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Chiu Fan Lee

Publications and source records attributed to Chiu Fan Lee.

At least 55 records · Page 3Linked to original sources

Incompressible polar active fluids in the moving phase

We study universal behavior in the moving 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 $d>2$.

cond-mat.soft↗

Equilibrium kinetics of self-assembling, semi-flexible polymers

Self-assembling, semi-flexible polymers are ubiquitous in biology and technology. However, there remain conflicting accounts of the equilibrium kinetics 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.

cond-mat.soft↗

Squeezed in three dimensions, moving in two: Hydrodynamic theory of 3D incompressible easy-plane polar active fluids

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 non-zero 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.

cond-mat.soft↗

Stress granule formation via ATP depletion-triggered phase separation

Stress granules (SG) are droplets of proteins and RNA that form in the cell cytoplasm during stress conditions. We consider minimal models of stress granule formation based on the mechanism of phase separation regulated by ATP-driven chemical reactions. Motivated by experimental observations, we identify a minimal model of SG formation triggered by ATP depletion. Our analysis indicates that ATP is continuously hydrolysed to deter SG formation under normal conditions, and we provide specific predictions that can be tested experimentally.

physics.bio-ph↗

Chemical reaction-controlled phase separated drops: Formation, size selection, and coarsening

Phase separation under non-equilibrium conditions is exploited by biological cells to organize their cytoplasm but remains poorly understood as a physical phenomenon. Here, we study a ternary fluid model in which phase-separating molecules can be converted into soluble molecules, and vice versa, via chemical reactions. We elucidate using analytical and simulation methods how drop size, formation, and coarsening can be controlled by the chemical reaction rates, and categorize the qualitative behavior of the system into distinct regimes. Ostwald ripening arrest occurs above critical reaction rates, demonstrating that this transition belongs entirely to the non-equilibrium regime. Our model is a minimal representation of the cell cytoplasm.

cond-mat.soft↗

Edge instability in incompressible planar active fluids

Interfacial instability is highly relevant to many important biological processes. A key example arises in wound healing experiments, which observe that an epithelial layer with an initially straight edge does not heal uniformly. We consider the phenomenon in the context of active fluids. Improving upon the approximation used in J. Zimmermann, M. Basan and H. Levine, Euro. Phys. J.: Special Topics 223, 1259 (2014), we perform a linear stability analysis on a two dimensional incompressible hydrodynamic model of an active fluid with an open interface. We categorise the stability of the model and find that for experimentally relevant parameters, fingering stability is always absent in this minimal model. Our results point to the crucial importance of density variation in the fingering instability in tissue regeneration.

cond-mat.soft↗

Droplet Ripening in Concentration Gradients

Living cells use phase separation and concentration gradients to organize chemical compartments in space. Here, we present a theoretical study of droplet dynamics in gradient systems. We derive the corresponding growth law of droplets and find that droplets exhibit a drift velocity and position dependent growth. As a consequence, the dissolution boundary moves through the system, thereby segregating droplets to one end. We show that for steep enough gradients, the ripening leads to a transient arrest of droplet growth that is induced by an narrowing of the droplet size distribution.

physics.bio-ph↗

Interface stability, interface fluctuations, and the Gibbs-Thomson relation in motility-induced phase separations

Minimal models of self-propelled particles with short-range volume exclusion interactions have been shown to exhibit signatures of phase separation. Here I show that the observed interfacial stability and fluctuations in motility-induced phase separations (MIPS) can be explained by modeling the microscopic dynamics of the active particles in the interfacial region. In addition, I demonstrate the validity of the Gibbs-Thomson relation in MIPS, which provides a functional relationship between the size of a condensed drop and its surrounding vapor concentration. As a result, the coarsening dynamics of MIPS at vanishing supersaturation follows the classic Lifshitz-Slyozov scaling law at the late stage.

cond-mat.soft↗

Statistical Mechanics and Kinetics of Amyloid Fibrillation

Amyloid fibrillation is a protein self-assembly phenomenon that is intimately related to well-known human neurodegenerative diseases. During the past few decades, striking advances have been achieved in our understanding of the physical origin of this phenomenon and they constitute the contents of this review. Starting from a minimal model of amyloid fibrils, we explore systematically the equilibrium and kinetic aspects of amyloid fibrillation in both dilute and semi-dilute limits. We then incorporate further molecular mechanisms into the analyses. We also discuss the mathematical foundation of kinetic modeling based on chemical mass-action equations, the quantitative linkage with experimental measurements, as well as the procedure to perform global fitting.

q-bio.BM↗

Surprising mappings of 2D polar active fluids to 2D soap and 1D sandblasting

Active fluids and growing interfaces are two well-studied but very different non-equilibrium systems. Each exhibits non-equilibrium behavior quite different from that of their equilibrium counterparts. Here we demonstrate a surprising connection between these two: the ordered phase of incompressible polar active fluids in two spatial dimensions without momentum conservation, and growing one-dimensional interfaces (that is, the 1+1-dimensional Kardar-Parisi-Zhang equation), in fact belong to the same universality class. This universality class also includes two equilibrium systems : two-dimensional smectic liquid crystals, and a peculiar kind of constrained two-dimensional ferromagnet. We use these connections to show that two-dimensional incompressible flocks are robust against fluctuations, and exhibit universal long-ranged, anisotropic spatio-temporal correlations of those fluctuations. We also thereby determine the exact values of the anisotropy exponent $ζ$ and the roughness exponents $χ_{_{x,y}}$ that characterize these correlations.

cond-mat.soft↗

Comment on "Anomalous Discontinuity at the Percolation Critical Point of Active Gels"

In their recent work Sheinman et al. [Phys. Rev. Lett. 114, 098104 (2015)] introduce a variation of percolation which they call no-enclaves percolation (NEP). The main claims are 1) the salient physics captured in NEP is closer to what happens experimentally; 2) The Fisher exponent of NEP, is $τ=1.82(1)$; 3) Due to the different Fisher exponent, NEP constitutes a universality class distinct from random percolation (RP). While we fully agree with 1) and found NEP to be a very interesting variation of random percolation, we disagree with 2) and 3). We will demonstrate that $τ$ is exactly $2$, directly derivable from RP, and thus there is no foundation of a new universality class.

cond-mat.soft↗

Percolation with trapping mechanism drives active gels to the critically connected state

Cell motility and tissue morphogenesis depend crucially on the dynamic remodelling of actomyosin networks. An actomyosin network consists of an actin polymer network connected by crosslinker proteins and motor protein myosins that generate internal stresses on the network. A recent discovery shows that for a range of experimental parameters, actomyosin networks contract to clusters with a power-law size distribution [Alvarado J. et al. (2013) Nature Physics 9 591]. Here, we argue that actomyosin networks can exhibit robust critical signature without fine-tuning because the dynamics of the system can be mapped onto a modified version of percolation with trapping (PT), which is known to show critical behaviour belonging to the static percolation universality class without the need of fine-tuning of a control parameter. We further employ our PT model to generate experimentally testable predictions.

cond-mat.soft↗

Critical Phenomenon of the Order-Disorder Transition in Incompressible Flocks

We study incompressible systems of motile particles with alignment interactions. Unlike their compressible counterparts, in which the order-disorder (i.e., moving to static) transition, tuned by either noise or number density, is discontinuous, in incompressible systems this transition can be continuous, and belongs to a new universality class. We calculate the critical exponents to $O(ε)$in an $ε=4-d$ expansion, and derive two exact scaling relations. This is the first analytic treatment of a phase transition in a new universality class in an active system.

cond-mat.soft↗

Thermal breakage of a semiflexible polymer: Breakage profile and rate

Understanding fluctuation-induced breakages in polymers has important implications for basic and applied sciences. Here I present for the first time an analytical treatment of the thermal breakage problem of a semi-flexible polymer model that is asymptotically exact in the low temperature and high friction limits. Specifically, I provide analytical expressions for the breakage propensity and rate, and discuss the generalities of the results and their relevance to biopolymers.

cond-mat.mtrl-sci↗

Thermodynamic costs of information processing in sensory adaption

Biological sensory systems react to changes in their surroundings. They are characterized by fast response and slow adaptation to varying environmental cues. Insofar as sensory adaptive systems map environmental changes to changes of their internal degrees of freedom, they can be regarded as computational devices manipulating information. Landauer established that information is ultimately physical, and its manipulation subject to the entropic and energetic bounds of thermodynamics. Thus the fundamental costs of biological sensory adaptation can be elucidated by tracking how the information the system has about its environment is altered. These bounds are particularly relevant for small organisms, which unlike everyday computers operate at very low energies. In this paper, we establish a general framework for the thermodynamics of information processing in sensing. With it, we quantify how during sensory adaptation information about the past is erased, while information about the present is gathered. This process produces entropy larger than the amount of old information erased and has an energetic cost bounded by the amount of new information written to memory. We apply these principles to the E. coli's chemotaxis pathway during binary ligand concentration changes. In this regime, we quantify the amount of information stored by each methyl group and show that receptors consume energy in the range of the information-theoretic minimum. Our work provides a basis for further inquiries into more complex phenomena, such as gradient sensing and frequency response.

cond-mat.stat-mech↗

Fluctuations and the role of collision duration in reaction-diffusion systems

In a reaction-diffusion system, fluctuations in both diffusion and reaction events, have important effects on the steady-state statistics of the system. Here, we argue through extensive lattice simulations, mean-field type arguments, and the Doi-Peliti formalism that the collision duration statistics -- i.e., the time two particles stay together in a lattice site -- plays a leading role in determining the steady state of the system. We obtain approximate expressions for the average densities of the chemical species and for the critical diffusion coefficient required to sustain the reaction.

cond-mat.soft↗

Active particles under confinement: Aggregation at the wall and gradient formation inside a channel

I study the confinement-induced aggregation phenomenon in a minimal model of self-propelled particles inside a channel. Starting from first principles, I derive a set of equations that govern the density profile of such a system at the steady-state, and calculate analytically how the aggregation at the walls varies with the physical parameters of the system. I also investigate how the gradient of the particle density varies if the inside of the channel is partitioned into two regions within which the active particles exhibit distinct levels of fluctuations in their directions of travel.

cond-mat.soft↗

Length distribution of stiff, self-assembled polymers at thermal equilibrium

We investigate the length distribution of self-assembled, long and stiff polymers at thermal equilibrium. Our analysis is based on calculating the partition functions of stiff polymers of variable lengths in the elastic regime. Our conclusion is that the length distribution of this self-assembled system follows closely the exponential distribution, except at the short length limit. We then discuss the implications of our results on the experimentally observed length distributions in amyloid fibrils.

cond-mat.soft↗