Table of Contents
Biophysics 101 Genomics and Computational Biology
Net1: Last week's take home lessons
Net2: Today's story & goals Bio101 28-Nov-2000
Algorithm Running Time
Algorithm Complexity
How to deal with NP-complete and NP-hard Problems
What can biology do for difficult computation problems
Net2: Today's story & goals Bio101 28-Nov-2000
Molecular Computing
DNA computing: Is there a Hamiltonian path through all nodes?
DNA Computing for st-Hamiltonian Path
Encode Graph into DNA Sequences
Create All st-Paths
DNA Computing Process
Molecular computation: RNA solutions to chess problems.
Problems of DNA Computing
Promises of DNA Computing
A sticker-based model for DNA computation.
3SAT
DNA Computing for 3SAT
DNA computing on surfaces
Net2: Today's story & goals Bio101 28-Nov-2000
Logical computation using algorithmic self-assembly of DNA triple-crossover molecules.
tiles
Nanoarray microscopy readout (vs gel assays)
Micro-ElectroMechanical Systems (MEMS)
Nano-ElectroMechanical Systems (NEMS)
Nanosensors
poly(dA)100 & poly(dC)100 at 15°C
Net2: Today's story & goals Bio101 28-Nov-2000
A synthetic oscillatory network of transcriptional regulators
Synthetic oscillator network
Synthetic oscillator network
Net2: Today's story & goals Bio101 28-Nov-2000
Genetic Algorithms (GA)
Genetic Operations
Step 1: Structure Representation
Protein Conformation and Structure Prediction
Step 2: Conformational Energy (fitness function)
Step 3: Genetic Operations
Assessment of Prediction
SAGA: Sequence Alignment by Genetic Algorithm
SAGA continues
Comparison of ClustalW & SAGA
Net2: Today's story & goals Bio101 28-Nov-2000
Artificial Neural Networks
Neural Networks
An ORF Classification Example
Measuring Exons
Linear Discriminate Function and Single Layer Neural Network
Activation Function
Determining Edge Weights from Training Sets
Non-linear Discrimination
The Multi-Layer Perceptron
GRAIL
Net2: Today's story & goals Bio101 28-Nov-2000
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