Table of Contents
Thermodynamics of Living Biochemical Processes
What is the Classic thermodynamics?
The mathematical methods of probability and stochastic processes, and statistical thermodynamics.
Classic biochemistry:
understanding biological processes inside living cells and organisms in
terms of atoms and molecules.
A non-living system approaches a thermodynamic equilibrium.
A elementary chemical reaction and
the law of mass action
Chemical equilibrium
Chemical nonequilibrium
steady-state
1st and 2nd Laws of Thermodynamics
Application to motor protein energy transduction
From Muscle to Actin & Myosin
Gliding of actin filaments
Experimental Images
How motor protein generate force?
Stochastic Kinetic Model of a Single Motor Protein
Nonequilibrium Steady-state
Energy Conservation
Efficiency of a motor protein:
Isometric Force and Equilibrium
Protein Structures
Free Energy Landscape of Motor Proteins: the Power Stroke and the Ratchet”
Equation for Motor Protein Movement
Stochastic Macromolecular Mechanics of Single Molecule
The Mathematics of Stochastic Macromolecular Mechanics
Application to GTPase signal transduction and kinetic timing hypothesis
Receptor-mediated GTPase: a timer
Exponential distribution
Kinetic Model for GTPase timer
Model Parameters
Waiting time distributions
Microscopy: wild-type Rab5
Microscopy: Q79L Rab5 mutant
Data: wild-type Rab5
Data: Q79L Rab5
Single Molecule Timer and Kinetic Timing Hypothesis
The Mathematical Basis of Kinetic Timing Hypothesis
Application to analyzing large-scale complex biochemical networks
Major Reactions of Metabolism
Stoichiometric Matrix
Flux Balance Analysis
A Simple Example
E. coli Growth Objective Function
Indentifying an essential gene when the maximal biomass output is sufficiently low
In silico Predictions
Energy Balance Analysis
How EBA work
Energy Balance Equation
How does EBA improve in silico
modeling
Biochemical Networki Theory
An Example
Gene regulation and biochemical conductance
Results
What do we learn from EBA?
Conclusions
Acknowledgement
|
