Applied Math & Statistics (AMS)
(Credits/Dept/Course #/Topic)

• 3 AMS 510: Calc/Lin Alg

• 3 AMS 535: Intro Comp Struc Bio

• 3 CSE 549: Comp Bio (Infomatics)

• 3 AMS 599: Research or ESL

• 0-3 AMS 531: Lab Rot*

• 0-1 AMS 532: J Club*

• 0-1 AMS 539: iPQB-Intro Phys Bio*

Biochemistry & Structural Biology (BSB)
(Credits/Dept/Course #/Topic)

• 3 MCB 520: Biochemistry

• 1 MCB 517: Biomembranes

• 1 BSB 515: Comp Method Biochem Struc Bio

• 1 BSB XXX: iQUANT- Quant Bio*

• 1 BSB 509: Colloquium in Biochemistry

• 3-6 BSB 531: Lab Rot*

• 0-1 AMS 539: iPQB-Intro Phys Bio

Year 1, Spring (12 credits)

Applied Math & Statistics (AMS)
(Credits/Dept/Course #/Topic)

• 3 AMS 533: Num Methd Algs CompBio

• 3 XXX XXX: Elective

• 3 AMS 599: Research

• 3 AMS 537: Biology Dyn & Network*

• 0-3 AMS 531: Lab Rot*

• 0-1 AMS 532: J Club (includes ethics)*

• 0-1 PHY 561: iBIO-Intro Bio
  

Biochemistry & Structural Biology (BSB)
(Credits/Dept/Course #/Topic)

• 2 BSB 512: Strc Bio & Spectroscopy

• 1 BSB 602: Colloquium in Biochemistry

• 1-6 BSB 510: Lab Rot

• 1 BSB 532: J Club

• 0 BIO 600: Teaching

• 1-4 MCB 656: Cell Biology (or elec)

   

Year 2, Fall (9 credits)

Applied Math & Statistics (AMS)
(Credits/Dept/Course #/Topic)

• 3 AMS 507: Probability

• 3 PHY 558: Phys Chem & Bio (elect)

• 3 CHE 541: Biochemistry

• 0-1 AMS 532: J Club*

Biochemistry & Structural Biology (BSB)
(Credits/Dept/Course #/Topic)

• 1 BSB 601: Colloquium in Biochemistry

• 1-12 BSB 599: Research

• 0 BIO 600: Teaching

• 3 MCB 503: Mol Genetics (or elec)

• 1 JRN 503: iCOMl-Improv for Sci**

• 3 CHE 558: Phys Chem & Bio (elect)

Year 2, Spring (9 credits)

Applied Math & Statistics (AMS)
(Credits/Dept/Course #/Topic)

• 3 AMS 699 Research

• X XXX XXX Elective

• X XXX XXX Elective

• 3 JRN 565 Communicating your Science

Biochemistry & Structural Biology (BSB)
(Credits/Dept/Course #/Topic)

• 1 BSB 602 Colloquium in Biochemistry

• 1-12 BSB 599 Research

• 1 BSB 532 J Club

• 1-3 XXX XXX Elective

• 0 GRD 500 RCR (or seminar ethics)

• 3 CHE 559 Biology Dyn & Network (elec)

• 1 JRN 501 iCOM2-Distill your Messg**

• 1 JRN 502 iCOM2-Writing Science***

• 3 XXX XXX Elective

• Electives: see BSB handbook
  
  

Electives

Applied Math & Statistics (AMS)
(Credits/Dept/Course #/Topic)

• AMS 530 Parallel Comput (lab, Deng)

• AMS 534 Sys Biology (lab, ***)

• AMS 536 Molec Modeling (lab, Rizzo)

• CHE 538 Statistical Mechanics

• CHE 533 Chemical Thermodynamics

• PHY 558 Phys Chem & Bio (elect)

Note:

*AMS 531 x-listed with PHY 584

*AMS 532 x-listed with PHY 665

*AMS 535 x-listed with CHE 535

*AMS 537 x-listed with CHE 559 & PHY 559

*AMS 539 paperwork submitted

Course Descriptions

AMS 507: Introduction to Probability

The topics include sample spaces, axioms of probability, conditional probability and independence, discrete and continuous random variables, jointly distributed random variables, characteristics of random variables, law of large numbers and central limit theorem, Markov chains.

3 credits, Letter grade

AMS 510: Analytical Methods for Applied Mathematics and Statistics

Review of techniques of multivariate calculus, convergence and limits, matrix analysis, vector space basics, and Lagrange multipliers.

Prerequisite: A course in linear algebra and in multivariate calculus

Fall, 3 credits, Letter grade

AMS 530: Principles in Parallel Computing

This course is designed for both academic and industrial scientists interested in parallel computing and its applications to large-scale scientific and engineering problems. It focuses on the three main issues in parallel computing: analysis of parallel hardware and software systems, design and implementation of parallel algorithms, and applications of parallel computing to selected problems in physical science and engineering. The course emphasizes hands-on practice and understanding of algorithmic concepts of parallel computing.

Prerequisite: A course in basic computer science such as operating systems or architectures or some programming experience.

Spring, 3 credits, Letter grade

AMS 531: Laboratory Rotations and Journal Club in Computational Biology

This is a two-semester course in which first year Ph.D. students spend at least 8 weeks in each of three different laboratories actively participating in the research of participating Computational Biology Faculty. At the end of each rotation, students give a presentation of their lab activates and accomplishments. The primary goal of rotations is to help students choose a research advisor and to help faculty members choose students. Students register for AMS 531 in both the Fall and Spring semesters of the first year.

0-3 credits, S/U grading, may be repeated for credit.

AMS 532: Laboratory Rotations and Journal Club in Computational Biology

The goal of this course is for students to hone critical reading and analytic skills through discussions of literature in the area of Computational Biology. Participants take turn being a "discussion leader" who informally guides the group through a peer-reviewed manuscript for which all Journal Club members will have to read in advance of the meeting. Meetings in the Spring semester will include in Person Training (IPT) in Responsible conduct of Research and Scholarship (RCRS) on topics that comprise (1) Integrity in Scholarship, (2) Scientific Misconduct, (3) Mentoring, (4) Ownership and Authorship, (5) Plagiarism, (6) Data Management, (7) Journalism and Science, (8) Human Subjects, and (9) Laboratory Animals.

0-1 credits, S/U grading, may be repeated for credit.

AMS 533: Algorithms and Model-Making

An in-depth survey of many of the key techniques used in diverse aspects of computational biology. A major focus of this class is on how to successfully formulate a statement of the problem to be solved, and how that formulation can guide in selecting the most suitable computational approach. Examples will be drawn from a wide range of problems in biology, including molecular modeling, biochemical reaction networks, microscopy and systems biology. No prior knowledge of biology is required.

3 credits, Letter grade

AMS 534: Introduction to Systems Biology

This course is geared towards teaching essential concepts and computational skills in Systems Biology. The course is centered upon two key programming languages: Matlab for modeling applications and the R language for statistical analysis and sequence manipulation.

Spring, 3 credits, Letter grade

AMS/CHE 535: Computational Structural Biology

This course will provide an introduction to Computational Structural Biology with application to Drug Design. Methods and applications that use computation to model biological systems involved in human disease will be emphasized. The course aims to foster collaborative learning and will consist of presentations by the instructor, guest lecturers, and by course participants with the goal of summarizing key methods, topics and papers relevant to Computational Structural Biology. This course is offered as both CHE 535 and AMS 535.

Fall, 0-3 credits, Letter grade

AMS 536: Molecular Modeling of Biological Molecules

This course is designed for students who wish to gain hands on experience modeling biological molecules at the atomic level. In conjunction with the individual interests, Molecular Mechanics, Molecular dynamics, Monte Carlo, Docking (virtual screening), or Quantum Mechanics software packages can be used to study relevant biological systems(s). Projects will include setup, execution, and analysis. Course participants will give literature presentations relevant to the simulations being performed and a final project report will be required. Familiarity with Unix (Linux) is desirable.

Spring, 0-3 credits, Letter grade

AMS 537: Dynamical Models of Gene Regulation and Biological Pattern Formation

This is a graduate course in the fundamental theory of genetic function and biological pattern formation in animal development. The course covers dynamical (sometimes called 'physiological') models of these processes at a variety of mathematical levels. Biologically, the emphasis will be on E. coli and the fruit fly Drosophila, with a careful discussion of key experimental results for non-specialists. We will study the use of both deterministic and stochastic differential equations to solve fundamental scientific problems such as the phage lambda lysis/lysogeny decision, the engineering of artificial gene circuits, and the determination and regulation of the morphogenetic field in animal development, particularly the segmentation field in Drosophila.

Spring, 3 credits, Letter grade, x-list with PHY/CHE 559

AMS 539: iPQB-Intro to Physical and Quantitative Biology

This course is a seminar series organized by the Laufer Center for Physical and Quantitative Biology and is aimed at any incoming graduate students who may be interested in doing research in computational, mathematical or physical biology. Each seminar will be given by a different faculty member about their research and will span a range of topics including computational structural biology, genomics/bioinformatics, metabolic and regulatory modeling, computational cell biology and evolutionary models.

Fall, 0-1 credits, S/U grading

AMS XXX: Research or ESL

Fall, 3 credits, Letter grade

BSB 515: Computational Methods in Biochemistry and Structural Biology

Data analysis and statistics using the R programming environment, sequence and graphical analysis of proteins and nucleic acids. Prerequisite: This class is restricted to first year BSB, HBM, MCB PHD, & HBH PhD students. Exception requires approval from the course instructor.

Fall, 1 credit, S/U grading

CHE 504: Structure and Reactivity in Organic Chemistry

Electronic and stereochemical theories relating to organic structure and reactions. Topics such as bonding, strain, aromaticity, MO theory, molecular rearrangements, pericyclic reactions, and photochemistry are covered. This course is intended to provide a foundation of knowledge at the beginning graduate level as preparation for advanced subjects in CHE 502 and CHE 503, and is complementary to CHE 501.

Fall, 3 credits, Letter grade

CHE 523: Chemical Thermodynamics

A rigorous development of the fundamentals of thermodynamics and its application to a number of systems of interest to chemists, such as electrochemical cells, gases, and homogeneous and heterogeneous equilibrium. An introduction to statistical mechanics will also be included.

Fall, 1-3 credits, Letter grade

CHE 528: Statistical Mechanics

Statistical theory of equilibrium systems and rate processes. Ensemble theory, spatial and time correlation functions. Model systems and methods of estimating their properties. Designed to enable the student to use the current literature dealing with application of statistical mechanics to problems in chemistry.

Spring, 3 credits, Letter grade

CHE 541: Biomolecular Structure and Analysis

The structures of biological macromolecules and the relationship of their structure to biological function are described. Methodology employed to study macromolecules is also discussed. Topics include chemical and physical properties of cell and tissue constituents, including carbohydrates, lipids, nucleic acids, proteins and peptides. Prerequisite: Strong foundation in physical and organic chemistry.

Fall, 3 credits, Letter grade

CHE 542: Chemical Biology

The reactivity and physiological function of biological macromolecules and their cofactors are described at the chemical biochemical level. The emphasis of this course reflects recent advances in chemical biology. Possible topics include catalysts, reaction mechanisms, correlation between three-dimensional structure and reactivity, receptor-ligand interactions in extracellular and intracellular signaling, protein folding in vitro and in vivo.

Spring, 3 credits, Letter grade

CHE 543: Chemical Approaches to Biology

The use of molecular concepts and methodology to solve problems in biology and medicine. The course covers methods to elucidate and control biological systems. Possible topics include chemical genomics, metabolomics, and chemotherapeutics.

Prerequisite: CHE 542

Fall, 3 credits, Letter grade

CSE 549: Computational Biology

This course focuses on current problems in computational biology and bioinformatics. Our emphasis will be algorithmic, on discovering appropriate combinatorial algorithm problems and the techniques to solve them. Primary topics will include DNA sequence assembly, DNA/protein sequence assembly, DNA/protein sequence comparison, hybridization array analysis, RNA and protein folding, and phylogenic trees.

Prerequisite: CSE 373 or CSE 548; or consent of instructor

Fall, 3 credits, Letter grade

BME 558/CHE 558/PHY 558: Physical and Quantitative Biology

This is a course on the quantitative principles of physical biology. We describe the nature of the forces and energies and entropies that drive molecular and cellular systems toward their states of equilibrium. We consider a broad range of applications throughout chemistry, biology, materials engineering and nanoscience. This course aims to give students an understanding of how the actions and behaviors of materials and biological systems arise from their constituents (atoms, molecules or cells). Topics of this course include but are not limited to: Time and space in cells; Structural basis of biology; Molecular solvation and lattice models; Chemical potential; Diffusion; Mass action and stochastic chemical kinetics; Electrostatics, potentials, dipoles, electrochemical potentials; Poisson-Boltzmann and Born models; Intermolecular potentials and force fields; Phase transitions; Lattice and Ising models; Adsorption; Binding polynomials; Binding cooperativity; Molecular machines; Molecular motors, energy conversion and transduction; Polymer theory; Flory-Huggins; Random flights; Elasticity; Helix-coil theory; Collapse transitions; Protein folding equilibria; Protein folding kinetics; Sequence space; Protein evolution; Protein elasticity and biological mechanics of proteins; Biophysics of the cell; Proteome stabilities, aggregation, kinetics; Gene regulation; Population and evolutionary dynamics.

Fall, 3 credits, Letter grade

CHE 559/PHY 559: Systems Biology and Network Dynamics

This course gives the foundations for systems biology. First, we discuss dynamical properties of chemical and biochemical networks, particularly in cells. Second, we give a broad introduction to the emerging science of networks including the internet, transportation systems, social nets such as Facebook, networks of disease propagation and others. We apply the principles learned on those systems to the networks of biochemical reactions in cells. Our aim is to prepare students to better understand the properties of cells and the principles for drug discovery of the future. Topics of this course include but are not limited to: Physical kinetics; Diffusion/ Smoluchowskii; Random flights; Waiting times; Poisson; Brownian ratchets; Chemical kinetics; Transition states; Stability, bifurcations, pattern development; Noise in cells: intrinsic and Extrinsic; Feedback; Biological Oscillators; Recurrence, period doubling, chaos; Networks; Topologies; Degree distribution, betweenness; Models of nets: Erdos-Renyi, scale-free, social, Watts-Strogatz, agents; Robustness, highly-optimized tolerance, bowties, epidemics; Biological networks: Protein-protein nets, regulatory and metabolic nets; Known biological circuits and their behaviors; How networks evolve: Preferential attachment, rewiring; Power laws; Fluxed through networks; Information and communication, entropy; Metabolic flux analysis; Artificial and Natural selection for traits; Darwinian evolution; Population dynamics.

Spring, 3 credits, Letter grade, x-list with AMS 537

CHE 581: Departmental Research Seminar

Meetings in which first-year graduate students learn about the research activities of the departmental faculty.

Fall, S/U grading

CHE 603: Special Topics in Bioorganic Chemistry

The subject matter varies depending on interests of students and faculty. Possible topics include asymmetric synthesis and natural product synthesis.

Fall, 1-3 credits, Letter grade, may be repeated for credit.

CHE 607: Modern Drug Design & Delivery

A seminar course covering modern aspects and approaches to drug design. This course combines presentations by faculty and by industry representatives to provide a cross-disciplinary view of the development of pharmaceuticals.

Fall, 1-3 credits, Letter grade

CHE XXX: Teaching

CHE XXX: Lab Rotation

CHE XXX: Journal Club

CSE 549: Computational Bioinformatics and Genomics

This course focuses on current problems in computational biology and bioinformatics. Our emphasis will be algorithmic, on discovering appropriate combinatorial algorithm problems and the techniques to solve them. Primary topics will include DNA sequence assembly, DNA/protein sequence assembly, DNA/protein sequence comparison, hybridization array analysis, RNA and protein folding, and phylogenic trees.

Prerequisite: CSE 373 or CSE 548; or consent of instructor

Fall, 3 credits, Letter grade

PHY 501: Classical Mechanics

Analytical classical mechanics including Lagrangian and Hamiltonian formulations and the Hamilton-Jacoby theory. Variational principles, symmetries and conservative laws. Selected advanced problems such as parametric and nonlinear oscillations, planetary motion, classical theory of scattering, rigid body rotation, and deterministic chaos. Basic notions of elasticity theory and fluid dynamics.

Fall, 3 credits, Letter grade

PHY 505: Classical Electrodynamics I

Electrostatics and Magnetostatics in vacuum and medium; Green's functions; Maxwell's equations and gauge invariance; Electromagnetic wave propagation; Radiation, scattering, interference, and diffraction; Special relativity; Radiation by relativistic charges; Additional topics as time permits. Three lecture hours plus two recitation hours per week.

Fall, 0-3 credits, Letter grade

PHY 511: Quantum Mechanics I

First course in a two-part sequence. Topics include basic quantum physics and mathematical apparatus; application to one dimensional examples and simple systems. Symmetries, angular momentum, and spin. Additional topics as time permits.

Fall, 3 credits, Letter grade

PHY 512: Quantum Mechanics II

Second course in a two-part sequence, covering variational principles, perturbation theory, relativistic quantum mechanics, quantization of the radiation field, many-body systems. Application to atoms, solids, nuclei and elementary particles, as time permits.

Spring, 3 credits, Letter grade

PHY 540: Statistical Mechanics

Brief review of thermodynamics, principles of physical statistics, systems of non- interacting particles: Boltzmann, Fermi-Dirac, and Bose-Einstein statistics. Applications to ideal gases, electrons and phonons in solids, and black body radiation. Approximate treatment of non-ideal gases. First-order and second-order phase transitions. Ising model, transfer matrix, and renormalization group approach. Fluctuations in thermal equilibrium, fluctuation-dissipation theorem, brief review of non-equilibrium fluctuations. Basic notions of ergodicity, classical and quantum chaos.

Spring, 3 credits, Letter grade

PHY 561: Biology for Physical Scientists

Topics of this course include but are not restricted to: Overview of living things; Six kingdoms, animal phyla. Physiology and organs; Chemistry of life; Noncovalent interactions; Hydrogen bonds; Solvation; Biochemistry: reactions, catalysis, ATP amino acids, nucleic acids, lipids; Cell structures: Nucleus, mitochondria, chromosomes, membranes; Basic paradigm: DNA makes RNA makes protein; How cell machines and circuits work; Cell cycle; The processes of evolution; Genetics and heredity; Diseases: how biological systems fail; How drugs are discovered; Tight-binding inhibitors; Antibodies; Current research: Cell division and cancer, genomics, bioinformatics, high throughput sequencing, systems and synthetic biology.

Spring, 1-3 credits, Letter grade

PHY 584: Rotation in Physical Biology

A two-semester course in which students spend at least 8 weeks in each of three different laboratories actively participating in the research of faculty associated with the Laufer Center. At least one of the rotations must be in experimental physical biology. Participants will give a research talk at the end of each eight week period.

Fall and Spring, 1-3 credits, Letter grade

PHY 600: Practicum in Teaching

This course provides hands-on experience in teaching. Activities may include classroom teaching, preparation and supervision of laboratory experiments, exams, homework assignments, and projects.

Fall and Spring, 0-3 credits, Letter grade, may be repeated for credit.

PHY 665: Journal Club in Physical Biology

Presentation of preliminary research results and current research problems by students and faculty. Required every semester for all graduate students in Physical Biology.

Fall and Spring, 0-1 credits 

XXX XXX: iCOM Communication 

XXX XXX: Research

3 credits