John F. Zimmermann
Current Organizations / Institutes
The organizations/institutes from the scholar's latest article
Previous Organizations / Institutes
The organizations / institutes from the scholar's other articles in the past ten years
John F. Zimmermann has a total of 107 co-authors. Here are the top co-authors by number of shared publications:
- Kevin Kit Parker
Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Boston, USA
11 shared publications - Bozhi Tian
The James Franck Institute, University of Chicago, Chicago, USA
8 shared publications - Herdeline Ann M. Ardona
Department of Chemical and Biomolecular Engineering, Samueli School of Engineering, University of California, Irvine, CA 92697, USA
8 shared publications - Qianru Jin
Disease Biophysics Group, John A. Paulson School of Engineering and Applied Science, Harvard University, Boston, MA 02134, USA
7 shared publications - Keel Yong Lee
Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, Republic of Korea
5 shared publications Luke A. MacQueen
Disease Biophysics Group, John A. Paulson School of Engineering and Applied Sciences, Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
4 shared publications
Latest Publications
- 23 February 2026
- Published by Royal Society of Chemistry (RSC) in Lab on a Chip
- Vol. 26 (9) , 2720-2733
Stroke volume analog on a chip – in vitro hydrodynamic model of cardiac pumping efficiency
We demonstrate the use of muscular thin films (MTFs) as a hydrodynamic assay to measure cardiac stroke volume on a chip, and quantify changes in response to ionotropic dosing; helping bridge the gap between in vitro and in vivo measurements.
- 23 February 2026
- Published by Royal Society of Chemistry (RSC) in Lab on a Chip
- Vol. 26 (9) , 2720-2733
Stroke volume analog on a chip – in vitro hydrodynamic model of cardiac pumping efficiency
We demonstrate the use of muscular thin films (MTFs) as a hydrodynamic assay to measure cardiac stroke volume on a chip, and quantify changes in response to ionotropic dosing; helping bridge the gap between in vitro and in vivo measurements.
- 26 February 2025
- Published by American Association for the Advancement of Science (AAAS) in Science Robotics
- Vol. 10 (99) , eadr6472
Bioinspired design of a tissue-engineered ray with machine learning
In biomimetic design, researchers recreate existing biological structures to form functional devices. For biohybrid robotic swimmers assembled with tissue engineering, this is problematic because most devices operate at different length scales than their naturally occurring counterparts, resulting in reduced performance. To overcome these challenges, here, we demonstrate how machine learning–directed optimization (ML-DO) can be used to inform the design of a biohybrid robot, outperforming other nonlinear optimization techniques, such as Bayesian optimization, in the selection of high-performance geometries. We show how this approach can be used to maximize the thrust generated by a tissue-engineered mobuliform miniray. This results in devices that can swim at the millimeter scale while more closely preserving natural locomotive scaling laws. Overall, this work provides a quantitatively rigorous approach for the engineering design of muscular structure-function relationships in an automated fashion.
- 26 February 2025
- Published by American Association for the Advancement of Science (AAAS) in Science Robotics
- Vol. 10 (99) , eadr6472
Bioinspired design of a tissue-engineered ray with machine learning
In biomimetic design, researchers recreate existing biological structures to form functional devices. For biohybrid robotic swimmers assembled with tissue engineering, this is problematic because most devices operate at different length scales than their naturally occurring counterparts, resulting in reduced performance. To overcome these challenges, here, we demonstrate how machine learning–directed optimization (ML-DO) can be used to inform the design of a biohybrid robot, outperforming other nonlinear optimization techniques, such as Bayesian optimization, in the selection of high-performance geometries. We show how this approach can be used to maximize the thrust generated by a tissue-engineered mobuliform miniray. This results in devices that can swim at the millimeter scale while more closely preserving natural locomotive scaling laws. Overall, this work provides a quantitatively rigorous approach for the engineering design of muscular structure-function relationships in an automated fashion.
- Open Access
- 1 December 2023
- Published by AIP Publishing in APL Bioengineering
- Vol. 7 (4) , 046114
Self-organizing behaviors of cardiovascular cells on synthetic nanofiber scaffolds
In tissues and organs, the extracellular matrix (ECM) helps maintain inter- and intracellular architectures that sustain the structure–function relationships defining physiological homeostasis. Combining fiber scaffolds and cells to form engineered tissues is a means of replicating these relationships. Engineered tissues' fiber scaffolds are designed to mimic the topology and chemical composition of the ECM network. Here, we asked how cells found in the heart compare in their propensity to align their cytoskeleton and self-organize in response to topological cues in fibrous scaffolds. We studied cardiomyocytes, valvular interstitial cells, and vascular endothelial cells as they adapted their inter- and intracellular architectures to the extracellular space. We used focused rotary jet spinning to manufacture aligned fibrous scaffolds to mimic the length scale and three-dimensional (3D) nature of the native ECM in the muscular, valvular, and vascular tissues of the heart. The representative cardiovascular cell types were seeded onto fiber scaffolds and infiltrated the fibrous network. We measured different cell types' propensity for cytoskeletal alignment in response to fiber scaffolds with differing levels of anisotropy. The results indicated that valvular interstitial cells on moderately anisotropic substrates have a higher propensity for cytoskeletal alignment than cardiomyocytes and vascular endothelial cells. However, all cell types displayed similar levels of alignment on more extreme (isotropic and highly anisotropic) fiber scaffold organizations. These data suggest that in the hierarchy of signals that dictate the spatiotemporal organization of a tissue, geometric cues within the ECM and cellular networks may homogenize behaviors across cell populations and demographics.
- 1 December 2023
- Published by AIP Publishing in APL Bioengineering
- Vol. 7 (4) , 046114
Open AccessSelf-organizing behaviors of cardiovascular cells on synthetic nanofiber scaffolds
In tissues and organs, the extracellular matrix (ECM) helps maintain inter- and intracellular architectures that sustain the structure–function relationships defining physiological homeostasis. Combining fiber scaffolds and cells to form engineered tissues is a means of replicating these relationships. Engineered tissues' fiber scaffolds are designed to mimic the topology and chemical composition of the ECM network. Here, we asked how cells found in the heart compare in their propensity to align their cytoskeleton and self-organize in response to topological cues in fibrous scaffolds. We studied cardiomyocytes, valvular interstitial cells, and vascular endothelial cells as they adapted their inter- and intracellular architectures to the extracellular space. We used focused rotary jet spinning to manufacture aligned fibrous scaffolds to mimic the length scale and three-dimensional (3D) nature of the native ECM in the muscular, valvular, and vascular tissues of the heart. The representative cardiovascular cell types were seeded onto fiber scaffolds and infiltrated the fibrous network. We measured different cell types' propensity for cytoskeletal alignment in response to fiber scaffolds with differing levels of anisotropy. The results indicated that valvular interstitial cells on moderately anisotropic substrates have a higher propensity for cytoskeletal alignment than cardiomyocytes and vascular endothelial cells. However, all cell types displayed similar levels of alignment on more extreme (isotropic and highly anisotropic) fiber scaffold organizations. These data suggest that in the hierarchy of signals that dictate the spatiotemporal organization of a tissue, geometric cues within the ECM and cellular networks may homogenize behaviors across cell populations and demographics.
- Top Cited Papers
- 27 July 2023
- Published by Springer Nature in Nature Materials
- Vol. 22 (8) , 1039-1046
Fibre-infused gel scaffolds guide cardiomyocyte alignment in 3D-printed ventricles
Hydrogels are attractive materials for tissue engineering, but efforts to date have shown limited ability to produce the microstructural features necessary to promote cellular self-organization into hierarchical three-dimensional (3D) organ models. Here we develop a hydrogel ink containing prefabricated gelatin fibres to print 3D organ-level scaffolds that recapitulate the intra- and intercellular organization of the heart. The addition of prefabricated gelatin fibres to hydrogels enables the tailoring of the ink rheology, allowing for a controlled sol–gel transition to achieve precise printing of free-standing 3D structures without additional supporting materials. Shear-induced alignment of fibres during ink extrusion provides microscale geometric cues that promote the self-organization of cultured human cardiomyocytes into anisotropic muscular tissues in vitro. The resulting 3D-printed ventricle in vitro model exhibited biomimetic anisotropic electrophysiological and contractile properties.
- 27 July 2023
- Published by Springer Nature in Nature Materials
- Vol. 22 (8) , 1039-1046
Top Cited PapersFibre-infused gel scaffolds guide cardiomyocyte alignment in 3D-printed ventricles
Hydrogels are attractive materials for tissue engineering, but efforts to date have shown limited ability to produce the microstructural features necessary to promote cellular self-organization into hierarchical three-dimensional (3D) organ models. Here we develop a hydrogel ink containing prefabricated gelatin fibres to print 3D organ-level scaffolds that recapitulate the intra- and intercellular organization of the heart. The addition of prefabricated gelatin fibres to hydrogels enables the tailoring of the ink rheology, allowing for a controlled sol–gel transition to achieve precise printing of free-standing 3D structures without additional supporting materials. Shear-induced alignment of fibres during ink extrusion provides microscale geometric cues that promote the self-organization of cultured human cardiomyocytes into anisotropic muscular tissues in vitro. The resulting 3D-printed ventricle in vitro model exhibited biomimetic anisotropic electrophysiological and contractile properties.
- Open Access
- 23 May 2023
- Published by AIP Publishing in APL Bioengineering
- Vol. 7 (2) , 026108
Light-triggered cardiac microphysiological model
Light is recognized as an accurate and noninvasive tool for stimulating excitable cells. Here, we report on a non-genetic approach based on organic molecular phototransducers that allows wiring- and electrode-free tissue modulation. As a proof of concept, we show photostimulation of an in vitro cardiac microphysiological model mediated by an amphiphilic azobenzene compound that preferentially dwells in the cell membrane. Exploiting this optical based stimulation technology could be a disruptive approach for highly resolved cardiac tissue stimulation.
- 23 May 2023
- Published by AIP Publishing in APL Bioengineering
- Vol. 7 (2) , 026108
Open AccessLight-triggered cardiac microphysiological model
Light is recognized as an accurate and noninvasive tool for stimulating excitable cells. Here, we report on a non-genetic approach based on organic molecular phototransducers that allows wiring- and electrode-free tissue modulation. As a proof of concept, we show photostimulation of an in vitro cardiac microphysiological model mediated by an amphiphilic azobenzene compound that preferentially dwells in the cell membrane. Exploiting this optical based stimulation technology could be a disruptive approach for highly resolved cardiac tissue stimulation.
- 8 July 2022
- Published by American Association for the Advancement of Science (AAAS) in Science
- Vol. 377 (6602) , 180-185
Recreating the heart’s helical structure-function relationship with focused rotary jet spinning
Helical alignments within the heart’s musculature have been speculated to be important in achieving physiological pumping efficiencies. Testing this possibility is difficult, however, because it is challenging to reproduce the fine spatial features and complex structures of the heart’s musculature using current techniques. Here we report focused rotary jet spinning (FRJS), an additive manufacturing approach that enables rapid fabrication of micro/nanofiber scaffolds with programmable alignments in three-dimensional geometries. Seeding these scaffolds with cardiomyocytes enabled the biofabrication of tissue-engineered ventricles, with helically aligned models displaying more uniform deformations, greater apical shortening, and increased ejection fractions compared with circumferential alignments. The ability of FRJS to control fiber arrangements in three dimensions offers a streamlined approach to fabricating tissues and organs, with this work demonstrating how helical architectures contribute to cardiac performance.
- 8 July 2022
- Published by American Association for the Advancement of Science (AAAS) in Science
- Vol. 377 (6602) , 180-185
Recreating the heart’s helical structure-function relationship with focused rotary jet spinning
Helical alignments within the heart’s musculature have been speculated to be important in achieving physiological pumping efficiencies. Testing this possibility is difficult, however, because it is challenging to reproduce the fine spatial features and complex structures of the heart’s musculature using current techniques. Here we report focused rotary jet spinning (FRJS), an additive manufacturing approach that enables rapid fabrication of micro/nanofiber scaffolds with programmable alignments in three-dimensional geometries. Seeding these scaffolds with cardiomyocytes enabled the biofabrication of tissue-engineered ventricles, with helically aligned models displaying more uniform deformations, greater apical shortening, and increased ejection fractions compared with circumferential alignments. The ability of FRJS to control fiber arrangements in three dimensions offers a streamlined approach to fabricating tissues and organs, with this work demonstrating how helical architectures contribute to cardiac performance.
- Top Cited Papers
- 10 February 2022
- Published by American Association for the Advancement of Science (AAAS) in Science
- Vol. 375 (6581) , 639-647
An autonomously swimming biohybrid fish designed with human cardiac biophysics
Biohybrid systems have been developed to better understand the design principles and coordination mechanisms of biological systems. We consider whether two functional regulatory features of the heart—mechanoelectrical signaling and automaticity—could be transferred to a synthetic analog of another fluid transport system: a swimming fish. By leveraging cardiac mechanoelectrical signaling, we recreated reciprocal contraction and relaxation in a muscular bilayer construct where each contraction occurs automatically as a response to the stretching of an antagonistic muscle pair. Further, to entrain this closed-loop actuation cycle, we engineered an electrically autonomous pacing node, which enhanced spontaneous contraction. The biohybrid fish equipped with intrinsic control strategies demonstrated self-sustained body–caudal fin swimming, highlighting the role of feedback mechanisms in muscular pumps such as the heart and muscles.
- 10 February 2022
- Published by American Association for the Advancement of Science (AAAS) in Science
- Vol. 375 (6581) , 639-647
Top Cited PapersAn autonomously swimming biohybrid fish designed with human cardiac biophysics
Biohybrid systems have been developed to better understand the design principles and coordination mechanisms of biological systems. We consider whether two functional regulatory features of the heart—mechanoelectrical signaling and automaticity—could be transferred to a synthetic analog of another fluid transport system: a swimming fish. By leveraging cardiac mechanoelectrical signaling, we recreated reciprocal contraction and relaxation in a muscular bilayer construct where each contraction occurs automatically as a response to the stretching of an antagonistic muscle pair. Further, to entrain this closed-loop actuation cycle, we engineered an electrically autonomous pacing node, which enhanced spontaneous contraction. The biohybrid fish equipped with intrinsic control strategies demonstrated self-sustained body–caudal fin swimming, highlighting the role of feedback mechanisms in muscular pumps such as the heart and muscles.
- Open Access
Structure-Function in Helical Cardiac Musculature Using Additive Textile Manufacturing
For more than fifty years, it has been hypothesized that the helical alignment of the heart gives rise to its mechanical function. Testing this hypothesis in an engineered environment is difficult, as the fine spatial features and complex three-dimensional (3D) structures of the cardiac musculature are challenging to reproduce using current biofabrication techniques. Addressing this, here we report a new form of additive textile manufacturing, Focused Rotary Jet Spinning (FRJS). FRJS allows for the rapid manufacturing of micro/nanofibers with controlled alignments. Using this method, we manufacture 3D models of the left ventricle, showing that helically aligned scaffolds display increased strain uniformity, axial shortening, cardiac output, and ejection fractions as compared to circumferential models. We then demonstrate how FRJS can enable the assembly of a full-sized model of the human heart’s musculature. This work experimentally confirms that ventricular alignment plays a critical role in ensuring healthy cardiac performance.
Open AccessStructure-Function in Helical Cardiac Musculature Using Additive Textile Manufacturing
For more than fifty years, it has been hypothesized that the helical alignment of the heart gives rise to its mechanical function. Testing this hypothesis in an engineered environment is difficult, as the fine spatial features and complex three-dimensional (3D) structures of the cardiac musculature are challenging to reproduce using current biofabrication techniques. Addressing this, here we report a new form of additive textile manufacturing, Focused Rotary Jet Spinning (FRJS). FRJS allows for the rapid manufacturing of micro/nanofibers with controlled alignments. Using this method, we manufacture 3D models of the left ventricle, showing that helically aligned scaffolds display increased strain uniformity, axial shortening, cardiac output, and ejection fractions as compared to circumferential models. We then demonstrate how FRJS can enable the assembly of a full-sized model of the human heart’s musculature. This work experimentally confirms that ventricular alignment plays a critical role in ensuring healthy cardiac performance.
- Open Access
Prednisolone rescues Duchenne Muscular Dystrophy phenotypes in human pluripotent stem cells-derived skeletal muscle in vitro
Duchenne Muscular Dystrophy (DMD) is a devastating genetic disease leading to degeneration of skeletal muscles and premature death. How dystrophin absence leads to muscle wasting remains unclear. Here, we describe an optimized protocol to differentiate human induced Pluripotent Stem Cells (iPSC) to a late myogenic stage. This allows to recapitulate classical DMD phenotypes (mislocalization of proteins of the Dystrophin-glycoprotein associated complex (DGC), increased fusion, myofiber branching, force contraction defects and calcium hyperactivation) in isogenic DMD-mutant iPSC lines in vitro . Treatment of the myogenic cultures with prednisolone (the standard of care for DMD) can dramatically rescue force contraction, fusion and branching defects in DMD iPSC lines. This argues that prednisolone acts directly on myofibers, challenging the largely prevalent view that its beneficial effects are due to anti-inflammatory properties. Our work introduces a new human in vitro model to study the onset of DMD pathology and test novel therapeutic approaches.
Open AccessPrednisolone rescues Duchenne Muscular Dystrophy phenotypes in human pluripotent stem cells-derived skeletal muscle in vitro
Duchenne Muscular Dystrophy (DMD) is a devastating genetic disease leading to degeneration of skeletal muscles and premature death. How dystrophin absence leads to muscle wasting remains unclear. Here, we describe an optimized protocol to differentiate human induced Pluripotent Stem Cells (iPSC) to a late myogenic stage. This allows to recapitulate classical DMD phenotypes (mislocalization of proteins of the Dystrophin-glycoprotein associated complex (DGC), increased fusion, myofiber branching, force contraction defects and calcium hyperactivation) in isogenic DMD-mutant iPSC lines in vitro . Treatment of the myogenic cultures with prednisolone (the standard of care for DMD) can dramatically rescue force contraction, fusion and branching defects in DMD iPSC lines. This argues that prednisolone acts directly on myofibers, challenging the largely prevalent view that its beneficial effects are due to anti-inflammatory properties. Our work introduces a new human in vitro model to study the onset of DMD pathology and test novel therapeutic approaches.
- 14 April 2020
- Published by Oxford University Press (OUP) in Integrative Biology
- Vol. 12 (3) , 64-79
Human brain microvascular endothelial cell pairs model tissue-level blood–brain barrier function
The blood–brain barrier plays a critical role in delivering oxygen and nutrients to the brain while preventing the transport of neurotoxins. Predicting the ability of potential therapeutics and neurotoxicants to modulate brain barrier function remains a challenge due to limited spatial resolution and geometric constraints offered by existing in vitro models. Using soft lithography to control the shape of microvascular tissues, we predicted blood–brain barrier permeability states based on structural changes in human brain endothelial cells. We quantified morphological differences in nuclear, junction, and cytoskeletal proteins that influence, or indicate, barrier permeability. We established a correlation between brain endothelial cell pair structure and permeability by treating cell pairs and tissues with known cytoskeleton-modulating agents, including a Rho activator, a Rho inhibitor, and a cyclic adenosine monophosphate analog. Using this approach, we found that high-permeability cell pairs showed nuclear elongation, loss of junction proteins, and increased actin stress fiber formation, which were indicative of increased contractility. We measured traction forces generated by high- and low-permeability pairs, finding that higher stress at the intercellular junction contributes to barrier leakiness. We further tested the applicability of this platform to predict modulations in brain endothelial permeability by exposing cell pairs to engineered nanomaterials, including gold, silver–silica, and cerium oxide nanoparticles, thereby uncovering new insights into the mechanism of nanoparticle-mediated barrier disruption. Overall, we confirm the utility of this platform to assess the multiscale impact of pharmacological agents or environmental toxicants on blood–brain barrier integrity.
- 14 April 2020
- Published by Oxford University Press (OUP) in Integrative Biology
- Vol. 12 (3) , 64-79
Human brain microvascular endothelial cell pairs model tissue-level blood–brain barrier function
The blood–brain barrier plays a critical role in delivering oxygen and nutrients to the brain while preventing the transport of neurotoxins. Predicting the ability of potential therapeutics and neurotoxicants to modulate brain barrier function remains a challenge due to limited spatial resolution and geometric constraints offered by existing in vitro models. Using soft lithography to control the shape of microvascular tissues, we predicted blood–brain barrier permeability states based on structural changes in human brain endothelial cells. We quantified morphological differences in nuclear, junction, and cytoskeletal proteins that influence, or indicate, barrier permeability. We established a correlation between brain endothelial cell pair structure and permeability by treating cell pairs and tissues with known cytoskeleton-modulating agents, including a Rho activator, a Rho inhibitor, and a cyclic adenosine monophosphate analog. Using this approach, we found that high-permeability cell pairs showed nuclear elongation, loss of junction proteins, and increased actin stress fiber formation, which were indicative of increased contractility. We measured traction forces generated by high- and low-permeability pairs, finding that higher stress at the intercellular junction contributes to barrier leakiness. We further tested the applicability of this platform to predict modulations in brain endothelial permeability by exposing cell pairs to engineered nanomaterials, including gold, silver–silica, and cerium oxide nanoparticles, thereby uncovering new insights into the mechanism of nanoparticle-mediated barrier disruption. Overall, we confirm the utility of this platform to assess the multiscale impact of pharmacological agents or environmental toxicants on blood–brain barrier integrity.