About

Professor Jongyoon Han is a faculty member at the Massachusetts Institute of Technology (MIT), serving as a Professor of Electrical Engineering and a Professor of Biological Engineering. He is the principal investigator of the Micro/Nanofluidic BioMEMS Group within the Research Laboratory of Electronics (RLE) at MIT. His research focuses on developing new tools and technologies for biomolecule separation and analysis using advanced microfluidics and nanofluidics. His work critically depends on understanding biological systems through the analysis of biomolecules and sub-cellular components, with advances in biology often coinciding with breakthroughs in the ability to separate and identify target biomolecules within complex intracellular environments. Professor Han received his B.S. and M.S. degrees from the Department of Physics at Seoul National University in Korea and earned his PhD from the School of Applied and Engineering Physics at Cornell University. Prior to joining the Department of Biological Engineering at MIT, he was a research scientist at Sandia National Laboratories, where he studied protein microfluidic separation systems. His research contributions include developing innovative tools for biomolecule analysis, which are essential for advancing biological understanding and medical applications.

Research topics

• Computer Science
• Physics
• Materials science
• Nanotechnology
• Optics
• Acoustics
• Engineering
• Geology
• Mechanical engineering
• Optoelectronics
• Classical mechanics
• Composite material
• Telecommunications
• Mathematics
• Chromatography
• Chemistry

Selected publications

• Continuous high-throughput microplastic removal using a fully automated self-cleaning benchtop system based on inertial microfluidics: a pilot study

  Journal of Water Process Engineering · 2026-04-03

  article
  PublisherDOI

• A sensitive sample preparation pipeline for adventitious virus detection using Oxford Nanopore sequencing

  Molecular Therapy — Methods & Clinical Development · 2025-04-24

  articleOpen access

  assays used for cell line qualification. Most short-read sequencing assays, however, still require over a week to obtain a final test result since the sequencing must be completed before bioinformatic analysis can begin, which is still too long for some cell and gene therapy products that must be released as soon as possible to reach critically ill patients. Oxford Nanopore sequencing can address these issues, as it provides real-time basecalling and sequence alignment, which can reduce the overall assay time. Still, as with any sequencing platform, the abundance of background nucleic acid from the human or mammalian host can mask the signal from a low-level viral contaminant. To address this, we have developed a sensitive sample preparation workflow using concentration, nuclease treatment, and agnostic PCR methods to eliminate background signals and amplify viral contaminant reads, leading to a 3-log improvement in the limit of detection that is comparable to or better than short-read sequencing approaches. This approach will lead to more rapid and improved detection of viral contaminants in cell and gene therapy manufacturing.

  PublisherDOI

• Thermophilic composting of dewatered sewage sludge under subzero temperatures using a full-scale pre-fermentation reactor: A 10-day valorisation strategy for year-round operation

  Journal of Environmental Management · 2025-11-19

  articleOpen access

  Thermophilic composting of sewage sludge under subzero temperatures remains a significant operational barrier to sustainable waste management. In this study, we report a full-scale composting process that treats 180 t of dewatered sewage sludge per day, achieving complete compost maturation within 10 days, even during freezing winter conditions. The system integrates a pre-fermentation reactor equipped with internal heating and aeration, enabling rapid thermophilic activation and maintaining aerobic stability despite ambient temperatures falling below −1.8 °C. Microbial community profiling revealed structured thermophilic succession even during the winter process, with Ureibacillus , Planifilum , and Mycolicibacterium enriched during peak activity. Short-chain fatty acid analysis indicated rapid acetate degradation during the reactor phase and a transient accumulation of butyrate following raw sludge remixing in winter, suggesting brief anaerobic microenvironments that were quickly resolved under resumed aerobic conditions. All major short-chain fatty acids were depleted by the maturation stage, reflecting a stable and sustained aerobic environment throughout the later composting phases. The final compost satisfied agronomic and safety criteria, including organic matter stabilisation, neutral pH, pathogen elimination, and heavy metal concentrations. These findings demonstrate the feasibility of year-round, thermophilic, and aerobically stable composting of dewatered sewage sludge at industrial scale. Furthermore, by minimizing anaerobic conditions during early decomposition, the system presents a strong potential for methane avoidance. We highlight its applicability as a scalable composting strategy for cold-climate regions, contributing to the development of sustainable sludge valorisation infrastructure within circular bioresource and climate-aligned waste management frameworks. • Industrial-scale composting system processed 180 tons/day of sewage sludge in 10 days, validated year-round. • Pre-fermentation reactor ensured thermophilic activation under subzero winter conditions. • Seasonal runs showed stable aerobic fermetation throughout composting. • Modeled carbon losses showed significant methane mitigation year-round. • Final composts met agronomic NPK and safety standards for soil application.

  PublisherDOI

• Cell trajectory modulation: rapid microfluidic biophysical profiling of CAR T cell functional phenotypes

  Nature Communications · 2025-05-22 · 5 citations

  articleOpen accessSenior author

  Chimeric Antigen Receptor (CAR) T cell therapy is a pivotal treatment for hematological malignancies. However, CAR T cell products exhibit batch-to-batch variability in cell number, quality, and in vivo efficacy due to donor-to-donor heterogeneity, and pre/post-manufacturing processes, and the manufacturing of such products necessitates careful testing, both post-manufacturing and pre-infusion. Here, we introduce the Cell Trajectory Modulation (CTM) assay, a microfluidic, label-free approach for the rapid evaluation of the functional attributes of CAR T cells based on biophysical features (i.e., size, deformability). CTM assay correlates with phenotypic metrics, including CD4:CD8 ratio, memory subtypes, and cytotoxic activity. Validated across multiple donors and culture platforms, the CTM assay requires fewer than 10,000 cells and delivers results within 10 minutes. Compared to labeled flow cytometry processing, the CTM assay offers real-time data to guide adaptive manufacturing workflows. Thus, the CTM assay offers an improvement over existing phenotypic assessments, marking a step forward in advancing CAR T cell therapy manufacturing. CAR T cell manufacturing faces significant challenges that impact cell quality and in vivo efficacy. This necessitates reliable cellular characterization methods. Here the authors present a real-time, label-free, microfluidic method that profiles cellular biophysical properties and correlates them to activation state and CAR T potency, facilitating the rapid phenotypic cell assessment during production.

  PublisherOA PDFDOI

• Whole blood biophysical immune profiling of newborn infants correlates with immune responses

  Pediatric Research · 2025-03-31

  articleOpen accessCorresponding

  BACKGROUND: There is a current, absence of reliable, blood-sparing, diagnostic tools to measure and trend real-time changes in the levels of inflammation and its effects on the immune cells in the infant. METHODS: We deployed the BiophysicaL Immune Profiling for Infants (BLIPI) system in the neonatal intensive care unit to describe immune cell biophysical profiles using 50 microliters of blood per sample from term and preterm infants. RESULTS: A total of 19 infants (8 term, 11 preterm) were recruited and 24 blood samples were collected in their first month. Based on the profiles of immune cells' size and deformation, there was a clear distinction between term and preterm infants, with 48/50 markers significantly different. A preterm infant with late-onset bacterial sepsis had notable size and deformability differences compared to the rest of the preterm cohort. There was a significant correlation between immune cell biophysical profiles and clinical markers such as C-reactive protein, white blood cell counts, and immature-to-total neutrophil (I:T) ratios, with Pearson correlation coefficients for linear regression models of 0.98, 0.97 and 0.94 respectively. CONCLUSION: This study highlights the potential for the biophysical immune cell profiling system to provide an overview of the infant's current immune activation and response. IMPACT: We present a novel, minimally invasive diagnostic system that leverages the physical properties of immune cells to provide a rapid and direct assessment of the immune status, requiring 20 times less blood volume than standard tests. This study demonstrates the potential of a compact, deployable system that is capable of performing biophysical profiling to assess immune cell activation in term and preterm infants, by revealing distinct differences in cell size and deformation between groups. The system's sensitive, quantitative measures were correlated with routine clinical biomarkers, highlighting its ability to provide a rapid, minimally invasive, real-time monitoring of neonatal immune status.

  PublisherOA PDFDOI

• Microfluidics with Machine Learning for Biophysical Characterization of Cells

  Annual Review of Analytical Chemistry · 2025-02-25 · 7 citations

  reviewOpen accessSenior author

  Understanding the biophysical properties of cells is essential for biological research, diagnostics, and therapeutics. Microfluidics enhances biophysical cell characterization by enabling precise manipulation and real-time measurement at the microscale. However, the high-throughput nature of microfluidic systems generates vast amounts of data, complicating analysis. Integrating artificial intelligence (AI) methods, including machine learning and deep learning, with microfluidic technologies addresses these challenges. AI excels at analyzing large, complex datasets, improving the accuracy and efficiency of microfluidic experiments and facilitating new biological discoveries. This review examines the synergy between microfluidics and machine learning for biophysical cell characterization, categorizing existing methods based on the types of input data used for machine learning analysis, highlighting recent advancements, and discussing challenges and future directions in this interdisciplinary field.

  PublisherDOI

• Improved Articular Cartilage Repair With Stratified Zonal Chondrocyte Implantation

  The American Journal of Sports Medicine · 2025-06-12 · 1 citations

  article

  BACKGROUND: The zonal organization of articular cartilage is critical for the biphasic mechanical properties of the tissue. Current treatments for articular cartilage have yet to regenerate this zonal architecture, compromising the functional efficacy of the repaired tissue, which could account for tissue failure in the long term. Autologous chondrocyte implantation (ACI) still suffers from inconsistent efficacy and a long recovery period stemming from implantation of a heterogeneous chondrocyte mixture. HYPOTHESIS: Stratified implantation of zonal chondrocytes would facilitate the recapitulation of articular cartilage zonal properties and improve the repair efficacy of ACI treatment. STUDY DESIGN: Controlled laboratory study. METHODS: Autologous chondrocytes extracted from porcine articular cartilage were subjected to dynamic microcarrier expansion followed by size-based segregation using a spiral microfluidic device for the enrichment of zonal chondrocytes. Zonal chondrocytes were implanted into a chondral defect as a bilayered hydrogel construct consisting of superficial zone chondrocytes overlaying middle/deep zone chondrocytes (n = 6). Twelve months after implantation, the repair efficacy was compared against implantation of full-thickness cartilage-derived heterogeneous chondrocytes expanded on tissue culture plates (n = 5) or microcarriers (n = 6). RESULTS: CT), compression modulus, and surface lubrication analysis, at 12 months demonstrated statistically significant improvement in cartilage and subchondral bone repair with zonal chondrocyte bilayered implantation. Magnetic resonance imaging (MRI) T2 mapping indicated progressive improvement in graft maturation as early as 3 months, reaching normalcy at 9 months. CONCLUSION: This study demonstrates that with appropriate expansion and isolation of zonal chondrocytes, stratified zonal chondrocyte implantation is able to facilitate restoration of articular cartilage zonal architecture and significantly enhance the functional repair as compared with current ACI treatment. CLINICAL RELEVANCE: With appropriate expansion and enrichment of zonal chondrocytes, stratified zonal chondrocyte implantation could represent a significant advancement over current ACI-based cartilage repair, with the potential to support quicker and better recovery.

  PublisherDOI

• Rapid Universal Detection of High‐Risk and Low‐Abundance Microbial Contaminations in CAR‐T Cell Therapy

  Small Methods · 2025-03-30 · 1 citations

  articleOpen access

  Live microbial contamination poses high risks to cell and gene therapies, threatening manufacturing processes and patient safety. Rapid, sensitive detection of live microbes in complex environments, such as CAR-T cell cultures, remains an urgent need. Here, an innovative sample-to-result workflow is introduced using digital loop-mediated isothermal amplification (dLAMP), enhanced by Electrostatic Microfiltration (EM)-based enrichment, for rapid sterility testing. By rationally designing primers targeting 16S and 18S rRNA, dLAMP assay enables both universal detection (covering >80% of known species) and strain-specific identification of bacterial and fungal contaminants in CAR-T cell spent medium and final products, directly from microorganism lysates. Enhanced by EM-based enrichment of low-abundance live microbes, the workflow achieves unparalleled sensitivity and speed, detecting contamination levels as low as 1 CFU/mL in complex CAR-T cell cultures within 6 h. Compared to qPCR and 14-day compendial methods, the approach demonstrates superior accuracy and significantly faster turnaround times. This workflow holds transformative potential for real-time monitoring in cell therapy manufacturing and rapid safety assessments of CAR-T cell products prior to patient infusion. Beyond cell therapy, the method is broadly applicable to infectious disease diagnostics, biomanufacturing monitoring, food safety, and environmental surveillance.

  PublisherOA PDFDOI

• The planarian dorsal–ventral boundary regulates anterior–posterior axis growth and patterning

  PLoS Biology · 2025-11-11

  articleOpen accessCorresponding

  Regeneration can involve the coordination of pattern formation in an outgrowth with the spatial pattern of pre-existing tissues, such as along body axes. Planarian adult axis patterning serves as a robust context for uncovering the mechanisms of such pattern integration. We investigated how the dorsal-ventral boundary (DVB), which surrounds the animal periphery at the dorsal-ventral (DV) median plane, regulates anterior-posterior (AP) axis growth and patterning. We define a spatial DVB gene expression atlas that includes genes encoding signaling, adhesion, and transcription factors. Wnt inhibition results in anterior positional information induction and ectopic head formation that is restricted to the DVB. DVB can be transplanted, and DVB identity can be experimentally induced at ectopic locations. Ectopic DVB is competent for anterior positional identity induction following Wnt inhibition, enabling the generation of animals with ectopic heads at experimentally dictated locations. DVB removal blocks the anteriorization that normally follows Wnt inhibition and prevents anterior positional information expression during head regeneration. Anterior positional information induction at the DVB after Wnt inhibition occurs independently from anterior pole formation, which promotes head patterning in regeneration. Our findings reveal a hierarchical model of pattern integration across body axes in which DV patterning is central by producing a DVB with competence to direct formation of large AP axis regions. This mechanism enables coordination of orthogonal positional information in the context of regeneration.

  PublisherDOI

• Rapid Determination of Iron in Serum and Plasma Using Micromagnetic Resonance Relaxometry (μMRR)

  Analytical Chemistry · 2025-07-02 · 3 citations

  articleSenior authorCorresponding

  Conventional iron determination methods, such as colorimetric assays, often lack sensitivity at low iron levels and are susceptible to interference from complex compositions in serum and plasma. In this study, we developed a rapid, sensitive, and accurate method for iron determination in 1 min utilizing an inexpensive benchtop 0.5-T micromagnetic resonance relaxometry (μMRR) system with acidification treatment of samples (pH < 1). The method yielded a highly linear calibration curve (R2 > 0.999) between the transverse relaxation rate R2 and iron concentration from 0.5 to 1000 μM, with a limit of detection (LOD) of 0.25 μM and a minimal assay volume of 5 μL. The accuracy of this method was validated by inductively coupled plasma mass spectrometry (ICP-MS) across a diverse range of biological samples. This μMRR-based approach offers a rapid and convenient alternative for serum and plasma iron measurements, which can substantially reduce clinical diagnostic time and support real-time iron monitoring for patients.

  PublisherDOI

Recent grants

• NIH Grant R01AI041637

  NIH · $5.1M · 2014

• CAREER: Nanofluidic Molecular Filters

  NSF · $400k · 2004–2009

• Novel Process Analytic Technology for Continuous Bioprocessses

  NIH · $4.8M · 2019–2023

• NIH Grant R21EB008177

  NIH · $185k · 2012

• Science and Engineering of Ion Concentration Polarization and Enhanced Electrokinetic Flow

  NSF · $240k · 2009–2012

Frequent coauthors

• Chwee Teck Lim

  National University of Singapore

  151 shared

• Han Wei Hou

  90 shared

• Ali Asgar S. Bhagat

  National University of Singapore

  70 shared

• Yong‐Ak Song

  58 shared

• Zirui Li

  57 shared

• Leon D. Li

  Massachusetts Institute of Technology

  54 shared

• Hiong Yap Gan

  Singapore Institute of Technology

  43 shared

• Zheng Yang

  43 shared

Education

• Ph.D., Biological Engineering

  Massachusetts Institute of Technology

  2006

• M.S., Biological Engineering

  Massachusetts Institute of Technology

  2002

• B.S., Bioengineering

  University of California, San Diego

  2000