Our group's research is focused at the intersection of mechanics and biology. We are interested in elucidating the underlying molecular mechanisms that give rise to the complex mechanical properties of cells, extracellular matrices, and tissues . Conversely, we are investigating how complex mechanical cues influence important biological processes such as cell division, differentiation, or cancer progression. Our approaches involve using force measurement instrumentation, such as atomic force microscopy, to exert and measure forces on materials and cells at the nanoscale, and the development of material systems for 3D cell culture that allow precise and independent manipulation of mechanical properties.

Academic Appointments

Administrative Appointments

  • Member, Bio-X (2013 - Present)
  • Assistant Professor, Department of Mechanical Engineering (2013 - Present)

Honors & Awards

  • Engineering Science Departmental Citation, University of California, Berkeley (2001)
  • Engineering Science Departmental Citation, University of California, Berkeley (2002)
  • Graduate Research Award, Biomedical Engineering Society (2006)
  • National Defense Science and Engineering Graduate Fellow, American Society for Engineering Education (2003 - 2006)
  • National Science Foundation Graduate Fellow, National Science Foundation (2006 - 2009)
  • National Research Service Award, National Institutes of Health (2010 - 2013)
  • Young Faculty Award, DARPA (2014 - 2016)

Professional Education

  • Postdoctoral Fellow, Harvard University, Biomaterials (2013)
  • Ph.D., University of California, Berkeley and San Francisco, Bioengineering (2009)
  • B.S., University of California, Berkeley, Engineering Physics (2003)

2016-17 Courses

Stanford Advisees

All Publications

  • Strain-enhanced stress relaxation impacts nonlinear elasticity in collagen gels PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Nam, S., Hu, K. H., Butte, M. J., Chaudhuri, O. 2016; 113 (20): 5492-5497


    The extracellular matrix (ECM) is a complex assembly of structural proteins that provides physical support and biochemical signaling to cells in tissues. The mechanical properties of the ECM have been found to play a key role in regulating cell behaviors such as differentiation and malignancy. Gels formed from ECM protein biopolymers such as collagen or fibrin are commonly used for 3D cell culture models of tissue. One of the most striking features of these gels is that they exhibit nonlinear elasticity, undergoing strain stiffening. However, these gels are also viscoelastic and exhibit stress relaxation, with the resistance of the gel to a deformation relaxing over time. Recent studies have suggested that cells sense and respond to both nonlinear elasticity and viscoelasticity of ECM, yet little is known about the connection between nonlinear elasticity and viscoelasticity. Here, we report that, as strain is increased, not only do biopolymer gels stiffen but they also exhibit faster stress relaxation, reducing the timescale over which elastic energy is dissipated. This effect is not universal to all biological gels and is mediated through weak cross-links. Mechanistically, computational modeling and atomic force microscopy (AFM) indicate that strain-enhanced stress relaxation of collagen gels arises from force-dependent unbinding of weak bonds between collagen fibers. The broader effect of strain-enhanced stress relaxation is to rapidly diminish strain stiffening over time. These results reveal the interplay between nonlinear elasticity and viscoelasticity in collagen gels, and highlight the complexity of the ECM mechanics that are likely sensed through cellular mechanotransduction.

    View details for DOI 10.1073/pnas.1523906113

    View details for Web of Science ID 000375977600024

    View details for PubMedID 27140623

  • Hydrogels with tunable stress relaxation regulate stem cell fate and activity NATURE MATERIALS Chaudhuri, O., Gu, L., Klumpers, D., Darnell, M., Bencherif, S. A., Weaver, J. C., Huebsch, N., Lee, H., Lippens, E., Duda, G. N., Mooney, D. J. 2016; 15 (3): 326-?


    Natural extracellular matrices (ECMs) are viscoelastic and exhibit stress relaxation. However, hydrogels used as synthetic ECMs for three-dimensional (3D) culture are typically elastic. Here, we report a materials approach to tune the rate of stress relaxation of hydrogels for 3D culture, independently of the hydrogel's initial elastic modulus, degradation, and cell-adhesion-ligand density. We find that cell spreading, proliferation, and osteogenic differentiation of mesenchymal stem cells (MSCs) are all enhanced in cells cultured in gels with faster relaxation. Strikingly, MSCs form a mineralized, collagen-1-rich matrix similar to bone in rapidly relaxing hydrogels with an initial elastic modulus of 17 kPa. We also show that the effects of stress relaxation are mediated by adhesion-ligand binding, actomyosin contractility and mechanical clustering of adhesion ligands. Our findings highlight stress relaxation as a key characteristic of cell-ECM interactions and as an important design parameter of biomaterials for cell culture.

    View details for DOI 10.1038/NMAT4489

    View details for Web of Science ID 000370967400019

    View details for PubMedID 26618884

  • Substrate stress relaxation regulates cell spreading. Nature communications Chaudhuri, O., Gu, L., Darnell, M., Klumpers, D., Bencherif, S. A., Weaver, J. C., Huebsch, N., Mooney, D. J. 2015; 6: 6364-?


    Studies of cellular mechanotransduction have converged upon the idea that cells sense extracellular matrix (ECM) elasticity by gauging resistance to the traction forces they exert on the ECM. However, these studies typically utilize purely elastic materials as substrates, whereas physiological ECMs are viscoelastic, and exhibit stress relaxation, so that cellular traction forces exerted by cells remodel the ECM. Here we investigate the influence of ECM stress relaxation on cell behaviour through computational modelling and cellular experiments. Surprisingly, both our computational model and experiments find that spreading for cells cultured on soft substrates that exhibit stress relaxation is greater than cells spreading on elastic substrates of the same modulus, but similar to that of cells spreading on stiffer elastic substrates. These findings challenge the current view of how cells sense and respond to the ECM.

    View details for DOI 10.1038/ncomms7365

    View details for PubMedID 25695512

  • Extracellular matrix stiffness and composition jointly regulate the induction of malignant phenotypes in mammary epithelium NATURE MATERIALS Chaudhuri, O., Koshy, S. T., da Cunha, C. B., Shin, J., Verbeke, C. S., Allison, K. H., Mooney, D. J. 2014; 13 (10): 970-978

    View details for DOI 10.1038/NMAT4009

    View details for Web of Science ID 000342743100018

  • Combined atomic force microscopy and side-view optical imaging for mechanical studies of cells NATURE METHODS Chaudhuri, O., Parekh, S. H., Lam, W. A., Fletcher, D. A. 2009; 6 (5): 383-U92


    The mechanical rigidity of cells and adhesion forces between cells are important in various biological processes, including cell differentiation, proliferation and tissue organization. Atomic force microscopy has emerged as a powerful tool to quantify the mechanical properties of individual cells and adhesion forces between cells. Here we demonstrate an instrument that combines atomic force microscopy with a side-view fluorescent imaging path that enables direct imaging of cellular deformation and cytoskeletal rearrangements along the axis of loading. With this instrument, we directly observed cell shape under mechanical load, correlated changes in shape with force-induced ruptures and imaged formation of membrane tethers during cell-cell adhesion measurements. Additionally, we observed cytoskeletal reorganization and stress-fiber formation while measuring the contractile force of an individual cell. This instrument can be a useful tool for understanding the role of mechanics in biological processes.

    View details for DOI 10.1038/NMETH.1320

    View details for Web of Science ID 000265661600020

    View details for PubMedID 19363493

  • Reversible stress softening of actin networks NATURE Chaudhuri, O., Parekh, S. H., Fletcher, D. A. 2007; 445 (7125): 295-298


    The mechanical properties of cells play an essential role in numerous physiological processes. Organized networks of semiflexible actin filaments determine cell stiffness and transmit force during mechanotransduction, cytokinesis, cell motility and other cellular shape changes. Although numerous actin-binding proteins have been identified that organize networks, the mechanical properties of actin networks with physiological architectures and concentrations have been difficult to measure quantitatively. Studies of mechanical properties in vitro have found that crosslinked networks of actin filaments formed in solution exhibit stress stiffening arising from the entropic elasticity of individual filaments or crosslinkers resisting extension. Here we report reversible stress-softening behaviour in actin networks reconstituted in vitro that suggests a critical role for filaments resisting compression. Using a modified atomic force microscope to probe dendritic actin networks (like those formed in the lamellipodia of motile cells), we observe stress stiffening followed by a regime of reversible stress softening at higher loads. This softening behaviour can be explained by elastic buckling of individual filaments under compression that avoids catastrophic fracture of the network. The observation of both stress stiffening and softening suggests a complex interplay between entropic and enthalpic elasticity in determining the mechanical properties of actin networks.

    View details for DOI 10.1038/nature05459

    View details for Web of Science ID 000243504700040

    View details for PubMedID 17230186

  • CD44 alternative splicing in gastric cancer cells is regulated by culture dimensionality and matrix stiffness. Biomaterials Branco da Cunha, C., Klumpers, D. D., Koshy, S. T., Weaver, J. C., Chaudhuri, O., Seruca, R., Carneiro, F., Granja, P. L., Mooney, D. J. 2016; 98: 152-162


    Two-dimensional (2D) cultures often fail to mimic key architectural and physical features of the tumor microenvironment. Advances in biomaterial engineering allow the design of three-dimensional (3D) cultures within hydrogels that mimic important tumor-like features, unraveling cancer cell behaviors that would not have been observed in traditional 2D plastic surfaces. This study determined how 3D cultures impact CD44 alternative splicing in gastric cancer (GC) cells. In 3D cultures, GC cells lost expression of the standard CD44 isoform (CD44s), while gaining CD44 variant 6 (CD44v6) expression. This splicing switch was reversible, accelerated by nutrient shortage and delayed at lower initial cell densities, suggesting an environmental stress-induced response. It was further shown to be dependent on the hydrogel matrix mechanical properties and accompanied by the upregulation of genes involved in epithelial-mesenchymal transition (EMT), metabolism and angiogenesis. The 3D cultures reported here revealed the same CD44 alternative splicing pattern previously observed in human premalignant and malignant gastric lesions. These findings indicate that fundamental features of 3D cultures - such as soluble factors diffusion and mechanical cues - influence CD44 expression in GC cells. Moreover, this study provides a new model system to study CD44 dysfunction, whose role in cancer has been in the spotlight for decades.

    View details for DOI 10.1016/j.biomaterials.2016.04.016

    View details for PubMedID 27187279

  • CD44 alternative splicing in gastric cancer cells is regulated by culture dimensionality and matrix stiffness BIOMATERIALS da Cunha, C. B., Klumpers, D. D., Koshy, S. T., Weaver, J. C., Chaudhuri, O., Seruca, R., Carneiro, F., Granja, P. L., Mooney, D. J. 2016; 98: 152-162
  • Engineered composite fascia for stem cell therapy in tissue repair applications ACTA BIOMATERIALIA Ayala, P., Caves, J., Dai, E., Siraj, L., Liu, L., Chaudhuri, O., Haller, C. A., Mooney, D. J., Chaikof, E. L. 2015; 26: 1-12


    A critical challenge in tissue regeneration is to develop constructs that effectively integrate with the host tissue. Here, we describe a composite, laser micromachined, collagen-alginate construct containing human mesenchymal stem cells (hMSCs) for tissue repair applications. Collagen type I was fashioned into laminated collagen sheets to form a mechanically robust fascia that was subsequently laser micropatterned with pores of defined dimension and spatial distribution as a means to modulate mechanical behavior and promote tissue integration. Significantly, laser micromachined patterned constructs displayed both substantially greater compliance and suture retention strength than non-patterned constructs. hMSCs were loaded in an RGD-functionalized alginate gel modified to degrade in vivo. Over a 7day observation period in vitro, high cell viability was observed with constant levels of VEGF, PDGF-β and MCP-1 protein expression. In a full thickness abdominal wall defect model, the composite construct prevented hernia recurrence in Wistar rats over an 8-week period with de novo tissue and vascular network formation and the absence of adhesions to underlying abdominal viscera. As compared to acellular constructs, constructs containing hMSCs displayed greater integration strength (cell seeded: 0.92±0.19N/mm vs. acellular: 0.59±0.25N/mm, p=0.01), increased vascularization (cell seeded: 2.7-2.1/hpf vs. acellular: 1.7-2.1/hpf, p<0.03), and increased infiltration of macrophages (cell seeded: 2021-3630μm(2)/hpf vs. acellular: 1570-2530μm(2)/hpf, p<0.05). A decrease in the ratio of M1 macrophages to total macrophages was also observed in hMSC-populated samples. Laser micromachined collagen-alginate composites containing hMSCs can be used to bridge soft tissue defects with the capacity for enhanced tissue repair and integration.Effective restoration of large soft tissue defects caused by trauma or treatment complications represents a critical challenge in the clinic. In this study, a novel composite construct was engineered and evaluated for stem cell delivery and tissue repair. Laser micromachining was used to fabricate patterned, microporous constructs designed with pores of defined size and distribution as a means to tune mechanical responses, accommodate and protect incorporated cells, and enhance tissue integration. The construct was embedded within an engineered alginate gel containing hMSCs. Upon repair of a full thickness abdominal wall defect in a rat model, the composite construct modulated host innate immunity towards a reparative phenotypic response, promoted neovascularization and associated matrix production, and increased the strength of tissue integration.

    View details for DOI 10.1016/j.actbio.2015.08.012

    View details for Web of Science ID 000362917200001

  • Substrate stress relaxation regulates cell spreading NATURE COMMUNICATIONS Chaudhuri, O., Gu, L., Darnell, M., Klumpers, D., Bencherif, S. A., Weaver, J. C., Huebsch, N., Mooney, D. J. 2015; 6

    View details for DOI 10.1038/ncomms7365

    View details for Web of Science ID 000350295800001

  • Biological materials and molecular biomimetics - filling up the empty soft materials space for tissue engineering applications JOURNAL OF MATERIALS CHEMISTRY B Miserez, A., Weaver, J. C., Chaudhuri, O. 2015; 3 (1): 13-24

    View details for DOI 10.1039/c4tb01267d

    View details for Web of Science ID 000346003300002

  • Influence of the stiffness of three-dimensional alginate/collagen-I interpenetrating networks on fibroblast biology BIOMATERIALS da Cunha, C. B., Klumpers, D. D., Li, W. A., Koshy, S. T., Weaver, J. C., Chaudhuri, O., Granja, P. L., Mooney, D. J. 2014; 35 (32): 8927-8936


    Wound dressing biomaterials are increasingly being designed to incorporate bioactive molecules to promote healing, but the impact of matrix mechanical properties on the biology of resident cells orchestrating skin repair and regeneration remains to be fully understood. This study investigated whether tuning the stiffness of a model wound dressing biomaterial could control the behavior of dermal fibroblasts. Fully interpenetrating networks (IPNs) of collagen-I and alginate were fabricated to enable gel stiffness to be tuned independently of gel architecture, polymer concentration or adhesion ligand density. Three-dimensional cultures of dermal fibroblasts encapsulated within matrices of different stiffness were shown to promote dramatically different cell morphologies, and enhanced stiffness resulted in upregulation of key-mediators of inflammation such as IL-10 and COX-2. These findings suggest that simply modulating the matrix mechanical properties of a given wound dressing biomaterial deposited at the wound site could regulate the progression of wound healing.

    View details for DOI 10.1016/j.biomaterials.2014.06.047

    View details for Web of Science ID 000341476500003

    View details for PubMedID 25047628

  • Oxidized alginate hydrogels for bone morphogenetic protein-2 delivery in long bone defects ACTA BIOMATERIALIA Priddy, L. B., Chaudhuri, O., Stevens, H. Y., Krishnan, L., Uhrig, B. A., Willett, N. J., Guldberg, R. E. 2014; 10 (10): 4390-4399
  • Highly stretchable and tough hydrogels NATURE Sun, J., Zhao, X., Illeperuma, W. R., Chaudhuri, O., Oh, K. H., Mooney, D. J., Vlassak, J. J., Suo, Z. 2012; 489 (7414): 133-136


    Hydrogels are used as scaffolds for tissue engineering, vehicles for drug delivery, actuators for optics and fluidics, and model extracellular matrices for biological studies. The scope of hydrogel applications, however, is often severely limited by their mechanical behaviour. Most hydrogels do not exhibit high stretchability; for example, an alginate hydrogel ruptures when stretched to about 1.2 times its original length. Some synthetic elastic hydrogels have achieved stretches in the range 10-20, but these values are markedly reduced in samples containing notches. Most hydrogels are brittle, with fracture energies of about 10 J m(-2) (ref. 8), as compared with ∼1,000 J m(-2) for cartilage and ∼10,000 J m(-2) for natural rubbers. Intense efforts are devoted to synthesizing hydrogels with improved mechanical properties; certain synthetic gels have reached fracture energies of 100-1,000 J m(-2) (refs 11, 14, 17). Here we report the synthesis of hydrogels from polymers forming ionically and covalently crosslinked networks. Although such gels contain ∼90% water, they can be stretched beyond 20 times their initial length, and have fracture energies of ∼9,000 J m(-2). Even for samples containing notches, a stretch of 17 is demonstrated. We attribute the gels' toughness to the synergy of two mechanisms: crack bridging by the network of covalent crosslinks, and hysteresis by unzipping the network of ionic crosslinks. Furthermore, the network of covalent crosslinks preserves the memory of the initial state, so that much of the large deformation is removed on unloading. The unzipped ionic crosslinks cause internal damage, which heals by re-zipping. These gels may serve as model systems to explore mechanisms of deformation and energy dissipation, and expand the scope of hydrogel applications.

    View details for DOI 10.1038/nature11409

    View details for Web of Science ID 000308347000049

    View details for PubMedID 22955625

  • STEM-CELL DIFFERENTIATION Anchoring cell-fate cues NATURE MATERIALS Chaudhuri, O., Mooney, D. J. 2012; 11 (7): 568-569

    View details for DOI 10.1038/nmat3366

    View details for Web of Science ID 000305638600006

    View details for PubMedID 22717486

  • Actin filament curvature biases branching direction PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Risca, V. I., Wang, E. B., Chaudhuri, O., Chia, J. J., Geissler, P. L., Fletcher, D. A. 2012; 109 (8): 2913-2918


    Mechanical cues affect many important biological processes in metazoan cells, such as migration, proliferation, and differentiation. Such cues are thought to be detected by specialized mechanosensing molecules linked to the cytoskeleton, an intracellular network of protein filaments that provide mechanical rigidity to the cell and drive cellular shape change. The most abundant such filament, actin, forms branched networks nucleated by the actin-related protein (Arp) 2/3 complex that support or induce membrane protrusions and display adaptive behavior in response to compressive forces. Here we show that filamentous actin serves in a mechanosensitive capacity itself, by biasing the location of actin branch nucleation in response to filament bending. Using an in vitro assay to measure branching from curved sections of immobilized actin filaments, we observed preferential branch formation by the Arp2/3 complex on the convex face of the curved filament. To explain this behavior, we propose a fluctuation gating model in which filament binding or branch nucleation by Arp2/3 occur only when a sufficiently large, transient, local curvature fluctuation causes a favorable conformational change in the filament, and we show with Monte Carlo simulations that this model can quantitatively account for our experimental data. We also show how the branching bias can reinforce actin networks in response to compressive forces. These results demonstrate how filament curvature can alter the interaction of cytoskeletal filaments with regulatory proteins, suggesting that direct mechanotransduction by actin may serve as a general mechanism for organizing the cytoskeleton in response to force.

    View details for DOI 10.1073/pnas.1114292109

    View details for Web of Science ID 000300495100052

    View details for PubMedID 22308368

  • Mechanics and contraction dynamics of single platelets and implications for clot stiffening NATURE MATERIALS Lam, W. A., Chaudhuri, O., Crow, A., Webster, K. D., Li, T., Kita, A., Huang, J., Fletcher, D. A. 2011; 10 (1): 61-66


    Platelets interact with fibrin polymers to form blood clots at sites of vascular injury. Bulk studies have shown clots to be active materials, with platelet contraction driving the retraction and stiffening of clots. However, neither the dynamics of single-platelet contraction nor the strength and elasticity of individual platelets, both of which are important for understanding clot material properties, have been directly measured. Here we use atomic force microscopy to measure the mechanics and dynamics of single platelets. We find that platelets contract nearly instantaneously when activated by contact with fibrinogen and complete contraction within 15 min. Individual platelets can generate an average maximum contractile force of 29 nN and form adhesions stronger than 70 nN. Our measurements show that when exposed to stiffer microenvironments, platelets generated higher stall forces, which indicates that platelets may be able to contract heterogeneous clots more uniformly. The high elasticity of individual platelets, measured to be 10 kPa after contraction, combined with their high contractile forces, indicates that clots may be stiffened through direct reinforcement by platelets as well as by strain stiffening of fibrin under tension due to platelet contraction. These results show how the mechanosensitivity and mechanics of single cells can be used to dynamically alter the material properties of physiologic systems.

    View details for DOI 10.1038/NMAT2903

    View details for Web of Science ID 000285339100022

    View details for PubMedID 21131961

  • Portrusive forces generated by dendritic actin networks during cell crawling Actin-Based Motility Chaudhuri, O., Fletcher, D. A. El Sevier. 2010: 359-379
  • Differential force microscope for long time-scale biophysical measurements REVIEW OF SCIENTIFIC INSTRUMENTS Choy, J. L., Parekh, S. H., Chaudhuri, O., Liu, A. P., Bustamante, C., Footer, M. J., Theriot, J. A., Fletcher, D. A. 2007; 78 (4)


    Force microscopy techniques including optical trapping, magnetic tweezers, and atomic force microscopy (AFM) have facilitated quantification of forces and distances on the molecular scale. However, sensitivity and stability limitations have prevented the application of these techniques to biophysical systems that generate large forces over long times, such as actin filament networks. Growth of actin networks drives cellular shape change and generates nano-Newtons of force over time scales of minutes to hours, and consequently network growth properties have been difficult to study. Here, we present an AFM-based differential force microscope with integrated epifluorescence imaging in which two adjacent cantilevers on the same rigid support are used to provide increased measurement stability. We demonstrate 14 nm displacement control over measurement times of 3 hours and apply the instrument to quantify actin network growth in vitro under controlled loads. By measuring both network length and total network fluorescence simultaneously, we show that the average cross-sectional density of the growing network remains constant under static loads. The differential force microscope presented here provides a sensitive method for quantifying force and displacement with long time-scale stability that is useful for measurements of slow biophysical processes in whole cells or in reconstituted molecular systems in vitro.

    View details for DOI 10.1063/1.2727478

    View details for Web of Science ID 000246073500032

    View details for PubMedID 17477674

  • Loading history determines the velocity of actin-network growth NATURE CELL BIOLOGY Parekh, S. H., Chaudhuri, O., Theriot, J. A., Fletcher, D. A. 2005; 7 (12): 1219-1223


    Directional polymerization of actin filaments in branched networks is one of the most powerful force-generating systems in eukaryotic cells. Growth of densely cross-linked actin networks drives cell crawling, intracellular transport of vesicles and organelles, and movement of intracellular pathogens such as Listeria monocytogenes. Using a modified atomic force microscope (AFM), we obtained force-velocity (Fv) measurements of growing actin networks in vitro until network elongation ceased at the stall force. We found that the growth velocity of a branched actin network against increasing forces is load-independent over a wide range of forces before a convex decline to stall. Surprisingly, when force was decreased on a growing network, the velocity increased to a value greater than the previous velocity, such that two or more stable growth velocities can exist at a single load. These results demonstrate that a single Fv relationship does not capture the complete behaviour of this system, unlike other molecular motors in cells, because the growth velocity depends on loading history rather than solely on the instantaneous load.

    View details for DOI 10.1038/ncb1336

    View details for Web of Science ID 000233748900015

    View details for PubMedID 16299496