Publications
106 results found
Chen L, Lee CF, Maitra A, et al., 2022, Incompressible Polar Active Fluids with Quenched Random Field Disorder in Dimensions d>2, Physical Review Letters, Vol: 129, ISSN: 0031-9007
We present a hydrodynamic theory of incompressible polar active fluids with quenched random field disorder. This theory shows that such fluids can overcome the disruption caused by the quenched disorder and move coherently, in the sense of having a nonzero mean velocity in the hydrodynamic limit. However, the scaling behavior of this class of active systems cannot be described by linearized hydrodynamics in spatial dimensions between 2 and 5. Nonetheless, we obtain the exact dimension-dependent scaling exponents in these dimensions.
Chen L, Lee CF, Maitra A, et al., 2022, Hydrodynamic theory of two-dimensional incompressible polar active fluids with quenched and annealed disorder, Physical Review E, Vol: 106, ISSN: 2470-0045
Chen L, Lee CF, Maitra A, et al., 2022, Packed Swarms on Dirt: Two-Dimensional Incompressible flocks with Quenched and Annealed Disorder, PHYSICAL REVIEW LETTERS, Vol: 129, ISSN: 0031-9007
Chen L, Lee CF, Maitra A, et al., 2022, Incompressible polar active fluids with quenched random field disorder in dimensions, Physical Review Letters, ISSN: 0031-9007
Chen L, Lee CF, Maitra A, et al., 2022, Packed swarms on dirt: two-dimensional incompressible flocks with quenched and annealed disorder, Physical Review Letters, ISSN: 0031-9007
We show that incompressible polar active fluids can exhibit an ordered, coherently moving phase even in the presence of quenched disorder in two dimensions. Unlike such active fluids with annealed disorder (i.e., time-dependent random white noise) only, which behave like equilibrium ferromagnets with long-range interactions, this robustness against quenched disorder is a fundamentally non-equilibrium phenomenon. The ordered state belongs to a new universality class, whose scaling laws we calculate using three different renormalization group schemes, which all give scaling exponents within 0.02 of each other, indicating that our results are quite accurate. Our predictions can be quantitatively tested in readily available artificial active systems, and imply that biological systems such as cell layers can move coherently in vivo, where disorder is inevitable.
Chen L, Lee CF, Maitra A, et al., 2022, Hydrodynamic theory of two-dimensional incompressible polar active fluids with quenched and annealed disorder, Physical Review E: Statistical, Nonlinear, and Soft Matter Physics, ISSN: 1539-3755
We study the moving phase of two-dimensional (2D) incompressible polar active fluids in the presence of both quenched and annealed disorder. We show that long-range polar order persists even in this defect-ridden two-dimensional system. We obtain the large-distance, long-time scaling lawsof the velocity fluctuations using three distinct dynamic renormalization group schemes. These are an uncontrolled one-loop calculation in exactly two dimensions, and two d = (dc − ε)-expansions to O(ε), obtained by two different analytic continuations of our 2D model to higher spatial dimensions:a “hard” continuation which has dc = ⁷/₃, and a “soft” continuation with dc = ⁵/₂. Surprisingly, the quenched and annealed parts of the velocity correlation function have the same anisotropy exponent and the relaxational and propagating parts of the dispersion relation have the same dynamic exponent in the nonlinear theory even though they are distinct in the linearized theory. This is due to anomalous hydrodynamics. Furthermore, all three renormalization schemes yield very similar values for the universal exponents, and, therefore, we expect the numerical values we predict forthem to be highly accurate.
Partridge B, Gonzalez Anton S, Khorshed R, et al., 2022, Heterogeneous run-and-tumble motion accounts for transient non-Gaussian super-diffusion in haematopoietic multi-potent progenitor cells, PLoS One, Vol: 17, Pages: 1-26, ISSN: 1932-6203
Multi-potent progenitor (MPP) cells act as a key intermediary step between haematopoietic stem cells and the entirety of the mature blood cell system. Their eventual fate determination is thought to be achieved through migration in and out of spatially distinct niches. Here we first analyze statistically MPP cell trajectory data obtained from a series of long time-course 3D in vivo imaging experiments on irradiated mouse calvaria, and report that MPPs display transient super-diffusion with apparent non-Gaussian displacement distributions. Second, we explain these experimental findings using a run-and-tumble model of cell motion which incorporates the observed dynamical heterogeneity of the MPPs. Third, we use our model to extrapolate the dynamics to time-periods currently inaccessible experimentally, which enables us to quantitatively estimate the time and length scales at which super-diffusion transitions to Fickian diffusion. Our work sheds light on the potential importance of motility in early haematopoietic progenitor function.
Bertrand T, Lee CF, 2022, Diversity of phase transitions and phase separations in active fluids, Physical Review Research, Vol: 4, ISSN: 2643-1564
Active matter is not only indispensable to our understanding of diverse biological processes, but also provides a fertile ground for discovering novel physics. Many emergent properties impossible for equilibrium systems have been demonstrated in active systems. These emergent features include motility-induced phase separation, a long-ranged ordered (collective motion) phase in two dimensions, and order-disorder phase coexistences (banding and reverse-banding regimes). Here, we unify these diverse phase transitions and phase coexistences into a single formulation based on generic hydrodynamic equations for active fluids. We also reveal a novel comoving coexistence phase and a multicritical point.
Pirillo C, Birch F, Tissot FS, et al., 2022, Metalloproteinase inhibition reduces AML growth, prevents stem cell loss, and improves chemotherapy effectiveness, BLOOD ADVANCES, Vol: 6, Pages: 3126-3141, ISSN: 2473-9529
Lee CF, 2022, An infinite set of integral formulae for polar, nematic, and higher order structures at the interface of motility-induced phase separation, NEW JOURNAL OF PHYSICS, Vol: 24, ISSN: 1367-2630
Killeen A, Bertrand T, Lee CF, 2022, Polar fluctuations lead to extensile nematic behavior in confluent tissues, Physical Review Letters, Vol: 128, Pages: 1-6, ISSN: 0031-9007
How can a collection of motile cells, each generating contractile nematic stresses in isolation, become an extensile nematic at the tissue-level? Understanding this seemingly contradictory experimental observation, which occurs irrespective of whether the tissue is in the liquid or solid states, is not only crucial to our understanding of diverse biological processes, but is also of fundamental interest to soft matter and many-body physics. Here, we resolve this cellular to tissue level disconnect in the small fluctuation regime by using analytical theories based on hydrodynamic descriptions of confluent tissues, in both liquid and solid states. Specifically, we show that a collection of microscopic constituents with no inherently nematic extensile forces can exhibit active extensile nematic behavior when subject to polar fluctuating forces. We further support our findings byperforming cell level simulations of minimal models of confluent tissues.
Lee CF, 2022, An infinite set of integral formulae for polar, nematic, and higher order structures at the interface of motility-induced phase separation, New Journal of Physics, Vol: 24, ISSN: 1367-2630
Motility-induced phase separation (MIPS) is a purely non-equilibriumphenomenon in which self-propelled particles phase separate without any attractive interactions. One surprising feature of MIPS is the emergence of polar, nematic, and higher order structures at the interfacial region, whose underlying physics remains poorly understood. Starting with a model of MIPS in which all many-body interactions are captured by an effective speed function and an effective pressure function that depend solely on the local particle density, I derive analytically an infinite set of integral formulae for the ordering structures at the interface. I then test these integral formulae by applying them to numerical data from direct particle dynamics simulation and find that they remain valid with a high accuracy.
Lee CF, 2021, Scaling law and universal drop size distribution of coarsening in conversion-limited phase separation, Physical Review Research, Vol: 3, Pages: 1-6, ISSN: 2643-1564
Phase separation is not only ubiquitous in diverse physical systems, but also plays an important organizational role inside biological cells. However, experimental studies of intracellular condensates (drops with condensed concentrations of specific collections of proteins and nucleic acids) have challenged the standard coarsening theories of phase separation. Specifically, the coarsening rates observed are unexpectedly slow for many intracellular condensates. Recently, Folkmann et al. [Science 373, 1218 (2021)] argued that the slow coarsening rate can be caused by the slow conversion of a condensate constituent between the state in the dilute phase and the condensate state. One implication of this conversion-limited picture is that standard theories of coarsening in phase separation (Lifshitz-Slyozov-Wagner theory of Ostwald ripening and drop coalescence schemes) no longer apply. Surprisingly, I show here that the model equations of conversion-limited phase separation can instead be mapped onto a grain growth model in a single-phase material in three dimensions. I further elucidate the universal coarsening behavior in the late stage using analytical and numerical methods.
Folkmann A, Putnam A, Lee CF, et al., 2021, Regulation of biomolecular condensates by interfacial protein clusters, Science, Vol: 373, Pages: 1218-1224, ISSN: 0036-8075
Pickering emulsions, droplet suspensions stabilized by solid particles, were discovered more than 100 years ago and are well studied in foods, oils, cosmetics, and pharmaceuticals. The particles adsorb to the droplet interface and prevent the emulsion from coarsening. Folkmann et al. report that P granules, biomolecular condensates in Caenorhabditis elegans, are an example of an intracellular Pickering emulsion (see the Perspective by Snead and Gladfelter). Biomolecular condensates are cellular compartments that form without traditional lipid membranes. This work raises the possibility that Pickering agents fulfill the role of membranes in biomolecular condensates. —DJ
Nesbitt D, Pruessner G, Lee CF, 2021, Uncovering novel phase transitions in dense dry polar active fluids using a lattice Boltzmann method, New Journal of Physics, Vol: 23, ISSN: 1367-2630
The dynamics of dry active matter have implications for a diverse collection of biological phenomena spanning a range of length and time scales, such as animal flocking, cell tissue dynamics, and swarming of inserts and bacteria. Uniting these systems are a common set of symmetries and conservation laws, defining dry active fluids as a class of physical system. Many interesting behaviours have been observed at high densities, which remain difficult to simulate due to the computational demand. Here, we show how two-dimensional dry active fluids in a dense regime can be studied using a simple modification of the lattice Boltzmann method. We apply our method on a model that exhibits motility-induced phase separation, and an active model with contact inhibition of locomotion, which has relevance to collective cell migration. For the latter, we uncover multiple novel phase transitions: two first-order and one potentially critical. We further support our simulation results with an analytical treatment of the hydrodynamic equations obtained via the Chapman-Enskog coarse-graining procedure.
Chen L, Lee CF, Toner J, 2020, Universality class for a nonequilibrium state of matter: A d=4−ε expansion study of Malthusian flocks, Physical Review E: Statistical, Nonlinear, and Soft Matter Physics, Vol: 102, Pages: 1-40, ISSN: 1539-3755
We show that “Malthusian flocks” – i.e., coherently moving collections of self-propelled entities(such as living creatures) which are being “born” and “dying” during their motion – belong toa new universality class in spatial dimensionsd >2. We calculate the universal exponents andscaling laws of this new universality class toO( ) in ad= 4− expansion, and find these aredifferent from the “canonical” exponents previously conjectured to hold for “immortal” flocks (i.e.,those without birth and death) and shown to hold for incompressible flocks with spatial dimensionsin the range of 2< d≤4. We also obtain a universal amplitude ratio relating the damping oftransverse and longitudinal velocity and density fluctuations in these systems. Furthermore, wefind a universal separatrix in real (r) space between two regions in which the equal time densitycorrelation〈δρ(r,t)δρ(0,t)〉has opposite signs. Our expansion should be quite accurate ind= 3,allowing precise quantitative comparisons between our theory, simulations, and experiments.
Chen L, Lee CF, Toner J, 2020, Moving, Reproducing, and Dying Beyond Flatland: Malthusian Flocks in Dimensions d > 2, PHYSICAL REVIEW LETTERS, Vol: 125, ISSN: 0031-9007
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Chen L, Lee CF, Toner J, 2020, Moving, reproducing, and dying beyond Flatland: Malthusian flocks in dimensions d>2, Physical Review Letters, ISSN: 0031-9007
We show that “Malthusian flocks” – i.e., coherently moving collections of self-propelled entities (such as living creatures) which are being “born” and “dying” during their motion – belong to a new universality class in spatial dimensions d>2. We calculate the universal exponents and scaling laws of this new universality class to O(ϵ) in an ϵ=4−d expansion, and find these are different from the “canonical” exponents previously conjectured to hold for “immortal” flocks (i.e., those without birth and death) and shown to hold for incompressible flocks in d>2. Our expansion should be quite accurate in d=3, allowing precise quantitative comparisons between our theory, simulations, and experiments.
Pytowski L, Lee CF, Foley AC, et al., 2020, Liquid–liquid phase separation of type II diabetes-associated IAPP initiates hydrogelation and aggregation, Proceedings of the National Academy of Sciences of USA, Vol: 117, Pages: 12050-12061, ISSN: 0027-8424
Amyloidoses (misfolded polypeptide accumulation) are among the most debilitating diseases our aging societies face. Amyloidogenesis can be catalyzed by hydrophobic–hydrophilic interfaces (e.g., air–water interface in vitro [AWI]). We recently demonstrated hydrogelation of the amyloidogenic type II diabetes-associated islet amyloid polypeptide (IAPP), a hydrophobic–hydrophilic interface-dependent process with complex kinetics. We demonstrate that human IAPP undergoes AWI-catalyzed liquid–liquid phase separation (LLPS), which initiates hydrogelation and aggregation. Insulin modulates these processes but does not prevent them. Using nonamyloidogenic rat IAPP, we show that, whereas LLPS does not require the amyloidogenic sequence, hydrogelation and aggregation do. Interestingly, both insulin and rat sequence delayed IAPP LLPS, which may reflect physiology. By developing an experimental setup and analysis tools, we show that, within the whole system (beyond the droplet stage), macroscopic interconnected aggregate clusters form, grow, fuse, and evolve via internal rearrangement, leading to overall hydrogelation. As the AWI-adsorbed gelled layer matures, its microviscosity increases. LLPS-driven aggregation may be a common amyloid feature and integral to pathology.
Lee CF, 2020, Formation of liquid-like cellular organelles depends on their composition, NATURE, Vol: 581, Pages: 144-145, ISSN: 0028-0836
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Partridge B, Lee CF, 2019, Critical motility-induced phase separation belongs to the Ising universality class, Physical Review Letters, Vol: 123, Pages: 1-6, ISSN: 0031-9007
A collection of self-propelled particles with volume exclusion interactions can exhibit the phenomenology of a gas-liquid phase separation, known as motility-induced phase separation (MIPS). The nonequilibrium nature of the system is fundamental to the phase transition; however, it is unclear whether MIPS at criticality contributes a novel universality class to nonequilibrium physics. We demonstrate here that this is not the case by showing that a generic critical MIPS belongs to the Ising universality class with conservative dynamics.
Sartori P, Lee CF, 2019, Scaling behaviour of non-equilibrium planar N-atic spin systems under weak fluctuations, New Journal of Physics, Vol: 21, Pages: 1-6, ISSN: 1367-2630
Starting from symmetry considerations, we derive the generic hydrodynamic equation of nonequilibrium XY spin systems with N-atic symmetry under weak fluctuations. Through a systematictreatment we demonstrate that, in two dimensions, these systems exhibit two types of scalingbehaviours. For N = 1, they have long-range order and are described by the flocking phase of drypolar active fluids. For all other values of N, the systems exhibit quasi long-range order, as in theequilibrium XY model at low temperature.
Overby DR, Spenlehauer A, Cairoli A, et al., 2019, Actomyosin contractility and the vimentin cytoskeleton influence giant vacuole life-cycle in Schlemm's canal endothelial cells, Annual Meeting of the Association-for-Research-in-Vision-and-Ophthalmology (ARVO), Publisher: ASSOC RESEARCH VISION OPHTHALMOLOGY INC, ISSN: 0146-0404
Weber C, Zwicker D, Juelicher F, et al., 2019, Physics of active emulsions, Reports on Progress in Physics, Vol: 82, Pages: 1-40, ISSN: 0034-4885
Phase separating systems that are maintained away from thermodynamic equilibrium via molecular processes represent a class of active systems, which we call \textit{ active emulsions}. These systems are driven by external energy input for example provided by an external fuel reservoir. The external energy input gives rise to novel phenomena that are not present in passive systems. For instance, concentration gradients can spatially organise emulsions and cause novel droplet size distributions. Another example are active droplets that are subject to chemical reactions such that their nucleation and size can be controlled and they can spontaneously divide. In this review we discuss the physics of phase separation and emulsions and show how the concepts that governs such phenomena can be extended to capture the physics of active emulsions. This physics is relevant to the spatial organisation of the biochemistry in living cells, for the development novel applications in chemical engineering and models for the origin of life.
Chen L, Lee CF, Toner J, 2018, Incompressible polar active fluids in the moving phase in dimensions d>2, New Journal of Physics, Vol: 20, ISSN: 1367-2630
We study universal behavior in the moving (polar ordered) phase of a generic system of motile particles with alignment interactions in the incompressible limit for spatial dimensions d > 2. Using a dynamical renormalization group analysis, we obtain the exact dynamic, roughness, and anisotropy exponents that describe the scaling behavior of such incompressible systems. This is the first time a compelling argument has been given for the exact values of the anomalous scaling exponents of a flock moving through an isotropic medium in d > 2.
Lee C, Wurtz JD, 2018, Novel physics arising from phase transitions in biology, Journal of Physics D: Applied Physics, Vol: 52, ISSN: 0022-3727
Phase transitions, such as the freezing of water and the magnetisation of a ferromagnet upon lowering the ambient temperature, are familiar physical phenomena. Interestingly, such a collective change of behaviour at a phase transition is also of importance to living systems. From cytoplasmic organisation inside a cell to the collective migration of cell tissue during organismal development and wound healing, phase transitions have emerged as key mechanisms underlying many crucial biological processes. However, a living system is fundamentally different from a thermal system, with driven chemical reactions (e.g. metabolism) and motility being two hallmarks of its non-equilibrium nature. In this review, we will discuss how driven chemical reactions can arrest universal coarsening kinetics expected from thermal phase separation, and how motility leads to the emergence of a novel universality class when the rotational symmetry is spontaneously broken in an incompressible fluid.
Leiming C, Lee CF, John T, 2018, Squeezed in three dimensions, moving in two: hydrodynamic theory of three-dimensional incompressible easy-plane polar active fluids, Physical Review E, Vol: 98, ISSN: 1539-3755
We study the hydrodynamic behavior of three-dimensional (3D) incompressible collections of self-propelled entities in contact with a momentum sink in a state with nonzero average velocity, hereafter called 3D easy-plane incompressible polar active fluids. We show that the hydrodynamic model for this system belongs to the same universality class as that of an equilibrium system, namely, a special 3D anisotropic magnet. The latter can be further mapped onto yet another equilibrium system, a DNA-lipid mixture in the sliding columnar phase. Through these connections we find a divergent renormalization of the damping coefficients in 3D easy-plane incompressible polar active fluids, and obtain their equal-time velocity correlation functions.
Lee C, 2018, Equilibrium kinetics of self-assembling, semi-flexible polymers, Journal of Physics: Condensed Matter, Vol: 30, ISSN: 0953-8984
Self-assembling, semi-flexible polymers are ubiquitous in biology and technology. However, conflicting accounts of the equilibrium kinetics remain for such an important system. Here, by focusing on a dynamical description of a minimal model in an overdamped environment, I identify the correct kinetic scheme that describes the system at equilibrium in the limits of high bonding energy and dilute concentration.
Lee C, Leanne M, Liu L-N, et al., 2018, Insights into the origin of distinct medin fibril morphologies induced by incubation conditions and seeding., International Journal of Molecular Sciences, Vol: 19, ISSN: 1661-6596
Incubation conditions are an important factor to consider when studying protein aggregation in vitro. Here, we employed biophysical methods and atomic force microscopy to show that agitation dramatically alters the morphology of medin, an amyloid protein deposited in the aorta. Agitation reduces the lag time for fibrillation by ~18-fold, suggesting that the rate of fibril formation plays a key role in directing the protein packing arrangement within fibrils. Utilising preformed sonicated fibrils as seeds, we probed the role of seeding on medin fibrillation and revealed three distinct fibril morphologies, with biophysical modelling explaining the salient features of experimental observations. We showed that nucleation pathways to distinct fibril morphologies may be switched on and off depending on the properties of the seeding fibrils and growth conditions. These findings may impact on the development of amyloid-based biomaterials and enhance understanding of seeding as a pathological mechanism.
Wurtz J, Lee C, 2018, Stress granule formation via ATP depletion-triggered phase separation, New Journal of Physics, Vol: 20, Pages: 1-20, ISSN: 1367-2630
Stress granules (SG) are droplets of proteins and RNA that formin the cell cytoplasm during stress conditions. We consider minimal models ofstress granule formation based on the mechanism of phase separation regulatedby ATP-driven chemical reactions. Motivated by experimental observations, weidentify a minimal model of SG formation triggered by ATP depletion. Ouranalysis indicates that ATP is continuously hydrolysed to deter SG formationunder normal conditions, and we provide specific predictions that can be testedexperimentally.
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