Theoretical Physics for Biological Systems

Dr. Paola Lecca is Research Scientist at the Department of Mathematics of University of Trento (Italy), and Paola Lecca has a Master Degree in Theoretical Physics and a PhD in Computer Science and Telecommunications. She worked for several years since its foundations as researcher and principal investigator at the Microsoft Research - University of Trento, Centre for Computational and Systems Biology, where she was the leader of the research team "Knowledge inference and data management". She is currently researcher at the Department of Mathematics of University of Trento, scholarship holder at the Department of Medicine of University of Verona, and Senior Professional Member of Association for Computing Machinery. Her main research activities focus on computational modelling and algorithmic procedures implementing efficient solutions for identiafiability, controllability, and simulation of complex dynamical networks. The main applicative domains of these studies are network biology, biochemistry, biological physics, microbiology, and synthetic biology. Dr. Paola Lecca is author of about hundred publications including books and journal and conference papers on international journals in computer science, computational biology, bioinformatics, and biophysics. She carries on an intense editorial activity as editor and reviewer for high impact journals in these subjects. Angela Re obtained her Master degree in Physics in 2004 and Ph.D. degree in 2007 in the programme – Complex Systems Applied to Post-Genomic Biology – at the University of Turin. Since then, she has been conducting an active research program in international research centres, abroad and in Italy such as the Centre for Integrative Biology in Trento and the Centre for Sustainable Future Technologies in Torino. She has a long-proven track record working with mathematical conceptualization and statistical analysis of a variety of different biological data types. Specific areas of interest include the study of eukaryotic post-transcriptional regulatory mechanisms and their inclusion in cancer and stem cell pathways as well as the application of systems and synthetic biology approaches to bacterial RNA biology, proteomics and metabolism. She contributes to develop statistical software for the analysis of network modular organization and its dynamical properties, and she is interested into integrative multi-assay genomic data visualization and integration. She is in charge of editor ad reviewer activities in peer-reviewed scientific journals. 　 　 　 　

TABLE OF CONTENTS

Quantum Mechanics in Biology

General Definitions

The Time-independent Schrödinger Equation

Time-dependent Schrödinger Equation

Transition Probability Per Unit of Time

Quantum Coherence and Entanglement

Quantum Interference

Quantum Effects 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