Manuals

Contents

• Introduction

  ---

• Global fitting engine

  ---

• Model derivations, implementation and testing

  ---

• General purpose modules

  ---

• Data-specific modules

  ---

• Tutorials

  ---

Introduction

• Version history

• General concepts and structure of the project

Back to Contents

Global fitting engine

• Concepts of data fitting algorithms

• Understanding fitting results

• Dataset class and objects: structure and function

• TotalFit class and objects: structure and function

Back to Contents

Model derivations, implementation and testing

All non-trivial mathematical derivations that produced equations for various modules in BiophysicsLab are documented in the form of MuPad notebooks and their HTML representations.  I also conducted testing of BiophysicsLab implementations of most of them here. The user is invited to examine and rerun notebooks to better understand inner workings of the mathematical models used in fitting and simulations. The folder Mathematical_models/ contains definitions, derivation of equations and test simulations for:

• Equilibrium thermodynamic equations to compute equilibrium concentrations of species in solution.
  • Folder: Mathematical_models/Equilibrium_thermodynamic_models/
  • HTML index

    ---

• Transient kinetics
  • Folder: Kinetic_models/
  • HTML index

    ---

• NMR 1D line shape models (kinetic matrices for Bloch-McConnel equations)
  
  • Folder: Mathematical_models/NMR_line_shape_models/
  • HTML index

    ---

For more examples see Tutorials.

Back to Contents

General purpose modules

For the theory and test examples see Model derivations, implementation and testing and Tutorials.

• Calculation of equilibrium concentrations of species

• Calculation of non-equilibrium concentrations of species in kinetics

• Hypothesis testing

• Distributed processing

• Data presentation

Back to Contents

Data-specific modules

For the theory and test examples see Model derivations, implementation and testing and Tutorials.

1D NMR line shapes

Rapid-Mixing Kinetics

Back to Contents

Tutorials

See separate document: Tutorial_index.htm

Back to Contents