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Mechanical and Genetic Aspects of Cardiovascular Diseases (Professor Chih-Wen Ni)

All Bioengineering graduate students must take the two required courses of the program: BIOE 210 Advanced Bio-Thermodynamics, Bio-Kinetics and Bio-Transport, and BIOE 215 Biological Imaging and Spectroscopy; and BIOE 291 (Bioengineering Seminar Series). No other courses are uniformly required for all Bioengineering graduate students. Students should work with their advisors to determine which additional courses are best suited for their research areas and to satisfy the total unit requirements for the relevant degree: Master or Ph.D. Course selection should be discussed with advisors each year at the annual review meeting. This may include any letter-graded graduate level elective BIOE course (200 or higher) as well as graduate level courses in other areas with the consent of the advisor.

Normally these courses should be taken during the first two years of graduate study. Requirements for formal course work beyond the minimum are flexible and are determined by the individual student’s background and research topic in consultation with the student’s graduate research advisor. Exceptions of these requirements due to transference from another graduate program will be analyzed on an individual basis.


BIOE 210 Advanced Bio-Thermodynamics, Bio-Kinetics and Bio-Transport (4)

A graduate level course specifically designed for emerging engineering disciplines that deal with living systems, the course will focus on thermodynamic aspects, kinetics and transport within living and biochemical systems. This course aims to provide theoretical and conceptual principles underlying biomolecular and biological systems. The course will start with basic and advanced concepts in physical chemistry, mechanics, reaction engineering and thermodynamics and introduce statistical mechanics as a tool to understand biomolecular interactions. The applications will be of relevance to bioengineering and biology disciplines. The course will not shy away from mathematical formulations and will stress the molecular perspective. The first part of the course will deal with the first, second and third laws of thermodynamics and focusing on the concepts of Gibbs Free energy, entropy in active systems as well as the notion of temperature and pressure. The second part of the course will deal with chemical reactions, adhesion, diffusional transport and convective transport in these systems – both at the intra-cellular level as well as at the level of organelles and organs. Specifically, momentum transport (viscous flow) and chemical species transport (convection and diffusion) in living systems will be analyzed with a view to develop mathematical and conceptual descriptions of physiological systems, bio-inspired engineered systems and drug delivery. This course will be of value to students interested in bioengineering, biophysics, biomechanics, mathematical modeling, and biochemistry.

BIOE 215 Biological Imaging and Spectroscopy (4)

This course has been designed to introduce fundamental principles of imaging and spectroscopy of biological systems, including biomolecules, cells, tissue and organisms. The general principles of biological imaging and spectroscopy to be discussed include electromagnetic wave spectrum, optical photon generation, optical photon propagation inside tissue, x-ray photon generation, x-ray photon interaction inside objects. The course will also discuss a variety of imaging methods including optical microscopy, electron microscopy, x-ray imaging, emission tomography, single photon emission computed tomography, and magnetic resonance imaging; and a variety of spectroscopy techniques including optical and fluorescence spectroscopy of biomolecules, single molecule detection, x-ray and neutron diffraction, nuclear magnetic resonance spectroscopy, x-ray and neutron diffraction. Image analysis includes principles of digital image formation, random processes, Gaussian processes, matrices, and hypothesis testing.

BIOE 291 Bioengineering Seminar Series (1)

Seminar series where external speakers deliver one-hour talks on current research and development in various bioengineering fields relevant to the research carried out in the graduate program, including but not limited to cell and molecular biophysics, synthetic cell and molecular biology, biological imaging and spectroscopy, and biological modeling and simulation.



BIOE 205 Molecular and Cell Biophysics (4)

Using the conceptual and analytical models used in bioengineering the student will get quantitative insights into biophysical properties of living systems. Nucleic Acids, Proteins, and Lipids structure and function will be assessed using a biophysical approach. In addition, mechanical and electrical forces involved in cellular signal transduction will be explored with a top-down approach that goes from the tissue to the cell and to the molecule.

BIOE 230 Computation and Modelling for Interdisciplinary Biophysical Sciences, Biomaterials and Biotechnology (3)

This practical programming course provides a hands-on introduction to scientific and engineering computer with an emphasis on problems and approaches most relevant to bioengineering. Programming fundamentals will be covered on the Linux environment using R, Python and C scripting and programming languages. Topics include: simulations of equations of state on Gromacs, epidemic models, Monte Carlo simulations, multidimensional random walks, diffusion limited aggregation.

BIOE 231 Imaging and Spectroscopy for Interdisciplinary Biophysical Sciences, Biomaterials and Biotechnology (3)

Students will learn the practical application of various spectroscopic and imaging methods to study biological systems. Covered techniques include UV-visible absorbance spectroscopy, circular dichroism, fluorescence, single molecule, nuclear magnetic resonance and mass spectroscopy, and their application to the study of the structure of macromolecules, and other important biological problems are covered. The students will also learn to apply biochemical methods for obtaining proteins suitable for spectroscopic analysis, including DNA transformation, bacterial growth, expression, electrophoresis SDS-PAGE, and purification. The course includes extensive hands-on laboratory work.

BIOE 232 Nano and Bio Fabrication for Interdisciplinary Biophysical Sciences, Biomaterials and Biotechnology (3)

A practical introduction of nanofabrication methods and applications that covers top-down and bottom-up nanofabrication approaches and applications relevant to bioengineering and biology. Students will get hands-on experience on cleanroom operation, electrospinning, lithography, confocal imaging, cell culture.

BIOE 240 Biomolecular Engineering (3)

This course covers the structural and quantitative analysis as well as the design of custom biomolecules, including proteins, nucleic acids, and macromolecular complexes. The students will learn the fundamental concepts of biomolecular structure and function and the experimental and computational tools/approaches for engineering biomolecules and how to apply these new technologies to solving some of the most pressing problems in biotechnology, medicine and bioengineering. The covered approaches range from rational and computational design to combinatorial and evolutionary optimization and biophysical characterization, whereas the target products span customized enzymes, molecular switches and actuators, recombinant biosensors, therapeutic antibodies, and protein and DNA assemblies.

BIOE 242 BioMEMs and Lab on Chip (3)

This course will cover major themes and current topics in microfluidics, microfabrication, BioMEMs and Lab on a Chip (LoC). Students will be exposed to concepts in materials science, electrostatics, fluid mechanics, diagnostic technology (i.e. microbiology, immunology, cell biology), and surface chemistry, all of which are critically integrated in the design and operation of LoC devices. The course is ideal for the advanced undergraduate or beginning graduate student who wishes to be exposed to the latest research in miniaturization, and the impact miniaturization has had on the fields of chemistry, biology, and physics.

BIOE 244 Macromolecular Assemblies in Biology (3)

Proteins and other biological macromolecules associate to form large assemblies that carry out a variety of roles inside the cell. This course discussed different aspects of these macromolecular platforms, including their composition, structure, dynamics and function, biophysical techniques typically used to characterize them, and methods to design and engineer altered functionalities.

BIOE 250 Advanced Genetic Engineering (3)

Genetic engineering refers to the set of technologies that directly manipulate on an organism’s genes, change the genetic makeup of cells and add new traits that are not found in that organism. In this advanced course, we will cover topics such as gene targeting, nuclear transplantation, transfection of synthetic chromosomes or viral insertion. The emphasis is given to the design of the methods and tools as well as the related applications in agriculture, medicine, and biological research.

BIOE 246 Advanced Biomedical Imaging (3)

Advanced biomedical imaging is the study of the cutting edge biomedical imaging modalities. This course covers fluorescence molecular tomography (FMT), confocal microscopy, two photon microscopy, optical coherent tomography (OCT), photocoustic tomography, phase contrast X-ray imaging, and functional magnetic resonance imaging.

BIOE 247 Biomedical Imaging Reconstruction (3)

Biomedical imaging reconstruction is the study of the reconstruction algorithms of biomedical imaging modalities. This course covers filtered back projection (FBP) of computed tomography (CT), iterative reconstruction of CT and positron emission tomography (PET) and fluorescence molecular tomography (FMT). Different regularization methods in reconstruction algorithms are introduced. The forward modeling of FMT and CT will be also included.

BIOE 248 Biomedical Optics and Biophotonics (3)

Biomedical Optics and Biophotonics encompasses a multidisciplinary research area involving all light-based technologies applied to life and clinical sciences. This course introduces the underlying principles, basic techniques, and common instruments used in biomedical optics research and clinical medicine. The course included in-depth coverage of advanced optical therapeutic and diagnostic systems with a particular focus on novel instruments. Light-tissue interactions will also be covered.

BIOE 252 Microgels and Carbon Cycle (3)

Microgels are three-dimensional polymer networks proposed to play a pivotal role in regulating biogeochemical dynamics, especially in carbon cycle. Microgels also provide structure to the microbial loop by forming metabolic “hot spots.” Microgels structurally link biological production and microbial degradative processes at the ocean’s surface to biogeochemical dynamics at the ocean’s interior, cloud properties, radiative balance, and global climate.

BIOE 254 Mechanics in Biology (3)

Mechanics plays a crucial role in biology at subcellular, cellular and supracellular levels. Recent insights offer fertile grounds to develop formal descriptions and understand complex rules that govern living matter within the framework provided by the laws of mechanics. In this course, we will cover topics at molecular scales (protein folding, lipid mechanics and chemical cascades); the cellular level (motility, morphomechanics, mechanotransduction and differentiation) and the tissue scale (force generation, remodeling of tumors and ligaments, mechanics of cardiac tissue).

BIOE 256 Macromolecular Principles for Biosensor Design (3)

Proteins and RNAs are macromolecules with two remarkable properties: 1) biomolecular recognition, or the ability to bind to a particular ligand or analyte, whether another macromolecule, small organic molecule, or a metallic ion, with unprecedented selectivity, specificity and tunable affinity; 2) conformational flexibility, or the ability to change its molecular shape upon binding. These properties make proteins and RNAs magnificent scaffolds for a vast array of biosensing applications. Here we will discuss the fundamental principles for macromolecular-based biosensor design with an emphasis on how to couple molecular recognition process to a transducing mechanism via induced conformational changes and to a sensitive signal readout, whether optical or electrical.

BIOE 260 Advanced Nuclear Magnetic Resonance Spectroscopy (3)

State-of-the-art solution NMR methods applied to the biophysical study of biomacromolecules, including structure, dynamics, self-association, interactions and binding. This course covers the physical principles of NMR spectroscopy and experimental design to obtain isotropic and anisotropic information in solution, as well as kinetics of conformational and chemical processes.

BIOE 263 Molecular and Cellular Cardiology (3)

Molecular, cellular and systemic integration of novel concepts in cardiac physiology. Neuro Cardiology. Cardiac Pharmacology. Cardiac physiopathology: ischemic diseases and arrhythmias. Topics covered include: diffusion and transport in cardiac cells, resting membrane potential, ionic channels, action potential, Hodgkin and Huxley Model in the heart, synaptic transition and synaptic potentials, autonomic nervous system, the heart as a pump, delay after depolarization and early after depolarization, electrocardiogram and arrhythmias, hemodynamics, microcirculation

BIOE 295 Graduate Research (1 – 12)

Supervised research.

BIOE 298 Directed Group Study (1 – 6)

Group project under faculty supervision.

BIOE 299 Directed Independent Study (1 – 6)

Independent project under faculty supervision