Principal Investigator
Dr. Mona Minkara
Mona Minkara, Ph.D.
Assistant Professor of Bioengineering
Affiliated Faculty of Chemistry and Chemical Biology

Dr. Mona Minkara is an Assistant Professor in the Department of Bioengineering and an Affiliate Faculty in the Department of Chemistry and Chemical Biology at Northeastern University. She received her Bachelor of Arts from Wellesley College and her Ph.D. in Chemistry from the University of Florida. Dr. Minkara is the head of the Minkara COMBINE (Computational Modeling for Biointerface Engineering) Lab, which focuses on the study of pulmonary surfactant, a complex protein-lipid substance secreted by the alveoli in the lungs and its potential therapeutic applications in the medical field. Dr. Minkara specializes in using an array of computational tools to apply to biomolecular problems, and her laboratory is developing innovative approaches that combine protein and surfactant modeling to investigate the PS system computationally. As a blind scientist, she is committed to making science more accessible and inclusive through engineering new tools for blind and partially sighted scientists, and she is involved in several projects dedicated to promoting accessibility in STEM fields. The importance of interdisciplinary research is emphasized in her work, which highlights the efficacy of computational methods in drug discovery and elucidating the complexities of the pulmonary surfactant (PS) system.

PhD Students
Deng Li

Deng Li is a first-year Ph.D. student in the Department of Bioengineering. His research focuses on the application of molecular dynamics simulations to explore the molecular mechanisms of the pulmonary surfactant system, particularly those of surfactant protein D (SP-D). In 2020, Deng graduated from the National Taiwan University, having received a Master's degree in Civil Engineering where he investigated the molecular mechanisms of cartilage tissue degradation. He likes climbing mountains and running marathons. He has climbed one-third of the One Hundred Peaks of Taiwan, each of which has an altitude over 3000 meters.

Master's Students
Aastha Mahapatra

Hello! my name is Aastha, and I am pursuing master’s in regulatory affairs at the college of professional studies. I recently joined the Dr. Minkara’s lab as a research assistant. My research mainly focuses on applying the molecular docking analysis technique on pulmonary surfactant proteins to establish a distinction between the binding patterns of these proteins with different molecules. This research will give me a base to expand further and use molecular dynamics to study the molecular level mechanisms of the pulmonary surfactant system, mainly that of pulmonary surfactant A (SP-A). I have completed my bachelor’s degree in pharmacy my concentration being computer aided drug designing from Siksha O Anusandhan University, Bhubaneswar, India. I also like playing basketball and travelling to different places.

Undergraduate Students
Paloma Figueroa

Hi! My name is Paloma and I am a second-year bioengineering student with a concentration in Medical Devices and Bioimaging. I am from Dallas, Texas but originally born in San Juan, Puerto Rico. I have been involved in the COMBINE Lab since September 2021. My research focuses on analyzing the relationship between Mannose Binding Lectin and Tuberculosis using Molecular Dynamics. Outside of the lab, I enjoy music, traveling to new places, and going to the gym!

Amit Shenoy

I love solving puzzles. And I love asking questions. That led me straight to my concentration – Computational Biology (Major: Bioengineering w/ a Minor in Math), and soon after, to the COMBINE Lab. Thrilled to serve as a trainee and grab as much knowledge and ""git gud"" before I start researching! If I'm not in the lab or in class, you'll either find me reading a book (highly recommend the Climate Book by Greta Thunberg), mobile gaming (Brawl Stars fan to this day), or spending time with my friends/family (our go-tos are card games, movies, and Mariokart). I also engage with sustainability, disability, and free software advocacy through Sustainability Committee (SGA), Ambassadors for Change, and GNU@NU! P.S. If you're looking for a reason to join this lab, it's always the right time!!! P.P.S. Mona has a youtube channel called ""Planes Trains and Canes"", I highly recommend watching literally any video, you're guaranteed lots of laughs and a whole lot of perspective 😄

Ann Titus

Hi! My name is Ann Titus and I am a first-year bioengineering major who is planning on concentrating in cell and tissue engineering! I am really looking forward to improving my coding skills and implementing them towards a research purpose. I am from the Boston area but was born in India. Outside of school I am a dancer on the New England Bhangra Club, will be a Residential Assistant in the fall, play the violin and love traveling!

Amanda Ferrante

Hi! I’m Amanda, a rising second-year student, pursuing a major in bioengineering and biochemistry on the pre-med track with a concentration in cell and tissue engineering. I am thrilled to be part of the COMBINE Lab, where I will have the opportunity to delve deeper into the fascinating realms of computational biology and chemistry and their implications in the field of medicine and understanding the pulmonary surfactant system. I’m originally from Long Island, New York. In my free time, I like spending time with friends and exploring Boston. I am eagerly looking forward to the exciting opportunities and experiences that lie ahead.

Emma Colaco

My name is Emma Colaco and I am a third-year Biochemistry and Data Science student from Westborough, MA. I recently joined the COMBINE Lab and after gaining wet lab experience during my cancer biology co-op at Bristol Myers Squibb, I am excited to build my knowledge and skills in computational modeling to better understand the pulmonary surfactant system. Outside of school, I enjoy going to the gym and trying out new cafes around Boston!

Tyler Locke

Tyler was an undergraduate researcher in the COMBINE lab from 2020-2023. During that time, he focused on understanding the lipid-modulating function of surfactant Protein B using comparative modeling and molecular dynamics simulation. He is currently pursuing a phD in Biomedical engineering at Cornell Univeristy, working with novel optical microscopy techniques to study heart disease.

Jake Duffy

My name is Jake, and I’m a computer science and physics student. I grew up about 45 minutes north of Chicago. I’m working on Monte Carlo simulations of pentadecanoic acid (PDA), and I’m excited to be conducting research in computational chemistry as it both applies my computer science curriculum as well as extends my knowledge to a new field.

Rohit Paradkar

Rohit Paradkar is a sophomore at Newton South High School. He’s originally from Colorado Springs, Colorado, and loves to ski and spend time outdoors. He’s very passionate about chemistry, biology, and computer science. He also loves to play tennis and watch football. His work in COMBINE lab deals with molecular docking for SARS-CoV-2 drug discovery.

Lydia Ruffner

Lydia Ruffner is a Postdoctoral Research Associate in the Department of Bioengineering. Her research in the COMBINE lab focuses on exploring the function of proteins in the pulmonary surfactant system such as surfactant protein C (SP-C). She recently defended her PhD from the Department of Chemistry and Chemical Biology at Northeastern University in early 2021. Her dissertation work used enzyme structure to determine the global and local structural differences in dynamics that may lead to the functional characterization of important disease related enzymes in uncharacterized metabolic pathways for pharmaceutical application. She is an alumna of Spelman College (C’14) where she majored in Biochemistry with a minor in Mathematics. Born in a DMV (DC, Maryland and Virginia) native who loves to traveling and enjoys spending times with family and friends.

Carolina Escobar Palacio

Hello! My name is Carolina and I’m a third-year bioinformatics student. I finished high school in 2013 in Medellin, Colombia (where I was also born) and I’ve been living in the U.S. for 6 years now. In the combine lab, I’m using molecular dynamics simulations to study SARS-CoV-2 proteins. I’m very excited about my project as I will be using different concepts of bioinformatics and apply them to such a relevant topic! My long-term goal is to pursue a PhD and do research related to computational chemistry.

Catherine Zhou

Hi! I’m Catherine, and I’m a first-year Chemical Engineering and Biochemistry major pursuing the pre-med track. I’m from the suburbs north of Dallas, TX. I will soon be working on researching the vapor liquid coexistence of pentadecanoic acid and palmitic acid using Monte Carlo Simulations. I am excited to apply my chemical engineering knowledge to real-world research, and to further sharpen my programming skills along the way.

Liam Farley

My name is Liam, I am a senior year chemistry student at Reed College. I am Brazilian-American who loves snowboarding, hiking, and the ocean. I am excited to be expanding my knowledge into the field of biology and developing my computational research skills. Currently, I am using molecular docking and molecular dynamics simulations to study SARS-CoV-2 proteins and identify possible drug leads.