Membrane trafficking
Quantitative studies of clathrin-mediated endocytosis and intracellular dynamics.
How cells sense, reshape, and interact with their environment
Welcome to the Intracellular Dynamics Laboratory at The Ohio State University.
Cells are not passive-they constantly feel their surroundings, push and pull on their membranes, and bring in nutrients, signals, and other materials from the outside. We study how these processes work and how they are controlled inside living cells.
To do this, we build new microscopes and analysis tools that let us watch these events unfold in real time. By understanding how cells move, reshape their membranes, and internalize material, we aim to uncover general principles of cell behavior.
By uncovering these mechanisms, we aim to identify new ways to influence cell behavior in disease, including approaches that target how cells respond to their environment.
Interested in our work! We are always looking for highly motivated postdoctoral scholars, graduate students, and undergraduate students with interests in cell biology, physics, or imaging to join our group.
Highlights
Selected visual highlights from the lab's work in endocytosis, mechanobiology, and imaging innovation.
Mechanobiology and disease
How cell mechanics influence signaling, apoptosis, and cancer-related phenotypes.
Imaging innovation
Instrumentation and computational methods for super-resolution and live-cell imaging.
Clathrin coat structure
Studying how coated pits and plaques form, curve, and internalize.
Computational microscopy
Image analysis pipelines that reveal dynamic intracellular organization.
Collaborative lab culture
An interdisciplinary group at the interface of physics and cell biology.
Members
Principal Investigator
B.Sc. Bilkent University, Physics, 2002
Ph.D. University of Illinois at Urbana-Champaign, Biophysics and Computational Biology, 2007
Postdoctoral Training: Harvard Medical School, Immune Disease Institute, 2008-2012
Graduate Students
Emily Chan
Tianyao Wu
Cris Thompson
Valeria Arteaga Muniz
Aritra Mondal
Undergraduate Students
Hermes Hermes
Arvin Alam
Henry Jiang
Alumni
Hirak Basu
Umida Djakbarova, Ph.D.
Marlin Keller
Caleb Smith
Connor Luellen
Yasaman Madraki
Ata Akatay
Jama Hersi
Lauren Riede
Hoda Akl, M.Sc.
Nathan Willy, Ph.D.
Salih Silahli, Ph.D.
Scott Huber, Ph.D.
Joshua P. Ferguson, Ph.D.
Ali Adali, Ph.D.
Farah Hasan
Spencer P. Heidotting
Matthew Webber
Daniel Hoying
Esra Aygun
Sevde Goker
Tugba Atabey
Vannimul Hem
Research
Advanced Microscopy
Our lab develops and applies advanced fluorescence microscopy approaches to study intracellular dynamics with high spatial and temporal resolution. A central goal is to push beyond the diffraction limit while still imaging living cells under physiologically relevant conditions.
We use techniques such as TIRF microscopy, structured illumination microscopy (SIM), and variable-angle illumination to selectively visualize membrane-proximal processes like clathrin-mediated endocytosis. These approaches allow us to resolve nanoscale organization and quantify protein recruitment, assembly kinetics, and structural transitions in real time.
In parallel, we develop computational imaging methods that incorporate deep learning, temporal information, and three-dimensional data to extract super-resolution information from live-cell datasets. This enables us to infer dynamic nanoscale features from limited or noisy data, bridging the gap between high-resolution imaging and fast cellular dynamics.
More recently, we are incorporating machine learning and deep learning methods to analyze high-dimensional imaging datasets. These approaches enable automated feature extraction, prediction of dynamic behaviors from single snapshots, and identification of hidden patterns that are not accessible through traditional analysis.
By integrating optical instrumentation, quantitative analysis, and machine learning, we aim to uncover how molecular-scale events give rise to emergent cellular behaviors in space and time.
Advanced Analytics
Our lab develops quantitative and computational approaches to extract mechanistic insight from complex live-cell imaging data. Because intracellular processes are highly dynamic and heterogeneous, a major focus is on building analysis frameworks that move beyond descriptive imaging toward rigorous, quantitative inference.
We design algorithms to track and analyze large populations of dynamic structures, such as clathrin-coated pits, across space and time. These include particle detection and tracking methods, intensity-based growth-rate analysis, and classification of trajectories into distinct dynamical subpopulations. This allows us to quantify variability in assembly, maturation, and internalization across different cellular conditions.
In addition, we use statistical modeling and data-driven approaches to infer underlying kinetic parameters from imaging data. By combining experimental measurements with analytical and computational models, we aim to link observed fluorescence signals to molecular processes such as adaptor recruitment, curvature generation, and vesicle formation.
Overall, our goal is to transform rich imaging datasets into predictive, mechanistic understanding of cellular processes.
Therapeutics
Our lab explores how cellular mechanics and membrane trafficking can be leveraged to improve therapeutic outcomes, particularly in cancer. A central idea is that the physical state of a cell-its stiffness, membrane tension, and trafficking activity-can directly influence how it responds to external signals, including those from the immune system.
We have shown that perturbing endocytic pathways can sensitize cancer cells to apoptosis by altering receptor availability at the cell surface. By modulating clathrin-mediated endocytosis and related trafficking processes, it is possible to enhance the effectiveness of immune-mediated killing and other therapeutic interventions.
Building on this, we investigate small molecules that act as "mechanosensitizers," shifting the physical and trafficking properties of tumor cells to make them more vulnerable. This includes repurposing clinically relevant compounds that affect cytoskeletal dynamics, membrane tension, or signaling pathways linked to endocytosis.
Our approach integrates biophysics, live-cell imaging, and translational research to identify strategies that complement existing therapies such as immunotherapy. The long-term goal is to develop new treatment paradigms where tuning the mechanical and trafficking state of cells enhances therapeutic efficacy while maintaining safety.
Software
TraCKer
TraCKer is a simple but fast two-dimensional particle tracking program. It uses a threshold determined over a Mexican hat filtered image for detection of fluorescent spots. Detected maxima are then connected in time by linking mutually nearest neighbors.
The required input is the path to the desired movie as a two-dimensional multipage TIFF. The output is saved as a MAT file containing tracked positions and intensities.
Slope Finder
Slope Finder determines clathrin coat growth-rate distributions from intensity traces. It takes the TraCKer intensity output, the movie frame rate, and a global background value for the movie corresponding to a signal with SNR = 1.
The output is a cell array of normalized slope values. Since endpoints are padded with zeros, those zeros should be excluded when forming a proper slope histogram.
Trace Library
createTraceLibrary groups clathrin coat intensity traces into clusters that share similar trace lengths and intensity profiles. Similarity is judged using trace_dist, which generates a distance metric between traces.
Each cluster has an average intensity trace and an associated growth-rate histogram. The cluster can then serve as a library for future comparisons using libraryLookup.
Publications
- Spatial Regulation of Endocytosis and Adhesion Formation Governs Breast Cancer Cell Migration Under Confinement
- Single-image Inference of Clathrin-mediated Endocytosis Dynamics via Deep Learning
- Spatial Regulation of Endocytosis and Adhesion Formation Governs Breast Cancer Cell Migration Under Confinement
- Approaching Maximum Resolution In Structured Illumination Microscopy Via Accurate Noise Modeling
- Targeting Endocytosis to Sensitize Cancer Cells to Programmed Cell Death
- Mechano-inhibition of endocytosis sensitizes cancer cells to Fas-induced Apoptosis
- Endocytosis at Extremes: Formation and Internalization of Giant Clathrin-1 coated Pits Under Elevated Membrane Tension
- De novo Endocytic Clathrin Coats Develop Curvature at Early Stages of Their Formation
- CALM supports clathrin-coated vesicle completion upon membrane tension increase
News & Pictures
2025
Valeria Arteaga-Muniz received the Molecular Biophysics Training Program best oral presentation award. Congratulations Valeria.
Emily Chan received the Biophysics Graduate Program best oral presentation award. Congratulations Emily.
Approaching Maximum Resolution in Structured Illumination Microscopy Via Accurate Noise Modeling is now accepted for publication by NPJ Imaging.
2024
Mechano-inhibition of Endocytosis Sensitizes Cancer Cells to Fas-induced Apoptosis is now accepted for publication in Cell Death and Disease.
Targeting endocytosis to sensitize cancer cells to programmed cell death is now accepted for publication in Biochemical Society Transactions.
2023
Umida Djakbarova has been awarded a Pelotonia Scholars Symposium Award. Congratulations Umida.
Cris Thompson has been awarded a National Society of Black Physicists (NSBP) best poster award. Congratulations Cris.
2022
Emily Chan has been awarded a Biophysical Society Travel Award. Congratulations Emily.
We have raised $1,900 for Pelotonia. Good job team.
Endocytosis at Extremes: Formation and Internalization of Giant Clathrin-coated Pits Under Elevated Membrane Tension is now accepted for publication by Frontiers Molecular Biosciences.
Our Dual-view Inverted Selective Plane Illumination Microscope (diSPIM) is up and running.
Emily Chan has been awarded a Pelotonia Doctoral Fellowship. Congratulations Emily.
See more
2021
De novo Endocytic Clathrin Coats Develop Curvature at Early Stages of Their Formation is now accepted for publication by Developmental Cell.
Farewell lunch for Connor. We wish him all the best at UC Berkeley.
We have raised $2,800 for Pelotonia. Good job team.
CALM supports clathrin-coated vesicle completion upon membrane tension increase is published in Proceedings of the National Academy of Sciences.
Dynamic interplay between cell membrane tension and clathrin-mediated endocytosis is published in Biology of the Cell.
2020
Emily is a Molecular Biophysics Training Program trainee now. Congratulations Emily.
2019
Caught by a pleasant surprise.
Dr. Umida Djakbarova has been awarded a Pelotonia Postdoctoral Fellowship. Congratulations Umida.
Deep learning enables cross-modality super-resolution in fluorescence microscopy is published in Nature Methods.
Scott has defended his dissertation. Congratulations Dr. Huber.
2018
Nathan has defended his dissertation. Congratulations Dr. Willy.
Josh has defended his dissertation. Congratulations Dr. Ferguson.
2017
Comert has received a National Science Foundation Early CAREER Development Award.
Joshua Ferguson has been awarded a Presidential Fellowship. Congratulations Josh.
We are on the cover of Molecular Biology of the Cell.
Nathan gave a platform presentation at the Fourth Midwest Membrane Trafficking and Signaling Symposium.
Our proposal to the Advanced Imaging Center has been accepted. We are going to the Janelia Research Campus.
Our paper Membrane Mechanics Govern Spatiotemporal Heterogeneity of Endocytic Clathrin Coat Dynamics is now accepted by Molecular Biology of the Cell.
Our paper Mechanoregulation of Clathrin-mediated Endocytosis is now accepted by the Journal of Cell Science.
Josh gave a platform presentation at the Biophysical Society Meeting.
2016
Daunorubicin-Loaded DNA Origami Nanostructures Circumvent Drug-Resistance Mechanisms in a Leukemia Model is published in Small.
Our paper Deciphering dynamics of clathrin-mediated endocytosis in a living organism is published in Journal of Cell Biology.
2015
Our paper Asymmetric formation of coated pits on dorsal and ventral surfaces at the leading edges of motile cells and on protrusions of immobile cells is published in Molecular Biology of the Cell.
EtpE Binding to DNase X Induces Ehrlichial Entry via CD147 and hnRNP-K Recruitment, Followed by Mobilization of N-WASP and Actin is published in mBio.
2014
Spencer is accepted for the OSU 2014 Undergraduate Summer Research Scholarship.
2013
Matthew is selected to be a judge at The Ohio Academy of Science's State Science Day, encouraging students to pursue learning in science, engineering, technology, and education.
Our paper Similar uptake but different trafficking and escape routes of reovirus virions and infectious subvirion particles imaged in polarized Madin Darby canine kidney cells is published in Molecular Biology of the Cell.
Our spinning disk head has arrived.
We are now officially culturing Drosophila melanogaster fly stocks and using our spinning-disk and light-sheet microscopy systems to image endocytic dynamics during embryogenesis.
2012
Matthew is awarded a Career Development Grant from the Ohio State University Council of Graduate Students to attend the 2013 annual meeting of the Biophysical Society in Philadelphia, Pennsylvania.
Our paper Dynamics of Intracellular Clathrin/AP1- and Clathrin/AP3-Containing Carriers is published in Cell Reports.
Openings
We are interested in hiring postdoctoral scholars, graduate students, and undergraduate students.
To apply, email Comert with your CV and a short note about your interests.
Location
Physics Research Building, 191 W Woodruff Ave, Columbus, OH 43210