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Author:

Burgard, Anthony P.

Title:

OPTIMIZATION-BASED FRAMEWORKS FOR THE ANALYSIS AND REDESIGN OF METABOLIC NETWORKS

Graduate Program:

Chemical Engineering

Keywords:

metabolic network
stoichiometric modeling
microbial strain design

File:

Download Thesis_Complete.pdf

Committee Members:

Costas D Maranas, Committee Chair/Co-Chair
Andrew Zydney, Committee Member
Darrell Velegol, Committee Member
Reka Z Albert, Committee Member

Author:

Zomorrodi, Ali Reza

Title:

OPTIMIZATION-DRIVEN DESIGN OF SYNTHETIC GENETIC CIRCUITS USING BIOBRICKS

Graduate Program:

Industrial Engineering

Keywords:

Biobrick
MIT registry of standard biological parts
Synthetic genetic circuits
Integer linear programming

File:

Download MS_thesis_Ali_R_Zomorrodi_Final.pdf

Committee Members:

Costas D Maranas, Thesis Advisor/Co-Advisor
Costas D Maranas, Thesis Advisor/Co-Advisor
Soundar Rajan Tirupatikumara, Thesis Advisor/Co-Advisor

Author:

Lehmann, Andreas

Title:

Molecular Design in Chemical and Biological Systems

Graduate Program:

Chemical Engineering

Keywords:

quantum chemistry
molecular design
protein design
protein engineering

File:

Download andreas_thesis.pdf

Committee Members:

Costas D Maranas, Committee Chair/Co-Chair
Margaret K Duda, Committee Member
Kristen Ann Fichthorn, Committee Member
Barbara Jane Garrison, Committee Member

Author:

Varshney, Amit

Title:

Optimization and control of multiscale process systems using model reduction: Application to thin-film growth

Graduate Program:

Chemical Engineering

Keywords:

Carleman Linearization
System Identification
Optimization
Dynamic Optimization
Modeling
Multiscale
Stochastic
Model Predictive Control
Receding Horizon Control
Thin film growth
Epitaxy

File:

Download mythesis.pdf

Committee Members:

Antonios Armaou, Committee Chair/Co-Chair
Costas D Maranas, Committee Member
Ali Borhan, Committee Member
Joan Marie Redwing, Committee Member
Andrew Zydney, Committee Member

Author:

Christensen, Claire Petra

Title:

INFERENCE, SIMULATION, MODELING, AND ANALYSIS OF COMPLEX NETWORKS, WITH SPECIAL EMPHASIS ON COMPLEX NETWORKS IN SYSTEMS BIOLOGY

Graduate Program:

Physics

Keywords:

systems biology
gene regulatory networks
graph theory
networks
disease dynamics
computational modeling

File:

Download Christensen_thesis.pdf

Committee Members:

Reka Z Albert, Committee Chair/Co-Chair
Dezhe Jin, Committee Member
Peter E Schiffer, Committee Member
Costas D Maranas, Committee Member

Author:

Vital-Lopez, Francisco Gamaliel

Title:

DEVELOPMENT OF HYBRID INTRACELLULAR/EXTRACELLULAR MODELS OF BRAIN TUMOR PROGRESSION AND MEDICATION STRATEGIES

Graduate Program:

Chemical Engineering

Keywords:

Modeling
Brain tumor
Angiogenesis
Temozolomide
Chemotaxis
Simulation

File:

Download Vital-Lopez_Dissertation.pdf

Committee Members:

Antonios Armaou, Dissertation Advisor/Co-Advisor
Antonios Armaou, Committee Chair/Co-Chair
Costas D Maranas, Committee Chair/Co-Chair
Ali Borhan, Committee Member
Patrick Cirino, Committee Member
Christine Dolan Keating, Committee Member
Andrew Zydney, Committee Member

Author:

Khoury, George Adeeb

Title:

COMPUTATIONAL DESIGN TO SWITCH PROTEIN COFACTOR SPECIFICITY AND CREATE ENZYMATIC ACTIVITY

Graduate Program:

Chemical Engineering

Keywords:

evolution
protein design
protein engineering
computation
mutagenesis
cofactor

File:

Download thesisdraftfinal.pdf

Committee Members:

Costas D Maranas, Thesis Advisor/Co-Advisor
Costas D Maranas, Thesis Advisor/Co-Advisor

Author:

Moore, Gregory Lee

Title:

Modeling and Optimization in Directed Evolution Protocols and Protein Engineering

Graduate Program:

Chemical Engineering

Keywords:

directed evolution
protein engineering
optimization

File:

Download thesis.pdf

Committee Members:

Costas D Maranas, Committee Chair/Co-Chair
Ali Borhan, Committee Member
Patrick Cirino, Committee Member
Stephen James Benkovic, Committee Member
Andrew Zydney, Committee Member

Author:

Li, Hui

Title:

PROTEIN ENGINEERING OF STRUCTURALLY HOMOLOGOUS PROTEINS

Graduate Program:

Integrative Biosciences

Keywords:

protein evolution
protein engineering
purine biosynthetic pathway
domain swapping
(β/α)8 barrel protein

File:

Download ThesisMaster.pdf

Committee Members:

Stephen James Benkovic, Committee Chair/Co-Chair
Costas D Maranas, Committee Member
Squire J Booker, Committee Member
Ming Tien, Committee Member

Author:

Fazelinia, Hossein

Title:

COMPUTATIONAL DESIGN AND EXPERIMENTAL CHARACTERIZATION OF PROTEINS WITH NOVEL FUNCTIONS

Graduate Program:

Chemical Engineering

Keywords:

OptGraft
Protein engineering
Computational protein design
Enzyme cofactor alteration
IPRO

File:

Download Fazelinia_Dissertation.pdf

Committee Members:

Costas D Maranas, Dissertation Advisor/Co-Advisor
Costas D Maranas, Committee Chair/Co-Chair
Patrick Cirino, Committee Chair/Co-Chair
David D Boehr, Committee Member
Andrew Zydney, Committee Member