Канал: Physical Biology of the Cell (Caltech BE APh 161)

Why physics needs biology

Why physics needs biology

Why equilibrium?

Why equilibrium?

Dynamics of symporter

Dynamics of symporter

ATP biological battery: phosphorylation-dephosphorylation dynamics

ATP biological battery: phosphorylation-dephosphorylation dynamics

Phosphorylation energetics

Phosphorylation energetics

ATP battery

ATP battery

Cashing in concentration gradients symporters

Cashing in concentration gradients symporters

Allostery no physicists allowed

Allostery no physicists allowed

Binding via chemical potential

Binding via chemical potential

Science is not a smorgasbord

Science is not a smorgasbord

Science is not a smorgasbord: Germ theory disease

Science is not a smorgasbord: Germ theory disease

Viruses As infectious agents

Viruses As infectious agents

The relaxation to equilibrium

The relaxation to equilibrium

The great Gibbs and the chemical potential

The great Gibbs and the chemical potential

Biological batteries

Biological batteries

Stat mech ion channel

Stat mech ion channel

Molecules as documents of evolutionary history

Molecules as documents of evolutionary history

Genomics without genomes: Hemoglobin

Genomics without genomes: Hemoglobin

Entropic elasticity DNA

Entropic elasticity DNA

Statistical mechanics protocol

Statistical mechanics protocol

Continuum theory protocol

Continuum theory protocol

Paradigms for patterning

Paradigms for patterning

I wonder - pattern formation

I wonder - pattern formation

Origins of field theory

Origins of field theory

Toner-Tu theory intro

Toner-Tu theory intro

Collective animal motions

Collective animal motions

Frog osmotic shock

Frog osmotic shock

Linear transport laws

Linear transport laws

Interlude on entropy

Interlude on entropy

Frogs sao tome puzzle

Frogs sao tome puzzle

Physics of frogs in saltwater

Physics of frogs in saltwater

Osmotic pressure

Osmotic pressure

Ocean currents dispersal

Ocean currents dispersal

Bar tailed godwit migration

Bar tailed godwit migration

Mitochondrial surface volume

Mitochondrial surface volume

Nucleolar scaling

Nucleolar scaling

Semantics on scale

Semantics on scale

Scaling of diffusion time

Scaling of diffusion time

A feeling for the organism

A feeling for the organism

Biological numeracy exam (answers)

Biological numeracy exam (answers)

Biological numeracy exam

Biological numeracy exam

I wonder...

I wonder...

Order of magnitude toolkit

Order of magnitude toolkit

Course accomplishments

Course accomplishments

Imposters, success and failure

Imposters, success and failure

PBoC: Understanding

PBoC: Understanding

Musings on mechanism

Musings on mechanism

Biological numeracy

Biological numeracy

Night science

Night science

Flory–Huggins theory

Flory–Huggins theory

Membraneless organelles and phase separation

Membraneless organelles and phase separation

C elegans actomyosin

C elegans actomyosin

The Real Biology

The Real Biology

Self-organization in Chara

Self-organization in Chara

Incompressibility

Incompressibility

Stokes equations for the cytoplasmic streaming in Chara

Stokes equations for the cytoplasmic streaming in Chara

Viscoelasticity in tissues

Viscoelasticity in tissues

Introduction to cytoplasmic streaming in Chara

Introduction to cytoplasmic streaming in Chara

Dimensionless Navier-Stokes, Reynolds number

Dimensionless Navier-Stokes, Reynolds number

Derivation of the Navier–Stokes equations

Derivation of the Navier–Stokes equations

Stress in fluids

Stress in fluids

Force balance in fluids

Force balance in fluids

Elasticity of beams

Elasticity of beams

Gut folding

Gut folding

Stress and strain

Stress and strain

Introduction to elasticity

Introduction to elasticity

What is field theory

What is field theory

Introduction to active matter

Introduction to active matter

Kinetic proofreading

Kinetic proofreading

Fidelity as defiance

Fidelity as defiance

Proton motive force

Proton motive force

Chemotaxis adaptation

Chemotaxis adaptation

Entropy production

Entropy production

Sameness

Sameness

MWC model of chemoreceptors

MWC model of chemoreceptors

Cost of forming the Bicoid gradient

Cost of forming the Bicoid gradient

Introduction to adaptation: Chemotaxis

Introduction to adaptation: Chemotaxis

Drawing energy from a concentration gradient

Drawing energy from a concentration gradient

Dissipation required to maintain a concentration gradient

Dissipation required to maintain a concentration gradient

Cost of transport up a gradient

Cost of transport up a gradient

Phenomenology not a dirty word

Phenomenology not a dirty word

Linear departure from equilibrium

Linear departure from equilibrium

Boltzmann as equilibrium recast

Boltzmann as equilibrium recast

Thermal energy scale

Thermal energy scale

Calculus of equilibrium

Calculus of equilibrium

Turing: Closing the loop

Turing: Closing the loop

Life as defiance: Introduction

Life as defiance: Introduction

Continuous version of Turing

Continuous version of Turing

Turing ring of cells

Turing ring of cells

In the steps of Turing

In the steps of Turing

Meeting Turing

Meeting Turing

Positional information: Reaction-diffusion equation

Positional information: Reaction-diffusion equation

Positional information: The French flag model

Positional information: The French flag model

On positional information

On positional information

Chemical master equation for the two-state model of transcription, part 2

Chemical master equation for the two-state model of transcription, part 2

Chemical master equation for the two-state model of transcription, part 1

Chemical master equation for the two-state model of transcription, part 1

Chemical master equation for the cytoskeleton

Chemical master equation for the cytoskeleton

Ode to precision

Ode to precision

Chemical Master Constitutive Promoter

Chemical Master Constitutive Promoter

Every distribution has its moments

Every distribution has its moments

Reconciling statistical mechanics and thermodynamics (continued)

Reconciling statistical mechanics and thermodynamics (continued)

Closing the theory-experiment loop

Closing the theory-experiment loop

MWC model

MWC model

On surprise in spectroscopy

On surprise in spectroscopy

Rate equations for the double negative regulation

Rate equations for the double negative regulation

Double negative feedback hypothesis for the Aleutians

Double negative feedback hypothesis for the Aleutians

Interlude on surprise

Interlude on surprise

Rate equations for pandemics

Rate equations for pandemics

Why I am so boring

Why I am so boring

Rate equations for microtubule length control

Rate equations for microtubule length control

Reconciling thermodynamic and statistical mechanical views of binding

Reconciling thermodynamic and statistical mechanical views of binding

Rate equations for genetic oscillators

Rate equations for genetic oscillators

Mutual repression switch: Fixed points

Mutual repression switch: Fixed points

Stability analysis for the mutual repression switch

Stability analysis for the mutual repression switch

Rate equations for the mutual repression switch

Rate equations for the mutual repression switch

Rate equations for auto-activation

Rate equations for auto-activation

Introduction to gene networks

Introduction to gene networks

Borges and you

Borges and you

Statistical mechanics: Binding cooperativity

Statistical mechanics: Binding cooperativity

Statistical mechanics: Binding

Statistical mechanics: Binding

Statistical mechanics: Introduction

Statistical mechanics: Introduction

Rate equations for compartmentalized enzymes

Rate equations for compartmentalized enzymes

On the literature

On the literature

Dynamics of enzymes

Dynamics of enzymes

Dynamics of ligand-receptor binding

Dynamics of ligand-receptor binding

Rate equations for mRNA dynamics

Rate equations for mRNA dynamics

Introduction to dynamics beyond diffusion

Introduction to dynamics beyond diffusion

Diffusion: Master equation

Diffusion: Master equation

Diffusion: Continuum theory

Diffusion: Continuum theory

Diffusion: Coin flips

Diffusion: Coin flips

Diffusion: Introduction

Diffusion: Introduction

Biological numeracy exam

Biological numeracy exam

Doing physics to it

Doing physics to it

Schrödinger's "What Is Life?"

Schrödinger's "What Is Life?"

Transformative technologies

Transformative technologies

Order-of-magnitude thinking

Order-of-magnitude thinking

A feeling for the organism

A feeling for the organism

Rate limiting hypothesis: Summary

Rate limiting hypothesis: Summary

Rate limiting hypothesis: Ribosomes

Rate limiting hypothesis: Ribosomes

Rate limiting hypothesis: Transcription

Rate limiting hypothesis: Transcription

Rate limiting hypothesis: Surface-to-volume ratio

Rate limiting hypothesis: Surface-to-volume ratio

Rate limiting hypothesis: ATP synthase

Rate limiting hypothesis: ATP synthase

Rate limiting hypothesis: Carbon transport

Rate limiting hypothesis: Carbon transport

Rate limiting hypothesis: Proteomics

Rate limiting hypothesis: Proteomics

Laws of cellular growth

Laws of cellular growth

What sets the bacterial division time?

What sets the bacterial division time?

Scaling of cellular structures

Scaling of cellular structures

Diffusion time by the numbers

Diffusion time by the numbers

Scaling of diffusion time

Scaling of diffusion time

Semantics on scale

Semantics on scale

Interlude on passion

Interlude on passion

Bacterial size control: Adder

Bacterial size control: Adder

Bacterial size control: Timer

Bacterial size control: Timer

Interlude on Taylor series

Interlude on Taylor series

Biological puzzles and probabilistic thinking

Biological puzzles and probabilistic thinking

Ion channels and exponential waiting time distriubtion

Ion channels and exponential waiting time distriubtion

Carboxysomes and binomial partitioning

Carboxysomes and binomial partitioning

mRNAs and Poisson distribution

mRNAs and Poisson distribution