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