Bulletin of the American Physical Society
APS March Meeting 2023
Volume 68, Number 3
Las Vegas, Nevada (March 5-10)
Virtual (March 20-22); Time Zone: Pacific Time
Session G14: Bio-inspired Phase Separation IFocus
|
Hide Abstracts |
Sponsoring Units: DSOFT DPOLY Chair: Omar Saleh, University of California, Santa Barbara; Sam Wilken, University of California, Santa Barbara Room: Room 206 |
Tuesday, March 7, 2023 11:30AM - 12:06PM |
G14.00001: Biologically-Inspired Active Droplets: from Reaction Crucibles to Robots(?) Invited Speaker: Eric R Dufresne Living cells need to organize chemical reactions. In school, we learned how lipid bilayers create and maintain compartments with distinct compositions. Most attempts to mimic biological compartmentalization have re-capitulated this strategy, with impressive results. However, since thermodynamics favors the formation of symmetric compositions across the bilayer, efficient encapsulation requires precise control of kinetic pathways, often using microfluidic devices. |
Tuesday, March 7, 2023 12:06PM - 12:18PM |
G14.00002: Hyperuniform Phase-separated DNA Droplets Sam Wilken, Aria Chaderjian, Omar A Saleh Many recent studies of phase separation in biology focus on phase separation as a dynamic control mechanism for cellular function, but it can also result in complex mesoscopic structures. Here, we investigate the long-range structures formed by a model phase-separating DNA system. We use DNA nanostars, a system of finite-valence, attractive particles roughly 10nm in size whose sequence is designed such that they self-assemble into liquid droplets on the micron scale via a binodal phase transition. We acquire images of fluorescent DNA nanostar droplets, and calculate from the images the scattering function χ(q)=<ρ(q)ρ(-q)>. We find that the structure is hyperuniform, corresponding to a disordered structure with anomalously small long range density fluctuations, χ(q→0)∼qα with α=2. Droplet diffusion tends to erase this structure, while measurements of multi-phase nanostar systems show hyperuniformity only occurs within, but not across, liquid species. Overall, our observations are consistent with a hyperuniform structure that is driven by spinodal decomposition, and modulated by Brownian motion. We expect the hyperuniformity exhibited by the model phase separating system of DNA nanostars will provide insight into certain phase-separated structures seen in nature. |
Tuesday, March 7, 2023 12:18PM - 12:30PM |
G14.00003: Inverse engineering of phase separating bio-condensates Fan Chen, William M Jacobs Liquid-liquid phase separation (LLPS) can result in complex phase diagrams even when the components comprising a fluid experience simple pairwise interactions. However, these interactions may not be independent of one another, since they arise from a limited set of physicochemical molecular features. Inspired by the observation that intracellular protein/RNA mixtures phase separate into many immiscible membraneless organelles, we seek to design pairwise interactions that can arise from a small number of physicochemical molecular features and yet give rise to complex phase diagrams. We first propose an algorithm for determining the minimum number of physicochemical features required to establish a target phase diagram within a mean-field theory. We then demonstrate the validity of our approach by designing polymer sequences and patchy colloidal particles with a small number of monomer and patch types, respectively, and verifying that the target phase diagram is realized. Our approach provides a principled way to explore the relationship between the physicochemical properties of biomolecules and intracellular LLPS, as well as a systematic design strategy for engineering complex biomolecular condensates de novo. |
Tuesday, March 7, 2023 12:30PM - 12:42PM |
G14.00004: Interface dynamics of active/passive mixtures Fernando Caballero, Paarth Gulati, M Cristina Marchetti Understanding the interfacial properties of phase separating mixtures of active and passive fluids is relevant to both biological processes and to the design of new functional materials. Recent experiments on mixtures of active microtubule-based liquid crystals and passive fluids have shown that activity can arrest and suppress phase separation, drive propagating surface waves, and strongly enhance interfacial fluctuations, resulting in new nonequilibrium scaling forms of the height fluctuation spectrum. We present analytical work on the behavior of the interface between an active nematic and a passive fluid. Starting from a continuum model of the mixture formulated in terms of the nematic concentration, the active liquid crystalline order parameter and flow, we derive analytically a reduced description of the interface dynamics in terms of coupled equations for the interface height and the nematic director field at the interface. We show that the linearized form of the equations captures activity-driven instabilities and propagating waves, leading to microphase separated states with droplet size distribution and growth laws observed experimentally and numerically. The nonlinear terms in the equations might shed light on the nonequilibrium properties of the height correlation spectrum. |
Tuesday, March 7, 2023 12:42PM - 12:54PM |
G14.00005: Depletion-Driven Morphological Control of Bundled Actin Networks James H Clarke, Francis M Cavanna, Anne D Crowell, Lauren Melcher, Justin R Houser, Kristin Graham, Allison M Green, Jeanne C Stachowiak, Thomas M Truskett, Delia Milliron, Adrianne M Rosales, Moumita Das, José R Alvarado The actin cytoskeleton is a semiflexible biopolymer network whose morphology is controlled by a wide range of biochemical and physical factors. Actin is known to undergo a phase transition from a single-filament state to a bundled state by the addition of polyethylene glycol (PEG) molecules in sufficient concentration. While the depletion interaction experienced by these biopolymers is well-known, the effect of changing the molecular weight of the depletant is less well understood. Here, we experimentally identify a phase transition in solutions of actin from networks of filaments to networks of bundles by varying the molecular weight of PEG polymers, while holding the concentration of these PEG polymers constant. We examine the states straddling the phase transition in terms of micro and macroscale properties. We find that the mesh size, bundle diameter, persistence length, and intra-bundle spacing between filaments across the line of criticality do not show significant differences, while the relaxation time, storage modulus, and degree of bundling change between the two states do show significant differences. Our results demonstrate the ability to tune actin network morphology and mechanics by controlling depletant size, a property which could be exploited to develop actin-based materials with switchable rigidity. |
Tuesday, March 7, 2023 12:54PM - 1:06PM |
G14.00006: Tuning nucleation kinetics via nonequilibrium chemical reactions Yongick Cho, William M Jacobs Unlike fluids at thermal equilibrium, biomolecular mixtures in living systems can sustain nonequilibrium steady states, in which active processes modify the conformational states of the constituent molecules. Despite qualitative similarities with liquid-liquid phase-separation at thermal equilibrium, the extent to which the phase-separation kinetics differ in nonequilibrium steady states remains unclear. Here we consider the influence of driven chemical reactions, which couple molecular conformational changes to a chemical fuel source. We show that driven chemical reactions can alter the nucleation kinetics of liquid-liquid phase separation in a manner that is consistent with classical nucleation theory, but can only be rationalized by introducing a nonequilibrium interfacial tension. We demonstrate that deviations from equilibrium kinetics arise when the chemical reactions are driven inhomogeneously between the phases, leading to different effective thermodynamics on either side of the interface. Finally, we identify conditions under which nucleation can be accelerated without changing the energetics or supersaturation, thus breaking the correlation between fast nucleation and strong driving forces that is typical of phase separation and self-assembly at thermal equilibrium. |
Tuesday, March 7, 2023 1:06PM - 1:18PM |
G14.00007: Biomolecular condensates as nonequilibrium soft materials Sebastian T Coupe, Nikta Fakhri Biomolecular condensates are biopolymer bodies within cells thought to act as cellular biochemical organizing centers. The protein-protein, protein-nucleic acid, and nucleic acid-nucleic acid interactions within these membraneless organelles dictate condensate formation, dynamics, and material state. Enzyme activity has been proposed to regulate these interactions and thereby regulate condensate properties, with DEAD-box helicases as a prime candidate class of enzymes for fulfilling this role. In this work, we connect the ATP-dependent RNA helicase activity of a well-studied DEAD-box helicase to the properties of reconstituted condensates. By varying the ability for the RNA substrate to self-interact and through varying chemical energy available to the helicase, we are able to assess the impact of the enzyme's activity on the dynamics and material state of the protein-RNA condensates. Interestingly, enzyme activity also drives mesoscopic structural features of these systems, which are also highly dependent on chemical energy. These results demonstrate how an enzyme can directly impact the dynamics of a biomolecular condensate, revealing broader insights into the interactions that govern condensate structure and dynamics. Furthermore, this system represents a novel class of nonequilibrium soft matter materials with dynamically regulatable properties. |
Tuesday, March 7, 2023 1:18PM - 1:30PM |
G14.00008: Arresting Spinodal-like Structures in Elastic Matrices Carla Fernandez-Rico, Eric R Dufresne, Robert Style, Charlotta Lorenz |
Tuesday, March 7, 2023 1:30PM - 1:42PM |
G14.00009: Liquid droplet coarsening in an active biomimetic fluid Jeremy Laprade, Hriday Talreja, Anthony Gillespie, William B Rogers, Guillaume Duclos Membraneless organelles that are found in the cell cytoplasm perform many necessary functions for the cell's survival. These organelles often display liquid-like dynamics and can grow and coarsen over time. It is not yet clear how the out of equilibrium nature of the cell cytoplasm contributes to organelle coarsening. In this work, we immerse phase separating DNA particles in microtubule-based active fluids to investigate the impact of cytoplasmic flows on droplet coarsening dynamics. We will quantify the motion of objects in an actively mixed fluid, and examine average size scaling and size distributions of droplets advected by active chaotic flows. We will show that actively mixed droplets exhibit a wider size distribution while maintaining a diffusive-like average size scaling. These results shine new light on how the physics of the cytoplasm is distinct from the physics of conventional fluid at thermodynamic equilibrium. |
Tuesday, March 7, 2023 1:42PM - 1:54PM |
G14.00010: Modular RNA motifs for orthogonal phase-separated compartments Elisa Franco, Shiyi Li, Anli Tang, Jaimie M Stewart, Melissa A Klocke, Paul Rothemund
|
Tuesday, March 7, 2023 1:54PM - 2:06PM |
G14.00011: Re-entrant demixing behavior due to differences in diffusivity in active matter at intermediate and high densities Erin McCarthy, Ojan K Damavandi, Raj Kumar Manna, M Lisa L Manning Spontaneous phase separation, or demixing, is an emergent behavior important in biological phenomena such as cell sorting/patterning, and the formation of non-membrane bound organelles. In particulate matter, differences in size, shape and persistent motion have all been shown to cause large-scale demixing. An open question is whether differences in diffusivity, i.e. the magnitude of translational noise, between particle types – which is possible in active matter out of equilibrium – can drive demixing. Recently, researchers found that in a two-species particle-based packing, differential diffusivity drives complete phase separation up to a packing fraction of 0.7. We use an improved particle-based simulation with a faster run time to investigate whether this demixing persists at higher densities, approaching the limit of confluency. We find that for particle packing fractions between 0.7 and 1.0, the system demixes for certain diffusivity ratios. However, we observe that the system remains mixed at higher packing fractions, exposing reentrant behavior in the phase diagram. This result suggests the importance of free-space between particles to this mechanism of activity-based demixing. Using a Voronoi model, we examine a confluent system with differential diffusivity and find no evidence of phase-separation, consistent with the highest-density particle-based simulations. |
Tuesday, March 7, 2023 2:06PM - 2:18PM |
G14.00012: Phase Separation and Gelation of Chemically Reactive Macromolecules Ruoyao Zhang, Sheng Mao, Mikko Haataja Phase transitions are ubiquitous in inanimate systems, and recent discoveries have shown that they also play a key role in living cells. Many membraneless, liquid-like organelles ("biomolecular condensates") have been shown to form via liquid-liquid phase separation (LLPS). Intriguingly, several such condensates display irreversible aging behavior akin to gelation. In this work, we first construct a theoretical framework to investigate the phase behavior of multi-component macromolecular systems in which chemical reactions, phase separation and gelation are present concurrently. We then formulate a thermodynamically consistent phase-field model to study coupled compositional and structural phase transformation phenomena in chemically reactive, multi-component biomolecular systems undergoing LLPS. The mesoscale nature of phase-field models enables the study of spatially extended systems over macroscopic timescales. Results such as phase diagrams that capture LLPS and gelation, size distribution of droplets and morphology of gel-state condensates will be presented. |
Tuesday, March 7, 2023 2:18PM - 2:30PM |
G14.00013: Active Turbulence leads to Microphase Separation Paarth Gulati, Fernando Caballero, M Cristina Marchetti Phase-separating active-passive mixtures are a new class of non-equilibrium binary fluids. Recent experiments have demonstrated a number of unconventional properties of these systems, including propagating interfacial waves and stable microphase separated states. We use a continuum model of active nematics coupled to a scalar phase field to study these phenomena. As with previous models of scalar active matter coupled to flow, we find that activity can arrest the transition to bulk phase separation. The active flows lead to a steady state composed of splitting and merging extensile droplets – an active emulsion. We find that there is a steady droplet size distribution with a mean radius controlled by the activity. To capture the evolution to this dynamical steady state and its properties, we describe the emulsion using coagulation-fragmentation equations for the droplet sizes. Using this model, we derive the coarsening exponents. We finally compare our results to experiments in a mixture of a passive fluid and an active microtubule suspension. |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700