Nature has perfected obtaining robust collective behavior and global order from simple local interactions. The challenge for us is to engineer similar systems at various scales that are composed of many agents, ranging from self-propelled nanoparticles in solution to cars in traffic, and to be able to control their emergent collective properties, their emergent “intelligence”.
Computer simulations have the unique opportunity and responsibility to lead the way in searching, understanding, controlling and designing these new materials that are catalysts for technological innovation.
Read more about our work here.
From invited perspective article in Soft Matter (2019).
Assembling polyhedra. From Soft Matter (2018)
From invited perspective article in Soft Matter (2019).
Check out the klogW virtual series seminars by the Topical Group on Statistical and Nonlinear Physics of the American Physical Society, featuring some amazing speakers, once a month!
News
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11/2022 Our paper on Reciprocal swimming at intermediate Reynolds numbers was published in the Journal of Fluid Mechanics. It was a fun collaboration with Chris Rycroft and Nick Derr.
In Stokes flow, Purcell's scallop theorem forbids objects with time-reversible (reciprocal) swimming strokes from moving. In the presence of inertia, this restriction is eased and reciprocally deforming bodies can swim. Recent work has investigated a simple model swimmer, an asymmetric spherical dimer of oscillating length, in a variety of contexts. Analytical, numerical, and experimental studies have shown a dense (i.e. inertial) dimer swims in Stokes flow. Similarly, numerical study shows a dimer in fluid of intermediate Reynolds number (Re = 1-1000) swims in a direction that varies depending on the degree of fluid inertia. Here, we introduce a general model for the inertial flow produced by an oscillating dimer at small amplitudes. We find the model's predictions match those of the dense Stokes swimmers in the appropriate limit, and that the behavior in inertial fluid is consistent with previous numerical analysis.
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07/2022 Pairwise interactions between model swimmers at intermediate Reynolds numbers - Published in PRF!!
How do mesoscale swimmers interact with one another when there is finite inertia? Do they repel, attract, how do they arrange? We numerically study simple model swimmers at intermediate Reynolds numbers and find that they form specific stable pairs depending on system parameters (e.g. Reynolds number). By looking at the flow fields, we relate the assemblies with nonlinear hydrodynamic interactions, namely steady streaming flows and discuss implications for the collective behavior beyond pairs.
Pairwise interactions between model swimmers at intermediate Reynolds numbers
Thomas Dombrowski, Hong Nguyen & Daphne Klotsa
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03/10/2022 Our paper on Fluid inertia and the scallop theorem has been submitted and is on the arXiv. This was a collaboration with Chris Rycroft and Nick Derr.
In Stokes flow, Purcell's scallop theorem forbids objects with time-reversible (reciprocal) swimming strokes from moving. In the presence of inertia, this restriction is eased and reciprocally deforming bodies can swim. Recent work has investigated a simple model swimmer, an asymmetric spherical dimer of oscillating length, in a variety of contexts. Analytical, numerical, and experimental studies have shown a dense (i.e. inertial) dimer swims in Stokes flow. Similarly, numerical study shows a dimer in fluid of intermediate Reynolds number (Re = 1-1000) swims in a direction that varies depending on the degree of fluid inertia. Here, we introduce a general model for the inertial flow produced by an oscillating dimer at small amplitudes. We find the model's predictions match those of the dense Stokes swimmers in the appropriate limit, and that the behavior in inertial fluid is consistent with previous numerical analysis.
Fluid inertia and the scallop theorem
Nicholas J. Derr, Thomas Dombrowski, Chris H. Rycroft & Daphne Klotsa
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06/15/2021 Our paper on Phase behavior and surface tension of soft active Brownian particles has been published in Soft Matter (2021 Soft Matter Emerging Investigators themed collection), check it out here.
Phase behavior and surface tension of soft active Brownian particles
Nicholas Lauersdorf, Thomas Kolb, Moslem Moradi, Ehssan Nazockdast & Daphne Klotsa
We study quasi two-dimensional, monodisperse systems of active Brownian particles (ABPs) for a range of activities, stiffnesses, and densities. We develop a microscopic, analytical method for predicting the dense phase structure formed after motility-induced phase separation (MIPS) has occurred, including the dense cluster's area fraction, interparticle pressure, and radius. Our predictions are in good agreement with our Brownian dynamics simulations. We, then, derive a continuum model to investigate the relationship between the predicted interparticle pressure, the swim pressure, and the macroscopic pressure in the momentum equation. We find that formulating the point-wise macroscopic pressure as the interparticle pressure and modeling the particle activity through a spatially variant body force – as opposed to a volume-averaged swim pressure – results in consistent predictions of pressure in both the continuum model and the microscopic theory. This formulation ...
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04/22/2021 Our paper on Pairwise and collective behavior between model swimmers at intermediate Reynolds numbers just appeared on the arxiv, check it out here.
Pairwise and collective behavior between model swimmers at intermediate Reynolds numbers
Thomas Dombrowski, Hong Nguyen, Daphne Klotsa
We computationally studied the pair interactions and collective behavior of asymmetric, dumbbell swimmers over a range of intermediate Reynolds numbers and initial configurations. Depending on the initial positions and the Re, we found that two swimmers either repelled and swum away from one another or assembled one of four stable pairs: in-line and in-tandem, both parallel and anti-parallel. When in these stable pairs, swimmers were coordinated, swum together, and generated fluid flows as one. We compared the stable pairs' speeds, swim direction and fluid flows to those of the single swimmer. The in-line stable pairs behaved much like the single swimmer transitioning from puller-like to pusher-like stroke-averaged flow fields. In contrast, for the in-tandem pairs we discovered differences in the swim direction transition, as well as the stroke-averaged fluid flow directions. Notably, the in-tandem V pair switched its swim direction at a higher Re than the single swimmer while the in-tandem orbiting pair switched at a lower Re. We also studied a system of 122 swimmers and found the collective behavior transitioned from in-line network-like connections to small, transient in-tandem clusters as the Reynolds number increased, consistent with the in-line to in-tandem pairwise behavior. Details in the collective behavior involved the formation of triples and other many-body hydrodynamic interactions that were not captured by either pair or single swimmer behavior. Our findings demonstrate the richness and complexity of the collective behavior of intermediate-Re swimmers.
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04/20/2021 Our paper on the Negative regulation of a ribonucleoprotein condensate driven by dilute phase oligomerization just appeared on the bioaRxiv, check it out here.
Ribonucleoprotein bodies are exemplars of membraneless biomolecular condensates that can form via spontaneous or driven phase transitions. The fungal protein Whi3 forms compositionally distinct ribonucleoprotein condensates that are implicated in key processes such as cell-cycle control and cell polarity. Whi3 has a modular architecture that includes a Q-rich intrinsically disordered region and a tandem RNA recognition module. Here, we uncover localized order-todisorder transitions within a 21-residue stretch of the Q-rich region. This region, which can form alpha-helical conformations, is shown to modulate protein density within Whi3-RNA condensates by driving dilute phase oligomerization. Specifically, enhancing helicity within this region enhances oligomerization in the dilute phase. This weakens the associations among disordered Qrich regions thereby diluting the concentration of Whi3 in condensates. The opposite behavior is observed when helicity within the 21-residue stretch of the Q-rich region is abrogated. Thus, dilute phase oligomers, driven by a specific sequence motif, lead to negative regulation of the stoichiometry of protein versus RNA in the dense phase. Our findings stand in contrast to other systems where oligomerization is known to enhance the drive for phase separation. Our results highlight distinctive regulatory effects over phase behavior due to local order-to-disorder transitions within intrinsically disordered regions. This provides a way to leverage molecular scale conformational preferences and coupled intermolecular associations to regulate mesoscale phase behavior and material properties of condensates.
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04/15/2021 Congratulations to our graduate student Nick Lauersdorf, who was awarded the 2021 National Defense Science and Engineering Graduate (NDSEG) Fellowship! Read Nick's interview to the Applied Physical Sciences Department here.
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04/13/2021 CONGRATULATIONS to Dr. Thomas Dombrowski who successfully defended his PhD thesis today!
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04/13/2021 Daphne gave a virtual talk at the Centre for Theoretical and Computational Physics (CFTC), Lisbon University. You can watch the recording here.
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04/13/2021 Daphne gave a talk virtually in Berlin at the Thematic Einstein Semester on Geometric and Topological Structure.
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01/07/2021 A long article "Cooperation over competition" about the research in the Klotsa group is published in Endeavors magazine, by Alyssa LaFaro.
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12/04/2020 Daphne did a Q&A on the group's research in Endeavors magazine, check it out here
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12/03/2020 Daphne gave the Fluids and Materials seminar in Bristol, UK!
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11/16/2020 Daphne was an invited speaker in session Spotlights in Thermodynamics and Computational Molecular Science (Invited Session) at the Annual meeting of the American Institute of Chemical Engineers.
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10/23/2020 Daphne gave a talk at the Fluids Seminar Series at the University of Illinois at Urbana-Champaign, UIUC.
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09/10/2020 Daphne gave a seminar at Cornell, Materials Science and Engineering Department, details here
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07/22/2020 Daphne gave a talk in the virtual seminar series organized by the BioActive UKFluids Network, you can see a recording of her talk "A touch of nonlinearity: mesoscale swimmers and active matter in fluids at intermediate Reynolds numbers" on their youtube channel and below:
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07/08/2020 Thomas Kolb successfully defended his PhD thesis! Congratulations Tom! And below some highlights from the Zoom event and socially-distanced party afterwards!
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06/24/2020 Thomas Dombrowski's paper published in Phys. Rev. Fluids and selected as Editor's suggestion!
Kinematics of a simple reciprocal model swimmer at intermediate Reynolds numbers
We study the kinematics, power and recovery strokes, fluid flows, and efficiency of a reciprocal dumbbell swimmer with finite inertia. We find the swimmer's average flow field is dominated by the flow during its power stroke, and it switches from puller-like to pusher-like depending on the Reynolds number.
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02/26/2020 Tom Kolb's paper published in Soft Matter and on the back cover - check it out here!
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02/06/2020 Thomas Dombrowski's paper "Kinematics of a simple reciprocal model swimmer at intermediate Reynolds numbers" appears on the arXiv!
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12/20/2019 Tom Kolb's paper published in Soft Matter - check it out here!
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11/14/2019 Daphne's perspective article appears in Soft Matter and on the cover, check it out here!
As Above, So Below, and also in Between: Mesoscale active matter in fluids
Living matter, such as biological tissue, can be viewed as a nonequilibrium hierarchical assembly, where at each scale self-driven components come together by consuming energy in order to form increasingly complex structures. The remarkable properties of living or “active-matter” systems, as they are generally known, such as versatility, self-healing, and self-replicating, have prompted the following questions: 1) do we understand the biology and biophysics that give rise to these properties? 2) can we achieve similar functionality with synthetic active materials? In this perspective we specifically focus on why it is important to study active matter in fluids with finite inertia. Finite inertia is relevant for mesoscale organisms that swim or fly covering at least three orders of magnitude in size (≈0.5mm-50cm) and their collective behavior is generally unknown. As a result, we are limited both in our understanding of the biology of mesoscale swarms and processes but also in our design of self-powered machines and robots at those scales. We expect interesting collective behavior to emerge because with finite inertia, come nonlinearities and the many-body hydrodynamic interactions between the organisms/particles can become quite complex, potentially leading to phenomena, such as novel flocking states and nonequilibrium phase transitions that have not been observed before and which could have great impact in materials applications.
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10/24/2019 Daphne gives a talk on active matter at the 91st Annual Meeting of The Society of Rheology
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09/18/2019 Daphne gives a talk at the Physics Department at UPenn
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09/09/2019 Tom's paper appears on the arXiv, check it out here!
Active binary mixtures of fast and slow hard spheres
We computationally studied the phase behavior and dynamics of binary mixtures of active particles, where each ‘species’ had distinct activities leading to distinct velocities, fast and slow. We obtained phase diagrams demonstrating motility-induced phase separation (MIPS) upon varying the activity and concentration of each species, and extended current kinetic theory of active/passive mixtures to active/active mixtures. We discovered two regimes of behavior quantified through the participation of each species in the dense phase compared to their monodisperse counterparts. In regime I (active/passive and active/weakly-active), we found that the dense phase was segregated by particle type into domains of fast and slow particles. Moreover, fast particles were suppressed from entering the dense phase while slow particles were enhanced entering the dense phase, compared to monodisperse systems of all-fast or all-slow particles. These effects decayed asymptotically as the activity of the slow species increased, approaching the activity of the fast species until they were negligible (regime II). In regime II, the dense phase was homogeneously mixed and each species participated in the dense phase as if it were it a monodisperse system; each species behaved as if it weren’t mixed at all. Finally, we collapsed our data defining two quantities that measure the total activity of the system. We thus found expressions that predict, a priori, the percentage of each particle type that participates in the dense phase through MIPS.
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02/08/2019 Thomas and Shannon's paper published today in Phys. Rev. Fluids, check it out here
We propose a reciprocal, self-propelled model swimmer at intermediate Reynolds numbers (Re). Our swimmer consists of two unequal spheres that oscillate in antiphase, generating nonlinear steady streaming (SS) flows. We show computationally that the SS flows enable the swimmer to propel itself, and also switch direction as Re increases. We quantify the transition in the swimming direction by collapsing our data on a critical Re and show that the transition in swimming directions corresponds to the reversal of the SS flows. Based on our findings, we propose that SS can be an important physical mechanism for motility at intermediate Re.
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Daphne was elected member-at-large (2019), Group of Statistical and Nonlinear Physics (GSNP) American Physical Society.
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08/23/2018 Paper on self-assembly of thousands of different polyhedra published in Soft Matter and featured on the cover!
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Daphne gave an invited talk at the 30th International Conference on Science and Technology of Complex Fluids that took place in San Luis Potosi, Mexico June 18-22, 2018.
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04/26/2018 The Klotsa Lab participated in Science is Awesome Day@UNC organized by the Physics Department. Three dual-language elementary schools in the Carrboro/Chapel Hill area came to UNC to spend a whole day dedicated to science! Graduate student Ian Seim helped out with hands-on activities and labs throughout the day! Daphne gave a presentation on the physics of penguin huddling, and WON best presentation voted by the students.
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Shannon Jones just submitted the first group paper Transitions in motility mechanism due to inertia in a model self-propelled two-sphere swimmer -- currently under review -- find it here in the meantime and watch the video.
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The group and Daphne Klotsa just received the NSF-CAREER award: From Single Swimmers to Swarms: A Computational Study of Mesoscale Active Matter In Fluids. We are grateful to the NSF for the support, and to colleagues and friends at Chapel Hill and broadly, who have helped and supported us!
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Tom won first prize in UNC-CHANL's 9th annual scientific art competition:
Vector Sunset, Tom Kolb. "This work characterizes the struggles of a graduate student in the computational realm. The image illustrates an effect known as ‘aliasing’ wherein previous frames of a video bleed through to the current frame. The small triangles are colored to represent direction of velocity vectors of individual particles, and, by sheer luck (or lack thereof) the artistic work ‘vector sunset’ was born."
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Tom Kolb passed his prelim!
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Tom Kolb received the NSF graduate fellowship, congratulations Tom :)
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Daphne Klotsa is invited to give the Physical Mathematics seminar at MIT on April 11th, 2017
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Daphne Klotsa is giving an invited talk at FNANO17 in Snowbird Utah in April 10-13th, 2017
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Shannon Jones and Tom Kolb gave talks at the APS March meeting 2017 in New Orleans
