilation and Vasoconstriction
            4. Cardiac Cycle
               1. Systole
               2. Diastole
               3. Heart Sounds
         5. Respiratory Physiology
            1. Lung Structure and Function
               1. Alveolar Structure
               2. Respiratory Membrane
               3. Surfactant
            2. Gas Exchange Mechanisms
               1. Diffusion
               2. Ventilation-Perfusion Matching
               3. Oxygen and Carbon Dioxide Transport
            3. Regulation of Breathing
               1. Respiratory Centers
               2. Chemical Control
               3. Neural Control
         6. Musculoskeletal Physiology
            1. Muscle Contraction Mechanisms
               1. Sliding Filament Theory
               2. Excitation-Contraction Coupling
               3. Energy Metabolism
            2. Bone Structure and Remodeling
               1. Bone Matrix
               2. Osteoblasts and Osteoclasts
               3. Bone Remodeling Cycle
            3. Joint Function and Movement
               1. Joint Types
               2. Range of Motion
               3. Biomechanics of Movement
   2. Foundational Chemistry
      1. General Chemistry Principles
         1. Atomic Structure
            1. Electron Configuration
            2. Periodic Trends
            3. Atomic Orbitals
         2. Chemical Bonding
            1. Ionic Bonding
            2. Covalent Bonding
            3. Metallic Bonding
            4. Intermolecular Forces
         3. Chemical Reactions and Stoichiometry
            1. Reaction Types
            2. Balancing Equations
            3. Limiting Reagents
            4. Yield Calculations
         4. Acids, Bases, and Buffers
            1. pH and pOH
            2. Acid-Base Theories
            3. Buffer Systems
            4. Henderson-Hasselbalch Equation
         5. Solutions and Concentrations
            1. Molarity
            2. Molality
            3. Mole Fraction
            4. Colligative Properties
      2. Organic Chemistry
         1. Functional Groups
            1. Hydrocarbons
               1. Alkanes
               2. Alkenes
               3. Alkynes
               4. Aromatic Compounds
            2. Oxygen-containing Groups
               1. Alcohols
               2. Ethers
               3. Aldehydes
               4. Ketones
               5. Carboxylic Acids
               6. Esters
            3. Nitrogen-containing Groups
               1. Amines
               2. Amides
               3. Nitriles
         2. Biomolecules
            1. Carbohydrates
               1. Monosaccharides
                  1. Glucose
                  2. Fructose
                  3. Galactose
               2. Disaccharides
                  1. Sucrose
                  2. Lactose
                  3. Maltose
               3. Polysaccharides
                  1. Starch
                  2. Glycogen
                  3. Cellulose
            2. Lipids
               1. Fatty Acids
                  1. Saturated Fatty Acids
                  2. Unsaturated Fatty Acids
               2. Triglycerides
               3. Phospholipids
               4. Steroids
                  1. Cholesterol
                  2. Steroid Hormones
            3. Proteins
               1. Amino Acids
                  1. Essential Amino Acids
                  2. Non-essential Amino Acids
                  3. Amino Acid Properties
               2. Peptide Bonds
               3. Protein Structure
                  1. Primary Structure
                  2. Secondary Structure
                  3. Tertiary Structure
                  4. Quaternary Structure
            4. Nucleic Acids
               1. Nucleotides
                  1. Purines
                  2. Pyrimidines
                  3. Phosphate Groups
               2. DNA Structure
               3. RNA Structure
      3. Biochemistry
         1. Enzyme Kinetics
            1. Enzyme Structure and Function
               1. Active Site
               2. Cofactors and Coenzymes
               3. Enzyme Classification
            2. Michaelis-Menten Kinetics
               1. Km and Vmax
               2. Lineweaver-Burk Plot
               3. Enzyme Efficiency
            3. Enzyme Inhibition
               1. Competitive Inhibition
               2. Non-competitive Inhibition
               3. Uncompetitive Inhibition
            4. Allosteric Regulation
               1. Positive Regulation
               2. Negative Regulation
               3. Cooperative Binding
         2. Metabolic Pathways
            1. Glycolysis
               1. Glucose Phosphorylation
               2. Pyruvate Formation
               3. ATP Generation
            2. Citric Acid Cycle
               1. Acetyl-CoA Entry
               2. NADH and FADH2 Production
               3. CO2 Release
            3. Oxidative Phosphorylation
               1. Electron Transport Chain
               2. ATP Synthase
               3. Chemiosmotic Theory
            4. Photosynthesis
               1. Light Reactions
               2. Calvin Cycle
               3. Chloroplast Structure
            5. Metabolic Regulation
               1. Anabolic Pathways
               2. Catabolic Pathways
               3. Metabolic Control
   3. Foundational Physics and Engineering Mechanics
      1. Classical Mechanics
         1. Statics
            1. Forces and Equilibrium
               1. Force Vectors
               2. Moment and Torque
               3. Static Equilibrium Conditions
            2. Free-Body Diagrams
               1. Force Identification
               2. Diagram Construction
               3. Problem-Solving Methods
         2. Dynamics
            1. Newton's Laws of Motion
               1. First Law
               2. Second Law
               3. Third Law
            2. Work, Energy, and Power
               1. Work-Energy Theorem
               2. Kinetic Energy
               3. Potential Energy
               4. Conservation of Energy
            3. Momentum and Impulse
               1. Linear Momentum
               2. Conservation of Momentum
               3. Impulse-Momentum Theorem
      2. Electricity and Magnetism
         1. Electric Charge and Coulomb's Law
            1. Electric Charge Properties
            2. Force Between Charges
            3. Superposition Principle
         2. Electric Fields and Potentials
            1. Electric Field Definition
            2. Electric Potential
            3. Equipotential Surfaces
         3. Electric Circuits
            1. Ohm's Law
            2. Series Circuits
            3. Parallel Circuits
            4. Kirchhoff's Laws
         4. Magnetism and Electromagnetic Induction
            1. Magnetic Fields
            2. Faraday's Law
            3. Lenz's Law
            4. Electromagnetic Applications
      3. Thermodynamics
         1. Laws of Thermodynamics
            1. Zeroth Law
            2. First Law
            3. Second Law
            4. Third Law
         2. Energy Conservation
            1. Internal Energy
            2. Enthalpy
            3. Work and Heat
         3. Heat Transfer Mechanisms
            1. Conduction
               1. Fourier's Law
               2. Thermal Conductivity
            2. Convection
               1. Natural Convection
               2. Forced Convection
            3. Radiation
               1. Stefan-Boltzmann Law
               2. Emissivity
         4. Entropy and Free Energy
            1. Entropy Definition
            2. Gibbs Free Energy
            3. Spontaneous Processes
      4. Fluid Mechanics
         1. Properties of Fluids
            1. Density
            2. Viscosity
            3. Compressibility
            4. Surface Tension
         2. Fluid Statics
            1. Hydrostatic Pressure
            2. Buoyancy
            3. Archimedes' Principle
         3. Fluid Dynamics
            1. Continuity Equation
            2. Bernoulli's Principle
         4. Flow Characteristics
            1. Laminar Flow
            2. Turbulent Flow
            3. Reynolds Number
         5. Viscous Flow
            1. Poiseuille's Law
            2. Flow in Tubes
            3. Drag Forces
      5. Mass and Energy Balances
         1. Conservation of Mass
            1. Mass Balance Equations
            2. Steady-State Systems
            3. Transient Systems
         2. Conservation of Energy
            1. Energy Balance Equations
            2. Heat Generation
            3. Energy Storage
         3. Control Volume Analysis
            1. System Boundaries
            2. Input and Output Streams
            3. Accumulation Terms
         4. Applications in Biological Systems
            1. Metabolic Balances
            2. Reactor Design
            3. Process Optimization
   4. Foundational Mathematics
      1. Calculus
         1. Limits and Continuity
            1. Limit Definition
            2. Limit Laws
            3. Continuity Conditions
         2. Differentiation
            1. Derivative Definition
            2. Differentiation Rules
            3. Chain Rule
            4. Implicit Differentiation
         3. Integration
            1. Antiderivatives
            2. Definite Integrals
            3. Integration Techniques
         4. Applications in Rate Processes
            1. Rate of Change
            2. Optimization Problems
            3. Related Rates
      2. Differential Equations
         1. First-Order Differential Equations
            1. Separable Equations
            2. Linear Equations
            3. Exact Equations
         2. Second-Order Differential Equations
            1. Homogeneous Equations
            2. Non-homogeneous Equations
            3. Characteristic Equations
         3. Systems of Differential Equations
            1. Linear Systems
            2. Phase Plane Analysis
            3. Stability Analysis
         4. Applications in Biological Modeling
            1. Population Dynamics
            2. Pharmacokinetics
            3. Enzyme Kinetics
      3. Linear Algebra
         1. Vectors and Matrices
            1. Vector Operations
            2. Matrix Operations
            3. Matrix Types
         2. Matrix Operations
            1. Addition and Subtraction
            2. Multiplication
            3. Inverse and Transpose
         3. Eigenvalues and Eigenvectors
            1. Characteristic Polynomial
            2. Diagonalization
         4. Linear Systems of Equations
            1. Gaussian Elimination
            2. Matrix Methods
            3. Solution Techniques
      4. Probability and Statistics
         1. Descriptive Statistics
            1. Measures of Central Tendency
            2. Measures of Variability
            3. Data Visualization
         2. Probability Distributions
            1. Discrete Distributions
            2. Continuous Distributions
            3. Normal Distribution
         3. Hypothesis Testing
            1. Null and Alternative Hypotheses
            2. Test Statistics
            3. P-values
            4. Type I and Type II Errors
         4. Regression and Correlation
            1. Linear Regression
            2. Correlation Coefficients
            3. Model Validation
         5. Experimental Design and Data Analysis
            1. Design of Experiments
            2. ANOVA
            3. Statistical Software