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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:

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:

Ravikirthi, Prabhasa

Title:

CONSTRUCTION OF A GENOME-SCALE ATOM MAPPING MODEL OF E.COLI FOR METABOLIC FLUX ANALYSIS

Graduate Program:

Cell and Developmental Biology

Keywords:

MFA
metabolic flux analysis
isotope mapping models

File:

Download Ravikirthi_MS_Thesis.pdf

Committee Members:

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

Author:

Saha, Rajib

Title:

RECONSTRUCTION OF A GENOME-SCALE METABOLIC MODEL OF MAIZE METABOLISM

Graduate Program:

Chemical Engineering

Keywords:

metabolic model
maize
Genome-scale

File:

Download Saha_MS_thesis_v2.pdf

Committee Members:

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

Author:

Grisewood, Matthew Jeffery

Title:

OptZyme: a computational tool for altering enzymatic specificity

Graduate Program:

Chemical Engineering

Keywords:

beta-glucuronidase
enzyme
redesign
molecular mechanics
OptZyme
transition state analogue
specificity

File:

Download Grisewood_Masters_Thesis.pdf

Committee Members:

Costas D Maranas, Thesis Advisor/Co-Advisor
Michael John Janik, Thesis Advisor/Co-Advisor

Author:

Islam, Mohammad Mazharul

Title:

Metabolic modeling of microbial communities

Graduate Program:

Chemical Engineering

Keywords:

dynamic
microbial communities
modeling
d-OptCom
Uranium reduction
Auxotrophic mutants. metabolic modeling

File:

Download MS_Thesis_Mohammad_Mazharul_Islam.pdf

Committee Members:

Costas D Maranas, Thesis Advisor/Co-Advisor

Author:

Gifford, Nathanael Paul

Title:

Computational Redesign of Acyl-acp Thioesterases for Increased Substrate Specificity

Graduate Program:

Chemical Engineering

Keywords:

Thioesterase
IPRO
Computational
Protein Engineering
Chemical Engineering

File:

Download Masters_Thesis_final.pdf

Committee Members:

Michael John Janik, Thesis Advisor/Co-Advisor
Costas D Maranas, Thesis Advisor/Co-Advisor

Author:

Ghaffari, Soodabeh

Title:

COMPUTATIONAL REDESIGN OF EZYMES AND CHANNEL PROTEINS

Graduate Program:

Chemical Engineering (MS)

Keywords:

computational protein designs
channel proteins
Rosetta
IPRO
enzyme engineering
optmization

File:

Download Soodabeh_Ghaffari_MS.pdf

Committee Members:

Costas D Maranas, Thesis Advisor/Co-Advisor
Scott Thomas Milner, Committee Member
Phillip Savage, Program Head/Chair
Esther Gomez, Committee Member

Author:

Mc Lellan, James

Title:

Engineering a Neural Network-Like Genetic Circuit In Escherichia coli

Graduate Program:

Chemical Engineering (MS)

Keywords:

CRISPRi
Genetic Circuits
Synthetic Biology

File:

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Committee Members:

Phillip Savage, Program Head/Chair
Howard M Salis, Thesis Advisor/Co-Advisor
Costas D Maranas, Committee Member
Esther Gomez, Committee Member

Author:

Shi, Pei

Title:

Study of fluorinated ether-based electrolyte for high-voltage lithium ion batteries and functional porous sulfur cathode for lithium sulfur batteries

Graduate Program:

Chemical Engineering

Keywords:

Lithium ion battery
electrolyte
Lithium sulfur battery
Porous cathode
High voltage electrolyte

File:

Download Thesis-Pei_Shi.pdf

Committee Members:

Donghai Wang, Thesis Advisor/Co-Advisor
Phillip E Savage, Program Head/Chair
Seong Han Kim, Committee Member
Costas D Maranas, Committee Member