*New Course* - Fundamentals of non-Newtonian fluid mechanics and rheology as applied to biological fluids. Fundamentals of mass and momentum conservation, dimensional analysis, continuity equations, Generalized Newtonian Fluid models, and the solution of fluid flow problems using empirical constitutive relationships. 

*New Course* - Metabolic engineering role in transition from fossil resources to a bio-based society. Design-build-test-learn cycle of metabolic engineering. Design, genetic engineering and optimization of microbial biocatalysts. Metabolic network analysis, constraint-based modelling of metabolism, microbial production of valuable chemicals. 

Introduction to bioengineering; engineering calculations; physical foundations of bioengineering; conservation laws; fundamentals of conservation principles; conservation of mass; energy; charge and momentum. Mechanical, chemical, electrical, and thermodynamic driving forces in biological systems. Design principles of biological systems.

Mechanisms of optical and electrical detection, transmission, and processing in biology. Vision, luminescence, photosynthesis, nerve conduction, ion channels. Speciation and evolutionary optimization as a design platform. Biomimetic opto-electric engineering. Optics and electronics in instrumentation for biological measurements.

An introduction to molecular and cell biology from a physical perspective. Techniques and methodologies, both experimental and computational, are included in the presentation of each thematic module.

Laboratory safety. Conceptual understanding of measurement principles and instrumentation. Introduction to experimental techniques requiring sterile conditions. Mechanical measurements of solid and thermofluid quantities. Optical sensing techniques. Measurements of biological and chemical properties. Design of experiments and statistical and uncertainty analyses.

Fundamental concepts of Thermodynamics: Internal Energy, Work, The 3 Laws of Thermodynamics, Enthalpy, and Entropy. Basic concepts of energy in living organisms: distribution of energy, energy conservation in living organisms, isothermal systems, Gibbs free energy in chemical coupling, reversible processes and redox reactions. Application of Thermodynamics in defining biological processes and components.

Forward & reverse engineering of biomolecular systems. Principles of biomolecular thermodynamics & kinetics. Structure and function of the main classes of biomolecules including proteins, nucleic acids, & lipids. Biomolecular systems as mechanical, chemical, & electrical systems. Rational design & evolutionary methods for engineering functional proteins & gene circuits.

Basic concepts in transport phenomena, including fluid dynamics (momentum transport) and heat transfer (energy transport), with applications to biological systems, both medical & non-medical. Topics in fluid dynamics include: properties of Newtonian & non-Newtonian fluids; dimensional analysis; drag; integral/macroscopic balances (Bernoulli's equation and linear momentum theorem); differential/microscopic balances (continuity and Navier-Stokes equations); boundary layer approximations; turbulence. Topics in heat transfer include elements of conduction & convection.

Basic mechanics of biological building blocks, focusing on the cytoskeleton, with examples from pathology. At the macromolecular level: weak/variable crosslinking and hydrolysis driven athermal processes. At the cellular/tissue level: cell architecture and function. Discussion of modern analytical techniques capable of single-molecule to tissue scale measurements.

The history, scope, challenges, ethical considerations, and potential of tissue engineering. In vitro control of tissue development, differentiation, and growth, including relevant elements of immunology compared to in vivo tissue and organ development. Emphasis on the materials, chemical factors, and mechanical cues used in tissue engineering.

Fundamental principles of mass transport and its application to a variety of biological systems. Membrane permeability and diffusive transport. Convection. Transport across cell membranes. Ion channels. Blood rheology. Active transport. Intra- and inter-cellular transport.

Discrete- and continuous-time signals; basic system properties. Linear time-invariant systems; convolution. Frequency domain analysis; filtering; sampling. Laplace and Fourier transforms; transfer functions; poles and zeros; transient and steady state response. Z-transforms. Dynamic behaviour and PID control of first- and second-order processes. Stability.Applications to biological systems, such as central nervous, cognitive, and motor systems. 

Description of chemical systems with the help of theories of physics and application of its techniques: reaction kinetics, physical and chemical equilibria in biological systems. Review of energy transfer and thermodynamics. Chemical and physical equilibria in biology: variation of Gibbs energy with temperature, energy, composition. Theories of reaction kinetics and the reaction mechanism in biological phenomena: polymerization, protein folding, enzymes.

Introduction to the fundamental principles of experimental design, statistical analysis, and scientific communications applied to bioengineering research.Laboratory topics include: DNA engineering and cloning, in vitro motility assays, mammalian cell culture and immunofluorescence, and microfabrication.

Introduction to computational biomolecular engineering. Biomolecular simulation: deterministic simulation, stochastic simulation. Biomolecular modeling: energy minimization, coarse-grained methods. Computational biomolecular design: protein design, protein docking, and drug design. Computational systems and synthetic biology: computer simulation of biomolecular circuits.
 

Introduction to the field of high throughput screening (HTS) analytical techniques and devices used for genomics, proteomics and other approaches, as well as for diagnostics, or for more special cases, e.g., screening for biomaterials. Introduction into the motivation of HTS and its fundamental physico-chemical challenges; techniques used to design, fabricate and operate HTS devices, such as microarrays and new generation DNA screening based on nanotechnology. 

Basic aspects of human physiology. Applications of general balance equations and control theory to systems physiology. The course will cover: circulatory physiology, nervous system physiology, renal physiology and the musculoskeletal system.

A capstone group design project on an industrially relevant engineering problem of a biological nature. Student teams work in consultation with faculty and industrial consultants in the design of functional and practical systems, devices, or processes, taking into account safety, sustainability, management and economic considerations.

Individual guided research projects in bioengineering. Under the guidance of a research adviser, students will propose and implement a research plan that addresses a current gap in knowledge or industry need. Projects will be designed to provide experience in critical evaluation of primary research literature, experimental approaches and methodologies, quantitative analysis, mathematical modelling, and effective written and oral presentation of scientific ideas.

Selected special topics in bioengineering, given by current and visiting staff.

Introduction to the interdisciplinary field of biomedical uses of nanotechnology. Emphasis on emerging nanotechnologies and biomedical applications including nanomaterials, nanoengineering, nanotechnology-based drug delivery systems, nano-based imaging and diagnostic systems, nanotoxicology and immunology, and translating nanomedicine into clinical investigation.

Microscopy techniques with application to biology and medicine. Practical introduction to optics and microscopy from the standpoint of biomedical research. Discussion of recent literature; hands-on experience. Topics include: optics, contrast techniques, advanced microscopy, and image analysis.

Introduction to electron microscopy and 3D imaging. Dual-beam microscopy (FIB-SEM, or focused ion beam – scanning electron microscope); conventional and cryogenic preparation methods for biological materials. Complementary methods such as X-ray diffraction, X-ray tomography, atom probetomography. 3D image processing and analysis, and the fundamentals of deep learning in imaging.

Storage and processing of information in biological systems, both natural and artificially-created, ranging from biomolecules, cells, and populations of cells. Information storage in DNA and DNA computation; molecular surfaces of proteins; computation with motile biological agents in networks; and biological and biologically-inspired algorithms.

The fundamental of diagnosis devices from design concepts to implementation in real-life application, a brief review of the gold standard diagnostic methods and their limitations, the building blocks of an ideal diagnostic device with a focus on point-of-care applications, biomolecular recognition elements including different one-step and multistep assays based on nucleic acids and proteins, and the fundamental of sample delivery systems and fluid flow based on microfluidics, the integration of bioassays and microfluidics in lab-on-chip devices for automated sample preparation and detection, real-life application of lab-onchip devices in medical diagnosis and the commercialized approaches.

Fundamentals of motor proteins in neuronal transport, force generation e.g. in muscles, cell motility and division. A survey of recent advances in using motor proteins to power nano fabricated devices. Principles of design and operation; hands-on-experience in building a simple device.
 

Introduction into the motivation of analytical biosensors as well as its fundamental physicochemical challenges. Techniques used to design, fabricate and operate biosensors. Specific applications.

Introduction to the role of active forces, e.g. cell and tissue contraction, in the mechanics of biological systems. Review of passive and actively driven viscoelastic systems and momentum transport underlying the material properties of biology. The course involves a literature survey and a team project application.

Engineering principles in biology, BioBricks and standardization of biological components, parts registries, advanced molecular biology tools for DNA assembly, genome editing, high-throughput genetic manipulation methods, construction of biological pathways, strategies for transcriptional control, examples of engineered systems.

Basic principles of cell culture engineering, cell line development and cell culture products; genomics, proteomics and post-translational modifications; elements of cell physiology for medium design and bioprocessing; bioreactor design, scale-up for animal cell culture and single use equipment; challenges in downstream processing of cell-culture derived products; process intensification: fed-batch, feeding strategies and continuous manufacturing; scale-down and process modeling; Process Analytical technologies and Quality by Design (QbD) concept.

Building on recent developments and expansion in the mammalian cell culture for production of complex biologics such as viral vaccines and viral vectors, the following topics will be covered: Principles of immunology and industrial virology; Cell physiology for vaccine production; Cell lines for vaccine production; Upstream process development and process intensification strategies; Purification and downstream processing of viral vaccines; Analytical and potency assays; Formulations and delivery of vaccines; Basics of clinical trials and regulatory principles; Immunization policies. Case studies on bioprocessing/manufacturing licensed vaccines.