Faculty Research Projects

Please select your top 5 projects

(rank 1 to 5 on your application)

Summer 2023 Projects

Acharya
Title: Mechanistic Investigation of Respiration Through the Marine Bacterial Outer Membrane
Project Description: Utilization of multi-heme cytochromes (MHCs) in the “respiration” of anaerobic bacteria makes them attractive candidates for emerging biotechnological applications like bioremediation of contaminated soil, microbe-to-electrode and electrode-to-microbe charge transport (CT) in microbial fuel cells and biofuel production. Therefore, the ability to control the rate of CT to/from redox-active toxins and electrodes will be instrumental for these technologies. Gram-negative anaerobic bacteria’s outer membrane (OM) modulates the CT rates influencing their respiration. We aim to understand the mechanism of “respiration” machinery in anaerobic marine bacteria with an emphasis on the role of the OM. The participant of the REU program will model the OM of the metal-reducing bacteria Shewanella oneidensis, followed by simulating an MHC complex in the OM environment. More details and related publications on MHC are available on our website (www.acharyalab.com).
Atanu Acharya, Ph.D.
Assistant Professor, Dept of Chemistry
Syracuse University
Lab Website: www.acharyalab.com

Bah
Title: Post-translational Control of Intrinsically Disordered Protein Function.
Project Description: Elucidate the structure, dynamics and functions of intrinsically disordered proteins and protein regions (IDPs/IDRs) and their biological regulation by Post-translational modifications. The BahLab is particularly interested in characterizing such regulation at atomic resolution using Nuclear Magnetic Resonance (NMR) spectroscopy and other biophysical tools such as microcalorimetry and fluorescence spectroscopic techniques. A recent and exciting emerging field in the IDP world is the realization that this class of proteins, either alone or in concert with Nucleic acids, can drive phase separation of biomolecules, resulting in the formation of membraneless organelles with extremely high protein concentrations. Such organelles form both within the cytoplasm (e.g. RNA granules) and the nucleus (e.g. nucleolus) as well as in the extracellular matrix (elastin coacervation). The goal of my lab is not only to understand the PTM-mediated conformational transitions (e.g. folded vs. disorder transitions) and/or monomer: phase-separation transitions in specific examples, but to also develop tools/protocols to enable characterization of such properties in other biological systems.
Alaji Bah, Ph.D.
Assistant Professor, Dept of Biochemistry & Molecular Biology
SUNY Upstate Medical University
Lab Website: Faculty Profile | Biochemistry and Molecular Biology | SUNY Upstate Medical University

Finkelstein
Title: Vascularization of 3D Polymer scaffolds
Project Description: Vascularization is a critical challenge for generating functional 3D tissue engineering scaffolds. In collaboration with the Monroe Biomaterials Lab at Syracuse University, we are using a preclinical model to determine if 3D scaffolds made by the Monore Lab promote vascular network formation The vascularization model employs vascular membranes of the developing chicken embryo. Different polymer foams are incubated on the vascular membranes followed by histological evaluation of the resulting scaffolds to see how tissue (and vascular networks) become incorporated with the polymer material. Once the baseline response to a scaffold formulation is known, we can alter the formulation to promote vascularization or use cell-laden scaffolds.
Eric Finkelstein, PhD
Research Assistant Professor, Department of Biomedical and Chemical Engineering, Syracuse University
Syracuse Biomaterials Innovation Facility
Website: https://bioinspired.syr.edu/sbi/

Ma
Title: Integrated data analytics for cardiac organoid physiomics
Project Description: With the advancement of stem cell technology, researchers have developed approaches to use cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) for drug-induced cardiotoxicity. We propose to develop an integrated physiomics analytical platform to establish human cardiomyocyte contractility profile, which can be used to monitor the responsiveness of human cardiomyocytes toward drug treatments. By applying unsupervised learning algorithms to the datasets, we will optimize the clustering model to visualize the difference and relevance of cardiomyocyte contraction profiles under drug treatments, which could facilitate drug development in medicine.
Zhen Ma, Ph.D.
Associate Professor, Department of Biomedical and Chemical Engineering
BioInspired Syracuse: Institute for Material and Living Systems
Lab Website: myheart.syr.edu

Monroe
Title:  Smart Materials for Biomedical Applications
Project Description:  We have developed ‘smart’ polymeric materials with a range of functionalities for wound healing in traumatic wounds, chronic wounds, and Crohn’s fistulas. The desired functions of these materials include blood clotting, degradability, antimicrobial properties, desired cell interactions, and controlled drug delivery. This REU project will focus on incorporation and/or characterization of one or more of these properties with an overall goal of improving healing outcomes. The research will involve a range of skills development, including polymer synthesis, scaffold fabrication, and chemical, physical, and biological characterization of biomaterials. 
Mary Beth Monroe, Ph.D.
Assistant Professor, Department of Biomedical and Chemical Engineering
Syracuse University
Lab Website: https://monroebiomaterials.syr.edu/

Movileanu
Title: Single-molecule detection of proteins using engineered nanopores.
Project Description: This project is aimed at designing, developing, optimizing, and validating bioinspired pore-based nanostructures for detecting proteins at single-molecule precision. These studies will involve techniques of protein engineering and high-resolution electrical recordings through single biological nanopores.
Liviu Movileanu, Ph.D.
Professor, Department of Physics
Syracuse University
Lab Website: http://lmovilea.expressions.syr.edu

Nangia
Title: Treating Alzheimer’s and disease using computational modeling approaches.
Project Description: Finding pathways across biological barriers for delivering life-saving drugs is entering a new era with the rapid advancement of computational resources. Our research group focuses on developing simulation methods to elucidate the interfacial phenomenon associated with biological barriers that play a role in life-threatening diseases such as Alzheimer’s, cancer, and chronic infections. Our goal is to influence this experimentally dominated research field by providing mechanistic, structural, and molecular insights into the barrier functions that were computationally unattainable before our work. In the past few years, we have made breakthroughs in understanding the molecular architecture of the blood-brain barrier and developed strategies to enhance the barrier’s permeability for the treatment of neurodegenerative disease. In the summer, we will perform simulations to investigate the blood-brain barrier and provide a perspective on the treatment of Alzheimer’s disease.
Shikha Nangia, Ph.D.
Associate Professor, Department of Biomedical and Chemical Engineering
Director, NSF Site: Interactive Biomaterials REU Program, Syracuse University
Lab Website: https://multiscale.syr.edu/

Paulsen
Title: Wet-a-materials: Harnessing elasto-capillarity and structural instability to design novel wet metamaterials
Project Description: The ability to fabricate soft structures with precisely controlled geometries has revolutionized materials science by enabling the development of metamaterials. Combining several materials further enhances the ability to design new functionalities, but so far the combination of fluids and elastic solids has remained mostly untapped. Many insects, snails, and even frogs have pads with hierarchical arrays of hairs that allow them to adhere to wet, rough, or mucus-covered surfaces, and some of these biologically-inspired topographies have found use to engineer wet-adhesive surfaces for biomedical technology and climbing robots. Fluids also move in response to elastic deformation, so that structured metamaterials could be used to manipulate fluids. In biology, hairy surfaces are implicated in the efficient drinking of particularly viscous fluids (honey, nectar, etc.) in hummingbirds, bats, and insects. Inspired by these biological examples, this project will work to develop a class of soft textured materials, and study their interactions with liquid droplets, as these materials are bent, stretched, or twisted.
Joseph Paulsen, Ph.D.
Associate Professor, Department of Physics
Lab website: https://paulsengroup.wordpress.com
Syracuse University

Pepling
Title: The Role of Cell Adhesion in Oocyte Development
Project Description: The reproductive lifespan of the mammalian female is determined by the time of birth. Essential for fertility is the establishment of a finite pool of primordial follicles, or oocytes that are surrounded by a layer of somatic cells called granulosa cells. During primordial follicle formation which occurs perinatally, clusters of oocytes separate into individual cells. Cell adhesion molecules are expressed in the mouse ovary during this process. E-cadherin is expressed in oocytes and its proposed role is to keep oocytes in clusters prior to primordial follicle formation. E-cadherin must then be down regulated for primordial follicle formation to occur. To test this idea, function blocking antibodies against E-cadherin will be used in mouse ovary organ culture. After culture, ovaries will be labeled with an oocyte marker and analyzed by confocal microscopy.
Melissa Pepling, Ph.D.
Professor, Department of Biology
Syracuse University
Website: https://thecollege.syr.edu/people/faculty/pepling-melissa-e/

Qin
Title: Biosensing and bioinspired music creation during mycelium growth.
Project Description: As the vegetative part of a fungus, mycelium fibers grow from agricultural wastes and integrate the wastes from pieces to continuous composite materials. Its growth is sensitive to the distribution of nutrition and environmental factors and is regulated by fluid delivery within the fiber network. Using electric sensors and microcontrollers, you will collect electric conductivity data during the mycelium growth. You will use the data and learn a machine-learning method to investigate the correlation between electric signals and environmental factors (e.g., temperature, humidity, and light). You will have the opportunity to use electric signals and artificial intelligence algorithms to create innovative music.
Zhao Qin, Ph.D.
Assistant Professor, Civil and Environmental Engineering
Syracuse University
Lab website: http://zhaoqinresearch.com/

Ren
Title: New antifouling materials to control bacterial biofilm formation.
Project Description: Bacterial colonization of implanted biomaterials causes biofilm formation and drug resistant infections. To address this challenge, the student will work with other team members to engineer novel antifouling materials based on physical and chemical modifications of silicon. Specifically, a new catheter will be engineered with micron-size pillars to prevent bacterial colonization. The student will have an opportunity to learn microfabrication, surface modification, microscopy, bacterial culturing, and imaging analysis.
Dacheng Ren, Stevenson Endowed Professor
Department of Biomedical and Chemical Engineering
Syracuse University
Lab website: https://renlab.syr.edu/

Ross
Title:  Programming Microtubule Materials
Project Description:  Microtubules are structural elements in the cell that give it structure and shape. Self-organizing and self-assembling structures made from these long, rigid rods have formed the basis for many biological materials. Here, we will investigate the ability of liquid phase separated droplets of a microtubule-associated and crosslinking protein from plants, MAP65, to control the size and shape of microtubule organizations. This work will be coupled with theoretical modeling from the Schwarz research group.
Jennifer Ross, Ph.D. 
Professor and Chair, Department of Physics
Syracuse University
Lab website: https://www.rosslabbiophysics.com/

Santangelo
Title: Computation simulations of self-shaping structures
Project Description: Inspired by materials in biology that can change their shape and internal geometry in response to stimuli, we will study how to design structures whose mechanical properties can be tuned by an external stimulus. The project is purely computational; we will perform numerical simulations of model stimuli-responsive structures to learn how to design them to realize desired target properties. We are a theoretical physics group that studies materials geometry – materials whose properties are governed by and can be understood through their geometry. Students will have the opportunity to learn scientific computing and get exposure to the ways we think about modern, soft materials. Designing new materials from first principles is a rapidly expanding area of interest with countless potential applications, and theoretical opportunities for undergraduates are still rare. There will also be opportunities for 3D printing to verify models for interested students.
Christian Santangelo, Ph.D.
Professor, Department of Physics
Syracuse University
Lab website: cdsantan.expressions.syr.edu

Wang
Title: Design, manufacturing, and testing of pyrolytic carbon fiber lattice structures (On-campus only)
Project Description: The recent advances in additive manufacturing techniques have allowed structures with complex geometries to be directly printed with high precision. Lattice structures are among one of such structures, which were shown to provide significant weight savings and outstanding mechanical properties, such as high compressive strength, fracture toughness, and impact resistance. Pyrolytic carbon fiber lattice structures are lattice structures that are comprised of 3D interconnected pyrolytic carbon fiber networks. They can be manufactured by 3D printing the polymer lattice structures first, followed by pyrolyzing the polymer structures under high temperatures. However, currently, there are still many challenges exist in developing such structures, including ensuring the geometric accuracy during the printing step, avoiding warpage during the pyrolyzing step, and determining the accurate volume shrinkage before and after the pyrolyzing step. To address these challenges, this project aims to design and manufacture such pyrolytic carbon fiber lattice structures and identify optimum set of printing parameters for 3D printing step and the processing parameters for the pyrolyzing step (e.g., heating cycle, gas flow rate) through the design-of-experiments method. Moreover, this project will also investigate the compressive strength of the manufactured lattice structures and its dependence on the printing and processing parameters. The obtained compressive strengths will also be compared with those of the traditional non-lattice structures. This project will provide guidance in designing and manufacturing pyrolytic carbon fiber lattice structures for engineering applications, such as building, infrastructure, aerospace, marine, and energy structures.
Yeqing Wang, Ph.D.
Assistant Professor, Mechanical and Aerospace Engineering
Syracuse University
Lab website: http://composites.syr.edu/