IQScience1_Sylllabusx - Department of Math & Computer Science

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2 Οκτ 2013 (πριν από 3 χρόνια και 8 μήνες)

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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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Text book

info

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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)