Paul Ruijgrok

All Publications

• Design and characterization of optically controllable filamentous myosins Zemsky, S., Ruijgrok, P. V., Bryant, Z. CELL PRESS. 2022: 292A

  View details for Web of Science ID 000759523001683

• Machine learning active-nematic hydrodynamics. Proceedings of the National Academy of Sciences of the United States of America Colen, J., Han, M., Zhang, R., Redford, S. A., Lemma, L. M., Morgan, L., Ruijgrok, P. V., Adkins, R., Bryant, Z., Dogic, Z., Gardel, M. L., de Pablo, J. J., Vitelli, V. 2021; 118 (10)

  Abstract

  Hydrodynamic theories effectively describe many-body systems out of equilibrium in terms of a few macroscopic parameters. However, such parameters are difficult to determine from microscopic information. Seldom is this challenge more apparent than in active matter, where the hydrodynamic parameters are in fact fields that encode the distribution of energy-injecting microscopic components. Here, we use active nematics to demonstrate that neural networks can map out the spatiotemporal variation of multiple hydrodynamic parameters and forecast the chaotic dynamics of these systems. We analyze biofilament/molecular-motor experiments with microtubule/kinesin and actin/myosin complexes as computer vision problems. Our algorithms can determine how activity and elastic moduli change as a function of space and time, as well as adenosine triphosphate (ATP) or motor concentration. The only input needed is the orientation of the biofilaments and not the coupled velocity field which is harder to access in experiments. We can also forecast the evolution of these chaotic many-body systems solely from image sequences of their past using a combination of autoencoders and recurrent neural networks with residual architecture. In realistic experimental setups for which the initial conditions are not perfectly known, our physics-inspired machine-learning algorithms can surpass deterministic simulations. Our study paves the way for artificial-intelligence characterization and control of coupled chaotic fields in diverse physical and biological systems, even in the absence of knowledge of the underlying dynamics.

  View details for DOI 10.1073/pnas.2016708118

  View details for PubMedID 33653956

• Optical control of fast and processive engineered myosins in vitro and in living cells. Nature chemical biology Ruijgrok, P. V., Ghosh, R. P., Zemsky, S. n., Nakamura, M. n., Gong, R. n., Ning, L. n., Chen, R. n., Vachharajani, V. T., Chu, A. E., Anand, N. n., Eguchi, R. R., Huang, P. S., Lin, M. Z., Alushin, G. M., Liphardt, J. T., Bryant, Z. n. 2021

  Abstract

  Precision tools for spatiotemporal control of cytoskeletal motor function are needed to dissect fundamental biological processes ranging from intracellular transport to cell migration and division. Direct optical control of motor speed and direction is one promising approach, but it remains a challenge to engineer controllable motors with desirable properties such as the speed and processivity required for transport applications in living cells. Here, we develop engineered myosin motors that combine large optical modulation depths with high velocities, and create processive myosin motors with optically controllable directionality. We characterize the performance of the motors using in vitro motility assays, single-molecule tracking and live-cell imaging. Bidirectional processive motors move efficiently toward the tips of cellular protrusions in the presence of blue light, and can transport molecular cargo in cells. Robust gearshifting myosins will further enable programmable transport in contexts ranging from in vitro active matter reconstitutions to microfabricated systems that harness molecular propulsion.

  View details for DOI 10.1038/s41589-021-00740-7

  View details for PubMedID 33603247

• Spatiotemporal control of liquid crystal structure and dynamics through activity patterning. Nature materials Zhang, R. n., Redford, S. A., Ruijgrok, P. V., Kumar, N. n., Mozaffari, A. n., Zemsky, S. n., Dinner, A. R., Vitelli, V. n., Bryant, Z. n., Gardel, M. L., de Pablo, J. J. 2021

  Abstract

  Active materials are capable of converting free energy into mechanical work to produce autonomous motion, and exhibit striking collective dynamics that biology relies on for essential functions. Controlling those dynamics and transport in synthetic systems has been particularly challenging. Here, we introduce the concept of spatially structured activity as a means of controlling and manipulating transport in active nematic liquid crystals consisting of actin filaments and light-sensitive myosin motors. Simulations and experiments are used to demonstrate that topological defects can be generated at will and then constrained to move along specified trajectories by inducing local stresses in an otherwise passive material. These results provide a foundation for the design of autonomous and reconfigurable microfluidic systems where transport is controlled by modulating activity with light.

  View details for DOI 10.1038/s41563-020-00901-4

  View details for PubMedID 33603187

• Optical Control of Fast and Processive Engineered Myosins In Vitro and in Living Cells Ruijgrok, P. V., Ghosh, R. P., Nakamura, M., Zemsky, S., Chen, R., Vachharajani, V., Liphardt, J. T., Bryant, Z. CELL PRESS. 2019: 259A

  View details for DOI 10.1016/j.bpj.2018.11.1410

  View details for Web of Science ID 000460779801296

• Controllable molecular motors engineered from myosin and RNA. Nature nanotechnology Omabegho, T. n., Gurel, P. S., Cheng, C. Y., Kim, L. Y., Ruijgrok, P. V., Das, R. n., Alushin, G. M., Bryant, Z. n. 2017

  Abstract

  Engineering biomolecular motors can provide direct tests of structure-function relationships and customized components for controlling molecular transport in artificial systems 1 or in living cells 2 . Previously, synthetic nucleic acid motors 3-5 and modified natural protein motors 6-10 have been developed in separate complementary strategies to achieve tunable and controllable motor function. Integrating protein and nucleic-acid components to form engineered nucleoprotein motors may enable additional sophisticated functionalities. However, this potential has only begun to be explored in pioneering work harnessing DNA scaffolds to dictate the spacing, number and composition of tethered protein motors 11-15 . Here, we describe myosin motors that incorporate RNA lever arms, forming hybrid assemblies in which conformational changes in the protein motor domain are amplified and redirected by nucleic acid structures. The RNA lever arm geometry determines the speed and direction of motor transport and can be dynamically controlled using programmed transitions in the lever arm structure 7,9 . We have characterized the hybrid motors using in vitro motility assays, single-molecule tracking, cryo-electron microscopy and structural probing 16 . Our designs include nucleoprotein motors that reversibly change direction in response to oligonucleotides that drive strand-displacement 17 reactions. In multimeric assemblies, the controllable motors walk processively along actin filaments at speeds of 10-20 nm s-1. Finally, to illustrate the potential for multiplexed addressable control, we demonstrate sequence-specific responses of RNA variants to oligonucleotide signals.

  View details for PubMedID 29109539

• Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity. eLife Gurel, P. S., Kim, L. Y., Ruijgrok, P. V., Omabegho, T. n., Bryant, Z. n., Alushin, G. M. 2017; 6

  Abstract

  Despite extensive scrutiny of the myosin superfamily, the lack of high-resolution structures of actin-bound states has prevented a complete description of its mechanochemical cycle and limited insight into how sequence and structural diversification of the motor domain gives rise to specialized functional properties. Here we present cryo-EM structures of the unique minus-end directed myosin VI motor domain in rigor (4.6 Å) and Mg-ADP (5.5 Å) states bound to F-actin. Comparison to the myosin IIC-F-actin rigor complex reveals an almost complete lack of conservation of residues at the actin-myosin interface despite preservation of the primary sequence regions composing it, suggesting an evolutionary path for motor specialization. Additionally, analysis of the transition from ADP to rigor provides a structural rationale for force sensitivity in this step of the mechanochemical cycle. Finally, we observe reciprocal rearrangements in actin and myosin accompanying the transition between these states, supporting a role for actin structural plasticity during force generation by myosin VI.

  View details for PubMedID 29199952

• Damping of Acoustic Vibrations of Single Gold Nanoparticles Optically Trapped in Water NANO LETTERS Ruijgrok, P. V., Zijlstra, P., Tchebotareva, A. L., Orrit, M. 2012; 12 (2): 1063-1069

  Abstract

  We combine ultrafast pump-probe spectroscopy with optical trapping to study homogeneous damping of the acoustic vibrations of single gold nanospheres (80 nm diameter) and nanorods (25 nm diameter by 60 nm length) in water. We find a significant particle-to-particle variation in damping times. Our results indicate that vibrational damping occurs not only by dissipation into the liquid, but also by damping mechanisms intrinsic to the particle. Our experiment opens the study of mechanisms of intrinsic mechanical dissipation in metals at frequencies 1-1000 GHz, a range that has been difficult to access thus far.

  View details for DOI 10.1021/nl204311q

  View details for Web of Science ID 000299967800090

  View details for PubMedID 22251064

• Brownian Fluctuations and Heating of an Optically Aligned Gold Nanorod PHYSICAL REVIEW LETTERS Ruijgrok, P. V., Verhart, N. R., Zijlstra, P., Tchebotareva, A. L., Orrit, M. 2011; 107 (3)

  Abstract

  We present the first quantitative measurements of the torque exerted on a single gold nanorod in a polarized three-dimensional optical trap. We determined the torque both by observing the time-averaged orientation distribution and by measuring the dynamics of the rotational brownian fluctuations. The measurements are in good agreement with calculations, where the temperature profile around the hot nanorod gives rise to a reduced, effective viscosity. The maximum torque on a 60  nm×25  nm nanorod was 100  pN·nm, large enough to address single-molecule processes in soft and biological matter.

  View details for DOI 10.1103/PhysRevLett.107.037401

  View details for Web of Science ID 000292597400024

  View details for PubMedID 21838403

• Making gold nanoparticles fluorescent for simultaneous absorption and fluorescence detection on the single particle level PHYSICAL CHEMISTRY CHEMICAL PHYSICS Gaiduk, A., Ruijgrok, P. V., Yorulmaz, M., Orrit, M. 2011; 13 (1): 149-153

  Abstract

  We demonstrate a simple way of making individual 20 nm gold nanoparticles fluorescent (with a fluorescence quantum yield of about 10(-6)) in glycerol. Gold NPs prepared in such a way have bright fluorescence for a long time under moderate excitation, and their fluorescence remains when the solvent is exchanged to water. We propose to use these nanoparticles as a calibration standard for simultaneous detection of fluorescence and absorption (by means of photothermal detection), and experimentally demonstrate the theoretically predicted shift in axial positions of these signals. Simultaneous absorption and fluorescence detection of such stable labels makes them attractive for multidimensional tracking and screening applications.

  View details for DOI 10.1039/c0cp01389g

  View details for Web of Science ID 000285099800017

  View details for PubMedID 21042602

• Room-Temperature Detection of a Single Molecule's Absorption by Photothermal Contrast SCIENCE Gaiduk, A., Yorulmaz, M., Ruijgrok, P. V., Orrit, M. 2010; 330 (6002): 353-356

  Abstract

  So far, single-molecule imaging has predominantly relied on fluorescence detection. We imaged single nonfluorescent azo dye molecules in room-temperature glycerol by the refractive effect of the heat that they release in their environment upon intense illumination. This photothermal technique provides contrast for the absorbing objects only, irrespective of scattering by defects or roughness, with a signal-to-noise ratio of ~10 for a single molecule in an integration time of 300 milliseconds. In the absence of oxygen, virtually no bleaching event was observed, even after more than 10 minutes of illumination. In a solution saturated with oxygen, the average bleaching time was of the order of 1 minute. No blinking was observed in the absorption signal. On the basis of bleaching steps, we obtained an average absorption cross section of 4 angstroms(2) for a single chromophore.

  View details for DOI 10.1126/science.1195475

  View details for Web of Science ID 000282986700036

  View details for PubMedID 20947760

• Spontaneous emission of a nanoscopic emitter in a strongly scattering disordered medium OPTICS EXPRESS Ruijgrok, P. V., Wuest, R., Rebane, A. A., Renn, A., Sandoghdar, V. 2010; 18 (6): 6360-6365

  Abstract

  Fluorescence lifetimes of nitrogen-vacancy color centers in individual diamond nanocrystals were measured at the interface between a glass substrate and a strongly scattering medium. Comparison of the results with values recorded from the same nanocrystals at the glass-air interface revealed fluctuations of fluorescence lifetimes in the scattering medium. After discussing a range of possible systematic effects, we attribute the observed lengthening of the lifetimes to the reduction of the local density of states. Our approach is very promising for exploring the strong threedimensional localization of light directly on the microscopic scale.

  View details for Web of Science ID 000276002500109

  View details for PubMedID 20389659

• Detection limits in photothermal microscopy Chem. Sci. Gaiduk A, Ruijgrok PV, Yorulmaz M, Orrit M 2010; 1 (3): 343-350
• Probing the acoustic vibrations of single gold nanoparticle by ultrashort laser pulses Laser Photonics Rev. Tcheborateva AL, Ruijgrok PV, Zijlstra P, Orrit M 2010; 4 (4): 581-597
• Acoustic and Optical Modes of Single Dumbbells of Gold Nanoparticles CHEMPHYSCHEM Tchebotareva, A. L., van Dijk, M. A., Ruijgrok, P. V., Fokkema, V., Hesselberth, M. H., Lippitz, M., Orrit, M. 2009; 10 (1): 111-114

  View details for DOI 10.1002/cphc.200800289

  View details for Web of Science ID 000262870500015

  View details for PubMedID 18688828