The Countoscope: Measuring Self and Collective Dynamics without Trajectories
Abstract: Driven by physical questions pertaining to quantifying particle dynamics, microscopy can now resolve complex systems at the single particle level, from cellular organisms to individual ions. Yet, available analysis techniques face challenges reconstructing trajectories in dense and heterogeneous systems where accurately labelling particles is difficult. Furthermore, the inescapable finite field of view of experiments hinders the measurement of collective effects. Inspired by Smoluchowski, we introduce a broadly applicable analysis technique that probes dynamics of interacting particle suspensions based on a remarkably simple principle: counting particles in finite observation boxes. Using colloidal experiments, advanced simulations and theory, we first demonstrate that statistical properties of fluctuating counts can be used to determine self-diffusion coefficients, so alleviating the hurdles associated with trajectory reconstruction. We also provide a recipe for practically extracting the diffusion coefficient from experimental data at variable particle densities, which is sensitive to steric and hydrodynamic interactions. Remarkably, by increasing the observation box size, counting naturally enables the study of collective dynamics in dense suspensions. Using our novel analysis of particle counts, we uncover a surprising enhancement of collective behaviour, as well as a new length scale associated with hyperuniform-like structure. Our counting framework, the Countoscope, thus enables efficient measurements of self and collective dynamics in dense suspensions and opens the way to quantifying dynamics and identifying novel physical mechanisms in diverse complex systems where single particles can be resolved.
- Islam, M. Einstein–smoluchowski diffusion equation: a discussion. Physica Scripta 70, 120 (2004).
- Smoluchowski, M. v. Studien über kolloidstatistik und den mechanismus der diffusion. Kolloid-Zeitschrift 18, 48–54 (1916).
- Chandrasekhar, S. Stochastic problems in physics and astronomy. Reviews of modern physics 15, 1 (1943).
- Eine neue methode zur prüfung der gültigkeit des boyle-gay-lussacschen gesetzes für kolloide lösungen. Zeitschrift für Physikalische Chemie 77, 145–191 (1911).
- Smoluchowski, M. v. Drei vortrage uber diffusion, brownsche bewegung und koagulation von kolloidteilchen. Zeitschrift fur Physik 17, 557–585 (1916).
- Zur koagulation grobdisperser goldhydrosole. Zeitschrift für Physikalische Chemie 92, 750–762 (1918).
- Westgren, A. Bestimmungen der kompressibilität disperser systeme. Zeitschrift für anorganische und allgemeine Chemie 95, 39–63 (1916).
- Fluorescence fluctuation spectroscopy: ushering in a new age of enlightenment for cellular dynamics. Biophysical reviews 1, 105–118 (2009).
- Dynamic light scattering: with applications to chemistry, biology, and physics (Courier Corporation, 2000).
- Fluorescence correlation spectroscopy. i. conceptual basis and theory. Biopolymers: Original Research on Biomolecules 13, 1–27 (1974).
- Differential dynamic microscopy: probing wave vector dependent dynamics with a microscope. Physical review letters 100, 188102 (2008).
- Making sense of brownian motion: colloid characterization by dynamic light scattering. Langmuir 31, 3–12 (2015).
- Rose, K. A. et al. Particle tracking of nanoparticles in soft matter. Journal of Applied Physics 127 (2020).
- Methods of digital video microscopy for colloidal studies. Journal of colloid and interface science 179, 298–310 (1996).
- Einstein, A. Über die von der molekularkinetischen theorie der wärme geforderte bewegung von in ruhenden flüssigkeiten suspendierten teilchen. Annalen der physik 4 (1905).
- Perrin, J. Les atomes (Cnrs, 2014).
- Comtet, J. et al. Anomalous interfacial dynamics of single proton charges in binary aqueous solutions. Science Advances 7, eabg8568 (2021).
- Ronceray, N. et al. Liquid-activated quantum emission from native hbn defects for nanofluidic sensing. arXiv preprint arXiv:2204.06287 (2022).
- A review of progress in single particle tracking: from methods to biophysical insights. Reports on progress in physics 78, 124601 (2015).
- To cross or not to cross: Collective swimming of escherichia coli under two-dimensional confinement. Physical Review Research 4, 023105 (2022).
- Distnet2d: Leveraging long-range temporal information for efficient segmentation and tracking. arXiv preprint arXiv:2310.19641 (2023).
- Deforet, M. et al. Automated velocity mapping of migrating cell populations (avemap). Nature methods 9, 1081–1083 (2012).
- Inferring stochastic rates from heterogeneous snapshots of particle positions. arXiv preprint arXiv:2311.04880 (2023).
- Learning the non-equilibrium dynamics of brownian movies. Nature communications 11, 5378 (2020).
- Communication: Radial distribution functions in a two-dimensional binary colloidal hard sphere system. The Journal of Chemical Physics 140, 161106 (2014).
- Effect of hydrodynamic interactions on self-diffusion of quasi-two-dimensional colloidal hard spheres. Phys. Rev. Lett. 115, 268301 (2015).
- soft-matter/trackpy: Trackpy v0.5.0 (2021).
- Two-Dimensional Melting of Colloidal Hard Spheres. Phys. Rev. Lett. 158001, 1–5 (2017).
- Driven dynamics in dense suspensions of microrollers. Soft Matter 16, 7982–8001 (2020).
- Theory of simple liquids: with applications to soft matter (Academic press, 2013).
- Dean, D. S. Langevin equation for the density of a system of interacting langevin processes. Journal of Physics A: Mathematical and General 29, L613 (1996).
- Kawasaki, K. Microscopic Analyses of the Dynamical Density Functional Equation of Dense Fluids. Journal of Statistical Physics 93, 527–546 (1998). URL http://link.springer.com/10.1023/B:JOSS.0000033240.66359.6c.
- Marbach, S. Intrinsic fractional noise in nanopores: The effect of reservoirs. The Journal of Chemical Physics 154, 171101 (2021).
- Effusion of stochastic processes on a line. arXiv preprint arXiv:2303.08961 (2023).
- Di Bello, C. et al. Current fluctuations in stochastically resetting particle systems. arXiv preprint arXiv:2302.06696 (2023).
- Thorneywork, A. L. et al. Structure factors in a two-dimensional binary colloidal hard sphere system. Molecular Physics 116, 3245–3257 (2018).
- On analytical theories for conductivity and self-diffusion in concentrated electrolytes. arXiv preprint arXiv:2306.16737 (2023).
- Slow viscous motion of a sphere parallel to a plane wall—i motion through a quiescent fluid. Chemical engineering science 22, 637–651 (1967).
- Gomer, R. Diffusion of adsorbates on metal surfaces. Reports on progress in Physics 53, 917 (1990).
- Enhanced hyperuniformity from random reorganization. Proceedings of the National Academy of Sciences 114, 4294–4299 (2017).
- Torquato, S. Hyperuniform states of matter. Physics Reports 745, 1–95 (2018).
- The charge fluctuations in classical coulomb systems. Journal of Statistical Physics 22, 435–463 (1980).
- Fluctuations, large deviations and rigidity in hyperuniform systems: a brief survey. Indian Journal of Pure and Applied Mathematics 48, 609–631 (2017).
- Screening in ionic systems: simulations for the lebowitz length. Physical review letters 95, 145701 (2005).
- Search for hyperuniformity in mechanically stable packings of frictionless disks above jamming. Physical Review E 92, 052206 (2015).
- Large-scale structure of randomly jammed spheres. Physical Review E 95, 052125 (2017).
- Thermodynamics and correlation functions of plasmas and electrolyte solutions. Molecular Physics 38, 1179–1199 (1979).
- Lebowitz, J. L. Charge fluctuations in coulomb systems. Physical Review A 27, 1491 (1983).
- Fluctuations of water near extended hydrophobic and hydrophilic surfaces. The journal of physical chemistry B 114, 1632–1637 (2010).
- Molecular explanation for why talc surfaces can be both hydrophilic and hydrophobic. Journal of the American Chemical Society 133, 20521–20527 (2011).
- Understanding Hydrophobic Effects: Insights from Water Density Fluctuations. Annual Review of Condensed Matter Physics 13, 303–324 (2022). URL https://www.annualreviews.org/doi/10.1146/annurev-conmatphys-040220-045516.
- Generalized hydrodynamics of systems of brownian particles. Advances in Physics 32, 173–283 (1983).
- Diffusion of hard disks and rodlike molecules on surfaces. Physical Review E 64, 021204 (2001).
- 3d hydrodynamic interactions lead to divergences in 2d diffusion. Journal of Physics: Condensed Matter 27, 194113 (2015).
- Dhont, J. K. An introduction to dynamics of colloids (Elsevier, 1996).
- Qiu, X. et al. Hydrodynamic interactions in concentrated suspensions. Physical review letters 65, 516 (1990).
- Short-time brownian motion in colloidal suspensions: Experiment and simulation. Physical Review E 52, 5070 (1995).
- Experimental evidence for the divergence of a transport coefficient in a quasi-two-dimensional fluid. Physical Review E 51, 423 (1995).
- Lin, B. et al. Divergence of the long-wavelength collective diffusion coefficient in quasi-one-and quasi-two-dimensional colloidal suspensions. Physical Review E 89, 022303 (2014).
- Hydrodynamic interactions induce anomalous diffusion under partial confinement. Soft matter 10, 2945–2948 (2014).
- Peláez, R. P. et al. Hydrodynamic fluctuations in quasi-two dimensional diffusion. Journal of Statistical Mechanics: Theory and Experiment 2018, 063207 (2018).
- Influence of hydrodynamics on many-particle diffusion in 2d colloidal suspensions. The European Physical Journal E 13, 267–275 (2004).
- Hashemi, A. et al. Computing hydrodynamic interactions in confined doubly periodic geometries in linear time. The Journal of Chemical Physics 158, 154101 (2023). URL https://doi.org/10.1063/5.0141371.
- Stokes flow for a Stokeslet between two parallel flat plates. J. Eng. Math. 10, 287–303 (1976).
- Faxén, H. Einwirkung der Gefässwände auf den Widerstand gegen die Bewegung einer kleinen Kugel in einer zähen Flüssigkeit (Uppsala University, 1921).
- Nonequilibrium phenomena in driven and active coulomb field theories. Physica A: Statistical Mechanics and its Applications 127947 (2022).
- Collective motion and density fluctuations in bacterial colonies. Proceedings of the National Academy of Sciences 107, 13626–13630 (2010).
- Peruani, F. et al. Collective motion and nonequilibrium cluster formation in colonies of gliding bacteria. Physical review letters 108, 098102 (2012).
- Density fluctuations and energy spectra of 3d bacterial suspensions. Soft Matter 17, 10806–10817 (2021).
- Hydrodynamics and phases of flocks. Annals of Physics 318, 170–244 (2005).
- Athermal phase separation of self-propelled particles with no alignment. Physical review letters 108, 235702 (2012).
- Spatial structures and giant number fluctuations in models of active matter. Physical review letters 108, 238001 (2012).
- The interplay between chemo-phoretic interactions and crowding in active colloids. Soft Matter 19, 2297–2310 (2023).
- Thinking outside the box: fluctuations and finite size effects. European Journal of Physics 35, 035011 (2014).
- Chandler, D. Interfaces and the driving force of hydrophobic assembly. Nature 437, 640–647 (2005).
- The statistical mechanical theory of solutions. i. The Journal of chemical physics 19, 774–777 (1951).
- The thermodynamic properties of electrolyte solutions: Some formal results. The Journal of Chemical Physics 86, 5110–5116 (1987).
- Schnell, S. K. et al. Calculating thermodynamic properties from fluctuations at small scales. The Journal of Physical Chemistry B 115, 10911–10918 (2011).
- Kirkwood-buff integrals from molecular simulation. Fluid Phase Equilibria 486, 21–36 (2019).
- Cheng, B. Computing chemical potentials of solutions from structure factors. The Journal of Chemical Physics 157, 121101 (2022). URL https://aip.scitation.org/doi/10.1063/5.0107059. Publisher: American Institute of Physics.
- Hyperuniformity of critical absorbing states. Physical review letters 114, 110602 (2015).
- Computing the heat conductivity of fluids from density fluctuations. Physical Review Letters 125, 130602 (2020).
- Ionic fluctuations in finite volumes: fractional noise and hyperuniformity. Faraday Discussions (2023).
- Frequency and field-dependent response of confined electrolytes from brownian dynamics simulations. arXiv preprint arXiv:2212.09481 (2022).
- Classical dynamical density functional theory: from fundamentals to applications. Advances in Physics 69, 121–247 (2020). URL https://www.tandfonline.com/doi/full/10.1080/00018732.2020.1854965.
- Wilson, L. G. et al. Differential dynamic microscopy of bacterial motility. Physical review letters 106, 018101 (2011).
- Hallatschek, O. et al. Proliferating active matter. Nature Reviews Physics 1–13 (2023).
- Bacterial growth: a statistical physicist’s guide. Reports on Progress in Physics 82, 016601 (2018).
- Marchetti, M. C. et al. Hydrodynamics of soft active matter. Reviews of modern physics 85, 1143 (2013).
- Active turbulence. Annual Review of Condensed Matter Physics 13, 143–170 (2022).
- A statistical physics view of swarming bacteria. Movement ecology 7, 1–17 (2019).
- Sprinkle, B. et al. Sedimentation of a colloidal monolayer down an inclined plane. Phys. Rev. Fluids 6, 034202 (2021).
- Rational Construction of Stochastic Numerical Methods for Molecular Sampling. Applied Mathematics Research eXpress 2013, 34–56 (2012). URL https://doi.org/10.1093/amrx/abs010.
- Density fluctuation in brownian motion and its significance in olfaction. Mathematical and computer modelling 18, 19–30 (1993).
- Estimating diffusion coefficients from count data: Einstein-smoluchowski theory revisited. Annals of the Institute of Statistical Mathematics 49, 667–679 (1997).
- Smoluchowski processes and nonparametric estimation of functionals of particle displacement distributions from count data. arXiv preprint arXiv:2108.06954 (2021).
- Kawasaki, K. Stochastic model of slow dynamics in supercooled liquids and dense colloidal suspensions. Physica A: Statistical Mechanics and its Applications 208, 35–64 (1994).
- The conductivity of strong electrolytes from stochastic density functional theory. Journal of Statistical Mechanics: Theory and Experiment 2016, 023106 (2016).
- Diffusion of a tracer in a dense mixture of soft particles connected to different thermostats. Physical Review E 106, 064608 (2022).
- Transient fluctuation-induced forces in driven electrolytes after an electric field quench. New Journal of Physics 23, 073034 (2021).
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