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
Add Text book info
Add 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 Schedule
MWF 10:25 – X, TR 9:45 - X
Date
Aug 26
Sept 2
Sept 9
Sept 16
Topic
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)
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)
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)
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
Sept 30
Oct 7
Oct 14
Oct 21
Oct 28
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)
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)
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)
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)
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)
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
Nov 11
Nov 18
Nov 25
Dec 2
vii. Bond Enthalpy
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)
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)
[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)
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
Aug 25
Sept 1
Sept 8
Sept 15
Sept 22
Sept 29
Oct 6
Oct 13
Oct 20
Oct 27
Nov 3
Nov 10
Nov 17
Nov 24
Dec 1
Topic
Basic CS – objects (work with GUI(Graphical User Interface))
CS – declarations and assignments
CS – Strings, binary, ascii
CS – conditional execution
CS - looping
Physics – problem solving related to classical mechanics
Chem - Introduce MM – have them do a manual calculation of E(MM)
Fall break (students work PCR tutorial)
CS – writing methods in general; methods for E(MM)
CS and Chem - Monte Carlo methods
Intro to Cloning (options for cloning, specifics on TA cloning)
CS – intro to bioinformatics
CS – intro to bioinformatics
Team work on posters
Team work on posters
Laboratory Schedule
Thurs 1:30-4:30
Date
Aug 27
Sept 3
Sept 10
Topic
Measurement of mutation to antibiotic resistance in bacterial populations
Evaluation of mutation rates in response to antibiotic selection
Creation of sponge stem cell primmorphs/microbial symbiont tissue cultures treated
with multiple antibiotic regimes
Sept 17
Sept 24
Oct 1
Oct 8
Oct 15
Oct 22
Oct 29
Nov 5
Nov 12
Nov 19
Nov 26
Dec 3
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)
Creating agent based computer simulations to study the evolution of antibiotic
resistance in a hospital population
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
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 E
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)
Using the laws of classical physics to model molecular behavior: Introduction to
Molecular Mechanics
Understanding molecular dynamical behavior of antibiotics using Monte Carlo
models
PCR purification and quantification of bacterial 16S rDNA bands and cloning of
PCR products
Plasmid preparations of 16S rDNA clones for DNA sequence analysis; Background
work on algorithm used for sequence similarity searching
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)
Thanksgiving Break
Poster presentations (need to coach them along the way in how to be preparing their
poster piece-meal throughout the semester)