Daphne Klotsa

University of North Carolina at Chapel Hill

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Sharon C. Glotzer

University of Michigan–Ann Arbor

Thomas Dombrowski

University of North Carolina at Chapel Hill

Michael Engel

Friedrich-Alexander-Universität Erlangen-Nürnberg

Greg van Anders

Queen's University

Ehssan Nazockdast

University of North Carolina at Chapel Hill

Michael Swift

University of New Hampshire

Shannon Jones

University of Cincinnati

Amneet Pal Singh Bhalla

San Diego State University

Thomas Kolb

DVGW-Forschungsstelle am Engler-Bunte-Institut des Karlsruher Instituts für Technologie

Boyce E. Griffith

University of North Carolina at Chapel Hill

Cooperative Institutions

University of North Carolina at Chapel Hill

Applied Physical Sciences (United States)

University of Michigan–Ann Arbor

Duke University

University of Nottingham

Ann Arbor Center for Independent Living

BioSurfaces (United States)

University of North Carolina Health Care

Communities In Schools of Orange County

Flatiron Institute

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Kinematics of a simple reciprocal model swimmer at intermediate Reynolds numbers

Physical Review Fluids (2020)

Thomas Dombrowski Daphne Klotsa

We computationally study the kinematics of a simple model reciprocal swimmer (asymmetric dumbbell) as a function of the Reynolds number (Re) and investigate how the onset and gradual increase of inertia impacts the swimming behavior: a reversal in the swim direction, flow directions, and the swim stroke. We divide the swim stroke into the expansion and compression of the two spheres and relate them to power and recovery strokes. We find that the switch in swim direction also corresponds to a switch in power and recovery strokes. We obtain expressions for the mean swimming velocity by collapsing the net displacement during expansion and compression under power law relationships with respect to Re, the swimmer's amplitude, and the distance between the two spheres. Analyzing the fluid flows, we see the averaged flow field during expansion always resembles a pusher and compression always a puller, but when averaged over the whole cycle, the flow that dominates is the one that occurs during the power stroke. We also relate the power and recovery strokes to the swimming efficiency during times of expansion and compression, and we find that the power stroke is, surprisingly, not always more efficient than the recovery stroke. Our results may have important implications for biology and ultimately the design of artificial swimmers.

Reciprocal

10.1103/physrevfluids.5.063103

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Pairwise and collective behavior of dumbbell swimmers at intermediate Reynolds numbers

Bulletin of the American Physical Society (2021)

Thomas Dombrowski Hong T. Nguyen Daphne Klotsa

Dumbbell

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Controlling crystal self-assembly using a real-time feedback scheme

The Journal of Chemical Physics (2013)

Daphne Klotsa Robert L. Jack

We simulate crystallisation of hard spheres with short-ranged attractive potentials as a model self-assembling system. Using measurements of correlation and response functions, we develop a method whereby the interaction parameters between the particles are automatically tuned during the assembly process, in order to obtain high-quality crystals and avoid kinetic traps. The method we use is independent of the details of the interaction potential and of the structure of the final crystal—we propose that it can be applied to a wide range of self-assembling systems.

Crystal (programming language)

10.1063/1.4793527

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Predicting the self-assembly of a model colloidal crystal

Soft Matter (2011)

Daphne Klotsa Robert L. Jack

We investigate the self-assembly (crystallisation) of particles with hard cores and isotropic, square-well interactions, using a Monte Carlo scheme to simulate overdamped Langevin dynamics. We measure correlation and response functions during the early stages of assembly, and we analyse the results using fluctuation-dissipation theorems, aiming to predict which systems will self-assemble successfully and which will get stuck in disordered states. The early-time correlation and response measurements are made before significant crystallisation has taken place, indicating that dynamical measurements are valuable in measuring a system's propensity for kinetic trapping.

Langevin dynamics

Kinetic Monte Carlo

Colloidal particle

10.1039/c1sm05456b

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A self-propelled two-sphere swimmer

APS March Meeting Abstracts (2017)

Shannon Jones Amneet Pal Singh Bhalla Boyce E. Griffith Daphne Klotsa

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Propulsion of a Two-Sphere Swimmer

Physical Review Letters (2015)

Daphne Klotsa Kyle A. Baldwin R. Hill R. M. Bowley Michael Swift

We describe experiments and simulations demonstrating the propulsion of a neutrally-buoyant swimmer that consists of a pair of spheres attached by a spring, immersed in a vibrating fluid. The vibration of the fluid induces relative motion of the spheres which, for sufficiently large amplitudes, can lead to motion of the center of mass of the two spheres. We find that the swimming speed obtained from both experiment and simulation agree and collapse onto a single curve if plotted as a function of the streaming Reynolds number, suggesting that the propulsion is related to streaming flows. There appears to be a critical onset value of the streaming Reynolds number for swimming to occur. We observe a change in the streaming flows as the Reynolds number increases, from that generated by two independent oscillating spheres to a collective flow pattern around the swimmer as a whole. The mechanism for swimming is traced to a strengthening of a jet of fluid in the wake of the swimmer.

Neutral buoyancy

10.1103/physrevlett.115.248102

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Citations (52)

Clusters of polyhedra in spherical confinement

Carolina Digital Repository (University of North Carolina at Chapel Hill) (2016)

Erin G. Teich Greg van Anders Daphne Klotsa Julia Dshemuchadse Sharon C. Glotzer

Polyhedron

10.17615/x2gw-a357

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Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate

Ian Seim Ammon E. Posey Wilton T. Snead Benjamin M. Stormo Daphne Klotsa

Ribonucleoprotein bodies are exemplars of membraneless biomolecular condensates that can form via spontaneous or driven phase transitions. The fungal protein Whi3 forms ribonucleoprotein condensates with different RNA molecules, and these condensates are implicated in key processes such as cell-cycle control and generating cell polarity. Whi3 has a modular architecture that includes a Q-rich intrinsically disordered region (IDR) and a tandem RNA recognition module. Here, we demonstrate that a 21-residue stretch within the Q-rich IDR has a weak intrinsic preference for forming alpha-helical conformations. Through mutagenesis, we find that increased alpha helicity enhances oligomerization in the dilute phase. One consequence of enhanced oligomerization is a dilution of Whi3 in the dense phase. The opposite behavior is observed when helicity within the 21-residue stretch of the Q-rich region is abrogated. Thus, the formation of dilute phase oligomers, driven by a specific sequence motif and potential synergies with the rest of the IDR, opposes incorporation of the Whi3 protein into the dense phase, thereby altering the dense phase stoichiometry of protein to RNA. Our findings, which stand in contrast to other systems where oligomerization has been shown to enhance the drive for phase separation, point to a novel mechanism that might be operative for influencing compositions of condensates. Our work also points to routes for designing synthetic ribonucleoprotein condensates whereby modulation of protein oligomerization via homotypic interactions can impact dense phase concentrations, stoichiometries, and material properties.

Helicity

Heterogeneous nuclear ribonucleoprotein

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Onset of motion and collective behavior for two-sphere swimmers

Bulletin of the American Physical Society (2016)

Daphne Klotsa Kyle A. Baldwin R. Hill R. M. Bowley Michael Swift

Collective motion

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Digital Alchemy for Materials Design: Colloids and Beyond

Bulletin of the American Physical Society (2016)

Greg van Anders Daphne Klotsa Andrew S. Karas Paul M. Dodd Sharon C. Glotzer

Starting with the early alchemists, a holy grail of science has been to make desired materials by modifying the attributes of basic building blocks. Building blocks that show promise for assembling new complex materials can be synthesized at the nanoscale with attributes that would astonish the ancient alchemists in their versatility. However, this versatility means that making a direct connection between building-block attributes and bulk structure is both necessary for rationally engineering materials and difficult because building block attributes can be altered in many ways. Here we show how to exploit the malleability of the valence of colloidal nanoparticle “elements” to directly and quantitatively link building-block attributes to bulk structure through a statistical thermodynamic framework we term “digital alchemy”. We use this framework to optimize building blocks for a given target structure and to determine which building-block attributes are most important to control for self-assembly, through...

Holy Grail

Synchronicity

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