1. Projects in Microsclae Engineering for the Life Sciences

Projects in Microscale Engineering for the Life Sciences

• Course Home
• Syllabus
• Readings
• Lecture Notes
• Labs
• Assignments
• Download Course Materials

Spring 2007

Staff

Instructors:
Prof. Alexander Aranyosi
Prof. Dennis Freeman
Prof. Martha Gray

Course Meeting Times

Lectures:
Two sessions / week
3 hours / session

Level

Undergraduate

Members of the class inspect one of the wafers they created in lab. (Image by A. Aranyosi.)

Course Description

This course is a project-based introduction to manipulating and characterizing cells and biological molecules using microfabricated tools. It is designed for first year undergraduate students. In the first half of the term, students perform laboratory exercises designed to introduce
(1) the design, manufacture, and use of microfluidic channels,
(2) techniques for sorting and manipulating cells and biomolecules, and
(3) making quantitative measurements using optical detection and fluorescent labeling. In the second half of the term, students work in small groups to design and test a microfluidic device to solve a real-world problem of their choosing. Includes exercises in written and oral communication and team building.

Special Features

• Image gallery

Technical Requirements

Special software is required to use some of the files in this course: .m.

Syllabus

Contents - Engineering Systems at the Scale of Cells and Biomolecules

• How do you build tools that can manipulate cells?
  • Lithography: Shrinking patterns to the micro-scale
  • Soft lithography: Making bio-compatible fluid reservoirs
  • Rapid prototyping: Using existing microscale structures to test new ideas
• How do you measure properties of individual cells?
  • Optical imaging
  • Electrical signals
  • Cell sorting
  • Averaging

Teaching/Learning Activities

• Two lectures each week to introduce new material.
• Two lab sessions each week to provide hands-on experience.
• One project to help students learn to pose testable hypotheses, to conduct research, and to communicate results.
• Weekly homework assignments to encourage students to actively assimilate the course material.

Homework

Weekly homework assignments provide an opportunity to develop intuition for new concepts by actively applying the new concepts to solve problems and answer questions. The process of actively struggling with the use of new ideas until you understand them is an effective and rewarding form of education.

Weekly homework assignments will be distributed in class on Thursdays and will be due the following Thursday at the start of lecture. Late homework will not be accepted. Homework assignments will be corrected, graded, and returned the week after they are due. The solution to each homework assignment will generally be made available to the class a few days after the homework due date. Paper copies of homework assignments and solutions will not be distributed.

Homework problems will be chosen for their educational value. Reading someone's solution to a problem is not educationally equivalent to generating your own solution. If you skip the process of personally struggling with the use of new concepts, you will have destroyed your most important educational experience.

Collaboration Policy

We encourage students to discuss the homework with other students and with the teaching staff to better understand the concepts. However, we expect that you wrote the solutions that you submit under your name. Students should not use solutions of other students (from this year or from previous years) in preparing their own solutions. Students should not take credit for computer code or electronic plots generated by other students. Students should not share their solutions with other students. Any student caught plagiarizing will receive a grade of zero on the assignment. All incidents of plagiarism will be reported to the Committee on Discipline (COD). More information about what constitutes plagiarism can be found at MIT Academic Integrity.

Projects

This subject includes one project. In this project, students are asked to improve on an existing microfluidic design or technique. Students will be expected to demonstrate the improvement with a working prototype. The project provides an opportunity to learn about, planning R&D and experiments, acquiring, processing, and interpreting data, communicating the results to others. The project requires a written proposal, which includes a well-defined hypothesis and procedures to test the hypothesis. Students are encouraged to work in pairs for the project. Partners are encouraged to submit a joint proposal and to cooperate in design, in collecting and processing data, in discussing interpretations, and in preparing their reports. Partners are also encouraged to submit a joint report. We strongly believe that students learn more by working with other students than by working in isolation. The final report will be presented in the form of a short talk to the class. It should be 12 minutes in length and should be delivered during the next to last week of the semester. The report has a firm due date, which is listed on the subject calendar. There are severe lateness penalties for missing the due date.

Communications Intensive

This subject is communications intensive. We feel that communications skills are essential for professional engineers and scientists. We also feel that the process of creating written manuscripts and oral presentations can help clarify thinking and can be an effective way to learn technical material. Homework assignments will often ask you to explain something or to define something that you have been taught. In addition the project is communications intensive. For the project, you and your partner must submit a written proposal and revise the proposal until it is approved by the staff. You and your partner must prepare a formal report that is structured as a scientific oral presentation. First drafts of the report are due approximately one week before the final draft, and will be reviewed by the technical staff, staff from the Writing Program, and by student peers. You and your partner will be assigned to prepare a written critique of a first draft from a different team. The critiques will be discussed during a special session held between the first draft and final draft deadlines. Students can satisfy their freshman year communications requirement by taking this subject.

Grade

Because of the project-oriented nature of this subject, grades will depend strongly on the final project. It should be noted that this project grade itself has several components which will be graded separately (e.g., proposal, first draft, written critique, etc.). In addition, your final presentation will be graded on several metrics (technical content, effective use of slides, clarity of presentation, etc.). More detail on grading is provided in the assignments section of this site. The weighting factors for determining letter grades are:

Grading criteria.

ACTIVITIES	PERCENTAGES
Homework	50%
Lab project	50%

For students near grade boundaries, other factors may be taken into account, including participation in class, laboratory performance not evidenced in the laboratory grade, etc. The grades are determined by the staff.

Text

The course has no required text. Supplementary materials will be distributed over the course of the semester.

Calendar

Course calendar.

LEC #	TOPICS	KEY DATES
Introductory exercises
1	Microfluidics
2	Microfabrication
3	Cells and membranes
4	Cells and membranes (cont.)	Homework 1 due after five days
5	Models of diffusion and cell experiment
6	Laminar flow	Homework 2 due
7	Data analysis using MATLAB®
8	Research applications	Homework 3 due
9	Research paper discussion
10	Visit research lab	Homework 4 due
11	Cell traps
12	Cell traps (cont.)
13	Project brainstorming
Projects
14-18	Projects	Homework 5 due Lec #15 Project propsal due Lec #16
19	Device fabrication
20-23	Projects
24	Project presentation Dry runs
25	Projects
26	Project presentations

Training Programs

In addition to the specialized training programs designed as tracks within the Medical Engineering Medical Physics Doctoral Program, described above, HST offers three training programs in specific areas.

Biomedical Informatics Program

Biomedical informatics is concerned with the cognitive, information-processing, and communication tasks of medical practice, education, and research. It includes the information sciences and technology needed to support those tasks. The field is intrinsically interdisciplinary, drawing together all traditional medical disciplines, the science and technology of computing, biostatistics, epidemiology, decision sciences, and health care policy and management. In addition to a focus on clinical practice, additional areas of emphasis are in bioinformatics, and in informatics related to health services research.

HST's predoctoral and postdoctoral training program in biomedical informatics offers fellowships to qualified US citizens or permanent residents. Several training options are offered: the Master of Science in Biomedical Informatics from HST; the PhD in Computer Science from MIT's Department of Electrical Engineering and Computer Science; the PhD in Health Decision Science in the Department of Health Policy and Management at the Harvard School of Public Health; and research fellowship training at biomedical informatics laboratories in Boston-area hospitals carried out in conjunction with the HST Biomedical Informatics Master's Program. The master's program is available only to HST-enrolled medical students or to individuals who already have advanced training in the health sciences (e.g., a doctoral degree in medicine, dentistry, nursing, veterinary medicine, clinical psychology, or a PhD in a medical relevant field such as physiology).

The combined training program offers several opportunities for education, research, and interaction among the various training sites. Course offerings at MIT and Harvard, as well as a variety of seminars, journal clubs, and other opportunities to exchange information, provide all trainees with opportunities to learn about the work at various laboratories and affiliated institutions, as well as the broader field of biomedical and health informatics.

Predoctoral fellowship applicants must concurrently apply for admission to MIT or a Harvard doctoral degree program. Postdoctoral applicants typically have at least one year and preferably three years of clinical residency before beginning their fellowship. For more information about the Biomedical Informatics Training Program, visit http://www.mi-boston.org/Boston-Informatics/index.html or contact Dr. Lucila Ohno-Machado, Decision Systems Group, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, machado@dsg.harvard.edu.

Clinical Investigator Training Program

The Clinical Investigator Training Program (CITP) trains postdoctoral physicians from various clinical disciplines in the techniques and processes used in patient-oriented research. Trainees develop expertise in clinical investigation while participating in an extensive educational program. The two-year program is a cooperative effort between HST, Beth Israel Deaconess Medical Center, and Pfizer, Inc. The curriculum allows trainees to develop direct experience in performing clinical investigation while, simultaneously through didactic course work, providing a strong foundation in computational and statistical sciences, biomedical ethics, the principles of clinical pharmacology, in vitro and in vivo measurement techniques, and various aspects of the drug development process.

The fellowship program consists of a primary project and core curriculum, plus an elective curriculum and a project elective. Although not required, fellows may choose to pursue a Master of Medical Sciences degree from Harvard Medical School in conjunction with CITP. The degree is awarded at the end of the two-year period upon successful completion of didactic coursework, a research project, a thesis or thesis equivalent, and a qualifying examination. CITP is open to physicians who have completed the clinical requirements for Board eligibility in their chosen specialty or subspecialty. For more information or to obtain an application, visit http://www.bidmc.harvard.edu/citp/ or contact the CITP administrative manager, Linda Bard, Beth Israel Deaconess Medical Center, 330 Brookline Ave, GZ 811, Boston, MA 02215, lbard@bidmc.harvard.edu.

Graduate Education in Medical Sciences Certificate Program

The MIT Graduate Education in Medical Sciences (GEMS) Training Program is a part-time certificate program that can be taken concurrently with doctoral studies and research by students in the Schools of Engineering and Science to gain exposure to biomedical and clinical sciences, including translational medicine. This educational experience for PhD graduate students in the sciences and engineering fields addresses a national need articulated by the Howard Hughes Medical Institute: the growing gap between advances in basic biology and the translation of those advances into medically relevant therapies and tools for the improvement of human health.

The GEMS training program aims to integrate medical knowledge into graduate education at MIT by training a select group of PhD students to bridge the widening chasm between concept and functional execution with a supplementary curriculum that entails: (1) a human pathology course, including molecular and cellular mechanisms of disease, (2) a medical pathophysiology course, a kaleidoscope of HST's pathophysiology curriculum, (3) a student-individualized clinical experience, working with experienced mentors who move seamlessly between clinical medicine and basic biological research, (4) a seminar showcasing examples of translation, and (5) HST's Graduate Seminar—attended by all HST PhD candidates—focusing on professional skills needed to succeed in interdisciplinary research (ethics, responsible conduct of research, communication, etc.). GEMS participants will gain an understanding of the elements of translation, appreciate the science and art of medicine in a way that cannot be conveyed by textbooks, and develop relationships with students and faculty in the broad biomedical community.

Inquiries

Additional information on degree programs, admissions, and financial aid can be obtained from HST's Academic Office, Room E25-518, 617-492-4091.

Speech and Hearing Bioscience and Technology

HST's doctoral program in Speech and Hearing Bioscience and Technology (SHBT), formerly Speech and Hearing Sciences, prepares students with an undergraduate background in science or engineering to have a broad acquaintance with the field of speech and hearing, and to develop specialized knowledge that focuses on a particular approach in research.

The only program of its type in the country—and the only doctoral training program funded in this area by the National Institutes of Health—SHBT is designed to develop research scientists who can apply the concepts and methods of the physical and biological sciences to basic and clinical problems in speech and hearing using innovative research.

No other research training program provides the multidisciplinary depth and breadth offered by SHBT. The five-to-seven–year program leads to a PhD in speech and hearing bioscience and technology from MIT. SHBT's more than 50 participating faculty members represent 10 academic departments from Harvard and MIT, with research facilities at MIT, Harvard University, Harvard Medical School and affiliated teaching hospitals, and the Massachusetts Eye and Ear Infirmary (MEEI).

The small class size of this unique program (seven to eight students per class year) ensures personalized and high-quality training by a diverse and dedicated faculty from the two institutions.

SHBT's curriculum provides an effective method of training researchers by introducing the physical and biological bases of speech and hearing mechanisms involved in the communications process. While SHBT seeks to develop research scientists rather than clinical practitioners, there is a strong emphasis on providing students with exposure to clinical problems, approaches, and techniques. Graduates are thoroughly prepared for successful careers in basic and applied research in industry, universities, or government laboratories involved with biological and synthetic communication systems.

Typically, a student's first two years in the program are devoted to coursework, which is supplemented by significant exposure to various research projects. Courses in the first year assume familiarity with calculus and differential equations, college-level physics, probability and statistics, and biology. The core curriculum covers the anatomical, acoustical, physiological, perceptual, and cognitive basics, as well as the clinical approaches to speech and hearing problems.

The early introduction of important concepts in acoustics, anatomy, and physiology provides a solid base from which to pursue individual research interests. Early in the curriculum, students are introduced to various research laboratories that use different approaches to solving speech and hearing problems. 

This involvement in research provides an immediate application of classroom subjects. Students work with research advisors to develop a thorough understanding of basic concepts and tools in their fields of concentration. Later, students participate in subjects that require them to apply basic concepts to clinical problems and scientific research.

Throughout the curriculum, special attention is devoted to developing personal integrity, scientific values, and scholarly practice. With faculty guidance, each student plans a concentration tailored to the student's particular interest.

By the end of their second year, students identify an area of professional interest and choose a research project that forms the basis for their doctoral thesis. SHBT research in the speech and hearing sciences focuses on the biological and physical mechanisms underlying human communication by spoken language. 

The processes addressed by these sciences include the physical acoustics of sound and the perceptual neurophysiological bases of hearing, as well as the linguistic, cognitive, and motor levels of processing by talkers and listeners.

Applicants to the program should have a bachelor's degree in physical science, biology, psychology, linguistics, communication sciences and disorders, engineering, computer science, or a related field. Superior analytical skills are strongly recommended for all applicants. Additional information may be obtained at http://web.mit.edu/shbt/ or by contacting Dr. M. Christian Brown, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114, 617-573-9635, mcb@epl.meei.harvard.edu.

Sumber:

Harvard-MIT Division of Health Sciences and Technology

Harvard-MIT Division of Health Sciences and Technology

Doctoral Programs

Medical Engineering and Medical Physics

The Medical Engineering and Medical Physics (MEMP) Program is a five-to-seven–year program that leads to the PhD in Medical Engineering and Medical Physics awarded by MIT or by the Harvard Faculty of Arts and Sciences. The program trains students as engineers or physical scientists who also have extensive knowledge of the medical sciences. By understanding engineering and physical science applications, as well as their clinical implications, graduates of this program are well positioned to define new questions and formulate novel approaches in biomedical research.

The MEMP program is founded on a philosophy of openness and collaboration, characteristics that encourage innovative and independent thinking and creativity. This philosophy is fostered by the unique environment in which MEMP students study. While each MEMP student has depth in one classical discipline of engineering or physical science, the collective community has students in all disciplines. MEMP students also have peers with diverse career paths in medicine, science, engineering, business, and government. This community promotes an open exchange of ideas and exposes students to different perspectives on the health sciences.

Moreover, MEMP students have access to research opportunities in labs at Harvard, MIT, and the Harvard teaching hospitals. Students can do research with faculty at any of these institutions and have many opportunities through classes, events, and projects to interact with faculty from all of these institutions. 

The program's academic curriculum includes three phases that prepare students to be medical innovators who will advance human health. First, HST provides MEMP students with a thorough graduate education in a classical discipline of engineering or physical science. Each student selects a concentration area, such as mechanical engineering, chemistry and chemical engineering, materials science, electrical engineering, computer science, physics, aeronautics and astronautics, or nuclear engineering, and completes substantial coursework in this discipline.

Students then become conversant in the biological sciences through preclinical coursework followed by a series of clinical experiences. They acquire a hands-on understanding of clinical care, medical decision-making, and the role of technology in medical practice both in the classroom and in patient care. Because the interface of technology and clinical medicine represents a continuum that extends from the molecular to the whole-organism levels, MEMP offers two distinct but related curricular sequences in the biomedical sciences: the cellular and molecular medicine sequence and the systems physiology and medicine sequence.

Finally, MEMP students investigate important problems at the interfaces of science, technology, and clinical medicine through individualized research projects that prepare them to undertake independent research. MEMP students have the opportunity to perform thesis research in laboratories at MIT, Harvard, and the Harvard affiliated teaching hospitals.

Bioinformatics and integrative genomics (BIG), neuroimaging and bioastronautics are areas of specialization within MEMP for which HST offers specially designed training programs. MEMP candidates may choose to apply through MIT, Harvard, or both. Those applying to MEMP through MIT should submit a single application. Those applying to MEMP through Harvard must also apply to the School of Engineering and Applied Sciences or the Biophysics Program. Additional information about applying to MEMP is available at http://hst.mit.edu/public/admissions/.

Medical Sciences

HST's Medical Sciences Program leads to the MD degree from Harvard Medical School. It is oriented toward students with a strong interest and background in quantitative science, especially in the biological, physical, engineering, and chemical sciences. The subjects in human biology developed for this curriculum represent the joint efforts of life scientists, physicians, physical scientists, and engineers from the faculties of Harvard and MIT.

The programs of study are designed to meet the interests and needs of the individual student. The student is encouraged to pursue advanced study in areas of interest that may complement the subjects offered in the division. Such study may be undertaken as part of the MD degree requirements or may be pursued in a program that combines the MD with a master's or doctoral degree. HST students join the students of the regular Harvard Medical School curriculum in the clinical clerkships.

Because HST is committed to educating physicians who have a deep understanding of the scientific basis of medicine and who are well equipped for an interdisciplinary research career, HST encourages students in the MD curriculum to devote time to research and requires a thesis for completion of the degree. 

Many MD students desire even more research training than is possible during the standard four-year MD curriculum. For such students, one option is to pursue a formal PhD program in addition to an MD program. Another option expands the MD program to five or more years in order to include a major research training component. This option may lead to a master's degree in health sciences and technology in addition to the MD degree.

The general requirements for a master's degree at MIT are given under Graduate Education in Part 1. The subject requirements must be in addition to the minimum number of units required for the MD degree. Subjects may be chosen in scientific, technical, or clinical areas relevant to the student's research area. Thesis research may be conducted at MIT, Harvard, or at Harvard-affiliated teaching hospitals. The completed thesis must be approved by the thesis supervisor and submitted to HST's Graduate Committee. The master's thesis simultaneously fulfills the thesis requirement for HST's MD degree. The two degrees are not formally linked; the MD degree is not a prerequisite for the master's degree.

Further details on the Medical Sciences Program and application forms may be obtained from the Office of Admissions, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02115. Applications must be submitted by October 15 of the year before desired matriculation. For further information, candidates can contact HST's Medical Sciences Admissions Coordinator at hst-md-admissions@mit.edu.

Radiological Sciences Joint Program

The Radiological Sciences Joint Program (RSJP) offers a unique integration of engineering and physical sciences education with research opportunities in a broad spectrum of biomedical research laboratories. The RSJP doctoral program is administered in collaboration with MIT's Nuclear Science and Engineering Department and Boston-area teaching hospitals. Students complete a doctoral program in nuclear science and engineering in addition to a focused clinical experience that includes basic biomedical courses and a clinical practicum. 

Training is provided in ionizing and non-ionizing radiation systems engineering and applications to biological and biomedical issues. This is accomplished through an academic core of nuclear physics and radiation engineering supplemented by biomedical subjects and a focused clinical experience. Student research topics typically involve radiation therapy or imaging, such as magnetic resonance imaging (MRI), computer-aided tomography (CT), positron emission tomography (PET), or single-photon emission tomography (SPECT). Recent innovations in the areas of particle radiation therapy and medical imaging have made this area one of the most exciting in the field of applied nuclear and radiation science.

The core curriculum includes topics in nuclear and radiation physics, radiation biology, medical imaging, and the biomedical application of radiation. These subjects form the basis of the departmental doctoral examination taken by most students two years after entering the program. After successful completion of the exam, full-time thesis research is pursued in specialty areas of radiation therapy, medical imaging, radiation biology, and biophysics, or image processing and computer applications. 

To supplement the program's academic training, a one-month clinical practicum in one of the affiliated Boston-area hospitals is also required. Students submit a doctoral thesis and defend it before a committee of MIT faculty, including members from HST and the Department of Nuclear Science and Engineering, in accordance with the interdisciplinary nature of the program.

Admission to the RSJP program is decided jointly by HST and MIT's Department of Nuclear Science and Engineering. In addition to a strong background in the physical and engineering sciences, applicants should have completed two undergraduate subjects in biology or biochemistry before entering RSJP. Additional information may be obtained by contacting Clare Egan, Room 24-102, 617-253-3814, cegan@mit.edu.

Sumber:

Harvard-MIT Division of Health Sciences and Technology