NEXUS/Physics Search:

Table of Contents

• Interlude 0 - The NEXUS/Physics idea

  • Introduction to the class

    • Overview: Introduction
      • The disciplines: Physics, Biology, Chemistry, and Math
      • Science as making models
        • Phenomenology and mechanism
        • Reductionism and emergence
      • What physics can do for biologists
      • Thinking about thinking and knowing
        • The nature of scientific knowledge
        • Models of memory
          • An evolutionary model of memory
          • Working memory and long term memory
          • Making meaning: Association
          • Selective attention
        • Thinking fast and slow: One-step thinking
        • Tools for knowing: Epistemological icons
          • Choosing a channel on cat television
          • Shopping for ideas
          • Choosing foothold ideas
          • Playing the implications game
          • Seeking coherence: Building a safety net
          • Sense making
            • Sense making resolved
              • How about now?
          • Refining intuitions
          • Representation translation
          • Dangerous bend

  • Using math in science

    • Overview: Modeling with mathematics
      • How math in science is different from math in math
      • The structure of physical modeling
      • Measurement
      • Dimensionalities
        • Complex dimensions and dimensional analysis
          • Example: Creating equations using dimensional analysis
        • Changing units
        • Natural scales
          • Dimensionless equations (advanced)
        • Considering changing our arbitrary choices
        • The parameters of matter
      • Estimation
        • Scales in biology
        • Workout: Estimation
        • Example: Can trees save the planet?
        • Example: Sampling
        • Some useful numbers
      • Approximations
      • Mathematics Recap
        • Significant (and insignificant) figures
        • Scientific notation
        • The idea of algebra: Unknowns and relationships
          • Symbols in science
          • Variables, constants, and parameters
            • More complex constants and parameters
        • Functions
          • Units, Scaling, and functional dependence
          • Powers and exponentials
            • Log-log plots
          • The concept of field
        • Values, change, and rates of change
          • Derivatives
            • What is a derivative, anyway?
            • Workout: What is a derivative anyway?
            • Example: Using the derivative
            • Differential Equations
              • Example: Differential equations
            • The chain and product rules
              • Proving the chain and product rules (technical)
          • Integrals: The mathematical meaning
            • What do I have to know about integrals?
        • Trigonometry
          • The small angle approximation
          • Trig functions for any value of the argument
          • The derivatives of trig functions
        • Probability
          • Why probability matters
          • Expected values
          • Permutations and combinations
      • Building your mathematical toolbelt
        • The dimensional analysis tool
        • The scaling tool
        • The special case tool
        • Toy models
        • Reading the physics in a graph
          • Example: Reading the physics in a graph
        • Anchor equations -- Reading the physics in an equation
        • The repackaging tool: Changing physics equations to math (and back)
        • Building equations from the physics
          • Example: Building equations from the physics
        • Telling the story
        • The estimation tool
        • The diagram tool
        • Putting your tools together
• Interlude 1 - The Main Question: How do things move?

  • Kinematics: Where and When?

    • Overview: Where and when?
      • Location in space -- Coordinates
        • Vectors
          • Adding vectors
            • Workout: Adding multiple vectors
            • Example: Vector subtraction
            • Example: Vector addition
          • Multiplying vectors
            • The dot product
            • The cross product
          • The gradient -- a vector derivative
            • Example: Gradient of a Gaussian
      • Time
      • Kinematic variables
        • Workout: Kinematic variables
        • Velocity
          • Average velocity
          • Instantaneous velocity
            • Example: Velocity at the top
          • Calculating with average velocity
            • Example: Average velocity
        • Acceleration
          • Average acceleration
          • Instantaneous acceleration
          • Calculating with constant acceleration
            • Example: Constant acceleration
            • Workout: Calculating with constant acceleration
      • Kinematic Graphs
        • Kinematic graphs and consistency
          • Example: Kinematic graphs and consistency
          • Reading the content in the kinematic equations
• Interlude 2 - Dynamics: Causes of motion

  • Newton's Laws

    • Overview: Newton's Laws
      • Physical content of Newton's Laws
        • Object egotism
        • Inertia
        • Interactions
        • Superposition
        • Mass
        • Reciprocity
      • Formulation of Newton's Laws as foothold principles
        • Quantifying impulse and force
          • On the definition of force
          • Adding forces
        • Newton 0
          • Free-body diagrams
            • Workout: Free-body diagrams
          • System Schema Introduction
        • Newton's 1st law
          • Example: Newton 1
        • Newton's 2nd law
          • Reading the content in Newton's 2nd law
          • Newton 2 as a stepping rule
            • Newton 2 on a spreadsheet
          • Example: Applying Newton's 2nd law - simple case
          • Example: Applying Newton's 2nd law - complex case
          • Workout: Newton's 2nd law
        • Newton's 3rd law
          • Using system schemas for Newton's 3rd law
          • Reading the content in Newton's 3rd law
      • Center of mass
        • Example: Center of mass
        • Center of Mass: General (technical)

  • Modeling Forces

    • Overview: Modeling Forces
      • Springs -- Hooke's law
        • Realistic springs
        • Normal forces
          • A simple model of solid matter
        • Workout: Springs
      • Tension forces
      • Resistive forces
        • Friction
          • Workout: Friction
          • Reading the content in the friction equations
        • Viscosity
        • Drag
        • Reynolds number
      • Weight: Gravitational forces
        • Flat-earth gravity
          • Free-fall in flat-earth gravity
            • Example: The faster fall
          • The effect of air resistance
        • Newton's Universal gravitation
          • The Cavendish Experiment - weighing the earth
        • The gravitational field
      • Electric forces
        • Charge and the structure of matter
        • Polarization
          • Workout: Polarization
        • Coulomb's law
          • Workout: Coulomb's law
          • Coulomb's law -- vector character
            • Example: Coulomb's law
          • Reading the content in Coulomb's law
        • The Electric field
          • Workout: Electric field
          • Making sense of a vector field
          • Motivating simple electric models
            • A simple electric model: A line of charge
              • The line charge integral
            • A simple electric model: A sheet of charge
              • The sheet of charge integral (technical)
            • A simple electric model: A spherical shell of charge

  • Coherent vs random motion

    • Overview: Coherent vs random motion
      • Linear momentum
        • Restating Newton's 2nd law: momentum
          • Example: The impulse-momentum theorem
        • Momentum conservation
          • Workout: Momentum conservation
          • Example: Momentum conservation
      • The role of randomness: Biological implications
        • Newton's laws and chaos
      • Diffusion and random walks
        • Fick's law
          • Reading the content in Fick's law
        • Workout: Diffusion and random walks (Excel)
        • Workout: Diffusion and random walks (Plinko)
• Interlude 3 -Macro models of matter

  • Solids

    • Density -- Solids
    • Young's modulus
    • Breaking strain
    • Bulk modulus -- solids
    • Shear modulus
    • Soft matter
      • Mechanical properties of cells

  • Fluids

    • Overview: Fluids
      • Pressure
        • Measuring pressure
      • Archimedes' Principle
        • Workout: Archimedes' Principle
        • Example: Measuring blood pressure
      • Buoyancy
        • Workout: Buoyancy
      • Gases
      • Liquids
        • Bulk modulus -- liquids
        • Internal cohesion
          • Surface tension
            • Example: The Laplace Bubble Law
          • Negative pressue
      • Fluid flow
        • Quantifying fluid flow
        • The continuity equation
          • Workout: The continuity equation
        • Internal flow -- the HP equation
          • Internal flow -- the HP equation (advanced)
        • External flow -- lift and drag

  • Heat and temperature

    • Overview: Heat and temperature
      • Measuring Temperature
      • Thermal energy and specific heat
      • Heat capacity
        • Example: Heat capacity 1
        • Example: Heat capacity 2
        • Workout: Heat capacity
      • Heat transfer
        • Workout: Heat transfer
        • Conduction -- Fourier's law
          • Example: Heat Transfer - conduction
        • Example: Heat Transfer - radiation
        • Biology of heat transfer
      • The biological implications and consequences of temperature
• Interlude 4 - Energy: The Quantity of Motion and its Distribution

  • Mechanical Energy

    • Overview: Mechanical energy
      • Kinetic energy and the work-energy theorem
        • Reading the content in the Work-Energy theorem
        • Comparing the Impulse-Momentum and Work-Energy theorems
      • Energy of place -- potential energy
        • Gravitational potential energy
        • Spring potential energy
          • Workout: Spring potential energy
        • Electric potential energy
        • Forces from potential energy
          • Example: Getting forces from PE - 1D
          • Example: Getting forces from PE - 2D
          • Example: Getting forces from PE - 3D
      • The conservation of mechanical energy
        • Example: Energy conservation
        • Example: Using energy conservation with friction
        • Interpreting mechanical energy graphs
        • Mechanical energy loss-thermal energy
          • Example: Mechanical energy loss
        • Workout: The conservation of mechanical energy
      • Energy in fluid flow
        • The work-energy theorem in fluids
        • Bernoulli's principle
          • Reading the content in Bernoulli's principle
            • Workout: Reading the content in Bernoulli's principle
        • The work-energy theorem and the H-P equation

  • Chemical energy - An essential energy for life

    • Overview: Chemical Energy
      • Atomic and Molecular forces
        • Interatomic forces
          • The Lennard-Jones Potential
            • Workout: Atomic and molecular forces
          • Workout: Interatomic forces
      • Chemical bonding
        • Workout: Chemical bonding
        • Example: Chemical bonding
        • Example: Boiling hydrogen bonds
      • Controlling chemical reactions - enzymes
• Interlude 5 - The Micro to Macro Connection

  • Thermodynamics and statistical physics

    • Overview: Thermodynamics and Statistical Physics
      • Kinetic theory: The ideal gas law
        • Partial pressure - gases
        • Partial pressure - liquids
        • Reading the content in the ideal gas law
      • The 1st law of thermodynamics
        • Organizing the idea of energy
        • Enthalpy
        • Thermodynamic equilibrium and equipartition
          • Example: Degrees of freedom
      • The 2nd Law of Thermodynamics
        • The 2nd Law of Thermodynamics -- A Probabilistic Law
        • Entropy -- implications of the 2nd law of thermodynamics
          • Biological consequences of the 2nd law of thermodynamics
          • Why entropy is logarithmic
            • Workout: Why entropy is logarithmic
          • Sharing -- a way to think about entropy
          • Calculating entropy
            • Example: Arranging energy and entropy
            • Example: Entropy and heat flow
            • Example: Calculating entropy by counting microstates
        • Motivating Free Energy
          • Example: Free energy of an expanding gas
          • Example: The one atom gas
          • Gibbs free energy
        • Fluctuations -- How energy is distributed
          • Workout: How energy is distributed
          • The Boltzmann distribution
            • Example: The Boltzmann distribution
              • Workout: A Boltzmann distribution example
            • The Boltzmann distribution and the Gibbs free energy
            • Workout: The Boltzmann distribution
• Interlude 6 - Electricity, Magnetism, and Electromagnetism

  • Electricity

    • Overview: Electricity
      • The electric potential
        • Electrostatic concepts: Keeping them straight
      • Motivating Capacitance
        • Two parallel sheets of charge
        • The capacitor
          • The dielectric constant
          • Workout: The capacitor
        • The energy stored in a capacitor
      • Electric fields in matter
      • Electrical interactions in ionic solutions
        • Debye length
        • The Nernst potential
      • Electric currents
        • Quantifying electric current
        • Resistive electric flow -- Ohm's law
        • Ways to think about current -- a toolbox of models
        • Kirchhoff's principles
          • Example: Resistors in series
          • Example: Resistors in parallel
          • Example: Batteries in series and parallel
          • Example: A complex network
      • Electrical energy and power
• Interlude 7 - Oscillations and waves

  • The harmonic oscillator

    • Overview: Motivating the harmonic oscillator
      • Mass on a spring
        • Hanging mass on a spring
          • Workout: Hanging mass on a spring
        • Reading the content in the harmonic oscillator solution
        • Example: Oscillator graphs
        • Example: Oscillator calculations
      • The pendulum
      • Damped oscillators
        • Damped oscillators: The math (technical)
      • Driven oscillators
      • Quantum oscillators -- discrete states

  • Waves in one dimension

    • Overview: Waves in 1D
      • Waves on an elastic string
      • Wave pulses
        • Propagating a wave pulse -- the math
        • Example: Velocity patterns in a pulse
        • Workout: Wave pulses
      • Wave speed
        • Workout: Wave speed
      • Superposition of waves in 1D
        • Example: Cancelling pulses
        • Workout: Superposition of waves in 1D
      • Sinusoidal waves
        • Reading the content in a sinusoidal wave
        • Beats
          • Workout: Beats
        • Standing waves
        • Spectral analysis -- summing different wavelengths
          • Workout: Spectral analysis

  • Light

    • Overview: Three models of light
      • The ray model of light
        • Flat mirrors
          • Example: Flat mirrors
        • Curved mirrors
          • Curved mirror equations
            • Workout: Curved mirror equations
            • Example: Curved mirror equations
        • Lenses
          • Lens equations
      • The wave model of light
        • Electromagnetic radiation -- Maxwell's rainbow
        • Huygens' principle
          • Huygens' principle -- the math
        • Two-slit interference
          • Workout: Two-slit interference
        • Diffraction
          • Interference from two wide slits
            • Workout: Interference from two wide slits
      • The photon model of light
        • Basic principles of the photon model
          • Workout: The photon model
        • Black-body radiation
        • Fluorescence
        • Reconciling the wave and photon models - sort of
        • The photon model today
      • Color and light
        • Visual implications of color