Integrated Quantitative Science 1
Lecture meets in (regular classroom (with large whiteboard space, try to get 2
nd
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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Grading scheme (exams, labs, HW)
Some part of this score is graded, take

home assignments (collaborative)
Some part are graded take

home exams (non

collaborat
ive)
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 chan
ge, 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 b
y 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 he
althcare 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. Dia
magnetism 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 intermolec
ular 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, electrost
atics, 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 p
roblem, partial derivatives)
mathematica? Connections t
o 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 m
ove/vibrate [students might possibly learn to write
their
own z

matrix; students w
ill 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
–
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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 evol
ution 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
PE
measure velocity, confirm
conservation of E
Oct 15
Amplification of bacterial 16S rDNA from antibiotic treated sponge
primmorph/micro
bial 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 anti
biotics 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 si
milarity 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)
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