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Fangfu Ye

Publications and source records attributed to Fangfu Ye.

At least 19 recordsLinked to original sources

Moment analysis of two-dimensional active Brownian run-and-tumble particles

We study an active Brownian run-and-tumble particle (ABRTP) model, that consists of an active Brownian run state during which the active velocity of the particle diffuses on the unit circle, and a tumble state during which the active velocity is zero, both with exponentially distributed time. Additionally we add a harmonic trap as an external potential. In the appropriate limits the ABRTP model reduces either to the active Brownian particle model, or the run-and-tumble particle model. Using the method of direct integration the equation of motion, pioneered by Kac, we obtain exact moments for the Laplace transform of the time dependent ABRTP, in the presence or absence of a harmonic trap. In addition we estimate the distribution moments with the help of the Chebyshev polynomials. Our results are in excellent agreement with the experiments.

cond-mat.stat-mech

Interfacial Stability in Tensionless Phase-Separated Quorum-Sensing Systems

Interfacial phenomena of motility-induced phase separation of active particles challenge our conventional understanding of phase coexistence. Despite the ubiquity of nonmechanical communication couplings among real active particles, most works on active interface have concentrated on active Brownian systems with steric interparticle interactions. Here, we study the interfacial behavior of phase-separated active particles interacting solely via quorum-sensing communications using both theory and simulations. Strikingly, we find that the quorum-sensing active system exhibits vanishing mechanical surface tension but nonzero effective capillary surface tension. We further demonstrate that the mechanical equilibrium of the tensionless interface is sustained by polarization force at the interface; while its dynamics is governed by the surface stiffness, which arises from tangential particle flux induced by local interfacial deformation. Our work reveals the fundamental distinction between mechanical and capillary surface tensions in active matter and paves the way for future exploration of active interface phenomena.

cond-mat.soft

Intrinsic pressure as a convenient mechanical framework for dry active matter

The identification of local pressure in active matter systems remains a subject of considerable debate. Through theoretical calculations and extensive simulations of various active systems, we demonstrate that intrinsic pressure (defined in the same way as in passive systems) is an ideal candidate for local pressure of dry active matter, while the self-propelling forces on the active particles are considered as effective external forces originating from the environment. Such a framework is universal and especially convenient for analyzing mechanics of dry active systems, and it recovers the conventional scenario of mechanical equilibrium well-known in passive systems. Thus, our work is of fundamental importance to further explore mechanics and thermodynamics of complex active systems.

cond-mat.soft

Agent4S: The Transformation of Research Paradigms from the Perspective of Large Language Models

While AI for Science (AI4S) serves as an analytical tool in the current research paradigm, it doesn't solve its core inefficiency. We propose "Agent for Science" (Agent4S)-the use of LLM-driven agents to automate the entire research workflow-as the true Fifth Scientific Paradigm. This paper introduces a five-level classification for Agent4S, outlining a clear roadmap from simple task automation to fully autonomous, collaborative "AI Scientists." This framework defines the next revolutionary step in scientific discovery.

cs.AI

Coherent Turning Behaviors Revealed Across Adherent Cells

Adherent cells have long been known to display two modes during migration: a faster mode that is persistent in direction and a slower one where they turn. Compared to the persistent mode, the turns are less studied. Here we develop a simple yet effective protocol to isolate the turns quantitatively. With the protocol, we study different adherent cells in different morphological states and find that, during turns, the cells behave as rotors with constant turning rates but random turning directions. To perform tactic motion, the cells bias the sign of turning towards the stimuli. Our results clarify the bimodal kinematics of adherent cell migration. Compared to the rotational-diffusion-based turning dynamics - which has been widely implemented, our data reveal a distinct picture, where turns are governed by a deterministic angular velocity.

physics.bio-ph

Exact moments for a run and tumble particle in a harmonic trap with a finite tumble time

We study the problem of a run and tumble particle in a harmonic trap, with a finite run and tumble time, by a direct integration of the equation of motion. An exact 1D steady state distribution, diagram laws and a programmable Volterra difference equation are derived to calculate any order of moments in any other dimension, both for steady state as well as the Laplace transform in time for the intermediate states. We also use the moments to infer the distribution by considering a Gaussian quadrature for the corresponding measure, and from the scaling law of high order moments.

cond-mat.stat-mech

Universality in the dynamics of vesicle translocation through a hole

We analyze the translocation process of a spherical vesicle, made of membrane and incompressible fluid, through a hole smaller than the vesicle size, driven by pressure difference $ΔP$. We show that such a vesicle shows certain universal characteristics which is independent of the details of the membrane elasticity; (i) there is a critical pressure $ΔP_{\rm c}$ below which no translocation occurs, (ii) $ΔP_{\rm c}$ decreases to zero as the vesicle radius $R_0$ approaches the hole radius $a$, satisfying the scaling relation $ΔP_{\rm c} \sim (R_0 - a)^{3/2}$, and (iii) the translocation time $τ$ diverges as $ΔP$ decreases to $ΔP_{\rm c}$, satisfying the scaling relation $τ\sim (ΔP -ΔP_{\rm c})^{-1/2}$.

cond-mat.soft

Trapping Instability of an Active Particle in Steering Potential Fields

A particle driven by active self-propulsion can be subject to inhomogeneous potential fields, steering its orientation and leading to confinement and eventual trapping. Analytical treatment of capture and/or release dynamics for general steering potentials presents a challenge due to its coupling between external potential fields and intrinsic active noise. By using the projection operator method we obtain the coarse-grained Dynkin equations with orientation integrated out in the large fluctuations limit, and derive explicit analytical solutions for the mean first passage time in radially symmetric point source trapping potentials. We analyze the ensuing trapping instabilities related to a critical value of the steering potential strength below which the particle either cannot be lured into the trap, or above which it is unable to leave the trap after being lured into it.

cond-mat.soft

Emergent Stripes of Active Rotors in Shear Flows

The shear-induced self-organization of active rotors into stripy aggregates is studied by carrying out computational simulations. The rotors, modeled by monolayers of frictional spheres, develop to stripy microstructures only when they counterrotate with respect to the vorticity of the imposed shear flow. The average width of the stripes is demonstrated to be linearly dependent on the relative intensity of active torque to the shear rate. By giving insight into three collective particle behaviors, i.e., shear-induced diffusion, rotation-induced rearrangement, and edge flows, we explain the mechanisms of formation of the particle stripes. Additionally, the rheological result shows the dependence of shear and rotational viscosities on the active torque direction and the oddness of the normal stress response. By exhibiting a collective phenomenon of active rotors, our study paves the way to understanding chiral active matter.

cond-mat.soft

Model of metameric locomotion in active directional filaments

Locomotion in segmented animals, such as annelids and myriapods (centipedes and millipedes), is generated by a coordinated movement known as metameric locomotion, which can be also implemented in robots designed to perform specific tasks. We introduce a theoretical model, based on an active directional motion of the head segment and a passive trailing of the rest of the body segments, in order to formalize and study the metameric locomotion. The model is specifically formulated as a steered Ornstein-Uhlenbeck curvature process, preserving the continuity of the curvature along the whole body filament, and thus supersedes the simple active Brownian model, which would be inapplicable in this case. We obtain the probability density by analytically solving the Fokker-Planck equation pertinent to the model. We also calculate explicitly the correlators, such as the mean-square orientational fluctuations, the orientational correlation function and the mean-square separation between the head and tail segments, both analytically either via the Fokker-Planck equation or directly by either solving analytically or implementing it numerically from the Langevin equations. The analytical and numerical results coincide. Our theoretical model can help understand the locomotion of metameric animals and instruct the design of metameric robots.

cond-mat.soft

Ordering of adsorbed rigid rods mediated by the Boussinesq interaction on a soft substrate

Orientational ordering driven by mechanical distortion of soft substrates plays a major role in material transformation processes such as elastocapillarity and surface anchoring. We present a theoretical model of the orientational response of anisotropic rods deposited onto a surface of a soft, elastic substrate of finite thickness. We show that anisotropic rods exhibit a continuous isotropic-nematic phase transition, driven by orientational interactions between surface deposited rods. This interaction is mediated by the deformation of the underlying elastic substrate, and is quantified by the Boussinesq solution adapted to the case of slender, surface deposited rods. From the microscopic rod-rod interactions we derive the appropriate Maier-Saupe mean-field description, which includes the Boussinesq elastic free-energy contribution due to the substrate elasticity, derive the conditions for the existence of a continuous orientational ordering transition and discuss the implication of results in the soft (bio) systems context.

cond-mat.soft

Drying Pathways of an Evaporating Soft Matter Droplet

Micro-droplets of soft matter solutions have different morphologies upon drying, and can finally become wrinkled, buckled or cavitated particles. We investigate the morphology evolution of a drying soft matter droplet in this work: at the early stage of drying, wrinkling or cavitation instability can occur in the droplet, depending on the comparison between the critical wrinkling and cavitation pressure; at a later stage of drying, no wrinkle will appear if cavitation happens first, while there can still be cavitation if wrinkling happens first. A three-dimensional phase diagram in the space of elastic length, gel layer thickness and weight loss is provided for illustrating these drying pathways of a soft matter droplet, which can guide future fabrications of micro-particles with desired morphologies.

cond-mat.soft

Modeling Multi-Cellular Dynamics Regulated by ECM-Mediated Mechanical Communication via Active Particles with Polarized Effective Attraction

Collective cell migration is crucial to many physiological and pathological processes. Recent experimental studies have indicated that the active traction forces generated by migrating cells in fibrous extracellular matrix (ECM) can mechanically remodel the ECM, enabling long-range propagation of cellular forces and leading to correlated migration dynamics regulated by the mechanical communication among the cells. Motivated by these experimental discoveries, we develop an active-particle model with polarized effective attractions (APPA) for modeling emergent multi-cellular migration dynamics regulated by ECM-mediated mechanical communications. Active particles with polarized pairwise attractions exhibit enhanced aggregation behaviors compared to classic active Brownian particles, especially at lower particle densities and larger rotational diffusivities. Importantly, in contrast to the classic ABP system, the high-density phase of APPA system exhibits strong dynamic correlation, which is characterized by the slowly decaying velocity correlation functions with a correlation length comparable to the linear size of high-density phase domain (i.e., cluster of the particles). The strongly correlated multi-cellular dynamics predicted by the APPA model are subsequently verified in {\it in vitro} experiments using MCF-10A cells. Our studies also indicate the importance of incorporating ECM-mediated mechanical coupling among the migrating cells for appropriately modeling emergent multi-cellular dynamics in complex micro-environments.

cond-mat.soft

The role of deformability in determining the structural and mechanical properties of bubbles and emulsions

We perform computational studies of jammed particle packings in two dimensions undergoing isotropic compression using the well-characterized soft particle (SP) model and the deformable particle (DP) model that we developed for compressed bubbles and emulsions. In the SP model, circular particles are allowed to overlap, generating purely repulsive forces. In the DP model, particles minimize their perimeter, while deforming at fixed area to avoid overlap during compression. We directly compare the structural and mechanical properties of jammed particle packings generated using the SP and DP models as a function of the true packing fraction $ρ$, instead of the reduced number density $ϕ$. We show that near jamming onset the excess contact number $Δz=z-z_J$ and shear modulus ${\cal G}$ scale as $Δρ^{0.5}$ in the large system limit for both the SP and DP models, where $Δρ= ρ-ρ_J$ and $z_J \approx 4$ and $ρ_J \approx 0.842$ are the values at jamming onset. $Δz$ and ${\cal G}$ for the SP and DP models begin to differ for $ρ\gtrsim 0.88$. In this regime, $Δz \sim {\cal G}$ can be described by a sum of two power-laws in $Δρ$, i.e. $Δz \sim {\cal G} \sim C_0Δρ^{0.5} +C_1Δρ^{1.0}$ to lowest order. We show that the ratio $C_1/C_0$ is much larger for the DP model compared to to that for the SP model. We also characterize the void space in jammed packings as a function of $ρ$. We find that, unlike the SP model, the DP model is able to describe the formation of Plateau borders as the system approaches $ρ= 1$. We further show that the results for $z$ and the shape factor ${\cal A}$ versus $ρ$ for the DP model agree with recent experimental studies of compressed foams and emulsions.

physics.app-ph

Hydrogen Polarity of Interfacial Water Regulates Heterogeneous Ice Nucleation

Using all-atomic molecular dynamics(MD) simulations, we show that various substrates could induce interfacial water (IW) to form the same ice-like oxygen lattice but different hydrogen polarity order, and regulate the heterogeneous ice nucleation on the IW. We develop an efficient MD method to probe the shape, structure of ice nuclei and the corresponding supercooling temperatures. We find that the polarization of hydrogens in IW increases the surface tension between the ice nucleus and the IW, thus lifts the free energy barrier of heterogeneous ice nucleation. The results show that not only the oxygen lattice order but the hydrogen disorder of IW on substrates are required to effectively facilitate the freezing of atop water.

physics.comp-ph

Modeling cell migration regulated by cell-ECM micromechanical coupling

Cell migration in fibreous extracellular matrix (ECM) is crucial to many physiological and pathological processes such as tissue regeneration, immune response and cancer progression. During migration, individual cells can generate active pulling forces via actin filament contraction, which are transmitted to the ECM fibers through focal adhesion complexes, remodel the ECM, and eventually propagate to and can be sensed by other cells in the system. The microstructure and physical properties of the ECM can also significantly influence cell migration, e.g., via durotaxis and contact guidance. Here, we develop a computational model for cell migration regulated by cell-ECM micro-mechanical coupling. Our model explicitly takes into account a variety of cellular level processes including focal adhesion formation and disassembly, active traction force generation and cell locomotion due to actin filament contraction, transmission and propagation of tensile forces in the ECM, as well as the resulting ECM remodeling. We validate our model by accurately reproducing single-cell dynamics of MCF-10A breast cancer cells migrating on collagen gels and show that the durotaxis and contact guidance effects naturally arise as a consequence of the cell-ECM micro-mechanical interactions considered in the model. Moreover, our model predicts strongly correlated multi-cellular migration dynamics, which are resulted from the ECM-mediated mechanical coupling among the migrating cell and are subsequently verified in {\it in vitro} experiments using MCF-10A cells. Our computational model provides a robust tool to investigate emergent collective dynamics of multi-cellular systems in complex {\it in vivo} micro-environment and can be utilized to design {\it in vitro} micro-environments to guide collective behaviors and self-organization of cells.

q-bio.CB

A tensor model for nematic phases of bent-core molecules based on molecular theory

We construct a tensor model for nematic phases of bent-core molecules from molecular theory. The form of free energy is determined by molecular symmetry, which includes the couplings and derivatives of a vector and two second-order tensors, with the coefficients determined by molecular parameters. We use the model to study the nematic phases resulted from the hard-core potential. Unlike most macroscopic models, we are able to obtain the phase diagram about the molecular parameters, but not merely some phenomenological coefficients. The tensor model is applicable to other molecules with the same symmetry, which we demonstrate by studying the phase diagram of star molecules.

cond-mat.soft

Ultra-high-density local structure of liquid water

The local structure of liquid water plays a key role in determining the anomalous properties of water. We run all-atom simulations for three microscopic water models, and use multiple order parameters to analyse the local structure of water. We identify three types of local structures. In addition to the well known low-density-liquid and high-density-liquid structures, the newly identified third type possesses an ultra high density and overcoordinated H-bonds. The existence of this third type decreases the rate of transition from the high-density-structure to low-density-structure and increases the rate of the reverse one, leading to the enhancement of the high-density-structure stability.

cond-mat.soft