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From Molecules to Organs: Principles and Applications of Biomechanical Modeling

01SRWMV

A.A. 2018/19

Course Language

Inglese

Course degree

Master of science-level of the Bologna process in Biomedical Engineering - Torino

Course structure
Teaching Hours
Teachers
Teacher Status SSD h.Les h.Ex h.Lab h.Tut Years teaching
Teaching assistant
Espandi

Context
SSD CFU Activities Area context
ING-IND/34 6 B - Caratterizzanti Ingegneria biomedica
2018/19
Modern experimental and computational methods have provided us with unprecedented insight into the marvels of engineering at the scales ranging from nanometers to microns and beyond that characterize the structure and function of the building blocks of biological cells. This field of research connects biology, physics, chemistry, materials science and even information science. By incorporating concepts and methods from biophysics, biochemistry, bioengineering, structural engineering, materials science and biology, computational modeling methods and theoretical concepts allows us to gain better understanding how biological materials are organized and how they function separately and integrated into a unit such as the living cell. The course can be taken in both the first and second year of degree.
Modern experimental and computational methods have provided us with unprecedented insight into the marvels of engineering at the scales ranging from nanometers to microns and beyond that characterize the structure and function of the building blocks of biological cells. This field of research connects biology, physics, chemistry, materials science and even information science. By incorporating concepts and methods from biophysics, biochemistry, bioengineering, structural engineering, materials science and biology, computational modeling methods and theoretical concepts allows us to gain better understanding how biological materials are organized and how they function separately and integrated into a unit such as the living cell. The course can be taken in both the first and second year of degree.
The course offers a concise physical description of the organization of the cell and multi-cellular organisms and provides examples of the applications of biomolecular modeling at all levels of organization. Practical cases will be the objective of specific hands-on tutorials. The student will gain competencies on physics and biomechanics characterizing subcellular, cellular and tissue level biological systems. At the end of the course the student will be able to: understand and characterize the biomechanics of subcellular structures such as proteins, protein aggregates, membrane polymers filaments networks; understand and characterize the physical, chemical and mechanical behavior of cells and tissues in physiological and pathological conditions. This course will help students to develop their independent thinking through self-assessment tests. The course will help to improve both written and oral communication skills through classroom exercises, group and individual tutorials and through the development of a short project on a specific topic. The ability to learn is stimulated by a training program that alternates, in an organized schedule, methodological principles, application examples, and exercises. A short research on a chosen topic encourages the students to undertake surveys on websites, to view the scientific literature and to become aware of the applied research areas related to the course.
The course offers a concise physical description of the organization of the cell and multi-cellular organisms and provides examples of the applications of biomolecular modeling at all levels of organization. Practical cases will be the objective of specific hands-on tutorials. The student will gain competencies on physics and biomechanics characterizing subcellular, cellular and tissue level biological systems. At the end of the course the student will be able to: understand and characterize the biomechanics of subcellular structures such as proteins, protein aggregates, membrane polymers filaments networks; understand and characterize the physical, chemical and mechanical behavior of cells and tissues in physiological and pathological conditions. This course will help students to develop their independent thinking through self-assessment tests. The course will help to improve both written and oral communication skills through classroom exercises, group and individual tutorials and through the development of a short project on a specific topic. The ability to learn is stimulated by a training program that alternates, in an organized schedule, methodological principles, application examples, and exercises. A short research on a chosen topic encourages the students to undertake surveys on websites, to view the scientific literature and to become aware of the applied research areas related to the course.
Basic knowledge of the basics of engineering with particular attention to physics, mathematics, chemistry, biology, mechanics, materials science. The lecturer may consider filling specific background gaps by giving ad hoc lectures.
Basic knowledge of the basics of engineering with particular attention to physics, mathematics, chemistry, biology, mechanics, materials science. The lecturer may consider filling specific background gaps by giving ad hoc lectures.
The course will cover the following topics: Features of living systems • What is life? Differences between the animate and the inanimate matter • The machinery of a prokaryotic cell, photosynthetic revolution, origin of a diploidal eukaryotic cell • Hierarchy of organization, morphogenesis and embryonal development • Allometric laws in physiology • Entropy reduction in living systems Key Life Processes • Non-equilibrium thermodynamics: time scales for relaxation processes • Kinetics of single chemical reactions: diffusion through membrane and uni-molecular reactions; chemical affinity and chemical equation of state; kinetic equations , redox reactions, many coupled reactions – steady state approximation, hierarchy of time scales. • Steady states in enzymatic catalysis, derivation and interpretation of the Michaelis–Menten equations, pattern formation in reaction-diffusion systems. Structure, Mechanics and Dynamics of Biomolecules • Biological building blocks, amphipatic molecules in water environments, structure of nucleic acids, structure of proteins, protein filaments and super assemblies, translational and rotational diffusion, Brownian motion, diffusion equation, diffusion to capture. Membrane and membrane proteins, Ion channels and ion pumps. Molecular and Biological Motors and Machines • Biological Motions, Isothermal Machines: power input and output; efficiency, chemo-Chemical machines: chemical fluxes and forces, motors as chemo-chemical machines, flux-force relatiions. • Functional proteins. Motor proteins and their role in cellular processes: dynein, kinesin, dynactin, myosin, the molecular mechanisms of force generation. Ribosome’s and production of proteins. Chaperones and Protein Folding. • Metabolism: role of ATP, production of H+ gradients. Mitochondria and chloroplasts, cell energetics. Energy and material transport in and out of a cell. • Cell motility: cilia and flagella, beats and strokes. Structure, Mechanics and Dynamics of Biological Cells • General Characteristics of a Cell • Networks and meshworks of protein filaments, the cytoskeleton, stress fibers and tensegrity. Cell adhesion • Cytoplasm, cellular water and its characteristics, biological ferroelectricity. • Nucleus: nuclear chromatin, chromosomes, nuclear lamina. • Mitosis and meiosis; stages and checkpoints, the cleavage furrow, physical models and biological reality • Cell communication, cell intelligence • Neurotransmitters and the mechanism of exocytosis, Synchronization of excitable cells, coherence of firing, Neural network models. Tissue and Organ Biophysics and Biomechanics • Energy Management in the human body • Multiscale features of the nervous system • Models of the immune system • The biophysics of vision • The biomechanics of sound perception • Biophysics of Respiration • Anatomy and physiology of the human circulatory system: the physics of blood flow in arteries and capillaries, Dynamics of the heart (pump, rhythms, arrythmias, spiral waves). • Muscles Biomechanics • Bone stiffness and strength
The course will cover the following topics: Features of living systems • What is life? Differences between the animate and the inanimate matter • The machinery of a prokaryotic cell, photosynthetic revolution, origin of a diploidal eukaryotic cell • Hierarchy of organization, morphogenesis and embryonal development • Allometric laws in physiology • Entropy reduction in living systems Key Life Processes • Non-equilibrium thermodynamics: time scales for relaxation processes • Kinetics of single chemical reactions: diffusion through membrane and uni-molecular reactions; chemical affinity and chemical equation of state; kinetic equations , redox reactions, many coupled reactions – steady state approximation, hierarchy of time scales. • Steady states in enzymatic catalysis, derivation and interpretation of the Michaelis–Menten equations, pattern formation in reaction-diffusion systems. Structure, Mechanics and Dynamics of Biomolecules • Biological building blocks, amphipatic molecules in water environments, structure of nucleic acids, structure of proteins, protein filaments and super assemblies, translational and rotational diffusion, Brownian motion, diffusion equation, diffusion to capture. Membrane and membrane proteins, Ion channels and ion pumps. Molecular and Biological Motors and Machines • Biological Motions, Isothermal Machines: power input and output; efficiency, chemo-Chemical machines: chemical fluxes and forces, motors as chemo-chemical machines, flux-force relatiions. • Functional proteins. Motor proteins and their role in cellular processes: dynein, kinesin, dynactin, myosin, the molecular mechanisms of force generation. Ribosome’s and production of proteins. Chaperones and Protein Folding. • Metabolism: role of ATP, production of H+ gradients. Mitochondria and chloroplasts, cell energetics. Energy and material transport in and out of a cell. • Cell motility: cilia and flagella, beats and strokes. Structure, Mechanics and Dynamics of Biological Cells • General Characteristics of a Cell • Networks and meshworks of protein filaments, the cytoskeleton, stress fibers and tensegrity. Cell adhesion • Cytoplasm, cellular water and its characteristics, biological ferroelectricity. • Nucleus: nuclear chromatin, chromosomes, nuclear lamina. • Mitosis and meiosis; stages and checkpoints, the cleavage furrow, physical models and biological reality • Cell communication, cell intelligence • Neurotransmitters and the mechanism of exocytosis, Synchronization of excitable cells, coherence of firing, Neural network models. Tissue and Organ Biophysics and Biomechanics • Energy Management in the human body • Multiscale features of the nervous system • Models of the immune system • The biophysics of vision • The biomechanics of sound perception • Biophysics of Respiration • Anatomy and physiology of the human circulatory system: the physics of blood flow in arteries and capillaries, Dynamics of the heart (pump, rhythms, arrythmias, spiral waves). • Muscles Biomechanics • Bone stiffness and strength
Lectures, classroom exercises and hands on in computational lab.
Lectures, classroom exercises and hands on in computational lab.
The teacher will provide all the course material (slides and lecture notes). Suggested textbooks: • Tuszynski, J.A., 2008. Molecular and cellular biophysics. Chapman & Hall/CRC. • Boal, D., 2001. Mechanics of the Cell. Cambridge University Press, Cambridge. doi:10.1017/CBO9780511810954
The teacher will provide all the course material (slides and lecture notes). Suggested textbooks: • Tuszynski, J.A., 2008. Molecular and cellular biophysics. Chapman & Hall/CRC. • Boal, D., 2001. Mechanics of the Cell. Cambridge University Press, Cambridge. doi:10.1017/CBO9780511810954
Modalità di esame: Prova scritta (in aula); Prova orale facoltativa; Progetto di gruppo;
A written exam of 2-hour duration with access only to a calculator will take place. A mandatory small project will be developed by the student (bibliographic work) which will help to define the final score. The grades will range from 0 to 33 and those students scoring at or above 31 will be given a designation: "laude"
Exam: Written test; Optional oral exam; Group project;
A written exam of 2-hour duration with access only to a calculator will take place. A mandatory small project will be developed by the student (bibliographic work) which will help to define the final score. The grades will range from 0 to 33 and those students scoring at or above 31 will be given a designation: "laude"


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