Integrated Quantitative Science 1



Integrated Quantitative Science 1Lecture meets in (regular classroom (with large whiteboard space, try to get 2nd floor near comp res room) and comp res room)Lab meets in physics lab or B201 (genetics lab)Precept meets in physics labAdd Text book infoAdd Grading scheme (exams, labs, HW)Some part of this score is graded, take-home assignments (collaborative)Some part are graded take-home exams (non-collaborative)Lecture ScheduleMWF 10:25 – X, TR 9:45 - XDateTopicAug 26All - Introducing the theme of the course; framing the question (1)AH- Evolution by natural selection and antibiotic resistance, basics of DNA and mutation (2)LC- Intro to DE’s: rates of change, continuity, limits, derivatives (2)Sept 2LC - Intro to DE’s: rates of change, continuity, limits, derivatives, linearization, numerical methods for DEspopulation analysis, regression analysis. Person-Person disease models (5)Sept 9Connections to math – doing something w/agent based (Matt king), dynamics of agents governed by probab or deterministic models, start with deterministic, extend to probabilistic, i.e. using deterministic as a benchmark (Matt worked through a paper by Cooper-Midley&Scott.) Hospital ward, markov dynamics governed interactions between patients and healthcare workers, not too much calc, more probab., role of a weighted dieResponse to infection in the absence of antibioticsGeneral intro to limits of computing: finite representation (4)Exam 1 (Thursday, Sept 10) (1)Sept 16MF - Classical mechanics (physics)- modeling the behavior of antibiotic molecules using intermolecular forces, Hooke’s law, electrostatics, vectors, Newton’s Laws, kinematics, motion, forces, PE, KE (3)CP/MF - Intro to atoms and molecules - focusing on structure of antibiotics: (How do drugs behave?) (2)Quantum Theory and Electronic Structure of Atoms;i. Radiant Energy: wavelength, frequency, energyii. Bohr Model of the Atom a. Electronic Energy Levels & Transitions, Plank’s eqniii. Quantum Mechanical Description of the Atom a. Dual Nature of the Electron b. Quantum Mechanics: Heisenberg Uncertainty Principle c. Quantum Numbers d. Orbital Representation iv. Electron Configuration: Orbital Diagrams & Relative Energies a. Pauli Exclusion Principleb. Diamagnetism and Paramagnetismc. Hund’s Rulev. Aufbau Principle Sept 23CP/MF - Quantum Theory and Electronic Structure of Atoms cont (3)Periodic Relationships Between Elements (1)i. Electron Configurations and the Periodic Tableii. Atomic and Ionic Sizeiii. Ionization Energyiv. Electron Affinity v. Electronegativity(significant figures, dimensional analysis, working with units) (1)Sept 30MF - Classical mechanics (physics)- modeling the behavior of antibiotic molecules using intermolecular forces, Hooke’s law, electrostatics, vectors, Newton’s Laws, kinematics, motion, forces, PE, KE (4)Exam 2 (Thursday, October 1) (1) Oct 7 MF - Classical mechanics (physics)- modeling the behavior of antibiotic molecules using intermolecular forces, Hooke’s law, electrostatics, vectors, Newton’s Laws, kinematics, motion, forces, PE, KE (5)Oct 14Fall Break (2)MF - Classical mechanics (physics)- modeling the behavior of antibiotic molecules using intermolecular forces, Hooke’s law, electrostatics, vectors, Newton’s Laws, kinematics, motion, forces, PE, KE (3)Oct 21CP/BL/LC - Energy surfaces (multivariable geometry, basic functions-math, intro to minimization, intro to multiple minima problem, partial derivatives)mathematica? Connections to QM? (to set up these topics for lab) (4)Exam 3 (Thursday, October 22) (1)Oct 28BL/LC/CP - 2 possible approaches to using E(MM): different minimization algorithms vs sampling methods (Monte Carlo) (the latter being much easier for intro students). (1)CP - Energy surfaces -Small molecule to model behavior (Molecular Mechanics), look at energies of different molecular conformations, visualize slices through PE surface(1)BL - Introduction to analysis of algorithms (multiple ways to approach a problem; computational vs implementation complexity, the “Big Oh” issue (1)CP and BL - Students write code for finding minima, Barry writes routine so that internal coordinate output can be visualized by Maestro GUI; animate snapshots to see dynamics of how they move/vibrate [students might possibly learn to write their own z-matrix; students will use Barry’s routine to understand how the z-matrix variable are converted into a file format.). Find a good (antibiotic?) molecule for this. Advanced data structure.] (2)Nov 4CP - Chemical Bonding; (1)i. Lewis Dot Symbols and Ionic Bondingii. Covalent BondingLC- Taylor polynomial approximations (1)CP - Chemical Bonding; (3)iii. Bond Polaritiesiv. Lewis Structures and Formal Charges v. Resonancevi. Limitations of the Octet Rule vii. Bond Enthalpy Nov 11CP - Molecular Geometry and Hybridization of Atomic Orbitals (4/5)i. Shapes of Simple Molecules; VSEPR Theory ii. Bond Polarity and Molecular Polarity iii. Hybrid Orbitals/Valence Bond Theory iv. MO theory Exam 4 (Thursday, November 12) (1)Nov 18 AH - DNA structure and replication, non-covalent interactions and mutation, Transcription and Translation (3/4)CP - Leads to amino acids, secondary and tertiary structure, structure of proteins (briefly and simply) (1)Nov 25[2 lecture periods this week (off W-F for Thanksgiving)]BL/AH – Evaluation data from bioinformatic searches (1)Exam 5 Activity/Presentation related to lab results on bioinformatics (Tuesday, November 24) (1)Dec 2 BL - Good vs bad algorithms related to sequence comparison, (brute-force vs dynamic programming), scalability (1)AH - Mechanisms of gene regulationRead the literature or work on a problem on/in antibiotic resistance and relate to what they’ve learned in the semester (4)Precept ScheduleTues 1:30 – 2:30DateTopicAug 25Basic CS – objects (work with GUI(Graphical User Interface))Sept 1CS – declarations and assignmentsSept 8CS – Strings, binary, ascii Sept 15CS – conditional executionSept 22CS - loopingSept 29Physics – problem solving related to classical mechanicsOct 6 Chem - Introduce MM – have them do a manual calculation of E(MM) Oct 13Fall break (students work PCR tutorial)Oct 20CS – writing methods in general; methods for E(MM)Oct 27CS and Chem - Monte Carlo methodsNov 3Intro to Cloning (options for cloning, specifics on TA cloning)Nov 10CS – intro to bioinformaticsNov 17 CS – intro to bioinformaticsNov 24Team work on postersDec 1Team work on postersLaboratory ScheduleThurs 1:30-4:30DateTopicAug 27Measurement of mutation to antibiotic resistance in bacterial populationsSept 3Evaluation of mutation rates in response to antibiotic selectionSept 10Creation of sponge stem cell primmorphs/microbial symbiont tissue cultures treated with multiple antibiotic regimes Sept 17Isolation of microbial DNA from sponge primmorphs; preparation of tissue for electron microscopy; extraction of natural products from primmorphs containing different microbial communities (in response to antibiotic treatments) and assay for antimicrobial metabolite production (Post lab: evaluation of bioassay data)Sept 24Creating agent based computer simulations to study the evolution of antibiotic resistance in a hospital populationOct 1Motion, Force, and Newton's Laws – data collection of x(t) and F(t) using harmonic oscillator motion, verifying F=ma, introduction of friction forceOct 8 Work and Conservation of Mechanical Energy – emphasize W=f*d, measure F(d), work is the integral of collected data PE measure velocity, confirm conservation of EOct 15Amplification of bacterial 16S rDNA from antibiotic treated sponge primmorph/microbial populations; Using electron microscopy to look at microbial populations in sponge tissues from various antibiotic treatments; Run PCR products on DGGE and agarose gels (Post lab: Cut out bands unique to a particular antibiotic treatment; possible post lab for students – running EM with Carolyn in the evening – need to check with Carolyn)Oct 22Using the laws of classical physics to model molecular behavior: Introduction to Molecular MechanicsOct 29Understanding molecular dynamical behavior of antibiotics using Monte Carlo modelsNov 5PCR purification and quantification of bacterial 16S rDNA bands and cloning of PCR productsNov 12Plasmid preparations of 16S rDNA clones for DNA sequence analysis; Background work on algorithm used for sequence similarity searchingNov 19 Bioinformatics searches on bacterial sequences and group work on identification of specific bacterial taxa (post-lab – make biological relevance to the bioinformatics and experimental data)Nov 26Thanksgiving BreakDec 3Poster presentations (need to coach them along the way in how to be preparing their poster piece-meal throughout the semester) ................
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