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The directed migration of cells toward stiffer substrate regions or durotaxis is relevant to tissue development and tumor progression. Here, we introduce a phenomenological model for single cell durotaxis that incorporates both elastic deformation-mediated cell-substrate interactions and the stochasticity of cell migration. Our model is motivated by a key observation in an early demonstration of durotaxis: a single, contractile cell at a sharp interface between a softer and a stiffer region of an elastic substrate reorients and migrates towards the stiffer region. We model migrating cells as self-propelling, persistently motile agents that exert contractile traction forces on their elastic substrate. The resulting substrate deformations induce elastic interactions with mechanical boundaries, captured by an elastic potential. Cell dynamics are governed by two critical parameters: the strength of the traction-induced boundary interaction (A) and the persistence of cell motility (Pe). The resulting elastic forces and torques align cells perpendicular (parallel) to the boundary and accumulate (deplete) them at clamped (free) boundaries. A clamped boundary induces an attractive potential, promoting durotaxis, while a free boundary generates a repulsive potential, preventing anti-durotaxis. By analyzing steady-state position and orientation probabilities, we show how accumulation and depletion depend on elastic potential strength and motility. We compare our findings with biological microswimmers and other active particles that accumulate at confining boundaries. The model defines metrics for boundary accumulation and durotaxis, presenting a phase diagram with three regimes: durotaxis, adurotaxis, and motility-induced accumulation. Our model predicts how durotaxis depends on cell contractility and motility, offering insights and testable predictions for future experiments., Comment: 11 figures, 24 pages

A deep learning-based computational method has been proposed for soft matter dynamics -- the deep Onsager-Machlup method (DOMM), which combines the brute forces of deep neural networks (DNNs) with the fundamental physics principle -- Onsager-Machlup variational principle (OMVP). In the DOMM, the trial solution to the dynamics is constructed by DNNs that allow us to explore a rich and complex set of admissible functions. It outperforms the Ritz-type variational method where one has to impose carefully-chosen trial functions. This capability endows the DOMM with the potential to solve rather complex problems in soft matter dynamics that involve multiple physics with multiple slow variables, multiple scales, and multiple dissipative processes. Actually, the DOMM can be regarded as an extension of the deep Ritz method constructed using variational formulations of physics models to solve static problems in physics as discussed in our former work [Wang et al, Soft Matter, 2022, 18, 6015-6031]. In this work, as the first step, we focus on the validation of the DOMM as a useful computational method by using it to solve several typical soft matter dynamic problems: particle diffusion in dilute solutions, and two-phase dynamics with and without hydrodynamics. The predicted results agree very well with the analytical solution or numerical solution from traditional computational methods. These results show the accuracy and convergence of DOMM and justify it as an alternative computational method for solving soft matter dynamics., Comment: 15 pages, 6 figures

We report a systematic study of the dynamics of self-propelled particles (SPPs) over a one-dimensional periodic potential landscape, which is fabricated on a microgroove-patterned polydimethylsiloxane (PDMS) substrate. From the measured non-equilibrium probability density function of the SPPs, we find that the escape dynamics of the slow-rotating SPPs across the potential landscape can be described by an effective potential, once the self-propulsion force is included into the potential under the fixed angle approximation. This work demonstrates that the parallel microgrooves provide a versatile platform for a quantitative understanding of the interplay among the self-propulsion force, spatial confinement by the potential landscape, and thermal noise, as well as its effects on activity-assisted escape dynamics and transport of the SPPs.

We carry out a numerical study on the dynamics of a single non-Brownian flexible fiber in two-dimensional Couette flows at finite Reynolds numbers. We employ the bead-spring model of flexible fibers to extend the fluid particle dynamics (FPD) method that is originally developed for rigid particles in viscous liquids. We implement the extended FPD method using a multiple-relaxation-time (MRT) scheme of the lattice Boltzmann method (LBM). The numerical scheme is validated firstly by a series of benchmark simulations that involve liquid-solid coupling. The method is then used to study the dynamics of flexible fibers in Couette flows. We only consider the highly symmetric case where the fibers are placed on the symmetry center of Couette flows and we focus on the effects of the fiber stiffness, the confinement strength, and the finite Reynolds number (from 1 to 10). A diagram of the fiber shape is obtained. For fibers under weak confinement and a small Reynolds number, three distinct tumbling orbits have been identified. (1) Jeffery orbits of rigid fibers. The fibers behave like rigid rods and tumble periodically without any visible deformation. (2) S-turn orbits of slightly flexible fibers. The fiber is bent to an S-shape and is straightened again when it orients to an angle of around 45 degrees relative to the positive x direction. (3) S-coiled orbits of fairly flexible fibers. The fiber is folded to an S-shape and tumbles periodically and steadily without being straightened anymore during its rotation. Moreover, the fiber tumbling is found to be hindered by increasing either the Reynolds number or the confinement strength, or both., Comment: 16 pages, 10 figures

Hydra tissue fragments excised freshly from Hydra body bend spontaneously to some quasi-stable shape in several minutes. We propose that the spontaneous bending is driven mechanically by supracellular actomyosin bundles inherited from parent Hydra. An active-laminated-plate model is constructed, from which we predict that the fragment shape characterized by spontaneous curvature is determined by its anisotropy in contractility and elasticity. The inward bending to endoderm side is ensured by the presence of a soft intermediate matrix (mesoglea) layer. The bending process starts diffusively from the edges and relaxes exponentially to the final quasi-stable shape. Two characteristic time scales are identified from the dissipation due to viscous drag and interlayer frictional sliding, respectively. The former is about 0.01 seconds, but the latter is much larger, about several minutes, consistent with experiments., Comment: 26 pages, 10 figures

Variational methods have been widely used in soft matter physics for both static and dynamic problems. These methods are mostly based on two variational principles: the variational principle of minimum free energy (MFEVP) and Onsager's variational principle (OVP). Our interests lie in the applications of these variational methods to active matter physics. In our former work [Soft Matter, 2021, 17, 3634], we have explored the applications of OVP-based variational methods for the modeling of active matter dynamics. In the present work, we explore variational (or energy) methods that are based on MFEVP for static problems in active elastic solids. We show that MFEVP can be used not only to derive equilibrium equations, but also to develop approximate solution methods, such as Ritz method, for active solid statics. Moreover, the power of Ritz-type method can be further enhanced using deep learning methods if we use deep neural networks to construct the trial solutions of the variational problems. We then apply these variational methods and the deep Ritz method to study the spontaneous bending and contraction of a thin active circular plate that is induced by internal asymmetric active contraction. The circular plate is found to be bent towards its contracting side. The study of such a simple toy system gives implications for understanding the morphogenesis of solid-like confluent cell monolayers. In addition, we introduce a so-called activogravity length to characterize the importance of gravitational forces relative to internal active contraction in driving the bending of the active plate. When the lateral plate dimension is larger than the activogravity length (about 100 micron), gravitational forces become important. Such gravitaxis behaviors at multicellular scales may play significant roles in the morphogenesis and in the up-down symmetry broken during tissue development., Comment: 19 pages, 8 figures

The variational principle of minimum free energy (MFEVP) has been widely used in the study of soft matter statics. MFEVP can be used not only to derive equilibrium equations (including both bulk equations and boundary conditions), but also to develop direct variational methods (such as Ritz method) to find approximate solutions to these equilibrium equations. In this work, we applied these variational methods to study long-range force transmission in nonlinear elastic biopolymer gels. We showed that the slow decay of cell-induced displacements measured experimentally for fibroblast spheroids in three-dimensional fibrin gels can be well explained by variational approximations based on the three-chain model of biopolymer gels., Comment: 11 pages, 4 figures

We review continuum elastic models for the transmission of both external forces and internal active cellular forces in biopolymer gels, and relate them to recent experiments. Rather than being exhaustive, we focus on continuum elastic models for small affine deformations and intend to provide a systematic continuum method and some analytical perspectives to the study of force transmissions in biopolymer gels. We start from a very brief review of the nonlinear mechanics of individual biopolymers and a summary of constitutive models for the nonlinear elasticity of biopolymer gels. We next show that the simple 3-chain model can give predictions that well fit the shear experiments of some biopolymer gels, including the effects of strain-stiffening and negative normal stress. We then review continuum models for the transmission of internal active forces that are induced by a spherically contracting cell embedded in a three-dimensional biopolymer gel. Various scaling regimes for the decay of cell-induced displacements are identified for linear isotropic and anisotropic materials, and for biopolymer gels with nonlinear compressive-softening and strain-stiffening elasticity, respectively. After that, we present (using an energetic approach) the generic and unified continuum theory proposed in [Ben-Yaakov, Soft Matter, 2015, 11, 1412] about how the transmission of forces in the biogel matrix can mediate long-range interactions between cells with mechanical homeostasis. We show the predictions of the theory in a special hexagonal multicellular array, and relate them to recent experiments. Finally, we conclude this paper with comments on the limitations and outlook of continuum modeling, and highlight the needs of complementary theoretical approaches such as discrete network simulations to force transmissions in biopolymer gels and phenomenological active gel theories for multicellular systems.

Onsager's variational principle (OVP) was originally proposed by Lars Onsager in 1931 [L. Onsager, $Phys. Rev.$, 1931, $37$, 405]. This fundamental principle provides a very powerful tool for formulating thermodynamically consistent models. It can also be employed to find approximate solutions, especially in the study of soft matter dynamics. In this work, OVP is extended and applied to the dynamic modeling of active soft matter such as suspensions of bacteria and aggregates of animal cells. We first extend the general formulation of OVP to active matter dynamics where active forces are included as external non-conservative forces. We then use OVP to analyze the directional motion of individual active units: a molecular motor walking on a stiff biofilament and a toy two-sphere microswimmer. Next, we use OVP to formulate a diffuse-interface model for an active polar droplet on a solid substrate. In addition to the generalized hydrodynamic equations for active polar fluids in the bulk region, we have also derived thermodynamically consistent boundary conditions. Finally, we consider the dynamics of a thin active polar droplet under the lubrication approximation. We use OVP to derive a generalized thin film equation and then employ OVP as an approximation tool to find the spreading laws for the thin active polar droplet. By incorporating the activity of biological systems into OVP, we develop a general approach to construct thermodynamically consistent models for better understanding the emergent behaviors of individual animal cells and cell aggregates or tissues.

The classical Lorentz reciprocal theorem (LRT) was originally derived for slow viscous flows of incompressible Newtonian fluids under the isothermal condition. In the present work, we extend the LRT from simple to complex fluids with open or moving boundaries that maintain non-equilibrium stationary states. In complex fluids, the hydrodynamic flow is coupled with the evolution of internal degrees of freedom such as the solute concentration in two-phase binary fluids and the spin in micropolar fluids. The dynamics of complex fluids can be described by local conservation laws supplemented with local constitutive equations satisfying Onsager's reciprocal relations (ORR). We consider systems in quasi-stationary states close to equilibrium, controlled by the boundary variables whose evolution is much slower than the relaxation in the system. For these quasi-stationary states, we derive the generalized Lorentz reciprocal theorem (GLRT) and global Onsager's reciprocal relations (GORR) for the slow variables at boundaries. This establishes the connection between ORR for local constitutive equations and GORR for constitutive equations at boundaries. Finally, we show that the LRT can be further extended to non-isothermal systems by considering as an example the thermal conduction in solids and still fluids., Comment: 30 pages, 3 figures

In this work, we report a new method to simulate active Brownian particles (ABPs) in molecular dynamics (MD) simulations. Immersed in a fluid, each ABP consists of a head particle and a spherical phantom region of fluid where the flagellum of a microswimmer takes effect. The orientation of the active particle is governed by a stochastic dynamics, with the orientational persistence time determined by the rotational diffusivity. To hydrodynamically drive the active particle as a pusher, a pair of active forces are exerted on the head particle and the phantom fluid region respectively. The active velocity measured along the particle orientation is proportional to the magnitude of the active force. The effective diffusion coefficient of the active particle is first measured in free space, showing semi-quantitative agreement with the analytical result predicted by a minimal model for ABPs. We then turn to the probability distribution of the active particle in confinement potential. We find that the stationary particle distribution undergoes an evolution from the Boltzmann-type to non-Boltzmann distribution as the orientational persistence time is increased relative to the relaxation time in the potential well. From the stationary distribution in confinement potential, the active part of the diffusion coefficient is measured and compared to that obtained in free space, showing a good semi-quantitative agreement while the orientational persistence time varies greatly relative to the relaxation time.

Solvent vapor annealing (SVA) is known to be a simple, low-cost and highly efficient technique to produce defect-free diblock copolymer (BCP) thin films. Not only can the solvent weaken the BCP segmental interactions, but it can vary the characteristic spacing of the BCP microstructures. We carry out systematic theoretical studies on the effect of adding solvent into lamellar BCP thin films on the defect removal close to the BCP order-disorder transition. We find that the increase of the lamellar spacing, as is induced by addition of solvent, facilitates more efficient removal of defects. The stability of a particular defect in a lamellar BCP thin film is given in terms of two key controllable parameters: the amount of BCP swelling and solvent evaporation rate. Our results highlight the SVA mechanism for obtaining defect-free BCP thin films, as is highly desired in nanolithography and other industrial applications., Comment: 14 pages, 9 figures

Engineering surfaces that promote rapid drop detachment is of importance to a wide range of applications including anti-icing, dropwise condensation6, and self-cleaning. Here we show how superhydrophobic surfaces patterned with lattices of submillimetre-scale posts decorated with nano-textures can generate a counter-intuitive bouncing regime: drops spread on impact and then leave the surface in a flattened, pancake shape without retracting. This allows for a four-fold reduction in contact time compared to conventional complete rebound. We demonstrate that the pancake bouncing results from the rectification of capillary energy stored in the penetrated liquid into upward motion adequate to lift the drop. Moreover, the timescales for lateral drop spreading over the surface and for vertical motion must be comparable. In particular, by designing surfaces with tapered micro/nanotextures which behave as harmonic springs, the timescales become independent of the impact velocity, allowing the occurrence of pancake bouncing and rapid drop detachment over a wide range of impact velocities., Comment: 11 pages, 4 figures, 31 references, + 5 pages of supplementary information