Next:
List of Figures
Up:
No Title
Previous:
No Title
Contents
List of Figures
I
NTRODUCTION
Inverse Protein Folding
Hierarchical Optimisation
Tie Knots
Schematic Organisation
Publications
P
ROTEIN
F
OLDING
, I
NVERSE
P
ROTEIN
F
OLDING
AND
Energy L
ANDSCAPES
Protein Folding
Inverse Protein Folding
Energy Landscapes
Smooth vs. Rugged Landscapes
Folding Funnels and Free Energy Traps
L
ATTICE
M
ODELS
AND
T
HERMODYNAMIC
S
EQUENCE
S
ELECTION
Lattice Models
Folding Dynamics
Analytic Representation
Shakhnovich Selection Scheme
Minimisation of
E
Minimisation of
Z
S
TABILITY
AND
A
CCESSIBILITY
Introduction
Stability and Accessibility
Details of Simulation
Shift of Pair Potential
Protein Folding is Many to One
Accessibility-Stability Phase Space
Conclusion
I
NVERSE
P
ROTEIN
F
OLDING
AS
AN
A
SSOCIATIVE
M
EMORY
Introduction
Proteins as Associative Networks
Energy Function
Capacity from Energetics
Capacity from Information Theory
Retrieving Memories from Proteins
Conclusion
F
UNNEL
D
ESIGN
BASED
ON
U
NFOLDING
D
YNAMICS
Introduction
Generalisation to Weighted Training
Simple Blob Model of Unfolding
Training to a Funnel
Conclusion
K
INETICALLY
O
RIENTED
S
EQUENCE
S
ELECTION
Introduction
Kinetically Oriented Sequence Selection
Measuring Folding Time
Simulated Annealing
Probability of Moving Downhill
Thermodynamic Guidance
Results
Sequential
MFPT
Landscape is Smooth
Conclusion
H
IERARCHICAL
O
PTIMISATION
P
ROBLEMS
Traveling Salesman Problem
Probabilistic Traveling Salesman Problem
Hierarchical Optimisation Problems
Combinatoric and Hierarchical Complexity
Definition of Hierarchical Optimisation
General Optimality Equation
S
TOCHASTIC
A
NNEALING
Introduction
Simulated Annealing
Stochastic Annealing
Comparison of Simulated and Stochastic Annealing
Probabilistic Traveling Salesman Problem
Conclusion
E
XACTLY
S
OLVABLE
H
IERARCHICAL
O
PTIMISATION
P
ROB
LEM
Introduction
Description of Problem
Optimality Equation
Uniform Cost Distribution
General Cost Distribution
Interpretation as a Percolation Model
Conclusion
Appendix A: Applying the
General Optimality Equation
T
IE
K
NOTS
AND
R
ANDOM
W
ALKS
Introduction
Definition of Tie Knots
Tie Knots as Random Walks
Size of Knots
Shape of Knots
Symmetry
Balance
Untying
Topology
Conclusion
Appendix A: Distribution of End to End
Distance of Walks in the Class
E
PILOGUE
References
About this document ...
list of figures
Thomas Fink
Tue Jun 16 17:14:36 BST 1998