Theoretical Physics for Biological Systems

TABLE OF CONTENTS

Quantum Mechanics in Biology

General De?nitions

The Time-independent Schroedinger Equation

Time-dependent Schroedinger Equation

Transition Probability Per Unit of Time

Quantum Coherence and Entanglement

Quantum Interference

Quantum E?ects in Biology

Statistical Physics in Biology

Why Statistical Physics in Biology?

Markov Processes

The Chemical Master Equation

Chemical Master Equation and Curse of Dimensionality

Discrete Approach to Chemical Kinetics

Stochastic Simulation Algorithm

An Example of Real Enzymatic Reactions Simulated with Gillespie Algorithm

Graph Theory and Physics Meet Network Biology

Physics at the Birth of Network Biology

Mutual Information-Based Network Inference

Thermodynamics Applications in Biological Network Analysis

Electronic Physics Applications in Network Analysis

Assessment of Network Inference Methods and the Issue of Generation of Gold-Standard Data

Network Biology is Transformed by Physics

Applied Descriptors for Complexity and Centrality to Network Biology

Network Theory

Measures for Network Complexity and Centrality

Comparative Network Analysis

Applications

Perspectives

Systems Theory and Quantum Physics

Various Recapitulation Exercises

References

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• Biotecnologia
• Biologia, ciências da vida
• Biofísica
• A física quântica (mecânica quântica e teoria quântica de campos)

Quantum Walk;DNA Sequence Comparison;Statistical physics for biology;Ordinary Differential Equations;Graph theory approaches in biophysics and biology;Transcription Regulation Network;Biological network topology and dynamics;Network Entropy;Quantum biology;Protein Concentration Level;Systems biological physics;Protein Protein Interaction Networks;Stochastic Simulation Algorithm;Structural Static Properties;Gillespie Algorithm;Network Inference;Resistance Distance;Von Neumann Entropy;PageRank Algorithm;Biological Network Analysis;Network Topological Features;Entangled State;Quantum Coherence;Classical Random Walk;Vibrational Centrality;Scale Free Networks;Mi;Multilayer Network;Adjacency Matrix;Pure Quantum State