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Rensselaer Catalog 2017-2018 [Archived Catalog]
Courses
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BIOL 6360 - Geomicrobiology
This course examines relationships between microorganisms and Earth processes. Topics include the origins of life on earth, surface metabolism theory, biological and biochemical benchmarks. Earth is considred as a microbial habitat with an emphasis on the lithosphere and hydrosphere, including soils, seawater, lakes, rivers, and groundwater. Geomicrobial processes are discussed with an emphasis on microbes as catalysts of geochemical processes including conversion of inorganics and metals, and mineralization of organics. Molecular and non-molecular methods for detection, isolation, and identification of geo-microbially active organisms are introduced.
Prerequisites/Corequisites: BIOL 1010 or permission of instructor.
When Offered: Spring term annually.
Cross Listed: Credit cannot be obtained for both BIOL 4360 and BIOL6360. Cross listed as ENVE 4360 /6360. Students cannot obtain credit for both ENVE 4360/6360 and BIOL 4360/6360.
Credit Hours: 3
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BIOL 6410 - Sequence Analysis
This course covers the theory and practice of biological sequence analysis, including algorithms for pairwise sequence alignment, multiple sequence alignment, phylogenetic analysis, and database searching. Concepts covered include homology, sequence similarity, parsimony, mechanisms and metrics of molecular evolution, biological data bases, database search algorithms (BLAST), and statistical significance. Selected topics include hidden Markov models, bootstrap analysis, and gene finding. Modern sequence analysis software will be provided. Laptop computers are required. Knowledge of a programming language is strongly suggested. Meets jointly with BIOL 4540; both cannot be taken for credit.
Prerequisites/Corequisites: MATH 1020, BIOL 4620, CSCI 1200 or equilavent, or permission of the instructor.
When Offered: Fall term annually.
Credit Hours: 4
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BIOL 6420 - Molecular Modeling
This course covers the theory and practice of the structural modeling of proteins and other biomolecules using informatics-driven and energy-based approaches. Topics include template-based comparative modeling, secondary structure prediction, tertiary structure prediction, protein classification, sidechain rotamers, docking, protein design, energy minimization, electrostatics, molecular dynamics, and molecular surfaces. Molecular modeling software will be provided. Laptop computers are required. BIOL 4550, BIOL 6420, BCBP 4550, and BCBP 6420 meet jointly; only one of these courses can be taken for credit.
Prerequisites/Corequisites: MATH 1020, BIOL 4620, BIOL 4760.
When Offered: Spring term annually.
Cross Listed: BIOL 4550, BCBP 4550/6420.
Credit Hours: 4
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BIOL 6510 - Biology Core Course 1
An intensive course designed to provide instruction and stimulate discussion on important topics in biological research. It is loosely divided into 4 modules: 1) ethics, writing, and basic computational biology tools; 2) structural and computational biology; 3) protein and carbohydrate structure and function; 4) microbiology, ecology, and evolution. Students will gain a fundamental understanding of major topics in biology through formal didactic instruction and selected readings from the primary literature.
Prerequisites/Corequisites: Completed bachelor’s degree or permission of instructor.
When Offered: Fall term annually.
Credit Hours: 4
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BIOL 6520 - Biology Core Course II
An intensive course designed to provide instruction and stimulate discussion on important topics in biological research. It is loosely divided into three modules: 1) molecular biology and genetics; 2) cell biology; and 3) entrepreneurship/leadership. Students will gain a fundamental understanding of major topics in biology through formal didactic instruction and selected readings from the primary literature.
Prerequisites/Corequisites: Prerequisite: This is a continuation of the fall course BIOL 6510. Completed bachelor’s degree or permission of instructor.
When Offered: Spring term annually.
Credit Hours: 4
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BIOL 6650 - The Biology of Systems
This course is designed to be a first course in the study of “systems biology”, to introduce students to the field, the experimental and computational methods that are used within it, and the type of insights that the field can provide to biology. To fully appreciate the complexity of living systems, researchers gather systematic, quantitative measurements of a system’s components using cutting-edge omics techniques. In addition, researchers also leverage computing power to describe, model, and predict dynamic behaviors that could otherwise not be perceived in such large scale omics data. Along with these topics, students will learn to critically read current scientific literature. A student cannot get credit for both BIOL/BCBP 4660 and BIOL/BCBP 6650.
Prerequisites/Corequisites: BIOL 4620 Molecular Biology I and BCBP 4670 Molecular Biochemistry I or permission of the instructor
When Offered: Spring term annually.
Cross Listed: BIOL 4660, BCBP 6660, BCBP 4660
Credit Hours: 4
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BIOL 6660 - Muscle Mechanics and Modeling
This graduate/advanced undergraduate hybrid course examines the structural and physiologic properties of muscle, as well as its force production and overall biomechanical function. Muscle structure and function will be explored at the protein, single fiber, and whole tissue levels. Discussions will focus primarily on skeletal muscle, and topics will include muscle morphology, cross-bridge theory, molecular motor and actomyosin interaction, Hill-type and Huxley-type models, electromyography, fatigue, muscle inhibition, history-dependent phenomena, in vitro and in vivo muscle function, and the response to injury. Each topic will be introduced and developed utilizing seminal articles in the literature as well as excerpts from texts, and further discussion on current problems and state-of-the-art experimental techniques will draw on the current scientific literature.
Prerequisites/Corequisites: Senior standing or permission of instructor.
When Offered: Spring term annually.
Cross Listed: BMED 4660/6660. A student may receive credit for only one of BIOL 6660 or BMED 4660/6660.
Credit Hours: 3
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BIOL 6680 - Applied and Environmental Microbiology
A survey of applied aspects of microbiology including the application of microorganisms in industrial processes and the roles played by microorganisms in the environment. Emphasis is placed on ways in which microorganisms can be manipulated and controlled for human advantage. Current literature regarding manipulation and regulation of microbial activities is discussed.
Prerequisites/Corequisites: Prerequisite: BIOL 4310 or permission of instructor.
When Offered: Spring term even-numbered years.
Credit Hours: 3
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BIOL 6690 - Advanced Molecular Biology
Students will use a variety of tools (textbooks, scientific journals, and Internet resources including molecular databases and data mining tools) to increase understanding of genes, their expression, their products, and their inter-relatedness. (Meets together with BIOL 4630.)
Prerequisites/Corequisites: Undergraduate course in molecular biology, molecular genetics, and/or molecular biochemistry.
When Offered: Fall term annually.
Cross Listed: BIOL 4630. Both cannot be taken for credit.
Credit Hours: 3
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BIOL 6880 - The Global Environment
This 4 credit course will explore global environmental cycles, patterns, and changes. It will cover elemental cycles of phosphorus, nitrogen, and carbon, and pollutants such as mercury, lead, and CFCs, and how changes in these cycles influence organisms and ecosystems. Also discussed will be large-scale biotic processes and theory about ecosystem dynamics. Major environmental issues such as acid rain, eutrophication, climate change, and land use conversation will also be discussed. Students cannot get credit for both BIOL 4880 and BIOL 6880.
Prerequisites/Corequisites: Ecology (BIOL 4850 or by instructor permission).
When Offered: Spring term annually.
Cross Listed: BIOL 4880.
Credit Hours: 4
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BIOL 6900 - Seminar in Biology
Weekly discussion of selected topics in biology by graduate students and staff.
When Offered: Fall and spring terms annually.
Credit Hours: 1
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BIOL 6910 - Research Rotation l
The students take active part in research, under the supervision of a Biology faculty adviser by mutual agreement.
Prerequisites/Corequisites: Restricted to first year Biology graduate students.
When Offered: Fall term annually.
Graded: S/U
Credit Hours: 4
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BIOL 6920 - Research Rotation ll
The student will perform hands-on research in the lab of a Biology faculty member to learn basic research methods and techniques, accomplish a small research project and determine whether the lab is a good fit for thesis research.
Prerequisites/Corequisites: Restricted to first year Biology graduate students.
When Offered: Spring term annually.
Graded: S/U
Credit Hours: 2
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BIOL 6930 - Research Rotation lll
The student will perform hands-on research in the lab of a Biology faculty member to learn basic research methods and techniques, accomplish a small research project and determine whether the lab is a good fit for thesis research.
When Offered: Spring term annually.
Graded: S/U
Credit Hours: 2
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BIOL 6940 - Readings in Biology
Readings in the current literature designed to supplement the background of the student and provide greater depth in the area of his or her specialty.
Prerequisites/Corequisites: Prerequisite: permission of instructor.
When Offered: Fall, spring, and summer terms annually.
Credit Hours: 1 to 4
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BIOL 6970 - Professional Project
Active participation in a semester-long project, under the supervision of a faculty adviser. A Professional Project often serves as a culminating experience for a Professional Master’s program but, with departmental or school approval, can be used to fulfill other program requirements. With approval, students may register for more than one Professional Project. Professional Projects must result in documentation established by each department or school, but are not submitted to the Office of Graduate Education and are not archived in the library. Grades of A, B, C, or F are assigned by the faculty adviser at the end of the semester. If not completed on time, a formal Incomplete grade may be assigned by the faculty adviser, listing the work remaining to be completed and the time limit for completing this work.
Credit Hours: 1-9
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BIOL 6990 - Master’s Thesis
Active participation in research, under the supervision of a faculty adviser, leading to a master’s thesis. Grades of S or U are assigned by the adviser each term to reflect the student’s research progress for the given semester. Once the thesis has been presentend, approved by the adviser, and accepted by the Office of Graduate Education, it will be archived in a standard format in the library.
Credit Hours: 2 to 9
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BIOL 9990 - Dissertation
Active participation in research, under the supervision of a faculty adviser, leading to a doctoral dissertation. Grades of IP are assigned until the dissertation has been publicly defended, approved by the doctoral committee, and accepted by the Office of Graduate Education to be archived in a standard format in the library. Grades will then be listed as S.
Credit Hours: Variable
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BMED 2100 - Biomaterials Science and Engineering
Presents structure-property relationships of implant materials including metals, polymers, ceramics, and composites, with an emphasis on mechanical and surface properties in the broader context of implant design. Biological performance of biomaterials, case studies of traditional implants—as well as emerging, tissue-engineered materials— are emphasized.
When Offered: Spring term annually.
Credit Hours: 4
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BMED 2300 - Bioimaging and Bioinstrumentation
This course serves as an introduction to biomedical instrumentation and imaging with focus on the acquisition and monitoring of vital signals. Basic principles for the selection and appropriate use of instruments for solving bioengineering and medical problems such as microscopy, magnetic resonance imaging, and ultrasounds, among others are addressed.
Prerequisites/Corequisites: PHYS 1200.
When Offered: Spring term annually.
Credit Hours: 4
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BMED 2540 - Biomechanics
Application of mechanics to the study of normal, diseased, and traumatized musculo-skeletal system. Areas covered include determination of joint and muscle forces, mechanical properties of biological tissues, and structural analysis of bone-implant systems. Case studies are discussed to illustrate the role of biomechanics and biomaterials in the design of implants.
Prerequisites/Corequisites: Prerequisite: ENGR 1100.
When Offered: Spring term annually.
Credit Hours: 4
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BMED 2940 - Studies in Biomedical Engineering
When Offered: Fall and spring terms annually.
Credit Hours: 1 to 4
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BMED 2960 - Topics in Biomedical Engineering
When Offered: Fall and spring terms annually.
Credit Hours: 1 to 4
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BMED 4010 - Biomedical Engineering Laboratory
Theory and practice of biomedical measurements. An introduction to instrumentation and procedures for measurement of membrane transport, bioelectrical potentials, cell counting, biomechanical and biomaterial properties using invasive and noninvasive techniques. Transducers studied include strain gauge, differential transformer, spectrophometer, bipotential electrodes, microscope with camera, mechanical testing machine, piezoelectric transducer (or sensor). Also studied are instruments for determination of material properties.
Prerequisites/Corequisites: Corequisite: BMED 4200 or permission of instructor.
When Offered: Fall and spring terms annually.
Credit Hours: 4
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BMED 4110 - Investigative Medicine I
Students will be exposed to real time investigative biomedical research projects that are currently in development, taught the principles of research project development and exposed to clinical experiences at a level typically found in college graduates/post graduates who are entering medical school.
Prerequisites/Corequisites: Restricted to 3rd Year RPI students who are in the combined B.S./M.D. Physician Scientist Program with Albany Medical College or 4th Year RPI students who are in the B.S./M.D. Physician Engineer Program with Albany Medical College.
When Offered: Fall term annually.
Cross Listed: With BIOL 4110.
Credit Hours: 1 credit hour
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BMED 4120 - Investigative Medicine II
Students will be exposed to several clinical experiences at a level typically found in college graduates/post graduates who are entering medical school.
Prerequisites/Corequisites: BIOL 4110: Investigative Medicine I or BMED 4110: Investigative Medicine I. Restricted to 3rd Year RPI students who are in the combined B.S./M.D. Physician Scientist Program with Albany Medical College or 4th Year RPI students who are in the B.S./M.D. Physician Engineer Program with Albany Medical College.
When Offered: Spring term annually.
Cross Listed: With BIOL 4120.
Credit Hours: 1
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BMED 4130 - Biomedical Research
Independent research in health sciences, supervised by a faculty member, for the purpose of developing research skills. Such skills include defining a research project, both as a written and oral exercise for a scientific and general audience, and gathering preliminary research data enabling both a written and oral description of the project in the form of a research proposal and an oral defense. This is a communication-intensive course.
Prerequisites/Corequisites: Restricted to 3rd Year RPI students who are in the combined B.S./M.D. Physician Scientist Program with Albany Medical College or 4th Year RPI students who are in the B.S./M.D. Physician Engineer Program with Albany Medical College.
When Offered: Spring term annually.
Cross Listed: With BIOL 4980.
Credit Hours: 4
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BMED 4260 - Biomedical Product Development and Commercialization
Students are introduced to the major biomedical industries, markets, and stakeholders, with an emphasis on biomedical devices. Market drivers and hurdles are covered including regulatory, intellectual property, and reimbursement. The interactive class format includes case studies and industry experts providing a practical perspective. Students select topic areas for design projects and begin work toward the goal of developing functional design solutions to practical biomedical problems.
Prerequisites/Corequisites: Prerequisites: Senior BME status and ENGR 2050.
When Offered: Fall term annually.
Credit Hours: 3
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BMED 4410 - BioMEMs
This course discusses state-of-the-art techniques in patterning biomolecules, biosensors, machining three-dimensional microstructures, and building microfluidic devices (Lab-on-a-Chip). Seminal and current literature will be used to discuss topics in BioMEMs ranging from device fabrication to applications in cell biology and medicine. Students cannot get credit for both BMED 4410 and BMED 6410.
Prerequisites/Corequisites: Prerequisite: junior/senior standing.
When Offered: Spring term annually.
Credit Hours: 3
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BMED 4420 - Clinical Orthopaedics and Contemporary Research
An in-depth review of the underlying science, engineering, medicine, and contemporary research related to the nation’s highest priorities for musculoskeletal diseases and care. Musculoskeletal anatomy, pathophysiology, epidemiology, and contemporary treatments are covered. Special topics will be presented relating state-of-the-art biomedical research to clinical practice. The clinical perspective of each topic will be presented by practicing clinicians with case studies. Topics conclude with live webcasts or recorded surgery from Albany Medical Center or the Capital Region Bone and Joint Center. Students can not get credit for both BMED 4420 and BMED 6420.
Prerequisites/Corequisites: Prerequisites: BMED 4500 and senior standing or permission from instructor.
When Offered: Fall term annually.
Credit Hours: 4
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BMED 4440 - Biophotonics
Biophotonics, or biomedical optics, is a newly developing field, dealing with the application of optical science and technology to biomedical problems, including clinical applications. The course introduces students to the fundamentals in modern and classical optics, light-matter interaction and provides them with a broad overview of current topics and contemporary research in the area of optics and lasers in medicine and biology.
Prerequisites/Corequisites: Prerequisite: PHYS 1200.
When Offered: Fall term annually.
Cross Listed: With BMED 6440. Students cannot receive credit for both courses.
Credit Hours: 3
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BMED 4450 - Drug and Gene Delivery
The course presents several aspects of drug and gene delivery including: 1) definitions of what drugs or gene are; 2) pharmacokinetics and pharmacodynamics; 3) biomaterial selection considerations; 4) bioactivity considerations; 5) physiological and biochemical barriers to drug delivery; 6) diffusion controlled, dissolution controlled, and osmotic controlled drug delivery systems; 7) polymeric delivery systems; 8) ligand-based targeting and physical targeting; 9) viral mediated gene delivery; 10) non-viral gene delivery; 11) polymers in gene delivery.
Prerequisites/Corequisites: Prerequisites: BMED 2100 or equivalent, senior standing, or instructor permission.
When Offered: Fall term annually.
Credit Hours: 3
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BMED 4460 - Biological Imaging Analysis
Survey of image analysis applications in biology and biotechnology; introduction to biological microscopy and selected biomedical imaging systems; image reconstruction and pre-processing; grayscale and geometric corrections; image segmentation; blob analysis, cell/colony counting, and cell morphometry; vessel and neuron tracing algorithms with applications to neurobiology and medicine; feature extraction, pattern analysis, cluster analysis and classification; image registration algorithms with applications to mosaicing, spatial referencing, motion estimation, and change detection.
Prerequisites/Corequisites: Prerequisites: BMED 2300.
When Offered: Spring term annually.
Credit Hours: 3
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BMED 4500 - Advanced Systems Physiology
Applications of control theory and systems techniques to physiology. Emphasis is on entire systems and their interactions rather than isolated phenomena. Areas covered include cardiac, respiratory, renal, and gastrointestinal systems. Includes laboratory on the application of engineering techniques in the study of physiological systems. This course is taught at Albany Medical Center and enrollment is limited to BME students.
Prerequisites/Corequisites: Prerequisite: BIOL 2120 or equivalent.
When Offered: Spring term annually.
Credit Hours: 4
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BMED 4510 - Mechanobiology
Mechanical regulation of biological systems. Topics include principles and concepts of mechanobiology; evolution, embryogenesis, and histogenesis of tissues with particular references to skeletal system; mechanical regulation of cellular behavior, tissue growth and organ development; concept and application of strain energy regulation in biology; application of mechanobiology to tissue regeneration; limits of mechanical regulation.
Prerequisites/Corequisites: Prerequisites: BMED 2540 (Biomechanics) or permission from instructor (non-BME students).
When Offered: Spring term annually.
Credit Hours: 3
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BMED 4540 - Biomechanics II
Examines biomechanics of human body movement through developing various models (e.g., lumped mass, planar rigid body, 3D) and exploring current techniques in Forward and Inverse Dynamic approaches. Topics are developed on a classical mechanics foundation, and simulations are constructed using software (e.g., OpenSIM) to describe normal movements, and investigate possible sources of abnormalities due to injury, disease, or dysfunction.
Prerequisites/Corequisites: Prerequisites: BMED 2540 or equivalent, junior/senior standing or instructor permission.
When Offered: Fall term annually.
Credit Hours: 4
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BMED 4550 - Cell Biomechanics
This is an undergraduate/graduate course on the mechanics of biopolymers, cell cytoskeleton, cell membrane, the whole cell, and multicellular structures in the context of the modulation of cell function by mechanical stresses. Topics include state-of-the-art experimental techniques in cell biomechanics, and cutting-edge research in stem cell mechanobiology, cell motility, collective cell behavior, neurite growth, osteocyte sensing, cardiovascular diseases, and immunology.
Prerequisites/Corequisites: Prerequisite: BMED 2540 or equivalant.
When Offered: Fall term annually.
Cross Listed: With BMED 6550. Students cannot receive credit for both courses.
Credit Hours: 3
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BMED 4580 - Biomedical Fluid Mechanics
This course covers the dynamics of fluid flow in human physiological system. Engineering principles and fluid dynamic concepts will be taught in the context of cardiovascular system. Topics include: pulsatile flow in arteries, vascular compliance and wave propagation, impedance, cardiac mechanics, dynamic coupling of ventricle and systemic circulation, blood flow in vein, coronary circulation, microcirculation, blood flow at complex geometries, imaging techniques in clinical hemodynamic assessment, fluid mechanics in designing and testing circulatory implants.
Prerequisites/Corequisites: Prerequisite: ENGR 2250 and a basic knowledge of human physiology.
When Offered: Fall term annually.
Cross Listed: With BMED 6480. Students cannot receive credit for both courses.
Credit Hours: 3
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BMED 4590 - Medical Imaging
This course serves as an in-depth overview to medical imaging modalities. First, individual modalities are introduced, including CT, MRI, PET, SPECT, and US. Then, multimodality systems are described. A balance is made among physical, mathematical, algorithmic and architectural contents. Contemporary research and insights to improve the current systems are introduced throughout the course to inspire students and provide an understanding of newer tools under development.
Prerequisites/Corequisites: Prerequisites: BMED 2300 or approval of instructor.
When Offered: Fall term annually.
Cross Listed: With BMED 6590. Students cannot receive credit for both courses.
Credit Hours: 3
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BMED 4600 - Biomedical Engineering Design
A guided approach to development of design skills. Students work individually and in teams to tackle a biomedical design problem using methods drawn as necessary from engineering and from the physical and mathematical sciences. Discussion sessions involve students in presentations of work. This is a communication-intensive course.
Prerequisites/Corequisites: Prerequisite: BMED 4260 or permission of instructor.
When Offered: Spring term annually.
Credit Hours: 4
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BMED 4650 - Intro to Cell and Tissue Engineering
The principles and practice of tissue engineering are taught in this course. The principles underlying strategies for employing selected cells, biomaterial scaffolds, soluble regulators or their genes, and biomechanical loading and culture conditions, for the regeneration of tissues and organs in vitro and in vivo are addressed. Bioreactors, enabling technology and biomimetic approach for fabricating tissue-engineered products and devices for implantation are taught.
Prerequisites/Corequisites: Prerequisites: a basic course in mechanics (ENGR 2530 or BMED 2540), and a basic course in transport phenomena or fluid dynamics (ENGR 2250 or equivalent), or permission of instructor.
When Offered: Spring term annually.
Credit Hours: 3
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BMED 4660 - Muscle Mechanics and Modeling
This graduate/advanced undergraduate hybrid course examines the structural and physiologic properties of muscle, as well as its force production and overall biomechanical function. Muscle structure and function will be explored at the protein, single fiber, and whole tissue levels. Discussions will focus primarily on skeletal muscle, and topics will include muscle morphology, cross-bridge theory, molecular motor and actomyosin interaction, Hill-type and Huxley-type models, electromyography, fatigue, muscle inhibition, history-dependent phenomena, in vitro and in vivo muscle function, and the response to injury. Each topic will be introduced and developed utilizing seminal articles in the literature as well as excerpts from texts and further discussion on current problems and state-of-the-art experimental techniques will draw on the current scientific literature.
Prerequisites/Corequisites: Prerequisites: senior standing or permission of instructor.
Credit Hours: 3
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BMED 4720 - Applied Mathematical Methods in Materials
Students apply mathematical and numerical techniques to understand materials engineering topics such as materials structure, symmetry, diffusion, mechanics and physics of solids. Class uses examples from materials science and engineering core courses to introduce mathematical concepts and materials-related problem solving skills. Topics include linear algebra, eigenvalues and eigenvectors, quadratic forms, tensor operations, symmetry operations, calculus of several variables, ordinary and partial differential equations, Fourier analysis, integral transformations, numerical methods and calculus of variations.
Prerequisites/Corequisites: Prerequisites: MATH 2400, and access to Mathematica.
When Offered: Fall term annually.
Cross Listed: MTLE 4720.
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BMED 4940 - Studies in Biomedical Engineering
When Offered: Fall and spring terms annually.
Credit Hours: 1 to 4
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BMED 4960 - Topics in Biomedical Engineering
When Offered: Fall and spring terms annually.
Credit Hours: 1 to 4
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BMED 6410 - BioMEMs
This course discusses state-of-the-art techniques in patterning biomolecules, biosensors, machining three-dimensional microstructures and building microfluidic devices (Lab-on-a-Chip). Seminal and current literature will be used to discuss topics in BioMEMs ranging from device fabrication to applications in cell biology and medicine. Students cannot get credit for both BMED 4410 and BMED 6410.
When Offered: Spring term annually.
Credit Hours: 3
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BMED 6420 - Clinical Orthopaedics and Contemporary Research
An in-depth review of the underlying science, engineering, medicine, and contemporary research related to the nation’s highest priorities for musculoskeletal diseases and care. Musculoskeletal anatomy, pathophysiology, epidemiology, and contemporary treatments are covered. Special topics will be presented relating state-of-the-art biomedical research to clinical practice. The clinical perspective of each topic will be presented by practicing clinicians with case studies. Topics conclude with live Webcasts or recorded surgery from Albany Medical Center or the Capital Region Bone and Joint Center. Students cannot get credit for both BMED 4420 and BMED 6420.
Prerequisites/Corequisites: Prerequisites: BMED 4500 and senior standing or permission from instructor.
When Offered: Fall term annually.
Credit Hours: 4
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BMED 6440 - Biophotonics
Biophotonics, or biomedical optics, is a newly developing field, dealing with the application of optical science and technology to biomedical problems, including clinical applications. The course introduces students to the fundamentals in modern and classical optics, light-matter interaction and provides them with a broad overview of current topics and contemporary research in the area of optics and lasers in medicine and biology.
Prerequisites/Corequisites: Prerequisisite: PHYS 1200.
When Offered: Spring term annually.
Cross Listed: With BMED 4440. Students cannot receive credit for both.
Credit Hours: 3
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BMED 6450 - Drug and Gene Delivery
The course presents several aspects of drug and gene delivery including: 1) definitions of what drugs or gene are; 2) pharmacokinetics and pharmacodynamics; 3) biomaterial selection considerations; 4) bioactivity considerations; 5) physiological and biochemical barriers to drug delivery; 6) diffusion controlled, dissolution controlled, and osmotic controlled drug delivery systems; 7) polymeric delivery systems; 8) ligand-based targeting and physical targeting; 9) viral mediated gene delivery; 10) non-viral gene delivery; 11) polymers in gene delivery.
Prerequisites/Corequisites: Prerequisites: BMED 2100 or equivalent, senior standing, or instructor permission.
When Offered: Fall term annually.
Credit Hours: 3
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BMED 6460 - Biological Imaging Analysis
Survey of image analysis applications in biology and biotechnology; introduction to biological microscopy and selected biomedical imaging systems; image reconstruction and pre-processing; grayscale and geometric corrections; image segmentation; blob analysis, cell/colony counting, and cell morphometry; vessel and neuron tracing algorithms with applications to neurobiology and medicine; feature extraction, pattern analysis, cluster analysis and classification; image registration algorithms with applications to mosaicing, spatial referencing, motion estimation, and change detection.
When Offered: Spring term annually.
Credit Hours: 3
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BMED 6480 - Biomedical Fluid Mechanics
This course covers the dynamics of fluid flow in human physiological system. Engineering principles and fluid dynamic concepts will be taught in the context of cardiovascular system. Topics include: pulsatile flow in arteries, vascular compliance and wave propagation, impedance, cardiac mechanics, dynamic coupling of ventricle and systemic circulation, blood flow in vein, coronary circulation, microcirculation, blood flow at complex geometries, imaging techniques in clinical hemodynamic assessment, fluid mechanics in designing and testing circulatory implants.
Prerequisites/Corequisites: Prerequisite: ENGR 2250 and a basic knowledge of human physiology.
When Offered: Fall term annually.
Cross Listed: With BMED 4580. Students cannot receive credit for both courses.
Credit Hours: 3
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BMED 6500 - Mechanobiology
Mechanical regulation of biological systems will be discussed. Topics include principles and concepts of mechanobiology; embryogenesis, and histogenesis of tissues with particular references to skeletal system; physical forces at cellular, tissue, and organ level; mechanical regulation of cellular behavior, tissue growth, and organ development; limits of mechanical regulation; biochemical influences; application of mechanobiology to tissue regeneration.
Prerequisites/Corequisites: Prerequisite: BMED 2540 or ENGR 2530 with permission from the instructor. Graduate course.
When Offered: Spring term even-numbered years.
Credit Hours: 3
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BMED 6550 - Cell Biomechanics
This is an undergraduate/graduate course on the mechanics of biopolymers, cell cytoskeleton, cell membrane, the whole cell, and multicellular structures in the context of the modulation of cell function by mechanical stresses. Topics include state-of-the-art experimental techniques in cell biomechanics, and cutting-edge research in stem cell mechanobiology, cell motility, collective cell behavior, neurite growth, osteocyte sensing, cardiovascular diseases, and immunology.
Prerequisites/Corequisites: Prerequisite: BMED 2540 or equivalant.
When Offered: Fall term annually.
Cross Listed: With BMED 4550. Students cannot receive credit for both courses.
Credit Hours: 3
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BMED 6650 - Introduction to Cell and Tissue Engineering
The principles and practice of tissue engineering are taught in this course. The principles underlying strategies for employing selected cells, biomaterial scaffolds, soluble regulators or their genes, and biomechanical loading and culture conditions, for the regeneration of tissues and organs in vitro and in vivo are addressed. Bioreactor, enabling technology, and biomimetic approach for fabricating tissue-engineered products and devices for implantation are taught.
Prerequisites/Corequisites: Prerequisites: a basic course in mechanics (ENGR 2530 or BMED 2540), and a basic course in transport phenomena or fluid dynamics (ENGR 2250 or equivalent) or permission of instructor.
When Offered: Spring term anually.
Credit Hours: 3
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BMED 6660 - Muscle Mechanics and Modeling
This graduate/advanced undergraduate hybrid course examines the structural and physiologic properties of muscle, as well as its force production and overall biomechanical function. Muscle structure and function will be explored at the protein, single fiber and whole tissue levels. Discussions will focus primarily on skeletal muscle, and topics will include muscle morphology, cross-bridge theory, molecular motor and actomyosin interaction, Hill-type and Huxley-type models, electromyography, fatigue, muscle inhibition, history-dependent phenomena, in vitro and in vivo muscle function, and the response to injury. Each topic will be introduced and developed utilizing seminal articles in the literature as well as excerpts from texts, and further discussion on current problems and state-of-the-art experimental techniques will draw on the current scientific literature.
Prerequisites/Corequisites: Prerequisites: senior standing or permission of instructor.
Credit Hours: 3
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BMED 6800 - Discussions in Graduate Research
This is a seminar based graduate level course that provides (a) a broad exposure to contemporary topics of research in biomedical engineering by recognized experts in the field and; (b) hands-on exposure on various aspects of professional development to Ph.D. students including conference/thesis presentations, writing scientific manuscripts and pre-doctoral and post-doctoral fellowship grant applications. Students are required to attend and participate in the departmental seminar and present their own research and grant proposals.
Prerequisites/Corequisites: Prerequisites: graduate student status required.
When Offered: Fall and spring terms annually.
Credit Hours: 0
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BMED 6940 - Studies in Biomedical Engineering
When Offered: Fall and spring terms annually.
Credit Hours: 1 to 4
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BMED 6960 - Topics in Biomedical Engineering
New courses or special course offerings are given under this number from time to time. Graduate students in biomedical engineering may pursue special interests under this number when sponsored by a biomedical engineering faculty member and with the permission of the department.
When Offered: By individual arrangement.
Credit Hours: 1 to 4
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BMED 6970 - Professional Project
Active participation in a semester-long project, under the supervision of a faculty adviser. A Professional Project often serves as a culminating experience for a Professional Master’s program but, with departmental or school approval, can be used to fulfill other program requirements. With approval, students may register for more than one Professional Project. Professional Projects must result in documentation established by each department or school, but are not submitted to the Office of Graduate Education and are not archived in the library. Grades of A, B, C, or F are assigned by the faculty adviser at the end of the semester. If not completed on time, a formal Incomplete grade may be assigned by the faculty adviser, listing the work remaining to be completed and the time limit for completing this work.
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BMED 6980 - Master’s Project
Active participation in a master’s-level project under the supervision of a faculty adviser, leading to a master’s project report. Grades of IP are assigned until the master’s project has been approved by the faculty adviser. If recommended by the adviser, the Master’s Project may be accepted by the Office of Graduate Education to be archived in the Library. Grades will then be listed as S.
Credit Hours: 1 to 9
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BMED 6990 - Master’s Thesis
Active participation in research, under the supervision of a faculty adviser, leading to a master’s thesis. Grades of S or U are assigned by the adviser each term to reflect the student’s research progress for the given semester. Once the thesis has been presentend, approved by the adviser, and accepted by the Office of Graduate Education, it will be archived in a standard format in the library.
Credit Hours: 1 to 9
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BMED 9990 - Dissertation
Active participation in research, under the supervision of a faculty adviser, leading to a doctoral dissertation. Grades of IP are assigned until the dissertation has been publicly defended, approved by the doctoral committee, and accepted by the Office of Graduate Education to be archived in a standard format in the library. Grades will then be listed as S.
Credit Hours: Variable
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CHEM 1110 - Chemistry I with Advanced Lab
Covers the same lecture material as CHEM 1100, but laboratory experiments will be more technique-oriented to provide better preparation for students who plan to take future laboratory courses in chemistry. Students cannot get credit for both this course and CHEM 1100.
When Offered: Fall term annually.
Credit Hours: 4
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CHEM 1200 - Chemistry II
Continued examination of the principles of chemistry in more depth, considering thermodynamics, advanced concepts in chemical equilibrium and acid-base chemistry, kinetics of chemical reactions, and electrochemistry.
Prerequisites/Corequisites: Prerequisite: CHEM 1100 or CHEM 1110.
When Offered: Spring term annually.
Credit Hours: 4
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CHEM 1600 - Materials Science
Introduction to the scientific principles that dictate the structure and properties of engineering materials, including metals, ceramics, semiconductors, and polymers. Physical properties of materials (mechanical, electrical, thermal, optical) are discussed in terms of the underlying structure, spanning multiple length scales from atomic packing to micron scale defects, in practical engineering materials. Throughout the course, the material behaviors are understood from the viewpoint of thermodynamics and kinetics.
Prerequisites/Corequisites: Prerequisites: CHEM 1100.
When Offered: Fall and spring terms annually.
Cross Listed: ENGR 1600, PHYS 1600, and ISCI 1600. Students cannot receive credit for both this course and ENGR 1600, PHYS 1600, or ISCI 1600.
Credit Hours: 4
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CHEM 2030 - Inorganic Chemistry I
Descriptive chemistry of the elements. Properties, structures, and typical reactions of the elements of the periodic table and their compounds; basic principles of inorganic chemistry.
Prerequisites/Corequisites: Prerequisite: CHEM 1200 or ENGR 1600.
When Offered: Spring term annually.
Credit Hours: 3
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CHEM 2120 - Experimental Chemistry I: Analytical Techniques
A laboratory course dealing with wet and instrumental techniques of chemical analysis.
Prerequisites/Corequisites: Corequisite: CHEM 2110.
When Offered: Fall term annually.
Credit Hours: 2
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CHEM 2230 - Organic Chemistry Laboratory I
Laboratory experiments dealing with basic techniques used in the synthesis and characterization of organic compounds.
Prerequisites/Corequisites: Pre- or corequisite: CHEM 2250 or a similar course in organic chemistry.
When Offered: Fall term annually.
Credit Hours: 1
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CHEM 2240 - Organic Chemistry Laboratory II
A continuation of CHEM 2230, which is a prerequisite.
Prerequisites/Corequisites: Prerequisite: CHEM 2230 and CHEM 2260 or a similar course in organic chemistry should be taken with or prior to this course.
When Offered: Spring term annually.
Credit Hours: 1
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CHEM 2260 - Organic Chemistry II
A continuation of CHEM 2250, which is a prerequisite.
Prerequisites/Corequisites: Prerequisite: CHEM 2250.
When Offered: Spring term annually.
Credit Hours: 3
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CHEM 2290 - Experimental Chemistry II: Synthesis and Characterization
Laboratory experiments dealing with the synthesis and characterization of chemical compounds and practical experience in accessing the chemistry literature. Primary emphasis is organic chemistry. Intended for chemistry majors.
Prerequisites/Corequisites: Corequisite: CHEM 2260.
When Offered: Spring term annually.
Credit Hours: 3
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CHEM 2360 - Chemistry Laboratory: Selected Experiments
A selection of experiments taken primarily from other chemistry laboratory courses. Intended to permit an individualized laboratory course to be set up to enable transfer students to make up deficiencies in their laboratory background, to allow students from other departments to obtain experience in areas of interest to them, and to provide a course that students from other schools can use to fulfill laboratory requirements of their home institution on a transfer basis. Selection of experiments and credits determined by individual consultation with the academic adviser and instructor.
When Offered: Fall and spring terms annually.
Credit Hours: Arranged.
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CHEM 2540 - Introduction to Geochemistry
An introduction to the application of chemistry to the understanding of problems in the earth and environmental sciences. Topics include thermodynamics and phase equilibria as applied to mineral stability, rock evolution, and water chemistry; stable isotope systematics; radiogenic isotope systematics, trace element geochemistry, organic geochemistry, and geochemical cycles.
Prerequisites/Corequisites: Prerequisites: ERTH 1100 and/or ERTH 1200 or permission of instructor.
When Offered: Spring term annually.
Cross Listed: Cross listed as ERTH 2140. Students cannot receive credit for both this course and ERTH 2140.
Credit Hours: 4
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CHEM 2930 - Out-of-Classroom Experience in Chemistry
Students may obtain credit for chemistry-related experience in nonclassroom situations. For credit to be awarded, a brief proposal outlining the nature of the experience to be undertaken must be given to the department in advance for approval of its suitability. A written report is required at the end of the experience. A maximum of 4 credits is allowed, but this may be made up in more than one experience.
Graded: Graded Satisfactory/Unsatisfactory.
Credit Hours: 1 to 4
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CHEM 2940 - Special Projects in Chemistry
Study and experimental work in various fields of chemistry to develop an interest in and ability for independent study and investigation.
Prerequisites/Corequisites: Prerequisite: permission of instructor.
When Offered: Fall and spring terms annually.
Credit Hours: 1 to 4
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CHEM 2950 - Undergraduate Research
Hands-on research in a faculty research laboratory.
Prerequisites/Corequisites: Prerequisite: permission of instructor.
When Offered: Fall and spring terms annually.
Credit Hours: 1 to 4
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CHEM 4010 - Inorganic Chemistry II
A course dealing with more advanced topics of inorganic chemistry, including molecular symmetry, application of symmetry concepts to molecular orbital descriptions of polyatomic molecules, solid state and non-stoichiometric compounds, coordination chemistry, spectral and magnetic properties, organometallic chemistry, and bioinorganic chemistry.
Prerequisites/Corequisites: Prerequisite: CHEM 2030; it is recommended that CHEM 4410 be taken concurrently.
Credit Hours: 3
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CHEM 4020 - Experimental Chemistry III: Inorganic and Physical Methods
Laboratory exploration including synthesis and characterization of several types of inorganic compounds, with emphasis on the use of physical methods in inorganic chemistry. Communication of results in written and oral form is an integral part of the course. This is a communication-intensive course.
Prerequisites/Corequisites: Corequisites: CHEM 4010 and CHEM 4410.
When Offered: Fall term annually.
Credit Hours: 3
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CHEM 4110 - Instrumental Methods of Analysis
This course will introduce advanced instrumental physicochemical methods of chemical analysis and will include such topics as separations (chromatography), atomic spectroscopy, molecular spectroscopy, and electroanalytical chemistry. Non-majors, particularly those in Biochemistry and Engineering (Biomedical, Environmental, etc. except Chemical Engineering) are encouraged to take this course. Chemistry majors should register for CHEM 4120 concurrently.
Prerequisites/Corequisites: Prerequisites: CHEM 2110 and CHEM 2120 or permission of the instructor.
When Offered: Spring term annually.
Credit Hours: 2
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CHEM 4120 - Experimental Chemistry IV: Physical and Instrumental Methods
A laboratory course emphasizing the hands-on use of modern instrumental methods in analytical and physical chemistry applications, and the interpretation and discussion of the results obtained from them. This is a communication-intensive course.
Prerequisites/Corequisites: Experiments depend on the theoretical material in CHEM 4110 and CHEM 4420, which are corequisites.
When Offered: Spring term annually.
Credit Hours: 3
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CHEM 4300 - Medicinal Chemistry
Organic and medicinal chemistry play a crucial role in the discovery of agents used to treat human disease. The basis of this course is the study of the drug discovery process from the perspective of these chemical disciplines. Concepts to be studied are molecular targeted drug discovery, lead compound identification and optimization, biophysical and molecular modeling tools, biological barriers to drug action and ways chemistry can overcome them, and the biotech industry. Topics pertinent to drug development such as drug metabolism and clinical research will also be discussed.
Prerequisites/Corequisites: Prerequisite: CHEM 2260 or permission of instructor.
Credit Hours: 4
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CHEM 4310 - Bioorganic Mechanisms
The study of mechanisms of organic reactions in biochemical processes on a molecular level. Enzyme active sites, mechanisms of enzymatic transformations, catalysis, cofactors, enzyme kinetics, environmental toxicology. Strong emphasis on the design and mechanism of action of pharmaceutical agents. Meets with CHEM 6310; both courses cannot be taken for credit.
Prerequisites/Corequisites: Prerequisite: CHEM 2260 or permission of instructor.
When Offered: Fall term annually.
Credit Hours: 4
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CHEM 4330 - Drug Discovery
This course will examine how bioinformatics, functional genomics, and other modern biotechnologies are used to speed the discovery of new drugs, especially those small organic molecules to treat human diseases with large unmet therapeutic need. Special emphasis will be placed on molecular target identification and validation as well as high-throughput screening to identify a lead. Topics to be discussed will include transgenic mice, RNA interference, DNA and protein microarrays, homogenous time-resolved fluorescence bioassays, phage-display, combinatorial chemistry, and parallel synthesis. Students cannot receive credit for both this course and CHEM 6330.
Prerequisites/Corequisites: Prerequisite: CHEM 2260 or permission of instructor.
When Offered: Fall term annually.
Credit Hours: 3
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CHEM 4410 - Macroscopic Physical Chemistry
A course dealing with physicochemical properties of substances on a macroscopic scale. Chemical thermodynamics, electrochemistry, electric and magnetic phenomena, transport properties, and surface and colloid chemistry.
Prerequisites/Corequisites: Prerequisite: MATH 2400.
When Offered: Fall term annually.
Credit Hours: 3
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CHEM 4420 - Microscopic Physical Chemistry
A course dealing primarily with physicochemical properties of substances on a molecular basis. Chemical kinetics, quantum chemistry, spectroscopy, and statistical mechanics.
Prerequisites/Corequisites: Prerequisite: MATH 2400.
When Offered: Spring term annually.
Credit Hours: 3
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CHEM 4440 - Physical Chemistry for Life Sciences
Topics in physical chemistry that are important for understanding processes in biological systems. Included are: thermodynamics as applied to phase and chemical equilibria in chemical and biochemical systems; passive transport models for diffusion and electrical conductivity in electrolyte solutions; kinetic models for simple and complex chemical reactions, including enzyme mechanisms; quantum mechanical models used in spectroscopy.
Prerequisites/Corequisites: Prerequisites: CHEM 1200 and MATH 1010.
When Offered: Fall term annually.
Credit Hours: 4
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CHEM 4470 - Theoretical Chemistry
Introduction to quantum mechanics and applications in chemical systems. Atomic and molecular spectra and structure. Statistical thermodynamics.
Prerequisites/Corequisites: Prerequisite: CHEM 4410.
When Offered: Fall term annually.
Credit Hours: 3
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CHEM 4530 - Modern Techniques in Chemistry
A lecture/laboratory course for Chemical Engineering students. Discusses the principles and applications of modern instrumental methods of chemical analysis and provides laboratory experience in their use along with other chemical techniques. Principles of analytical, organic, and physical chemistry will be illustrated throughout the course.
Prerequisites/Corequisites: Prerequisites: CHEM 2250.
When Offered: Fall and spring terms annually.
Credit Hours: 4
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CHEM 4690 - Aqueous Geochemistry
Fundamentals of aqueous chemistry as applied to the evolution of natural waters. The course covers principles of chemical equilibrium, activity models for solutes, pH as a master variable, concentration and Eh-pH diagrams, mineral solubility, aqueous complexes, ion exchange, and stable isotopes. The carbonate system, weathering reactions, and acid rain are examined in detail. Emphasis is on the chemical reactions that control surface and groundwater evolution in natural and engineered (treatment process) settings. Students learn theory, computation methods, and the use of computer programs for calculation of speciation and mass balance.
Prerequisites/Corequisites: Prerequisite: permission of instructor.
When Offered: Fall term annually.
Cross Listed: Cross listed as ENVE 4110 and ERTH 4690. Students cannot receive credit for both this course and either ERTH 4690 or ENVE 4110.
Credit Hours: 4
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CHEM 4770 - Molecular Biochemistry II
The second semester of the Molecular Biochemistry sequence. Topics include lipids and lipid metabolism, amino acid metabolism and the coenzymes involved in this metabolism, nucleic acid synthesis and chemistry, protein synthesis and degradation, integration of metabolism, photobiology, and photosynthesis. This course is taught in studio mode. (Students cannot obtain credit for both this course and either BIOL 4770 or BCBP 4770.)
Prerequisites/Corequisites: Prerequisite: CHEM 4760 or equivalent.
When Offered: Spring term annually.
Credit Hours: 4
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CHEM 4810 - Chemistry of the Environment
Chemical processes important in the environment from naturally occurring and man-induced systems. Thermodynamic and chemical considerations of fuels; the thermodynamics of the atmosphere; atmospheric photochemistry; chemistry of natural water systems; chemistry of pesticides, fertilizers, and other important environmental contaminants; aspects of the carbon, nitrogen, and sulfur cycles.
Prerequisites/Corequisites: Prerequisites: CHEM 1200 and one prior or concurrent course in organic chemistry or permission of instructor.
When Offered: Spring term annually.
Cross Listed: Cross listed as ERTH 4810. Students cannot obtain credit for both this course and ERTH 4810.
Credit Hours: 4
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CHEM 4900 - Professional Development Seminar
Weekly seminars on topics of concern to students who are about to embark on their professional careers in Chemistry. Topics will include employment and career opportunities; graduate school; ethical requirements and expectations in the profession; patent considerations; new directions in research and other topical matters. Restricted to senior Chemistry majors.
When Offered: Fall term annually.
Graded: S/U
Credit Hours: 1
Contact, Lecture or Lab Hours: 1
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