2022-2023 Academic Catalog [ARCHIVED CATALOG]
Courses
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BIOL 256 - Biology of Symbiosis
This course focuses on the ecological and evolutionary aspects of symbioses, the intimate associations among different species that are ubiquitous in nature. Examples of symbioses include lichens, corals and pollination syndromes. Lectures introduce general theory regarding evolution and ecology of symbioses, and student-led discussions are based on close reading of primary research articles. Students write a review article on a specific symbiotic system.
Prerequisites: BIOL 102 and BIOL 118 or BIOL 105
Anticipated Terms Offered: Offered every other year
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BIOL 263 - Plant Breeding: The Past, Present, and Future of Agriculture
The food we buy in a grocery store freezer, from a fast food drive up window, and at the farmer’s market from a local vendor have a lot more in common than we might think. Their ingredients all have an extensive history of human intervention, which took them from meager, sometimes even dangerous wild plants to worldwide dietary staples. Through a combination of lectures, reading of primary literature, and interactive exercises, students will explore the history of plant breeding from early phenotypic selection practiced by our ancestors, to modern techniques based on genetics and genomics. We will also discuss modern breeding technologies such as RNAi and CRISPR, their applications, limitations, governmental regulations, and societal perspectives.
Prerequisites: BIOL 105 and BIOL 118 ; or permission
Anticipated Terms Offered: Fall annually
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BIOL 265 - Population Genetics
This course will focus on understanding how evolutionary forces affect population diversity form a genetic perspective. We will explore how to differentiate between selection and genetic drift, learn to calculate rates of genetic diversity between and across populations and study the variation in populations as driven by time by studying examples from primary and secondary literature.
Prerequisites: BIOL 105 , BIOL 106 , and BIOL 118
Anticipated Terms Offered: Fall, Bi-annually
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BIOL 266 - Chemical Ecology
This course explores the role of chemical compounds in mediating interactions between organisms. Through a mixture of lectures, labs and discussions, we will examine the diversity of species interactions, the structure and function of chemical compounds that mediate these interactions, and the methods used to detect these compounds. Examples will include defensive and offensive chemistry mediating antagonistic interactions in plants, insects and microorganisms; the evolution of defenses; chemicals mediating mutualisms, competition, sociality, and sexual selection; and how chemical ecology affects humans. This course will include paper discussions of relevant recent literature, exposure to laboratory techniques in chemical ecology, and a final project on a chemically mediated interaction.
Prerequisites: BIOL 216 OR CHEM 131 OR Permission
Anticipated Terms Offered: Spring Bi-annually
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BIOL 268 - Plant-Microbe Interactions
This is a research-based course to give students hands-on experience doing experiments and making their own observations about plant and microbiology.
Prerequisites: BIOL 109
Anticipated Terms Offered: Spring annually
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BIOL 274 - Biological Dynamics
This course is designed to introduce students to the invaluable tools involved in modeling and analyzing biological dynamics. It does so through the use of basic mathematical techniques from differential equations and linear algebra, including separable equations, numerical methods of integration, matrix multiplication, and eigenvalues. Applications will come from a wide range of areas in Biology - including population dynamics, epidemiology, molecular evolution, and population genetics, with the overarching goal of helping students gain the skills needed to use differential equations and/or linear algebra in their research. No prior knowledge of topics from differential equations or linear algebra will be assumed.
Prerequisites: Minimum of one course in Biology beyond Biol 101 & 102, and one course in calculus (BIOL 121 or MATH 120 or MATH 124 )
Anticipated Terms Offered: Bi-annually
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BIOL 276 - Biology of Social Insects
This course explores the biology of social insects including ants, bees, wasps and termites. Through a mixture of lectures, activities and discussions, we will examine the ecology, evolution and behavior of social insects. Examples of topics include social insect taxonomy; the evolution of sociality; nest architecture; mutualisms and commensalisms involving social insects; territoriality; and how social insects provide ecosystem services. This course will include paper discussions of relevant recent literature, exposure to methods used to study social insects, and a final presentation on a research topic of the student’s choice.
Prerequisites: BIOL 105 or BIOL 118 or Permission
Anticipated Terms Offered: Spring bi-annually
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BIOL 282 - BioFrontiers: Introductory Python for life sciences
Life is complex. So complex, in fact, that it borders the unknowable. Technological advancements have offered many ways to explore this complexity, often producing data that requires the use of computers to extract information that our brains can understand. As such, computers have quickly become as essential as microscopes and pipettes for all kinds of biology laboratories.
The goal of the online course is to introduce the students to the Python programming language, giving them the skills needed for low level programming (scripting), as well as the use of Python-based tools applied to biological sciences. The student will learn how to use several basic Python libraries for advanced mathematical and statistical operations, operating with biological sequences and data visualization. The student will learn how to install and access the documentation of new packages and will be introduced to several Python packages for more specific applications such as functional genome annotation, structural biology, phylogenetics, image processing and chemistry.
Prerequisites: BIOL 118 and one of BIOL 105 or BIOL 106
Anticipated Terms Offered: Winter intersession bi-annually
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BIOL 283 - BioFrontiers: Introduction to Quantitative Image Analysis
Introduction to Quantitative Image analysis will introduce students to the considerations and methods needed to analyze biological image data which is qualitative in nature and extract quantitative information. It will prepare students for a future in which quantitative analysis is becoming the norm in fields of academic and applied research.
Prerequisites: BIOL 105 and BIOL 118 and a math course (MBB 110 or MATH 120 or MATH 124 or BIOL 106 )
Anticipated Terms Offered: Winter intersession annually
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BIOL 284 - Data Visualization and Exploration for the Biosciences in the Tidyverse
This course serves as a guide to exploring and communicating biological data. Data visualization is a key component of understanding experimental data. Introductory Biostatistics provides students with the tools to analyze and answer questions about their data. This course provides students with the knowledge to determine if they are asking the right question or if they need to generate new hypotheses by visualizing data. Students will learn the fundamental components of statistical graphing focusing on the the grammar of graphics outlined in the tidyverse.
Prerequisites: BIOL 106 or Permission of instructor
Anticipated Terms Offered: Fall annually
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BIOL 290 - Science Careers & Effective Practice
Students will consider what science is, how it works, and what it means to be a scientist. They will learn about the limits of scientific inquiry, how the scientific method works, and how to test hypotheses and interpret results. Students will go on to study how scientists write and the types of things they write. This will culminate in the writing of a grant proposal. Students will also learn about and discuss scientific ethics, including the ethics behind doing good science, and those focused around publishing. Finally, students will learn about career options in science (both academic and not), how to write a CV, give a presentation, and apply to graduate school and for other academic positions. The goal of the course is to teach students about the rarely-discussed, but critically important aspects of being a successful scientist.
Prerequisites: Must be Seniors. Students should be research active (working in a professor’s lab). Students will need permission to enroll.
Anticipated Terms Offered: Offered every other spring
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BIOL 293 - Peer Learning Assistant
Peer Learning Assistants (PLAs) are undergraduate students who are selected by a faculty member to facilitate teaching and learning activities. These activities may include: helping to prepare for or assisting in laboratory sessions, providing feedback on drafts of writing assignments, leading small group discussions, working with individual students who are having difficulty, facilitating group project work (in or out of class), and/or facilitating online discussions. It is the practice at Clark that PLAs do not grade student work. PLAs generally work 10-15 hours per week but the precise schedule, activities, and units earned are determined on an individual basis with the supervising faculty/staff member. Students who receive credit for being a PLA participate in weekly meetings to review the experiences of PLAs, discuss various aspects of science education and student learning, and receive guidance on upcoming projects. Students will provide written reflections about their experiences and goals mid-semester and a final paper based on the teaching/learning experience at the end of the semester. This course is offered on a Pass/Fail basis. Registration is by instructor permission only and you must choose the number of units (0.5 or 1.0). May be repeatable for credit.
Prerequisites: Registration by instructor permission only.
Anticipated Terms Offered: Offered every semester
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BIOL 301 - Ecology of Atlantic Shores
This course explores the ecology of marine organisms found in diverse Atlantic habitats, ranging from the rocky intertidal of New England to the coral reefs of Bermuda. The course includes lectures, field research, and a one-week trip to the Bermuda Biological Station for Research during semester break. Students must pay a fee (approximately $2500) for the cost of lodging, meals and airfare to Bermuda.
Prerequisites: BIOL 101 or BIOL 103 , and BIOL 102 ; or permission. BIOL 114 or BIOL 216 recommended.
Anticipated Terms Offered: Offered every other fall.
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BIOL 306 - Advanced Biostatistics
During Advanced Biostatistics, students will build on the basic statistical skills they gained in Quantitative Methods and learn to apply more advanced techniques to real data. Students will also learn to read biostatistical literature, which will build their ability to learn other statistical techniques on their own. Students will learn a variety of techniques that are frequently used by Biology Faculty at Clark University, and so will enhance the skills students have to effectively do research in the department. Students will learn to do these statistics in the statistical computing language R, which has become the standard in the sciences for conducting complex statistical analysis. Students will get the opportunity to analyze data generated in Clark Biology laboratories to reinforce their learning and get valuable hands-on experience doing statistics.
Prerequisites: BIOL 106 or permission of the instructor
Anticipated Terms Offered: every other fall
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BIOL 307 - Conservation Biology
Conservation Biology focuses on the biological underpinnings of efforts to preserve biodiversity in the face of increasing impacts of human activities. This seminar builds upon student background in evolution and genetics, developing skills for assessment of the fundamental biological information needed to develop policy that can lead to the protection of threatened and endangered species/populations/ evolutionarily significant units.
Anticipated Terms Offered: Usually offered every spring.
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BIOL 309 - The Genome Project
The Genome Project offers students a unique opportunity to directly apply the bioinformatics and comparative genomics skills they acquired during Introduction to Bioinformatics (BINF 101) in the analysis of a novel genome. Each year, students will work collaboratively in small research teams to piece together the entire DNA blueprint of an organism with no existing reference genome. Students will evaluate and apply genome assembly, gene prediction, functional annotation, and variant discovery algorithms to better understand the genome structure, and functional biology of sequenced organisms. Analysis will be conducted within a LINUX environment through the Clark University Supercomputing Cluster.
Prerequisites: BIOL 123
Anticipated Terms Offered: Spring
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Biol 312 - Microbiomes
The course will explore current research on microbiomes found in a variety of habitats: human and plant associated, marine, and soil. Through a mixture of lectures and discussions, students will learn about core ecological concepts relevant to microbiomes and microbiology. Throughout the course, students will read primary scientific literature and gain practical skills in how to understand and interpret research articles. Students will learn about current sequencing and molecular techniques (including 16S rDNA sequencing, metagenomics, and metatranscriptomics) used to study microbiomes. Each student will give a final presentation on a microbiome research article of their choice.
Anticipated Terms Offered: offered every other year
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BIOL 316 - Ecology
Provides an overview of ecology as a scientific discipline. The primary emphasis is on efforts to explain and predict the distribution and abundance of organisms, how ecological communities are composed and why they vary in time and space.
Prerequisites: One or more courses from the organismal biology group and one college-level math course.
Anticipated Terms Offered: Offered every year
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BIOL 317 - Research
This is a variable unit graduate course for students engaged in research at the PhD level.
Anticipated Terms Offered: Every Semester, including summers
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BIOL 318 - Genetics and Disease
This course focuses on the genetic basis of human disease. Many important disorders are primarily of genetic origin, whereas others reflect the complex interplay between our genes and the environment. The Human Genome Project has provided a wide range of new tools that allow us to understand the genetic underpinnings of both kinds of disease. The course uses a mixed format, with both lecture and discussion of primary literature; students will also pick a human disorder/disease and present a literature review of it in the form of an essay and a poster presentation.
Anticipated Terms Offered: Offered periodically
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BIOL 321 - Developmental Biology
Considers the fundamentals of development from the molecular level up to the organismal. Emphasis is placed on the major animal model systems.
Prerequisites: BIOL 137 or permission of instructor.
Anticipated Terms Offered: Offered every other year.
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BIOL 322 - Physiological Ecology of Marine Algae
This course will introduce upper-division undergraduate and graduate students to algal diversity and the physiological ecology of marine algae. The course includes lectures, readings, discussions, and laboratory research. Topics of discussion include evolution, biochemistry, molecular biology, and physiology of photosynthetic cells. In the laboratory, students will learn various techniques including measurements of photosynthesis, determination of enzyme activity and methods used to examine gene expression. The topics and techniques covered in the course are readily applied to the physiology of a broad range of organisms.
Anticipated Terms Offered: Offered every other spring
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BIOL 323 - Topics in Marine Biology
This course provides an opportunity for advanced undergraduate and graduate students to explore in depth selected topics in marine biology. This writing intensive course uses discussions of the primary literature to explore topics in genomics, microbial ecology, oceanography and marine biology.
Anticipated Terms Offered: Offered every other spring
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BIOL 330 - The Human Genome
This course will provide a foundation for the basic concepts in human genomics. Topics covered will include: genome structure and function, human evolution and paleogenomics, human migration, natural selection in human populations, genetic disease, microbiomics, epigenetics, and personalized medicine and ethics. The format of the course will be a combination of group projects, discussion of primary literature, and lecture.
Anticipated Terms Offered: Varied
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BIOL 333 - Animal Locomotion
Students will learn about how animals move and how their locomotion is affected by their environment. They will learn how the musculoskeletal system works to allow animals to move, and the biophysics of locomotion. Animal Locomotion takes an inquiry-based approach to studying the subject. The course will integrate short lectures, demonstrations, reading and discussion of primary literature, and hands-on analysis of locomotion. During the course, students will undertake original research projects in small groups to learn about animal locomotion and publicly present their findings. Students will work with high-speed videos to learn to quantify different aspects of locomotion to test hypotheses that they come up with.
Anticipated Terms Offered: Offered every other spring
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BIOL 334 - Signal Transduction
An advanced course exploring the various molecular and biochemical pathways through which cells communicate with themselves and their environment. Topics include protein phosphorylation, G-proteins, phospholipid metabolism, the action of oncogenes and several ion signaling pathways. Class format includes both lectures and student presentations.
Prerequisites: BIOL 137 or BCMB 271 or permission of instructor.
Anticipated Terms Offered: Offered periodically
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BIOL 336 - Biology of Cancer
According to the World Health Organization, cancer is the cause of one in eight deaths around the world, and kills an even greater proportion of Americans. Over the past thirty years, great strides have been made in understanding the biological and environmental causes of cancer; we have also made stunning progress in the treatment of some cancers. This class will address the cellular, genetic and biochemical basis of cancer, as well as delve into current modes of treatment. Students will choose a human cancer and develop an essay, present a poster and give an oral presentation on it, based on a review of primary literature.
Prerequisites: BIOL 137 or BCMB 271 ; BIOL 118 recommended.
Anticipated Terms Offered: Offered periodically.
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BIOL 337 - Epigenetics
With the completion of the sequencing of the human genome, where does science go now? Many scientists have chosen to investigate our genome at the level “above genetics”, or Epigenetics. Epigenetic changes are not coded in the DNA sequence, yet they are heritable through mitotic or meiotic cell divisions. Although epigenetic phenomena have been noted for decades, seemingly disparate observations are only now coalescing into an emerging field of Biology. This seminar style course will investigate the molecular basis of epigenetics and allow students to present research articles and discuss the literature at the intersection of gene expression, chromosome structure, and chromatin dynamics.
Anticipated Terms Offered: Spring
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BIOL 338 - Seminar in Cell Biology
Discussion based on research papers from the current literature, will be focused on an area in cell biology selected by the participants on the first day. The weekly readings will be selected by both the students and the member. The scientific content, as well as the methodology will be discussed in detail.
Anticipated Terms Offered: Offered periodically
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BIOL 339 - Evolutionary Developmental Biology
Biology 339 is an upper level seminar in evolutionary developmental biology, or “evo-devo”. Evo-devo is a major, emerging field that integrates organismal evolutionary biology with molecular embryology, genetics, and genomics. The goal of this course is to understand how changes in developmental processes have given rise to the incredible biological diversity seen in nature. We will primarily focus on the evolution of metazoan, or animal, development, but we will also discuss evolution of non-metazoan organismal development. This course emphasizes analysis and discussion of primary literature dealing with phenomena and questions that interest evolutionary developmental biologists, including (but not limited to): 1) How embryonic development arose and evolved in the transition to multicellularity, 2) The role evolution of developmental processes plays in the evolutionary modification of existing features and the origin of novel structures, 3) Phenotypic plasticity and the linkage between genotype and phenotype, and 4) Interactions between developmental processes and environmental influences.
Prerequisites: BIOL 105 or permission of the instructor
Anticipated Terms Offered: Fall only
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BIOL 340 - Comparative & Human Physiology
Introduces the principles underlying physiological function. Lectures cover the subcellular, cellular and organ levels of organization and place a primary emphasis on the integrative processes whereby all of the diverse organs and systems contribute to the performance of the complete individual.
Prerequisites: BIOL 137 or BCMB 271 . Enrollment is normally restricted to juniors, seniors and graduate students.
Anticipated Terms Offered: Offered every year.
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BIOL 342 - Animal Behavior
Examines the causes and evolution of the behavior of animals. The largest part of this course will focus on the adaptive value and evolution of behavioral patterns, but a general overview of behavioral development and causation will be provided to offer the necessary background for interpretation of the ultimate causes of behavior.
Prerequisites: BIOL 105 or BIOL 220 and permission of instructor.
Anticipated Terms Offered: Offered every other year.
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BIOL 343 - Seminar in Evolution
Discussion of a topic in evolution selected by interested students the previous fall. Readings will be from original literature. The format will be a combination of lecture and discussion.
Anticipated Terms Offered: Offered odd years.
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BIOL 350 - Graduate Research Seminar
Invited lecturers present seminars on varied research topics. Required for all graduate students. Offered for variable credit.
Anticipated Terms Offered: Offered every semester
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BIOL 354 - Molecular and Evolutionary Systematics
This course is designed for students who are interested in genetics, evolutionary biology, environmental biology, and bioinformatics. Topics to be discussed include evolution of genes and genomes, methods used to estimate evolutionary relationships using molecular data, and applications of molecular data to general problems in biology. The course will include lectures, student-led discussions, laboratory projects using computer-based applications and presentations.
Anticipated Terms Offered: Offered periodically
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BIOL 355 - Viruses: friends or foes?
Viruses are the ultimate parasites-they hijack the molecular machinery of their host to make more copies of themselves. There are viruses that infect nearly every type of life, from bacteria to beluga whales and even other viruses! Through lectures and in-class reading of current research articles, and in-class discussion this class will explore the amazing biology of viruses, their impact on society and our planet, and several controversial topics relevant to viruses: the growing anti-vaccination movement, research on the evolution of more virulent avian flu viruses, and virus-derived genome editing technologies (e.g. CRISPR). Students will also give a final project presentation on a particular virus of their choosing.
Anticipated Terms Offered: Offered every fall
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BIOL 356 - Biology of Symbiosis
This course focuses on the ecological and evolutionary aspects of symbioses, the intimate associations among different species that are ubiquitous in nature. Examples of symbioses include lichens, corals and pollination syndromes. Lectures introduce general theory regarding evolution and ecology of symbioses, and student-led discussions are based on close reading of primary research articles. Students write a review article on a specific symbiotic system.
Anticipated Terms Offered: Offered every other year
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BIOL 363 - Plant Breeding: The Past, Present, and Future of Agriculture
The food we buy in a grocery store freezer, from a fast food drive up window, and at the farmer’s market from a local vendor have a lot more in common than we might think. Their ingredients all have an extensive history of human intervention, which took them from meager, sometimes even dangerous wild plants to worldwide dietary staples. Through a combination of lectures, reading of primary literature, and interactive exercises, students will explore the history of plant breeding from early phenotypic selection practiced by our ancestors, to modern techniques based on genetics and genomics. We will also discuss modern breeding technologies such as RNAi and CRISPR, their applications, limitations, governmental regulations, and societal perspectives.
Anticipated Terms Offered: Fall annually
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BIOL 365 - Population Genetics
This course will focus on understanding how evolutionary forces affect population diversity form a genetic perspective. We will explore how to differentiate between selection and genetic drift, learn to calculate rates of genetic diversity between and across populations and study the variation in populations as driven by time by studying examples from primary and secondary literature.
Anticipated Terms Offered: Fall, Bi-annually
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BIOL 366 - Chemical Ecology
This course explores the role of chemical compounds in mediating interactions between organisms. Through a mixture of lectures, labs and discussions, we will examine the diversity of species interactions, the structure and function of chemical compounds that mediate these interactions, and the methods used to detect these compounds. Examples will include defensive and offensive chemistry mediating antagonistic interactions in plants, insects and microorganisms; the evolution of defenses; chemicals mediating mutualisms, competition, sociality, and sexual selection; and how chemical ecology affects humans. This course will include paper discussions of relevant recent literature, exposure to laboratory techniques in chemical ecology, and a final project on a chemically mediated interaction.
Anticipated Terms Offered: Spring Bi-annually
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BIOL 368 - Plant-Microbe Interactions
This is a research-based course to give students hands-on experience doing experiments and making their own observations about plant and microbiology.
Anticipated Terms Offered: Spring annually
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BIOL 374 - Biological Dynamics
This course is designed to introduce students to the invaluable tools involved in modeling and analyzing biological dynamics. It does so through the use of basic mathematical techniques from differential equations and linear algebra, including separable equations, numerical methods of integration, matrix multiplication, and eigenvalues. Applications will come from a wide range of areas in Biology - including population dynamics, epidemiology, molecular evolution, and population genetics, with the overarching goal of helping students gain the skills needed to use differential equations and/or linear algebra in their research. No prior knowledge of topics from differential equations or linear algebra will be assumed.
Anticipated Terms Offered: Bi-annually
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BIOL 376 - Biology of Social Insects
This course explores the biology of social insects including ants, bees, wasps and termites. Through a mixture of lectures, activities and discussions, we will examine the ecology, evolution and behavior of social insects. Examples of topics include social insect taxonomy; the evolution of sociality; nest architecture; mutualisms and commensalisms involving social insects; territoriality; and how social insects provide ecosystem services. This course will include paper discussions of relevant recent literature, exposure to methods used to study social insects, and a final presentation on a research topic of the student’s choice.
Anticipated Terms Offered: Spring bi-annually
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BIOL 382 - BioFrontiers: Introductory Python for life sciences
Life is complex. So complex, in fact, that it borders the unknowable. Technological advancements have offered many ways to explore this complexity, often producing data that requires the use of computers to extract information that our brains can understand. As such, computers have quickly become as essential as microscopes and pipettes for all kinds of biology laboratories.
The goal of the online course is to introduce the students to the Python programming language, giving them the skills needed for low level programming (scripting), as well as the use of Python-based tools applied to biological sciences. The student will learn how to use several basic Python libraries for advanced mathematical and statistical operations, operating with biological sequences and data visualization. The student will learn how to install and access the documentation of new packages and will be introduced to several Python packages for more specific applications such as functional genome annotation, structural biology, phylogenetics, image processing and chemistry.
Anticipated Terms Offered: Winter intersession bi-annually
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BIOL 383 - BioFrontiers: Introduction to Quantitative Image Analysis
Introduction to Quantitative Image analysis will introduce students to the considerations and methods needed to analyze biological image data which is qualitative in nature and extract quantitative information. It will prepare students for a future in which quantitative analysis is becoming the norm in fields of academic and applied research.
Anticipated Terms Offered: Winter intersession annually
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BIOL 384 - Data Visualization and Exploration for the Biosciences in the Tidyverse
This course serves as a guide to exploring and communicating biological data. Data visualization is a key component of understanding experimental data. Introductory Biostatistics provides students with the tools to analyze and answer questions about their data. This course provides students with the knowledge to determine if they are asking the right question or if they need to generate new hypotheses by visualizing data. Students will learn the fundamental components of statistical graphing focusing on the the grammar of graphics outlined in the tidyverse.
Anticipated Terms Offered: Fall annually
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BIOL 385 - Proposal Writing
Offered for Variable credit for Biology PhD students who are writing their proposal.
Anticipated Terms Offered: Every Semester
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BIOL 390 - Science Careers & Effective Practice
Students will consider what science is, how it works, and what it means to be a scientist. They will learn about the limits of scientific inquiry, how the scientific method works, and how to test hypotheses and interpret results. Students will go on to study how scientists write and the types of things they write. This will culminate in the writing of a grant proposal. Students will also learn about and discuss scientific ethics, including the ethics behind doing good science, and those focused around publishing. Finally, students will learn about career options in science (both academic and not), how to write a CV, give a presentation, and apply to graduate school and for other academic positions. The goal of the course is to teach students about the rarely-discussed, but critically important aspects of being a successful scientist.
Prerequisites: Students must be Masters, or PhD in the natural sciences. They should be research active (working in a professor’s lab). Students will need permission to enroll.
Anticipated Terms Offered: Offered every other spring
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BIOL 394 - Dissertation Writing
This is a variable unit, graduate course for students engaged in writing a Ph.D. Dissertation.
Anticipated Terms Offered: Every Semester, including summers
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BIOL 396 - Master’s Thesis
This is a variable unit, graduate course for students engaged in writing a Master’s thesis.
Anticipated Terms Offered: Offered every year
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BIOL 397 - Doctoral Dissertation
Offered for variable credit.
Anticipated Terms Offered: Offered every year
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BIOL 398 - Internship
Academic experience taking place in the field with an opportunity to earn credit.
Anticipated Terms Offered: Offered Every Semester
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BIOL 2000 - Immunology
This course will provide students with a basic understanding of the human immune system through pictorial and scientific explanation of the cellular and molecular interactions of our human immune components such as lymphocytes and antibodies to control the normal defense of the human body against multiple diseases. The research and understanding from this discipline has contributed significantly to our ability to use antibodies and cellular immunotherapy for biopharmaceutical applications.
In this course, the fundamental principles of the mechanisms of human immune responses will be thoroughly discussed. Advances in immunology related researches provide a more complete view of the innate lymphoid cells, the biology of the inflammation activation, subsets of the memory lymphocytes, or the role of IgE in allergy. Our translational understanding of the human immune responses has helped us address questions in autoimmunity, immunodeficiencies, transplantation rejection, HIV infection, microbiome interaction, or cancer immunotherapy and many more. Furthermore, knowledge from this discipline has formed the cornerstone of many therapeutic products in the biotech industry, such as in the area of biologic antibodies therapeutics or cellular immunotherapy.
Prerequisites: BIOL 1010 Introduction to Biology I
CHEM 1010 - Introduction to Chemistry I
Anticipated Terms Offered: As needed. Course is a pre-requisite admission requirements for BS Biotechnology program.
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BIOT 1000 - Introduction to Biotechnology
Biotechnology began with technology innovation, leading to its commercial development and benefits to society. Hence, a historical and current review of the cutting edge technology will be presented and discussed in this course. Students will learn about the current global effort in the product development and commercialization of biotechnology for human health. This course will serve as a foundation to understand the history, promise, operation, development and commercialization of biotechnology. Key scientific principles in nucleic acid and proteins will be applied as important tools for the genomic and proteomic area, leading to commercial applications and product development.
Prerequisites: BIOL 1010 or BIOL 101 - Introduction to Biology I
BCMB 2000 or BCMB 371 - Biochemistry I
MATH 1150 - Statistics
Anticipated Terms Offered: fall, spring
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BIOT 1200 - Business Operations Management for Biotechnology
This course is designed for students to learn and apply skills and knowledge for the management of business operations in the Life Sciences industry. Topics will include concepts and techniques for planning, designing, controlling and improving business operations. Areas of focus include the process view of organizations, research and development, performance measures, product bio-manufacturing, product attributes, production processes, process competencies, procurement and regulatory requirements.
Prerequisites: BIOT 1000 - Introduction to Biotechnology
Anticipated Terms Offered: fall
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BIOT 1300 - Introduction to Bioinformatics
This course will provide students with a technical foundation and an understanding of the current advances in bioinformatics and database analytics searches. These fields have grown significantly and become an essential tool for professionals in health care, biotechnology, forensic science, diagnostic and medical research.
The course will focus on the science of DNA sequencing and databases assembly, leading to the extrapolation of protein structures through in silico modeling. Some discussion of the sequencing technology, hardware, software and programming languages are integrated into the course, so that students will appreciate the impact of the recent technical and technological advances propelling this discipline. Furthermore, the practice of artificial intelligence and machine learning will be critical for our understanding of gene expression, metabolic pathway, and system biology. Together, this integrative knowledge has allowed major breakthroughs in drug discovery for the biotech industry.
Prerequisites: BIOL 1010 Intro to Biology I
CHEM 1010 - Introduction to Chemistry I
BIOL 1180 Genetics
BCMB 2000 - Biochemistry I
Anticipated Terms Offered: fall, spring
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BIOT 2300 - Regulatory Affairs Process for Biopharmaceuticals
The course will explore the regulations and requirement of new product filing process by which the FDA has used successfully to safe guard the public interest from novel therapeutic drug products. Some of the key steps by which life science and pharmaceutical companies used to assemble their product development data on discovery, preclinical studies, CMC process, and clinical studies for FDA filing will be examined. This course will show the students the important process of regulatory filing for new drug development so that students may appreciate the extensive product development hurdles, documentation, validation, and quality control of every step to assure a successful filing. Although the course will focus on the known regulatory platforms in small molecule and biologic filings, some discussion on the new fields of cell and gene therapies will be compared and contrasted with the established filing platforms.
Prerequisites: BIOT 1000 - Introduction to Biotechnology
BIOT 1200 - Business Operations Management for Biotechnology
COMM 2100 - Scientific and Technical Communications for Biotech Industry
Anticipated Terms Offered: fall,
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BIOT 2400 - Project Management in Biopharmaceutical Development
This course provides training and skills for managing projects from discovery to development (e.g., Investigational New Drug (IND) submission for clinical studies) that are the regular stages of therapeutic product development. The primary focus of the course will be to review the different stages in the project lifespan and the different team and management needs at each stage from product discovery to product development. In addition, the course will describe the tools needed to successfully manage this process, including the concept of program management, people and team management, and development of communication and presentation skills for project leadership.
Prerequisites: BIOT 1000 Introduction of Biotechnology
BIOT 1100 Leadership Foundation in Biotechnology
BIOT 1200 Business Operations Management for Biotechnology
BIOT 2300 Regulatory Affairs Process for Biopharmaceuticals
COMM 2100 Scientific and Technical Communications
PHIL 2000 Bioethical Issues in Biotechnology
Anticipated Terms Offered: fall, spring
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BIOT 2999 - Capstone
The Capstone project is the culminating experience for the BS in Biotechnology program. The final deliverable is a demonstration of the student’s professional competencies and evidence of a foundation of theoretical knowledge applied to “real-world” issues. SPS offers students various options for completing their capstone requirement. Each option involves practicing their skills in collaboration, analysis, problem solving, research, writing and professional presentations. Students work with their advisor to determine the Capstone option that works best for their professional and academic development.
Prerequisites: BIOT 2400 - Project Management in Biopharmaceutical Development (may be taken concurrently with permission from program lead)
Anticipated Terms Offered: fall, spring
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CHEM 007 - Science of Weapons of Mass Destruction
The science behind weapons of mass destruction will be discussed. Topics include low-technology explosives, nerve agents, biological agents and nuclear devices. In each case, introductory science concepts will be used to explain how the device or agent works. Historical examples will be reviewed, such as the Oklahoma bombing, Wisconsin Army Research Lab bombing, Tokyo Sarin subway attack, World War I gas attacks, Kurdish gas attack, anthrax letters and Hiroshima/Nagasaki. The technical basis for preventing the use of these weapons will also be discussed as will be the availability of information on the Internet.
Course Designation/Attribute: SP
Anticipated Terms Offered: Offered every year
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CHEM 010 - Topics in Contemporary Chemistry
This course is designed for students majoring in a social science or the humanities and is intended to develop a qualitative feeling about chemistry as it relates to the modern world. Approximately half the course is concerned with the development of modern chemical concepts; the remainder deals with current societal problems such as nuclear weapons and reactors, air and water quality, drugs, food additives, polymers, poisons and others. In-class and final exams.
Course Designation/Attribute: SP
Anticipated Terms Offered: Offered every year
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CHEM 012 - The Science of Fermentation
The structure of this course is designed to highlight humanity’s rich history and tradition of preserving food and drinks through fermentation. The class will start by covering some general aspects about the fermentation process and then will focus on the application of microorganisms/biomacromolecules to different substrates to generate a wide variety of non-perishable foods, beverages and biomedically relevant substances. This class has a laboratory component where the students will make and characterize a wide variety of fermentation products, such as beer, wine, cheese and vegetables (sauerkraut, kimchi etc.). In accordance with University policy, the students will NOT consume alcoholic fermented derivatives product in class.
Through the lectures and laboratory experiments students will learn the basic principles of experimental design, the importance and need to control experimental parameters, rules of proportion, scaling and basic chemical concepts such as the difference between a physical mixture and a chemical reaction, solubility, acidity, density, gas laws, etc. In addition to this, the course will also cover topics such as the development of fat-free, lactose-free and low-calorie alternatives as examples of how public demands can affect scientific developments and how commercial research studies are structured, funded and regulated.
Course Designation/Attribute: SP
Anticipated Terms Offered: varies
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CHEM 030 - Kitchen Chemistry
Basic chemical principles can be applied to cooking. Considered to be the original, most widespread form of chemical research, cooking illustrates chemical and biological changes that occur in food. This course will explore properties in regards to food preparation, consumption, and nutrition with hands-on experiments and interactive learning.
Prerequisites: Must register for lab.
Course Designation/Attribute: SP
Anticipated Terms Offered: Offered Periodically
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CHEM 050 - Forensic Science
Forensic science is the application of science to the collection, examination, evaluation, and interpretation of evidence. This course will examine the basic applications of biological and chemical sciences to crime scene investigation. Specific topics may include analysis of physical evidence (i.e. fingerprinting, hair analysis, fiber analysis), principles of serology and blood analysis. DNA analysis, ballistics, drug detection and toxicology, as well as chemical separation and identification techniques. Famous cases will be reviewed, such as the John F. Kennedy assassination, the deaths of celebrities such as Heath Ledger and Anna Nicole Smith, the O.J. Simpson Trial, the case of Dr. Sam Sheppard, and the identity of Anastasia. An interactive laboratory will mirror the work of a crime lab with emphasis on collection of evidence and hands-on experience with experimental techniques used to solve crimes.
Course Designation/Attribute: SP
Anticipated Terms Offered: Offered every other year
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CHEM 0070 - Science of Weapons of Mass Destruction
The science behind weapons of mass destruction will be discussed. Topics include low-technology explosives, nerve agents, biological agents and nuclear devices. In each case, introductory science concepts will be used to explain how the device or agent works. Historical examples will be reviewed, such as the Oklahoma bombing, Wisconsin Army Research Lab bombing, Tokyo Sarin subway attack, World War I gas attacks, Kurdish gas attack, anthrax letters and Hiroshima/Nagasaki. The technical basis for preventing the use of these weapons will also be discussed as will be the availability of information on the Internet.
Course Designation/Attribute: SP (summer only)
Anticipated Terms Offered: varies
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CHEM 102 - Introductory Chemistry II
Continues CHEM 101 with a discussion of thermodynamics, equilibrium theory, kinetics, electrochemistry and the application of such theories to studies of structure and reactivity of molecules. The laboratory studies experimental techniques related to the lecture material. In-class and final exams, laboratory reports and quizzes.
Prerequisites: CHEM 101 or advanced placement.
Course Designation/Attribute: SP
Anticipated Terms Offered: Offered ever year
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CHEM 103 - Accelerated Introductory Chemistry
This is a one-semester course for students with a strong background in chemistry who do not need the traditional two-semester sequence. Upon completion of CHEM 103, students are eligible to go directly to CHEM 131 - Organic Chemistry Principles and CHEM 140 - Analytical Chemistry , thereby accelerating their program in chemistry by one semester and allowing for additional elective courses during their junior and senior years. Topics include atomic and molecular structure, geometry, bonding, reactions, equilibria, thermodynamics, acids and bases, basic kinetics and stoichiometry.
Prerequisites: Permission of instructor.
Course Designation/Attribute: SP
Anticipated Terms Offered: Offered every fall
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CHEM 131 - Organic Chemistry Principles
This course introduces students to the chemistry of carbon-based molecules. This family of molecules is broad and diverse, as it includes the molecules of natural biochemistry, synthetic materials, modern medicine, nutrition, and much more. Major topics include foundational knowledge of molecular structures, observable properties, analytical methods, chemical reactivity, and the relationships between these topics. As an intermediate-level natural science course, this course challenges students to become stronger thinkers and stronger students by improving their analytical and critical thinking skills and by becoming more proactive and engaged as learners. The course includes a weekly lab period.
Prerequisites: CHEM 102 , CHEM 103 or advanced placement
Anticipated Terms Offered: Offered every year
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CHEM 132 - Organic Chemistry in Depth
This advanced/intermediate-level course completes the American Chemical Society’s expectations for the organic chemistry portion of an ACS-certified chemistry degree. The course builds upon the foundational material and skills from the organic chemistry principles course by focusing on examples of molecular structures, analytical methods, and reactions that are more complex and more powerful than those seen before. Students will be challenged to incorporate together a large amount of organic chemistry material (from both courses) and to use that material to synthesize solutions to complex problems. The course includes a weekly lab period. Prerequisites: CHEM 131 with C- minimum grade.
Prerequisites: CHEM 131 with C- minimum grade
Anticipated Terms Offered: Offered every year
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CHEM 140 - Analytical Chemistry
This course introduces modern methods of quantitative analysis. Topics include UV-Vis spectroscopy, fluorescence spectroscopy, electrochemistry, separation methods, experimental error and uncertainty, acid-base equilibria, and fundamental analytical laboratory techniques. Must register for lab.
Prerequisites: CHEM 102 or CHEM 103
Anticipated Terms Offered: n/a
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CHEM 199 - Introduction to Research
For students seeking and introduction to laboratory experience in chemistry research. Involves participation in an ongoing laboratory research project. This course is strongly encouraged in order to participate in a laboratory based directed study (CHEM 299 ) or honors (CHEM 297 ). A quarter credit or half credit can be earned with this course. May be repeatable for credit.
Prerequisites: CHEM 103 or CHEM 131 or CHEM 140
Anticipated Terms Offered: Offered every semester
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CHEM 236 - Organometallic Chemistry
Covers material related to compounds containing one or more covalent metal-carbon bonds. The material progresses from the traditional organometallics, such as Grignards and cuprates, through the transition metal and main group complexes. Emphasis is placed on the properties of organometallic compounds and mechanisms of their formation and subsequent reactions. Because of the continuing development of the field, use of the primary literature is stressed. A comparison of traditional organic and inorganic chemistry is developed through this intermediate field.
Prerequisites: CHEM 132 and CHEM 250 or permission of instructor. Chem 250 may be taken as a co-requisite
Anticipated Terms Offered: Offered every other year
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CHEM 250 - Inorganic Chemistry
Deals with theories of structure and bonding and their utility in explaining the chemistry of inorganic substances, especially compounds of transition metals. Topics include: molecular orbital, valence bond, and crystal field theories of bonding and examples of the use of theories in explaining the structure and reactivities of inorganic molecules; acid base theory; spectroscopic methods; and kinetics. Emphasis is placed on the interpretation of structure and reactivity in terms of basic molecular and atomic parameters. In-class and final exams, laboratory reports.
Prerequisites: CHEM 131 and CHEM 132 or CHEM 140 or BCMB 271
Anticipated Terms Offered: Offered every year
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CHEM 256 - Inorganic Materials
Deals with structure-property relationships in inorganic materials. The range of topics includes a survey of the factors controlling structure, lattice energy, prominent structure types and variations in properties as a function of composition. Discussion of analysis methods, synthesis and the prominent uses of these materials will be incorporated into the course.
Prerequisites: Pre- or corequisite: CHEM 250 or CHEM 260 or PHYS 131 , or permission of instructor.
Anticipated Terms Offered: Offered every other year
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CHEM 258 - Crystallography, Diffraction, and Scattering Methods
This course will examine the determination of structure in biochemical, inorganic, and organic materials through diffraction methods. The effects of scattering on matter and symmetry in solids will be explored. Diffraction and scattering techniques used to characterize non-crystalline materials or measure and characterize dynamics in materials, such as small angle scattering and quasi-elastic neutron scattering, will also be covered.
Prerequisites: CHEM 260 or PHYS 131 , or permission.
Anticipated Terms Offered: Offered every other year.
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CHEM 260 - Physical Chemistry I
CHEM 260 covers thermodynamics and kinetics. Topics include the gas law, kinetic theory of gases, the laws of thermodynamics, Gibbs and Helmholtz energies and their applications, electrolyte and nonelectrolyte solutions, phase equilibria, chemical equilibria, and chemical kinetics.
Prerequisites: CHEM 131 or CHEM 140 and MATH 121 or MATH 125
Anticipated Terms Offered: Offered every year
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CHEM 262 - Physical Chemistry II
CHEM 262 covers basic principles of quantum mechanics and their application for understanding fundamental aspects of atomic structure and molecular bonding as well as spectroscopy.
Prerequisites: CHEM 260 .
Anticipated Terms Offered: Offered every year
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CHEM 281 - Polymer Science
This course is designed as an introduction to polymer science, incorporating previous knowledge from organic chemistry, basic inorganic chemistry and physical chemistry to illustrate the key aspects governing the structure-property relationships of macromolecules. An overview of both traditional and state of the art polymer synthesis and polymer characterization techniques will be provided. Several examples from primary scientific literature will serve to integrate the concepts covered in class and will expose the student to relevant technological advances that rely heavily on polymer science. This course seeks to provide students with a broad perspective on how chemistry can be used as the primary tool for developing new materials or modifying existing polymer systems to achieve specific performance targets.
Prerequisites: CHEM 132 or CHEM 134 , CHEM 260 (or BCMB 264 ) or permission of instructor.Completion of CHEM 231 , CHEM 250 and CHEM 262 are recommended, but not required for graduate students.
Anticipated Terms Offered: Offered periodically
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CHEM 283 - Polymeric Biomaterials
This course is designed to provide chemists and biochemists with a basic knowledge of polymer synthesis and structure property relationships, primarily focused on using synthetic strategies to control the structure and architecture of biomaterials. An overview of polymer synthetic routes and fabrication techniques utilized in biomedical engineering will be provided. Drug delivery systems, tissue engineering scaffolds, biodegradable and biocompatible implants will be used as model systems to explore the process of biomaterial design from synthesis to end applications. The main goal of this course is to provide students a set of chemical tools for the development of new biomaterials or the modification of existing polymer systems to achieve design targets. A design project will be utilized to engage students in their own research interests through the application and integration of the course material.
Prerequisites: CHEM 132 , CHEM 260 (or BCMB 264 ) or permission of instructor. This course assumes basic knowledge of organic chemistry, biology, thermodynamics and biochemistry. Completion of CHEM 231 , CHEM 250 , and CHEM 262 are recommended but not required for graduate students.
Anticipated Terms Offered: Offered periodically
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CHEM 285 - The Chemistry of Materials that Store Energy
Establishing zero-carbon societies is of paramount importance for our planet’s future and will require developing superior energy storage technologies. In this course, students will explore the chemistry of materials that store energy. Students will discover the multiple roles that nanostructured transition metal complexes, carbon allotropes and conducting polymers play in electrochemical capacitors and batteries. The fundamental chemical concepts that dictate electronic, capacitive and pseudocapacitive behavior of materials will be studied. This course strives to pinpoint chemical fundamentals by describing connections between molecular structure and charge transfer events responsible for energy storage. Characterization of materials via spectroscopic and electrochemical techniques as well as the fabrication of electrochemical cells will be investigated.
Prerequisites: CHEM 101 , CHEM 102 , or with permission by the instructor
Anticipated Terms Offered: Annually
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CHEM 289 - Research Methods
Deals with the application of analytical tools widely used in the laboratory. Topics include NMR, EPR, IR, Raman, UV-visible, mass and fluorescence spectroscopy, chromatography, electrophoresis, electrochemistry and other techniques. Emphasizes practical knowledge for data interpretation and instrument operation. Quarter-credit courses lasting four to five weeks are offered periodically. Graded as Pass/Fail.
May be repeatable for credit.
Fall 2022 Topic -LEEPING INTO A SCIENTIFIC CAREER - This course is intended for science students interested in learning how to successfully navigate the job market and secure a scientific job after completing their studies at Clark. Topics to be discussed include searching for job postings, having a professional online presence, assembling an application package, how to prepare for an interview, networking, and how to approach and groom your reference letter writers. Guest speakers from different professional scientific backgrounds will join the class to share their career paths. Attendance and class participation are mandatory.
Fall 2022 Topic - HPLC & MASS SPECT - This quarter unit course is a practical, hands-on introduction to using chromatography instruments such as high performance liquid chromatography, liquid chromatography / mass spectrometry, and gas chromatography / mass spectrometry instruments. These methods are widely used throughout both academic and industrial research settings for separating synthetic and biomolecular compounds. The course is intended for graduate students and research active undergraduates in the natural science departments.
SPRING 2022 TOPIC - MEDICINAL CHEMISTRY: This course provides an introduction to the field of Medicinal Chemistry. Students will first learn the basics of the structure of a drug focusing on how it binds to its target. Next, how the body interacts/modifies the drug will be discussed including the identification of liabilities that need to be avoided/minimized which lead to the development of guidelines for drug design. Finally, three medicinal chemistry case studies will be reviewed to provide real life examples of how medicinal chemistry impacts drug discovery.
By permission only. The course is intended for graduate students and research-active undergraduates in any of the natural science departments.
Prerequisites: By permission only.
Anticipated Terms Offered: Offered periodically
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CHEM 298 - Internship
Internships are arranged through the Career Services Office. Students may register under CHEM 298 provided that the Clark internship supervisor is a member of the Chemistry Department. May be repeatable for credit.
Anticipated Terms Offered: every semester
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CHEM 300 - Teaching
For more information please see Departmental Chair. May be repeatable for credit.
Anticipated Terms Offered: Varied
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CHEM 317 - Research
This is a variable unit graduate course for students engaged in research at the PhD level.
Anticipated Terms Offered: Every Semester, including summers
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CHEM 336 - Organometallic Chemistry
Covers material related to compounds containing one or more covalent metal-carbon bonds. The material progresses from the traditional organometallics, such as Grignards and cuprates, through the transition metal and main group complexes. Emphasis is placed on the properties of organometallic compounds and mechanisms of their formation and subsequent reactions. Because of the continuing development of the field, use of the primary literature is stressed. A comparison of traditional organic and inorganic chemistry is developed through this intermediate field.
Prerequisites: CHEM 250 and CHEM 260 or permission of instructor.
Anticipated Terms Offered: Offered every other year
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CHEM 350 - Inorganic Chemistry
Deals with theories of structure and bonding and their utility in explaining the chemistry of inorganic substances, especially compounds of transition metals. Topics include: molecular orbital, valence bond, and crystal field theories of bonding and examples of the use of theories in explaining the structure and reactivities of inorganic molecules; acid base theory; spectroscopic methods; and kinetics. Emphasis is placed on the interpretation of structure and reactivity in terms of basic molecular and atomic parameters. In-class and final exams, laboratory reports.
Anticipated Terms Offered: Varied
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