Integrated Quantitative Science 1

Lecture 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 lab

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Some part of this score is graded, take-home assignments (collaborative)

Some part are graded take-home exams (non-collaborative)

Lecture Schedule

MWF 10:25 – X, TR 9:45 - X

Date / Topic
Aug 26 / All - 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 2 / LC - Intro to DE’s: rates of change, continuity, limits, derivatives, linearization, numerical methods for DEs
population analysis, regression analysis. Person-Person disease models (5)
Sept 9 / Connections 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 die
Response to infection in the absence of antibiotics
General intro to limits of computing: finite representation (4)
Exam 1 (Thursday, Sept 10) (1)
Sept 16 / 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)
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, energy
ii. Bohr Model of the Atom
a. Electronic Energy Levels & Transitions, Plank’s eqn
iii. 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 Principle
b. Diamagnetism and Paramagnetism
c. Hund’s Rule
v. Aufbau Principle
Sept 23 / CP/MF - Quantum Theory and Electronic Structure of Atoms cont (3)
Periodic Relationships Between Elements (1)
i. Electron Configurations and the Periodic Table
ii. Atomic and Ionic Size
iii. Ionization Energy
iv. Electron Affinity
v. Electronegativity
(significant figures, dimensional analysis, working with units) (1)
Sept 30 / 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 (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 14 / Fall 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 21 / CP/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 28 / BL/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 4 / CP - Chemical Bonding; (1)
i. Lewis Dot Symbols and Ionic Bonding
ii. Covalent Bonding
LC- Taylor polynomial approximations (1)
CP - Chemical Bonding; (3)
iii. Bond Polarities
iv. Lewis Structures and Formal Charges
v. Resonance
vi. Limitations of the Octet Rule
vii. Bond Enthalpy
Nov 11 / CP - 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 regulation
Read the literature or work on a problem on/in antibiotic resistance and relate to what they’ve learned in the semester (4)

Precept Schedule

Tues 1:30 – 2:30

Date / Topic
Aug 25 / Basic CS – objects (work with GUI(Graphical User Interface))
Sept 1 / CS – declarations and assignments
Sept 8 / CS – Strings, binary, ascii
Sept 15 / CS – conditional execution
Sept 22 / CS - looping
Sept 29 / Physics – problem solving related to classical mechanics
Oct 6 / Chem - Introduce MM – have them do a manual calculation of E(MM)
Oct 13 / Fall break (students work PCR tutorial)
Oct 20 / CS – writing methods in general; methods for E(MM)
Oct 27 / CS and Chem - Monte Carlo methods
Nov 3 / Intro to Cloning (options for cloning, specifics on TA cloning)
Nov 10 / CS – intro to bioinformatics
Nov 17 / CS – intro to bioinformatics
Nov 24 / Team work on posters
Dec 1 / Team work on posters

Laboratory Schedule

Thurs 1:30-4:30

Date / Topic
Aug 27 / Measurement of mutation to antibiotic resistance in bacterial populations
Sept 3 / Evaluation of mutation rates in response to antibiotic selection
Sept 10 / Creation of sponge stem cell primmorphs/microbial symbiont tissue cultures treated with multiple antibiotic regimes
Sept 17 / Isolation 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 24 / Creating agent based computer simulations to study the evolution of antibiotic resistance in a hospital population
Oct 1 / Motion, Force, and Newton's Laws – data collection of x(t) and F(t) using harmonic oscillator motion, verifying F=ma, introduction of friction force
Oct 8 / Work and Conservation of Mechanical Energy – emphasize W=f*d, measure F(d), work is the integral of collected data à PE à measure velocity, confirm conservation of E
Oct 15 / Amplification 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 22 / Using the laws of classical physics to model molecular behavior: Introduction to Molecular Mechanics
Oct 29 / Understanding molecular dynamical behavior of antibiotics using Monte Carlo models
Nov 5 / PCR purification and quantification of bacterial 16S rDNA bands and cloning of PCR products
Nov 12 / Plasmid preparations of 16S rDNA clones for DNA sequence analysis; Background work on algorithm used for sequence similarity searching
Nov 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 26 / Thanksgiving Break
Dec 3 / Poster presentations (need to coach them along the way in how to be preparing their poster piece-meal throughout the semester)