The Riedel-Kruse lab combines basic research and engineering approaches by working on (1) biophysics of development and (2) biotic games.

(1) We investigate how genetic networks orchestrate the dynamics and mechanics of developing embryos with a focus on oscillatory processes and molecular forces, with the long-term motivation to advance our understanding on human disease and tissue engineering.

(2) Biotic games require biological process to run and could have a similar impact on society as conventional video games based on electronics; and we design and engineer biotic games specifically targeted at educational challenges and to support biomedical research.

We use theoretical / computational as well as experimental approaches based on molecular, cellular, developmental biology; zebrafish; imaging; physics; informatics / computer sciences; micro-fluidics; and engineering.

Academic Appointments

Honors & Awards

  • Beckman Fellowship, Caltech (2007)
  • Della Martin Fellowship, Caltech (2006)
  • Erasmus Fellowship, Erasmus Fellowship (1998)

Professional Education

  • PhD, Max Planck Institute, Biophysics (2005)

Current Research and Scholarly Interests

Biophysics of multi-cellular systems / (zebrafish) development / biotic games

2015-16 Courses

Stanford Advisees

All Publications

  • A biotic game design project for integrated life science and engineering education. PLoS biology Cira, N. J., Chung, A. M., Denisin, A. K., Rensi, S., Sanchez, G. N., Quake, S. R., Riedel-Kruse, I. H. 2015; 13 (3)


    Engaging, hands-on design experiences are key for formal and informal Science, Technology, Engineering, and Mathematics (STEM) education. Robotic and video game design challenges have been particularly effective in stimulating student interest, but equivalent experiences for the life sciences are not as developed. Here we present the concept of a "biotic game design project" to motivate student learning at the interface of life sciences and device engineering (as part of a cornerstone bioengineering devices course). We provide all course material and also present efforts in adapting the project's complexity to serve other time frames, age groups, learning focuses, and budgets. Students self-reported that they found the biotic game project fun and motivating, resulting in increased effort. Hence this type of design project could generate excitement and educational impact similar to robotics and video games.

    View details for DOI 10.1371/journal.pbio.1002110

    View details for PubMedID 25807212

  • Innocent Fun or "Microslavery"? AN ETHICAL ANALYSIS OF BIOTIC GAMES HASTINGS CENTER REPORT Harvey, H., Havard, M., Magnus, D., Cho, M. K., Riedel-Kruse, I. H. 2014; 44 (6): 38-46

    View details for DOI 10.1002/hast.386

    View details for Web of Science ID 000345510900014

  • Row with the flow. eLife Friedrich, B. M., Riedel-Kruse, I. H. 2014; 3


    Fluid forces are sufficient to keep flagella beating in synchrony.

    View details for DOI 10.7554/eLife.03804

    View details for PubMedID 25073929

  • Design, engineering and utility of biotic games LAB ON A CHIP Riedel-Kruse, I. H., Chung, A. M., Dura, B., Hamilton, A. L., Lee, B. C. 2011; 11 (1): 14-22


    Games are a significant and defining part of human culture, and their utility beyond pure entertainment has been demonstrated with so-called 'serious games'. Biotechnology--despite its recent advancements--has had no impact on gaming yet. Here we propose the concept of 'biotic games', i.e., games that operate on biological processes. Utilizing a variety of biological processes we designed and tested a collection of games: 'Enlightenment', 'Ciliaball', 'PAC-mecium', 'Microbash', 'Biotic Pinball', 'POND PONG', 'PolymerRace', and 'The Prisoner's Smellemma'. We found that biotic games exhibit unique features compared to existing game modalities, such as utilizing biological noise, providing a real-life experience rather than virtual reality, and integrating the chemical senses into play. Analogous to video games, biotic games could have significant conceptual and cost-reducing effects on biotechnology and eventually healthcare; enable volunteers to participate in crowd-sourcing to support medical research; and educate society at large to support personal medical decisions and the public discourse on bio-related issues.

    View details for DOI 10.1039/c0lc00399a

    View details for Web of Science ID 000285101700002

    View details for PubMedID 21085736

  • Synchrony dynamics during initiation, failure, and rescue of the segmentation clock SCIENCE Riedel-Kruse, I. H., Mueller, C., Oates, A. C. 2007; 317 (5846): 1911-1915


    The "segmentation clock" is thought to coordinate sequential segmentation of the body axis in vertebrate embryos. This clock comprises a multicellular genetic network of synchronized oscillators, coupled by intercellular Delta-Notch signaling. How this synchrony is established and how its loss determines the position of segmentation defects in Delta and Notch mutants are unknown. We analyzed the clock's synchrony dynamics by varying strength and timing of Notch coupling in zebra-fish embryos with techniques for quantitative perturbation of gene function. We developed a physical theory based on coupled phase oscillators explaining the observed onset and rescue of segmentation defects, the clock's robustness against developmental noise, and a critical point beyond which synchrony decays. We conclude that synchrony among these genetic oscillators can be established by simultaneous initiation and self-organization and that the segmentation defect position is determined by the difference between coupling strength and noise.

    View details for DOI 10.1126/science.1142538

    View details for Web of Science ID 000249764300037

    View details for PubMedID 17702912

  • A self-organized vortex array of hydrodynamically entrained sperm cells SCIENCE Riedel, I. H., Kruse, K., Howard, J. 2005; 309 (5732): 300-303


    Many patterns in biological systems depend on the exchange of chemical signals between cells. We report a spatiotemporal pattern mediated by hydrodynamic interactions. At planar surfaces, spermatozoa self-organized into dynamic vortices resembling quantized rotating waves. These vortices formed an array with local hexagonal order. Introducing an order parameter that quantifies cooperativity, we found that the array appeared only above a critical sperm density. Using a model, we estimated the hydrodynamic interaction force between spermatozoa to be approximately 0.03 piconewtons. Thus, large-scale coordination of cells can be regulated hydrodynamically, and chemical signals are not required.

    View details for DOI 10.1126/science.1110329

    View details for Web of Science ID 000230449800045

    View details for PubMedID 16002619

  • A Force Balance Can Explain Local and Global Cell Movements during Early Zebrafish Development BIOPHYSICAL JOURNAL Chai, J., Hamilton, A. L., Krieg, M., Buckley, C. D., Riedel-Kruse, I. H., Dunn, A. R. 2015; 109 (2): 407-414


    Embryonic morphogenesis takes place via a series of dramatic collective cell movements. The mechanisms that coordinate these intricate structural transformations across an entire organism are not well understood. In this study, we used gentle mechanical deformation of developing zebrafish embryos to probe the role of physical forces in generating long-range intercellular coordination during epiboly, the process in which the blastoderm spreads over the yolk cell. Geometric distortion of the embryo resulted inĀ nonuniform blastoderm migration and realignment of the anterior-posterior (AP) axis, as defined by the locations at which the head and tail form, toward the new long axis of the embryo and away from the initial animal-vegetal axis defined by the starting location of the blastoderm. We found that local alterations in the rate of blastoderm migration correlated with the local geometry of the embryo. Chemical disruption of the contractile ring of actin and myosin immediately vegetal to the blastoderm margin via Ca(2+) reduction or treatment with blebbistatin restored uniform migration and eliminated AP axis reorientation in mechanically deformed embryos; it also resulted in cellular disorganization at the blastoderm margin. Our resultsĀ support a model in which tension generated by the contractile actomyosin ring coordinates epiboly on both the organismal and cellular scales. Our observations likewise suggest that the AP axis is distinct from the initial animal-vegetal axis in zebrafish.

    View details for DOI 10.1016/j.bpj.2015.04.029

    View details for Web of Science ID 000358312800025

    View details for PubMedID 26200877

  • Tangible Interactive Microbiology for Informal Science Education Lee, S., Chung, A. M., Cira, N., Riedel-Kruse, I. H. 2015: 273

    View details for DOI 10.1145/2677199.2680561

  • Shape Mode Analysis Exposes Movement Patterns in Biology: Flagella and Flatworms as Case Studies PLOS ONE Werner, S., Rink, J. C., Riedel-Kruse, I. H., Friedrich, B. M. 2014; 9 (11)


    We illustrate shape mode analysis as a simple, yet powerful technique to concisely describe complex biological shapes and their dynamics. We characterize undulatory bending waves of beating flagella and reconstruct a limit cycle of flagellar oscillations, paying particular attention to the periodicity of angular data. As a second example, we analyze non-convex boundary outlines of gliding flatworms, which allows us to expose stereotypic body postures that can be related to two different locomotion mechanisms. Further, shape mode analysis based on principal component analysis allows to discriminate different flatworm species, despite large motion-associated shape variability. Thus, complex shape dynamics is characterized by a small number of shape scores that change in time. We present this method using descriptive examples, explaining abstract mathematics in a graphic way.

    View details for DOI 10.1371/journal.pone.0113083

    View details for Web of Science ID 000349145400033

    View details for PubMedID 25426857

  • Active Phase and Amplitude Fluctuations of Flagellar Beating PHYSICAL REVIEW LETTERS Ma, R., Klindt, G. S., Riedel-Kruse, I. H., Juelicher, F., Friedrich, B. M. 2014; 113 (4)
  • Integrated bioprinting and imaging for scalable, networkable desktop experimentation RSC ADVANCES Orloff, N. D., Truong, C., Cira, N., Koo, S., Hamilton, A., Choi, S., Wu, V., Riedel-Kruse, I. H. 2014; 4 (65): 34721-34728

    View details for DOI 10.1039/c4ra05932h

    View details for Web of Science ID 000341287500070

  • High-precision tracking of sperm swimming fine structure provides strong test of resistive force theory JOURNAL OF EXPERIMENTAL BIOLOGY Friedrich, B. M., Riedel-Kruse, I. H., Howard, J., Juelicher, F. 2010; 213 (8): 1226-1234


    The shape of the flagellar beat determines the path along which a sperm cell swims. If the flagellum bends periodically about a curved mean shape then the sperm will follow a path with non-zero curvature. To test a simple hydrodynamic theory of flagellar propulsion known as resistive force theory, we conducted high-precision measurements of the head and flagellum motions during circular swimming of bull spermatozoa near a surface. We found that the fine structure of sperm swimming represented by the rapid wiggling of the sperm head around an averaged path is, to high accuracy, accounted for by resistive force theory and results from balancing forces and torques generated by the beating flagellum. We determined the anisotropy ratio between the normal and tangential hydrodynamic friction coefficients of the flagellum to be 1.81+/-0.07 (mean+/-s.d.). On time scales longer than the flagellar beat cycle, sperm cells followed circular paths of non-zero curvature. Our data show that path curvature is approximately equal to twice the average curvature of the flagellum, consistent with quantitative predictions of resistive force theory. Hence, this theory accurately predicts the complex trajectories of sperm cells from the detailed shape of their flagellar beat across different time scales.

    View details for DOI 10.1242/jeb.039800

    View details for Web of Science ID 000276031900006

    View details for PubMedID 20348333

  • High-Resolution Three-Dimensional Extracellular Recording of Neuronal Activity With Microfabricated Electrode Arrays JOURNAL OF NEUROPHYSIOLOGY Du, J., Riedel-Kruse, I. H., Nawroth, J. C., Roukes, M. L., Laurent, G., Masmanidis, S. C. 2009; 101 (3): 1671-1678


    Microelectrode array recordings of neuronal activity present significant opportunities for studying the brain with single-cell and spike-time precision. However, challenges in device manufacturing constrain dense multisite recordings to two spatial dimensions, whereas access to the three-dimensional (3D) structure of many brain regions appears to remain a challenge. To overcome this limitation, we present two novel recording modalities of silicon-based devices aimed at establishing 3D functionality. First, we fabricated a dual-side electrode array by patterning recording sites on both the front and back of an implantable microstructure. We found that the majority of single-unit spikes could not be simultaneously detected from both sides, suggesting that in addition to providing higher spatial resolution measurements than that of single-side devices, dual-side arrays also lead to increased recording yield. Second, we obtained recordings along three principal directions with a multilayer array and demonstrated 3D spike source localization within the enclosed measurement space. The large-scale integration of such dual-side and multilayer arrays is expected to provide massively parallel recording capabilities in the brain.

    View details for DOI 10.1152/jn.90992.2008

    View details for Web of Science ID 000263745500045

    View details for PubMedID 19091921

  • How molecular motors shape the flagellar beat HFSP JOURNAL Riedel-Kruse, I. H., Hilfinger, A., Howard, J., Juelicher, F. 2007; 1 (3): 192-208


    Cilia and eukaryotic flagella are slender cellular appendages whose regular beating propels cells and microorganisms through aqueous media. The beat is an oscillating pattern of propagating bends generated by dynein motor proteins. A key open question is how the activity of the motors is coordinated in space and time. To elucidate the nature of this coordination we inferred the mechanical properties of the motors by analyzing the shape of beating sperm: Steadily beating bull sperm were imaged and their shapes were measured with high precision using a Fourier averaging technique. Comparing our experimental data with wave forms calculated for different scenarios of motor coordination we found that only the scenario of interdoublet sliding regulating motor activity gives rise to satisfactory fits. We propose that the microscopic origin of such "sliding control" is the load dependent detachment rate of motors. Agreement between observed and calculated wave forms was obtained only if significant sliding between microtubules occurred at the base. This suggests a novel mechanism by which changes in basal compliance could reverse the direction of beat propagation. We conclude that the flagellar beat patterns are determined by an interplay of the basal properties of the axoneme and the mechanical feedback of dynein motors.

    View details for DOI 10.2976/1.2773861

    View details for Web of Science ID 000258366600006

    View details for PubMedID 19404446

  • Ab initio calculation of the transmission coefficients from a superlattice electronic structure Phys. Rev. B Riedel, I., Zahn, P., Mertig, I. 2001; 63 (195403)