BME 100 Introduction to Biomedical Engineering

The goal of this course is to introduce Biomedical Engineering majors to the cutting edge of biomedical engineering, including the clinical challenges which arise in this discipline. The course focuses on work by internationally renowned bioengineers, including Stony Brook faculty, which cover areas such as biomechanics, medical imaging, biomaterials, tissue engineering, drug/medical device development, bioinformatics and functional genomics. Topics related to the impact of technology on medicine are also addressed, including ethics. The principal outcome of this course is to engage the new BME student with the opportunities of working at a research university, and to encourage them to enter the laboratory as a key part of their education.

BME 201 Bioengineering and Society

How engineers interact with others in the development of solutions to societal problems, with emphasis on engineering problems arising in the biological realm. The roles that bioengineers play in supporting the well being of urban and rural populations throughout the world, through the developments biomedical engineering, biotechnology, and in ergonomic design will be illuminated through the in depth evaluation of both successful and unsuccessfully introduced technologies. The course will provide skills for retrieval of information in biomedical engineering and enhance communication and writing skills by using scientific presentation formats to introduce topics in bioengineering. It will describe the basic engineering principles that can be applied to analyze life mechanisms and characterize medical devices (e.g., artificial joints, limbs, organs, valves, stents, CT scanners, diagnostic ultrasound). It will present ethical issues pertaining to biomedical engineering, from the perspective of societal needs and their interaction with technology and innovation, e.g., stem cell research, the mammography debate, etc. It will familiarize the students with cutting edge research in biomedical engineering through presentations by members of the Biomedical Engineering Department and their areas of research.

BME 212 BME Research Fundamentals

This class will provide insight into the research process in biomedical engineering, the result of which may lead to scientific discoveries and technological advances. This is a class that heavily relies on hands on experience in the lab with a lab to lecture ratio of 2:1. Within three different modules (biolelectricity, molecular bioengineering, and biomechanics), students are introduced to a great variety of laboratory techniques in biomedical engineering. Modern bioengineering tools are being used to accomplish measurements and quantitative analyses in biology. Examples include the design of Labview data collection algorithms to measure EMG signals, the quantification of DNA bands on agarose gels, or the mechanical behaviors of biological materials and structures. Importantly, the design of all labs is discovery-based rather than purely instruction-based. Particular emphasis is placed on the statistical analysis of the collected data which ranges from correlations/regressions, appropriate parametric and non-parametric tests, and power analyses; the concepts of which are taught in the lecture. This course also provides students with the opportunity to write and defend coherent reports based on the laboratory work, consistent with formats and standards found in scientific journals in biomedical engineering. At the beginning of each lecture, one group of students will give a Powerpoint presentation based on the experiment from the previous week.

BME 300 Writing in Biomedical Engineering

Technical writing and oral communication skills taken in conjunction with BME 300 level courses through the use of written scientific reports and oral presentations of experimental procedures and results. Fulfills the Upper-Division Writing Requirement.

BME 301 Bioelectricity

This class that equips students with basic concepts in the field of bioelectricity, using up-to-date information. The goal is to encourage students to apply quantitative engineering tools to typical problems dealing with excitable cells, to understand the biological origin and mechanisms associated with cell-generated electricity, and to appreciate its clinical importance. The class contents and methods stay as close as possible to the highly demanding, engineering-oriented style of Robert Plonsey and Roger Barr, pioneers in teaching bioelectricity and authors of the classical text in the field. At the same time, the goal is to entice students with recent molecular biology advancements and modern computational biology tools, and to challenge them to integrate all components. As a result, cable theory and Hodgkin-Huxley models are taught alongside bioelectronics using bacteriorhodopsin, cellular automata modeling and development of Java applets to solve bioelectricity problems. Unique feature of the class is the "Bioelectricity from Gene to Disease" project, which requires students to: 1) do in-depth research of a genetic disease, affecting bioelectrical function; 2) develop a scientific hypothesis about the effects of the gene mutations on the ion channel level; 3) mathematically express their hypothesis and implement the changes into a Java applet, produced by them, to predict functional effects on the whole cell level and to rationalize clinical reports.

BME 303 Biomechanics

Introduction to biomechanics for students in the biomedical engineering major or minor. A rigorous approach to understanding the interactions between mechanics and biology. Basic concepts of mechanics are covered and the mathematical tools necessary to explain the concepts, with a strong emphasis on the relevant biology. Topics covered include force vectors, moments and torque, analyses of systems in equilibrium, skeletal joints and muscles, stress and strain in living systems, material properties of biological tissues, multiaxial deformations and stress analyses, and mechanical modeling of biological tissues.

BME 304 Genetic Engineering

Provide an introduction into the realm of molecular bioengineering with specific focus on genetic engineering. This course introduces the structure and function of DNA, the flow of genetic information in a cell, genetic mechanisms, the methodology involved in recombinant DNA technology and its application in society in terms of cloning and genetic modification of plants and animals (transgenics), biotechnology (pharmaceutics, genomics), bioprocessing (production and process engineering with a specific focus on the production of genetically engineered products.), and gene therapy. Production factors such as time, rate, cost, efficiency, safety and desired product quality will also be covered. Further, societal issues involving ethical and moral considerations, consequences of regulation, as well as risks and benefits of genetic engineering will be discussed.

BME 305 Biofluids

From the organ to the subcellular level, life is supported by transport processes. The course objectives are to learn the fundamentals of fluid mechanics and heat and mass transfer in the context of physiological systems. Techniques for formulating and solving biofluid heat and mass transfer problems with emphasis on the special features and the different scales encountered in physiological systems will be covered, from the organ and the tissue level down to the molecular transport level. The course will cover Conservation Laws (mass, momentum, and energy); Macroscopic balance versus microscopic balance; Fundamentals of Fluid Mechanics; Mass and momentum balance equations; Bernoulli relation;, Navier-Stokes equations; Oscillatory flows, creeping flows, laminar and turbulent flows; Biorheology; Mechanical properties of blood and other physiological fluids; Models of organ circulations; Mechanics of flow in artificial organs; Molecular Transport Processes and Diffusion- Fick's law; Bio Heat Transfer including heat conduction, thermal diffusivity, and Fourier's law. Examples of the applications of techniques learned in the course will include bioengineering problems such as cardiovascular pathologies and prosthetic devices. This course will prepare students for advanced courses in heat and mass transfer in biological systems, and for competence in the workplace through computer-based learning and design skills.

BME 313 Bioinstrumentation

The course content is directed to the basic concept of biomedical instrumentation and medical device. Main focus is on the virtual instrumentation in biomedical engineering using the latest computer technology. The course covers the topics on basic sensors in biomedical engineering, biological signal measurement, conditioning, digitizing and analysis. In addition, the course will teach LabVIEW, a graphics programming tool for virtual instrumentation, and programming principles and working with the MATLAB package. This course will help students to develop skills to build virtual instrumentation for laboratory research and prototyping medical devices. It is a combination of lecture (2 hours/week) and laboratory (3 hours/week).

BME 353 Biomaterials

The engineering characteristics of materials, including metals, ceramics, polymers, composites, coatings, and adhesives, that are used in the human body. Emphasizes the need of materials that are considered for implants to meet the material requirements specified for the device application (e.g., strength, modulus, fatigue and corrosion resistance, conductivity) and to be compatible with the biological environment (e.g., nontoxic, noncarcinogenic, resistant to blood clotting if in the cardiovascular system). Crosslisted with ESE 353.

BME 381 Nanofabrication in Biomedical Applications

Three section one semester course to introduce the theory and applications of nanofabrication to upper level BME students. Section one will review aspects of nano-machines in nature with special attention to the role of self-lubrication, intracellular or interstitial viscosity, and protein guided adhesion (receptor ligand interactions). Section two will review current nanofabricated machines to perform the same tasks with special attention to the problems of lubrication, compliance and adhesion. Section three will outline self-assembly mechanisms of nanofabrication for the machines studied in Section two, with special attention to cutting edge discovery to overcome current challenges associated with nanofabricated machines.

BME 404 Essentials of Tissue Engineering

This course will provide an introduction to tissue engineering. Specific topics to be covered are as follows: developmental biology (nature's tissue engineering), mechanisms of cell-cell and cell-matrix interactions, biomaterial formulation, characterization of biomaterial properties, evaluation of cell interactions with biomaterials, principles of designing an engineered tissue. In addition, manufacturing parameters such as time, rate, cost, efficiency, safety and desired product quality will be considered as well as regulatory issues. The Course is a combination of lecture (1.5 hours/week) and laboratory experience (3 hours/week).

BME 420 Computational Biomechanics

The concepts of skeletal biology, mechanics of bone, ligament and tendon, and linear and nonlinear properties of biological tissues will be introduced. The principles of finite differences method (FDM) and finite elements method (FEM) will be introduced to solve biological problems. Both FDM and FEM are applied to solve the equations and problems in solid and porous media. Programming using Fortran or C languages will be required.

BME 430 Engineering Approaches to Drug & Gene Delivery

This course addresses the physiological and biopharmaceutical issues on designing and engineering of controlled delivery devices (for both drugs and DNA). DNA will be treated as another category of substance with pharmacological activity. A basic description on pharmaceutical sciences and the regulatory aspects governing the pharmaceutical industry will be given at the beginning of the course, in conjunction with a general overview on the implication of human physiology on drug absorption, and the rationales of designing drug delivery systems to optimize drug utilization. The concept of biocompatibility and site-specific action, and using biodegradable and non-biodegradable polymers for designing drug delivery systems will be discussed. Emphasis will be placed on comparing conventional drug therapy with therapy involving the use of controlled delivery technologies and the advantages of the latter. A simplified mathematical modeling of controlled release system will be incorporated. The primary emphasis on gene therapy will be placed on the practical applications in biomedical problems.

BME 440 Design in Bioengineering

Introduction to product development, presented from the perspective of solving biomedical, biotechnological, environmental, and ergonomic problems. Teamwork in design, establishing customer needs, writing specifications, legal and financial issues, are covered in the context of design as a decision based process. A semester long team design project provides the opportunity to apply the concepts covered in class.

BME 441 Senior Design Project

Formulation of optimal design problems in biomedical and physiological settings. Introduction to optimization techniques for engineering design. Modeling for compact and rapid optimization of realistic biomedical engineering problems. Necessary conditions for constrained local optimum, with special consideration for the constraints in which the designed product should function in terms of the settings (corporal, ex-corporal, biological, etc.) and the safety considerations involved which are unique to biomedical engineering. Students will carry out the detailed design of senior projects chosen in the beginning of the semester. A final design report is required. Not counted as a technical elective. Laboratory fee required.

BME 461 Biosystems Analysis

This is an upper-level undergraduate course which introduces biomedical signal analysis. The course covers linear aspects of biomedical signal processing, computational and system identification approaches to understanding and predicting the function, interactions, and physiological effects of various organ systems as well as data consisting of DNA, RNA, proteins, and related molecules and processes. The emphasis is on providing various statistical linear techniques to mine large noisy data sets. The course will emphasize various modeling methods and algorithms to handle both stationary and nonstationary data. Topics include Laplace and Z transforms, convolution, correlation, Fourier transform, transfer function, coherence function, various filtering techniques and time-invariant and time-varying spectral techniques. Emphasis will be placed on application of these linear techniques for DNA, RNA, protein structure prediction, as well as systems analysis of various organ systems (cardio-respiratory, neural control of breathing, and renal system).

BME 481 Biosensors

This course will start with a comprehensive introduction to the basic features of biosensors, discussing the types of most common biological agents (e.g., chromorphores, fluorescence dyes) and the ways in which they can be connected with a variety of transducers to create the complete biosensors for biomedicine. The general methods for signal readout and the performance characteristics of several typical biosensors (or biosensing systems) will be discussed. In addition to traditional bioelectrochemical sensors, emphases of this course will be placed optical techniques used in biosensors (e.g., fluorescence spectroscopy, microscopy and fiberoptic sensors) and their current and potential applications in biomedicine. Although not emphasized, new technologies such as molecular beacons, nanoparticles, Q-dots, bioMEMS, confocal microscopy and multiphoton microscopy, and OCT will be referenced.

BME 499 Research in Biomedical Engineering

Independent research project with faculty supervision during the academic year. Can be taken for 1-3 credits (reflecting the effort), and may be taken twice towards technical elective credits (up to 6 credits). The student is required to submit an extensive written report in the format of a research article.