Chronic viral hepatitis:
Human Disease and Animal Models
Arlin Rogers
MIT Division of Comparative Medicine
BE.450 April 20, 2005
Hepatitis viruses
HAV: Acute gastroenteritis and/or hepatitis
HBV: Acute or chronic hepatitis; significantly
increases ris
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
Professor Jacob K. White
20
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
P
Problem Set 4
Issued:
03/10/06
Due:
03/17/06
100 points total
20.462J/3.962J
Spring 2006
1. Physically associating polymers are used as drug carriers, tissue bulking agents, and cell
delivery scaffolds.
a. Explain why physical hydrogels are most often for
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
Professor Jacob K. White
20
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
P
20.462J/3.962J
Spring 2006
Figure removed due to copyright restrictions.
Please see:
Figure 1 in Mason, Mariah N., Andrew T. Metters, Christopher N. Bowman, and
Kristi S. Anseth. "Predicting Controlled-Release Behavior of Degradable
PLA-b-PEG-b-PLA Hydrog
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
Professor Jacob K. White
20
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
P
Problem Set 3
Issued:
03/02/06
Due:
03/09/06
100 points total
20.462J/3.962J
Spring 2006
1. Consider a hydrogel formed by polymerizing acrylate-encapped polylactide-b-poly(ethylene
glycol)-b-polylactide, as illustrated below. The gel will break down to wa
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
Professor Jacob K. White
20
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
P
Problem Set 2 Model Solutions
Issued:
02/23/06
Due:
03/02/06
100 points total
20.462J/3.962J
Spring 2006
1. From the reading for lecture 4 (Kumamoto et al., Nat. Biotech. 20, 64-69 (2002), we saw an
example of how controlled release materials can be app
Problem Set 2
Issued:
02/23/06
Due:
03/02/06
100 points total
20.462J/3.962J
Spring 2006
1. From the reading for lecture 4 (Kumamoto et al., Nat. Biotech. 20, 64-69 (2002), we saw an
example of how controlled release materials can be applied to create v
Problem Set 4 Model Solutions
Issued:
03/10/06
Due:
03/17/06
100 points total
20.462J/3.962J
Spring 2006
1. Physically associating polymers are used as drug carriers, tissue bulking agents, and cell
delivery scaffolds.
a. Explain why physical hydrogels ar
Problem Set 5
Issued:
04/04/06
Due:
04/13/06
100 points total
20.462J/3.962J
Spring 2006
1. (50 points) Compare and contrast a natural extracellular matrix based on collagen fibers with
a synthetic matrix formed by a covalent PEG-based hydrogel containi
7.91 Amy Keating
How do we use computational methods
to analyze, predict, or design
protein sequences and structures?
Theme:
Methods based on physics vs. methods
based on our accumulated empirical
knowledge of protein properties
For a molecular simula
STATISTICAL MECHANICS
BEH.410 Tutorial
Maxine Jonas
February 14, 2003
Why Statistical Mechanics?
Understand & predict the physical properties of
macroscopic systems from the properties of their
constituents
Deterministic approach
- need of 6N coordinates
20
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
Professor Jacob K. White
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
P
7.91 Amy Keating
Comparing Protein Structures
Why?
detect evolutionary relationships
identify recurring motifs
detect structure/function relationships
predict function
assess predicted structures
classify structures - used for many purposes
Algorithms for
Massachusetts Institute of Technology
Biological Engineering Division Department of Mechanical Engineering Department of Electrical Engineering and Computer Science BEH.410/2.798J/6.524J/10.539J Molecular, Cellular & Tissue Biomechanics, Spring 2003 Probl
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
Professor Jacob K. White
20
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
P
Problem Set 5 Model Solutions
Issued:
04/04/06
Due:
04/13/06
100 points total
20.462J/3.962J
Spring 2006
1. (50 points) Compare and contrast a natural extracellular matrix based on collagen fibers with
a synthetic matrix formed by a covalent PEG-based h
Problem Set 1 solutions
Issued:
02/07/06
Due:
02/16/06
10 points/problem
20.462J/3.962J
Spring 2006
1. Listed in the table below are chemical and schematic structures of poly(L-lactide) and a
number of derivatives of this polymer.
a. Using physicochem
MASSACHUSETTS INSTITUE OF TECHNOLOGY
Molecular, Cellular and Tissue Biomechanics
BEH.410 / 2.978J / 6.524J / 10.537J
Problem Set #2
Issued: 2/21/03
Due: 3/5/03 (in class)
Please staple each problem separately as we will have different graders grading
each
6.581J / 20.482J
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor Bruce Tidor
Professor Jacob K. White
6.581J / 20.482J
Foundations of Algorithms and Computational Techniques in Systems Biology
Professor
MASSACHUSETTS INSTITUE OF TECHNOLOGY
Molecular, Cellular and Tissue Biomechanics
BEH.410 / 2.978J / 6.524J / 10.537J
Problem Set #1
Issued: 2/13/03
Due: 2/19/03 (in class)
Please staple each problem separately as we will have different graders grading
eac