UC San Diego
Quantitative Biology Ph.D Specialization
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qBio Course Offering for the Ph.D Specialization

The program consists of three main components: theoretical analysis, quantitative measurements, and driving biological questions. For more information about the course requirements see our Program of Study page.

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Foundation of Biomechanics
Modern development of biomechanics at an advanced mathematical level. Description of internal stresses and deformation in living tissues and fluids, thermodynamics. Mechanics of soft connective tissue, extracellular matrix, cells, membranes, and cytoskeleton. Mechanotransduction, migration, adhesion. Blood flow in microvessels. Biomechanical analysis of tissue injury. Students that have taken BENG 222 cannot take BENG 226 for credit.

Course Number: BENG 226
Foundation of Biomechanics
Course Units: 4
Offered: Spring
Molecular imaging and quantitation in living cells
This course will introduce advanced quantitative fluorescence microscopy techniques used for imaging, manipulating, and quantifying the spatiotemporal characteristics of molecular events in live cells. The tentative topics will cover the fundamentals of optics, the concept of confocal microscopy, total internal fluorescence microscopy (TIRF), super-resolution methods (structured illumination, STORM, and PALM), Fluorescence recovery after photobleaching (FRAP), Fluorescence Lifetime Imaging (FLIM), and Forster Resonance Energy Transfer (FRET), imaging acquisition, processing, and segmentation, imaging tracking and cross-correlation analysis, molecular engineering of fluorescent biosensors, optogenetics and molecular actuators, manipulation and quantification of molecular signals in live cells. A laboratory component will be integrated into the course. Students will be organized into small teams to complete projects involving the preparation of cells, the introduction of molecular sensors or immuno-staining of the cells with photoswitchable dyes or fluorescent proteins, and the observation of molecular activities and features under the different imaging modalities of microscopies. The lecture content, wet lab experiments, and imaging acquisition and analysis will be coordinated in time based on different teams.

Course Number: BENG 235
Molecular imaging and quantitation in living cells
Course Units: 4
Offered: Spring
Seminar in Bioengineering
Weekly seminars by faculty, visitors, postdoctoral research fellows, and graduate students concerning research topics in bioengineering and related subjects. May be repeated for credit. Course does not apply toward MS graduation requirements.

Course Number: BENG 281 / BNFO 281
Seminar in Bioengineering
Course Units: 1
Offered: Winter Fall Spring
Introduction to quantitative biology
The goal of this course is to discuss and work through examples where quantitative biology approaches were necessary to yield novel biological insights. Problems will be presented with a historic perspective to instill a philosophy for when, how and why q-bio approaches are most effective. We will discuss q-bio principles governing biological interactions that span across scales: 1) among residues comprising proteins, 2) among genes and proteins comprising gene regulatory networks and 3) cellular and population level interactions. By showing how quantitative approaches reveal common featuresand behaviors that apply across scales, students will be exposed to a path that leads from observation (what?) to an understanding (how?) and ultimately to possible evolutionary principle (why?).

Course Number: BGGN 214
Introduction to quantitative biology
Course Units: 4
Offered: Fall
Graduate Research Seminar
Discussions of recent research in various aspects of biological research conducted by third- and fourth-year doctoral students in the Division of Biological Sciences.

Course Number: BGSE 205
Graduate Research Seminar
Course Units: 1
Offered: Winter Fall Spring
Ethics in Scientific Research
Overview of ethical issues in scientific research, conflicts of interest; national, statewide and campus issues and requirement; ethical issues in publications; authorship; retention of research records; tracing of research records; attribution; plagiarism; copyright considerations; primary, archival and meeting summary publications; ethical procedures and policies; NIH, NSF, California and UC San Diego; case studies and precedents in ethics.

Course Number: BIOM 219
Ethics in Scientific Research
Course Units: 1
Offered: Not Currently Offered
Bioinformatics Students Research Talks
Weekly presentations by Bioinformatics and Systems Biology students about Research Projects that are proposed or completed. Faculty mentors are present to contribute critiques and suggestions.

Course Number: BNFO 283
Bioinformatics Students Research Talks
Course Units: 1
Offered: Winter Fall Spring
Nonlinear Dynamics in Quantitative Biology
Qualitative, analytical and computational mathematical modeling techniques applied to regulatory networks and signaling network. Stability, bifurcations, oscillations, multistability, hysteresis, multiple time-scales, and chaos. Introduction to experimental data analysis and control techniques. Applications to synthetic biology, cellular population dynamics, ad canonical signaling networks (inflammation, tumor suppression, metabolism).

Course Number: BNFO 284
Nonlinear Dynamics in Quantitative Biology
Course Units: 4
Offered: Not Currently Offered
Signaling Circuits in Cells
Modulation cellular activity based on environmental factors involves biochemical signaling circuits that process information received by cellular receptors to controls cellular responses. Several information processing principles are important for the proper function of biochemical signaling networks including signaling dynamic, control of stochasticity, ant network-motifs and feedback structures. This course reviews underlying mechanisms and involves mathematical modeling using personal computer tools.

Course Number: CHEM 220
Signaling Circuits in Cells
Course Units: 4
Offered: Winter
Seminar in Chemistry
Regularly scheduled seminars by first-year graduate students provide opportunities for practice in seminar delivery and for the exploration of topics of general interest.

Course Number: CHEM 250
Seminar in Chemistry
Course Units: 2
Offered: Spring
Biochemistry Seminar
Formal seminars or informal puzzle sessions on topics of current interest in biochemistry, as presented by visiting lecturers, local researchers, or students.

Course Number: CHEM 295
Biochemistry Seminar
Course Units: 2
Offered: Not Currently Offered
Mechanics Inside the Cell
We will study quantitative models that describe the mechanics of processes relevant to eukaryotic cell functions such as cell migration or mechanotransduction. We cover methods to measure mechanical aspects cellular nature and behavior such as intracellular rheology, intracellular force distribution, cell adhesion strength, generation of propulsive forces during locomotion.

Course Number: MAE 263
Mechanics Inside the Cell
Course Units: 4
Offered: Not Currently Offered
Experimental Techniques for Quantitative Biology
A hands-on laboratory course in which the students learn and use experimental techniques, including optics, electronics, chemistry, machining, and computer interface, to design and develop simple instruments for quantitative characterization of living systems. Lab classes will comprise five two-week modules.

Course Number: PHYS 270A
Experimental Techniques for Quantitative Biology
Course Units: 4
Offered: Fall
Quantitative Biology Laboratory
A project-oriented laboratory course in which students will be guided to develop their own ideas and tools, along with using state-of-art instruments to investigate a biological problem of current interest. A range of current topics in quantitative biology are available, including microbiology, molecular and cell biology, developmental biology, synthetic biology, and evolution. These projects (5-week or 10-week long) are designed by QBIO faculties and are based on open research questions. Students will work closely with the sponsoring faculty in the qBio lab space, and will be expected to write a research paper and make verbal presentation. This course may be taken repeatedly for credits as long as students work on different projects.

Course Number: PHYS 270B
Quantitative Biology Laboratory
Course Units: 4
Offered: Winter Fall Spring
Biophysics Seminar
Presentation of current research in biological physics and quantitative biology by invited speakers from the U.S. and abroad.

Course Number: PHYS 254
Biophysics Seminar
Course Units: 1
Offered: Winter Fall Spring
Biophysics Research Talks
Discussion of recent research in biological physics and quantitative biology by current graduate students.

Course Number: PHYS 255
Biophysics Research Talks
Course Units: 1
Offered: Winter Fall Spring
Critical Reading in Quantitative Biology
Critical analysis of classic and current literature in quantitative biology, involving written critiques and group discussion.

Course Number: PHYS 256
Critical Reading in Quantitative Biology
Course Units: 1
Offered: Winter Fall Spring
Fundamentals of Biological Physics
This course teaches how quantitative models derived from statistical physics can be used to build quantitative, intuitive understanding of biological phenomena. This course is different from traditional biology/biophysics courses in that the organizational thread that links various topics of this course is based upon the underlying physics prospective. The idea of two-state variables and the Gibbs distribution will be employed to investigate ion channel gating, phosphorylation, and ligand-receptor binding and cooperativity. Physics of random walks will be used to explore the size of a genome and the geography of chromosomes, DNA looping and gene regulation, the emergence of entropic elasticity, and protein folding. We will examine the microscopic and continuum descriptions of diffusion, the Smoluchowski equation, and discuss diffusion as a transport mechanism and a mechanism for delivering ligands to receptors. The theory of rate equations will be applied to the dynamics of ion channels, enzyme kinetics, cytoskeletal assembly, and the dynamics of molecular motors. The propagation of nerve impulses will be discussed as a problem in biological electricity.

Course Number: PHYS 275
Fundamentals of Biological Physics
Course Units: 4
Offered: Fall
Quantitative Molecular Biology
A quantitative approach to gene regulation including transcriptional and post-transcriptional control of gene expression, as well as feedback and stochastic effects in genetic circuits. These topics will be integrated into the control of bacterial growth and metabolism.

Course Number: PHYS 276
Quantitative Molecular Biology
Course Units: 4
Offered: Winter
Physics of Bacterial Cells
The use of dynamic systems and nonequilibrium statistical mechanics to understand the biological cell. Topics chosen from chemotaxis as a model system, signal transduction networks and cellular information processing, mechanics of the membrane, cytoskeletal dynamics, nonlinear Calcium waves.

Course Number: PHYS 277
Physics of Bacterial Cells
Course Units: 4
Offered: Spring
Information Theory and Pattern Formation
Biological Systems: This course discusses how living systems acquire information on their environment and exploit it to generate structures and perform functions. Biological sensing of concentrations, reaction diffusion equations, the Turing mechanism and applications of information theory to cellular transduction pathways and animal behavior will be presented.

Course Number: PHYS 273
Information Theory and Pattern Formation
Course Units: 4
Offered: Winter
Stochastic Processes in Population Genetics
The course explores genetic diversity within biological populations. Genetics fundamentals, mutation/selection equilibria, speciation, Wright-Fisher model, Kimura’s neutral theory, Luria–Delbrück test, the coalescent theory, evolutionary games and statistical methods for quantifying genetic observables such as SNPs, copy number variations, etc., will be discussed.

Course Number: PHYS 274
Stochastic Processes in Population Genetics
Course Units: 4
Offered: Spring