This textbook covers the scientific basics of molecular bioengineering, a new field where technology meets biology and chemistry, and the fundamental knowledge required for students to understand molecular mechanisms beyond biological phenomena. The textbook focuses on the role of proteins in biomolecular machinery, and it is divided into 2 parts: Part I covers the molecular thermodynamics of biological systems, and Part II discusses the computational aspects behind protein structure prediction and molecular dynamics. In the first part of the textbook, students will find comprehensive explanations of thermodynamics and statistical mechanics, which are the basis to understand how molecular properties translate into macroscopic. Part I also offers an introduction to proteins and concepts like intermolecular forces, volumetric properties of fluids, ionization equilibria and salting-out, and protein binding and protein-protein interactions. In the second part of the textbook, students will learn about protein structure prediction and analysis, systems biology and structure-based protein networks, and computational tools and approaches for molecular dynamics simulations and protein binding and protein-protein interactions. This textbook adds to the scholarly debate with a unique contribution, addressing important new areas of biophysical chemistry and molecular biophysics not covered in currently available textbooks. Given its breadth, the textbook is suitable for courses in molecular biophysics, biochemistry, physical chemistry and bioengineering, and will also appeal to researchers and professionals in these fields. Part I of this book is a translation from its Italian original manuscript done with the help of artificial intelligence. A subsequent human revision of the content was done by the author. Springer Nature works continuously to further the development of tools for the production of books and on the related technologiesto support the authors.