Papers

Understanding how molecular interactions govern macroscopic behaviour is a central challenge in molecular sciences. However, conventional theory building cannot keep pace with the vast datasets modern experimentation routinely produces. Large language models offer a promising route to automating theory construction, but a spatiotemporal field cannot be directly placed in a prompt. Existing models generally learn about the data only through a score measuring how well each proposal fits it. Here we introduce data interpretation, a stage that measures the field into the quantities a theorist would consult and supplies them to the model as a direct input. On a benchmark of simulated fields, interpretation nearly triples the accuracy of recovered equations relative to showing the raw data, at negligible computational cost and without any training. By allowing a language model to read field data as a theorist does, data interpretation offers a practical route to automated field theory construction that can coevolve with experimentation.

Contractile cells and external loads reorganize the fibrous extracellular matrix, aligning and compacting fibers over distances far exceeding a cell's size, strongly affecting bioprocesses such as wound healing, angiogenesis and tumor invasion. We develop a continuum micromechanical theory that links, at every material point, the load-induced orientational order to the mechanical response that the reoriented network then exhibits. The network is described statistically, by the probability density of fiber orientations, and deforms affinely, so that a single-fiber stress-strain law is carried into the network stress, with the deformation set self-consistently by mechanical equilibrium. Critical to realistic biological relevant conditions, this theory allows both geometrical and material nonlinearities. Applied to a two-dimensional network under uniaxial stretch, the theory collapses onto a single anisotropy parameter that governs the orientation distribution, the nematic order, the Poisson ratio, and the densification of fibers. Our theory reveals that induced order and densification are highly positively correlated, and in the case of uniaxial stretch they collapse onto a nearly universal curve, independent of the single-fiber stiffness behavior. For a contracting cell, we find that buckling controls how far nematic orientational order and densification propagate. We find an algebraic decay of deformations with distance and solve for the dependence of the power-law exponent on the buckled-reduced stiffness of a single fiber. We validate our theory by comparison with non-affine discrete fiber-network simulations.

We used simulations of short single stranded DNA (ssDNA) homopolymers, based on the sequence dependent Three Interaction Site (TIS) model, to calculate the persistence length ($l_p$) in polyvalent cations. The TIS model accounts for stacking interactions and electrostatic interactions are treated using the Coulomb potential. We find that $l_p$ for $\mathrm{dT_{30}}$ (T is thymine) and $\mathrm{dA_{30}}$ (A is adenine) is quantitatively fit using $l_p = l_p^0 + \lambda \kappa^{-1}$ ($l_p^0$ is the bare persistence length, $\lambda$ is a dimensionless constant, and $\kappa$ is the inverse Debye length) in the divalent cations $\mathrm{Mg^{2+}}$ and $\mathrm{Ca^{2+}}$. The dependence of $l_p$ on $\kappa$ is surprising because it was derived for long flexible polyelectrolytes in which the charges interact via the Debye-Hückel potential. The $l_p^0$ values are 0.4 nm and 1.1 nm for polyT and polyA, respectively. Strikingly, $l_p$ is almost independent of the tetravalent spermine concentration. There is no clear theoretical explanation although simulations suggest that the number of spermine molecules that bind to the ssDNA saturates at a small value. A qualitative picture, based on the restrictions of access to the phosphate groups due to volume exclusion of the anisotropic structure of $\mathrm{Spm^{4+}}$, rationalizes the simulation results. The predicted dependence of $l_p$ in spermine awaits experimental test.

We study the equilibrium phase behavior of a fluid confined in a slit made from two patterned walls. Shearing the walls frustrates the fluid, due to a competition between capillary condensation and interface delocalization, forcing the formation of bridging phases with different pinning properties. This leads to an unusually rich phase diagram, displaying first-order and continuous phase transitions, depending sensitively on the slit width and shear. Generalized Kelvin equations determine the phase boundaries, while the bridging phases are characterized by large correlation lengths, predictions for which are tested using a microscopic density functional model.

Abrupt transitions between rest and motion can render the standard Newtonian description – based on position, velocity, and acceleration – incomplete, requiring higher-order derivatives such as the jerk, the third time derivative of position. Here, we show that the interplay between activity and dry friction gives rise to robust jerk-dominated dynamics in self-propelled particles: the particle speed increases quadratically with time under an active force, in contrast to the linear growth expected for conventional Newtonian dynamics. We demonstrate this behavior analytically, numerically, and experimentally using active vibrobots self-propelling on a vertically vibrating plate at low vibration amplitudes, where surface asperities generate dry friction and, thus, give rise to jerky motion when combined with activity. Our results establish dry friction as a simple mechanism for realizing higher-order dynamics in active matter and suggest that jerky dynamics may arise broadly in nonequilibrium systems with frictional contacts.

We investigate the diffusiophoretic motion of a chemically isotropic active colloid in a three-dimensional wedge formed by two distinct fluid media, in the limit of vanishing Péclet and Reynolds numbers. The concentration field is obtained using the Fourier-Kontorovich-Lebedev transform, yielding an exact representation for arbitrary wedge opening angles and interfacial contrasts. We introduce the interfacial parameter $\Gamma=(1-\lambda\ell)/(1+\lambda\ell)$, where $\lambda$ denotes the diffusivity contrast and $\ell$ the solute partition coefficient. For $\Gamma=\pm1$ and commensurate wedge angles, the solution reduces to finite image constructions, with distinct structures for even and odd commensurability. The general solution also recovers the planar-interface and semi-infinite-interface limits. The leading-order translational phoretic velocity is derived from the concentration field, revealing a strong interplay between wedge geometry and interfacial properties that governs both the magnitude and direction of particle motion. This work provides a framework for understanding and controlling phoretic transport in confined multiphase environments and offer a basis for extensions to finite-size geometries and mixed fluid–fluid and solid boundary conditions. Our results may find applications in the control of active-particle transport in confined multiphase environments, where interfacial properties and geometry can be exploited to tune phoretic motion.

Chain scission is a key molecular process underlying damage and fracture in polymer networks. In this Letter, we develop a statistical-mechanical framework for predicting chain-scission kinetics while accounting for three-dimensional (3D) conformational fluctuations. Within transition-state theory, scission is formulated as a multichannel first-rupture problem, with bond-specific rates governed primarily by self-consistent potentials of mean force. In the freely jointed limit, the additional 3D configurational freedom enhances rupture relative to the collinear 1D reference. Finite bending stiffness introduces orientational correlations that can reverse this enhancement and, at high stiffness, reduce rupture rates by orders of magnitude. These correlations also make rupture bond-position dependent, with higher rates near the chain ends and a common interior rate. For sufficiently long chains, the interior contribution dominates, yielding linear scaling of the chain-scission rate with chain length. These molecularly resolved rates provide physically grounded inputs for future network-scale models of polymer damage and fracture.

According to Purcell's scallop theorem, reciprocal single-degree-of-freedom shape deformations cannot achieve net propulsion in a viscous fluid. We show that this limitation is bypassed by thermal fluctuations in a two-parameter driven potential landscape. Formulating the stochastic shape dynamics via a Smoluchowski equation with position-dependent mobility $M_\mathrm{eff}(x)$, we utilize a generalized inverse operator to evaluate the slow-driving response. Cyclic modulation of the control parameters induces a non-zero Berry-Sinitsyn-Nemenman curvature $F_{12}(\bm{\theta})$, resulting in directed geometric propulsion. Simultaneously, the non-adiabatic excess dissipation is dictated by a Riemannian thermodynamic metric $g_{ij}(\bm{\theta})$. Our results provide a unified geometric foundation that bridges hydrodynamic friction, stochastic mechanics, and thermodynamic trade-offs in micro-swimmers.

Gaucher disease (GD), the most common lysosomal storage disorder, alters red blood cell (RBC) mechanics and circulation, contributing to vascular occlusions, bone infarcts, and splenomegaly. However, the individual roles of GD-RBC biophysical properties in these processes remain unclear. Here, we present a combined computational-experimental investigation to quantitatively characterize GD-RBC biophysical properties and determine how specific mechanical parameters drive abnormal RBC behavior. Informed by experimental data, we independently quantify key RBC properties, including shear modulus (mu), surface-to-volume ratio (S/V), and bending modulus (k_c). Based on these parameters, we construct three GD-RBC subtypes (GD-RBC1-3) to systematically isolate their individual contributions. At the single-cell level, optical tweezers simulations show up to ~27% reduction in axial diameter and ~42% reduction in transverse compression. Tank-treading dynamics exhibit non-monotonic behavior, with rotation frequencies increasing by up to ~70% or decreasing under elevated bending rigidity. In confined flow, traversal times through microchannel constrictions increase by more than a factor of two, while splenic slit passage times rise from ~250 ms (control) to >1200 ms for the severe GD-RBC subtype, approaching a functional no-passage threshold. At the population level, viscosity simulations demonstrate that these alterations collectively elevate blood viscosity, with small fractions (~4.0%) of highly rigid cells disproportionately increasing flow resistance. Overall, this study provides a quantitative and mechanistic framework that disentangles the contributions of key RBC parameters to abnormal behavior in GD, linking cellular-scale biophysics to hematologic dysfunction and microvascular occlusion.

Can a boundary determine the direction of circulation in a collectively moving active fluid? We study chiral self-propelled particles with nematic bulk alignment, confined by walls whose orientational coupling varies continuously from nematic to polar. For an isolated particle at a wall, we derive the exact parameter condition under which a stable orientation is tangent to the wall. With predominantly nematic wall coupling, however, the many-body circulation changes sign at a chirality that is nearly independent of the wall symmetry. This sign change follows a pronounced decrease in nematic order and disappears when bulk alignment is removed. As the polar wall coupling becomes dominant, opposite-handed circulation is suppressed and same-handed polar locking emerges. Thus local orientation at a wall and the direction of macroscopic circulation are selected by distinct physical processes: the wall determines the possible local orientations, whereas collective order determines whether those orientations control the global flow.

We present a robotic electrospinning platform and design method for depositing nanofiber membranes onto non-planar, three-dimensional conductive geometries. Conventional electrospinning relies on fixed emitters and planar grounded collectors, which restricts deposition to flat substrates: on concave geometries, field shielding prevents fibers from reaching recessed regions, and material bridges across elevated features instead. We address this with a custom end-effector integrated with a six-axis UR20 arm. The tool carries a localized stepper-driven syringe pump that maintains consistent polymer flow independent of orientation, and routes high-voltage DC (up to 25 kV) directly to a robot-mounted needle, turning the arm into a mobile emitter with full kinematic control over position, orientation, working distance, and traversal velocity. Toolpaths that continuously reorient the emitter along surface normals give access to concave topologies unreachable by fixed-axis systems. We characterize the resulting deposition behavior in two parts. A catalog of four bio-compatible polymer systems (PEO, PVA, keratin-PEO, silk-PEO) establishes the operating envelope, reporting deposition speed, jet stability, fiber size, alignment, and durability for each. A taxonomy of 3D-printed conductive scaffolds spanning geometric primitives, hybrid compositions, and square, triangular, and hexagonal lattices links collector geometry to fiber alignment, density, and cross-void bridging. We also demonstrate programmable grounding, in which selectively energized pins in an array steer deposition without changing physical geometry. Assembly instructions and toolpath-generation code are released as an open-source repository.

We study hard spherocylinders on a sphere with axes rigidly locked to a tangential director field at fixed angle $\tilt$ to the meridian, necessarily singular at the poles. Three lengths set the problem: the rod length $\Lrod$, the diameter $\Drod$, and the host radius $\Rsph$. Monte Carlo simulations across fifteen geometries and four coverages give two main results for the polar marginal, the azimuthal average of rod-center density. First, the tilt is a continuous handle on the width of the depleted region that packing induces around each singularity. Under meridian locking it is set principally by the rod length; turning the director toward the latitude contracts it substantially, the contraction being spent well before latitude locking. Second, how uniform the polar marginal can be made is limited by geometry, not tilt. The smallest variance on the sampled grid follows a power law in $\Lrod^{2}/(\Rsph\Drod)$, which measures how far a straight rod's ends stand off the curved surface in rod diameters, with an effective exponent between $1.1$ and $1.3$. Long rods on small hosts cannot be made uniform at any sampled tilt; the remedy is geometric, not orientational. The polar marginal is equator-heavy almost everywhere, inverting only at high coverage and tilt; meridian locking is the least uniform choice, and the variance-minimizing tilt usually lies in a sampled band from $31.7^{\circ}$ to $55^{\circ}$. The golden-ratio tilt $\arctan(1/\phigold)$ is one of those angles: a benchmark, not one the model selects. Both results describe the infinitely locked athermal ensemble.

Wicking in a capillary tube could happen as long as the liquid contact angle is smaller than 90 degrees, making it possible for weak hydrophilic liquids to spontaneously invade the tube. For textured surfaces, energy minimization argument predicts the same. However, wicking of weak hydrophilic liquids on textured surfaces has not been possible due to energy barriers induced by the textures. We demonstrate how these barriers could be avoided by adjusting the shape and arrangement of the pillars, thus the wettability required for wicking reaches the theoretical limit. An unprecedented wicking contact angle of 82 degrees is reported. More surprisingly, wicking coefficients of such surfaces can be larger than that of rectangular grooves at the same porosity. These findings may significantly advance biomedical and thermal management technologies.

AC nanocalorimetry was used to measure the reversing heat capacity Cp of low energy indomethacin glasses as they isothermally transform into the supercooled liquid. As the film thickness increases from 75 to 600 nm, the transformation time increases by more than an order of magnitude, consistent with a surface-initiated transformation mechanism. Eventually, the transformation time becomes constant for films between 1.4 and 30 microns indicating a distinct bulk transformation pathway. The observation of size-dependent transformation kinetics for glass samples approaching 1 micron is unprecedented. We interpret the crossover in thickness dependence at 1 micron to signify the average distance between transformation initiation sites in the bulk low energy glass.

In situ AC nanocalorimetry was used to measure the reversing heat capacity of vapor-deposited glasses of decahydronaphthalene (decalin). Glasses with low heat capacity and high kinetic stability, as compared to the corresponding liquid-cooled glass, were prepared from cis-decalin and from several cis/trans-decalin mixtures. This is the first report of highly stable glass formation for molecular mixtures. The 50/50 cis/trans-decalin mixture is the highest fragility material reported to produce an ultrastable glass. The 50/50 mixture exhibited high kinetic stability, with an ~500 nm film deposited at 116 K (0.86 Tg,) displaying a transformation time equivalent to 104.4 times the structural relaxation time of the supercooled liquid at the annealing temperature. Cis-decalin and the decalin mixture formed stable glasses that had heat capacities as much as 4.5% lower than the liquid-cooled glass.

We performed constant strain rate deformation and stress relaxation on a poly(methyl methacrylate) glass at Tg - 19 K, utilizing three strain rates and initiating the stress relaxation over a large range of strain values. Following previous workers, we interpret the initial rate of decay of the stress during the relaxation experiment as a purely mechanical measure of mobility for the system. In our experiments, the mechanical mobility obtained in this manner changes by less than a factor of 3 prior to yield. During these mechanical experiments, we also performed an optical measurement of segmental mobility based upon the reorientation of a molecular probe; we observe that the probe mobility increases up to a factor of 100 prior to yield. In the post-yield regime, in contrast, the mobilities determined mechanically and by probe reorientation are quite similar and show a similar dependence upon the strain rate. Dynamic heterogeneity is found to initially decrease during constant strain rate deformation and then remain constant in the post-yield regime. These combined observations of mechanical mobility, probe mobility, and dynamic heterogeneity present a challenge for theoretical modeling of polymer glass deformation.

Excitation-energy transfer underpins the conversion of light into usable energy in photosynthetic organisms and serves as a paradigm for evolutionary optimized transport in open quantum systems. Although this process is often described as incoherent thermally assisted hopping, such descriptions become inadequate when electronic coupling, vibronic interactions and environmental fluctuations occur on comparable energy scales. Determining how the environment controls transport therefore remains a fundamental challenge. Here, we use temperature-dependent 2DES to investigate energy transfer in the photosynthetic antenna protein allophycocyanin over the range 10 - 296 K. The dominant $\beta \rightarrow \alpha$ transfer step exhibits a pronounced non-monotonic temperature dependence: the transfer time decreases from 400 fs at 10 K to 200 fs near 30- 40 K before increasing again to 400 fs at 296 K. In contrast, the homogeneous optical dephasing time decreases monotonically across the same temperature range. To interpret these observations, we model APC as a vibronically coupled excitonic dimer interacting with a structured environment and solve the dynamics using hierarchical equations of motion. Conventional fixed-bath models, including Drude-Lorentz and explicit intermolecular-mode spectral densities, fail to reproduce the observed turnover. Quantitative agreement is obtained only when the low-frequency sector of the environmental spectral density is allowed to anharmonically evolve strongly with temperature, while the high-frequency bath remains essentially unchanged. More broadly, these findings demonstrate that transport efficiency is controlled not simply by the magnitude of environmental fluctuations, but by the distribution of environmental spectral weight across frequency space, providing new experimental constraints on theories of molecular transport in complex quantum environments.

Biomolecular condensates can undergo striking changes, such as transitioning from a liquid-like to a gel- or a solid-like aggregate due to changes in molecular interactions in response to changes in the biochemical environment. The question of how modified molecular interactions lead to such a transition in the material properties and spatial organization of condensates has not yet been elucidated. To address this question, we represent the biochemical environment as a triphasic mixture comprising a liquid-like protein-rich phase, a network-like protein-rich phase, and solvent. Owing to a change in the biochemical environment, protein molecules can reversibly switch between two conformational states. In a switched conformational state, the cross-linking domains of molecules are exposed which promote transient network formation in phase separated states. We develop a transient-network model and a continuum framework that couples phase separation, molecular switching, and dynamic cross-linking to predict condensate morphology and mechanics. The transient-network model predicts that a non-aging network behaves like a Maxwell fluid. When a network slowly ages via stabilization of cross-links, it shows Maxwell-like behavior and waiting time-dependent relaxation. However, a strongly aged network shows elastic recoil like characteristic of a Kelvin-Voigt solid. Our coupled continuum model demonstrates that the interplay of molecular switching and dynamic cross-linking in network formation shapes the spatial organization of condensate phases. In summary, this work demonstrates a mechanistic route explaining how conformational switching and molecular cross-linking regulate material properties and morphology of condensates.

Odd viscosity, the nondissipative part of the viscous response of a time-reversal-broken fluid, is notoriously difficult to measure precisely because it does no work. Here we show that parity-time ($\mathscr{PT}$) symmetry, familiar from non-Hermitian optics, converts this elusiveness into a measurement principle. The odd Navier-Stokes equations, that include the nonlinear inertial terms, are $\mathscr{PT}$-symmetric, follow from a Lagrangian, and linearize to a Schrödinger equation in which the odd viscosity plays the role of Planck's constant; potential vorticity obeys a generalized Ertel conservation law. A probe trapped in an odd liquid realizes a pair of oscillators coupled by odd friction, and supplying balanced loss and gain drives a twofold $\mathscr{PT}$ transition whose exceptional point and Rabi sidebands locate the odd viscosity with square-root-enhanced sensitivity. Upon quantization the spectrum is of Fock-Darwin form, and the dissipative pair exhibits a Liouvillian exceptional point separating linear from exponential heating. These results furnish mechanical, stochastic, and spectroscopic protocols for measuring odd transport coefficients in classical and quantum fluids.

The capillary rise of simple passive fluids in a tube is given by Jurin's law of capillary action, which balances surface tension and gravity. For fluids composed of active particles interacting via pairwise forces, a capillary rise was reported despite a negative mechanical surface tension, a phenomenon which remains unexplained. We establish the active form of Jurin's law from the microscopic dynamics. It includes a drag emerging from particle currents that we find responsible for capillary rise. These active currents, alongside negative surface tension, lead to complex and counterintuitive capillary action phenomena that are impossible in equilibrium. In particular the capillary rise of active fluids depends on the shape of the tube, not solely on the tube diameter.

We harness two established ingredients for collective demixing: differential speed and curvature to create a self-sorting device. In binary mixtures, motility differences drive spontaneous spatial segregation, while confinement geometry determines how rapidly and strongly this demixing develops. Using particle based simulations, we systematically identify the geometrical conditions that promote efficient segregation and use these results to guide the design of a finite sorting architecture. We then translate these physical mechanisms into a sequence of curved microfluidic units that progressively amplify the separation of the two species and direct them toward distinct collection regions. Experiments with binary Quincke-roller mixtures confirm that an initially mixed suspension progressively demixes as it propagates through the device, leading to strong enrichment downstream. Our results demonstrate how collective active demixing can be converted into a functional continuous sorting strategy, providing a route toward autonomous microfluidic separation based on particle motility and confinement geometry.

A downward fin thrust near a cohesive seabed lofts sediment. Whether this cloud settles or organizes into a self-sustaining down-slope current determines if a diver loses visibility briefly or catastrophically. We reduce the layer-averaged balances of fluid mass, sediment mass, and momentum to a temporal slab of fixed thickness in the weakly entraining limit. This yields an autonomous planar vector field in dimensionless near-bed speed and suspended load, governed by three dimensionless groups: drag against settling, erosion strength, and near-bed concentration. The field possesses a quiescent equilibrium at the origin and, above a critical bed slope obtained in closed form as the ratio of near-bed concentration times drag-settling number to erosion-strength number, an interior saddle equilibrium. The saddle's stable manifold partitions the state space into basins of decay and unbounded growth, establishing the exact threshold between self-limiting and igniting disturbances. On a flat bed, the origin attracts globally for all admissible erosion laws. For representative silt, the ignition threshold is near a 17-degree bed angle. The closed-form structure is confirmed numerically to machine precision. A closure study demonstrates the critical slope is robust in existence but closure-dependent in value, identifying the linear erosion law as the conservative choice. The model thus isolates bed slope as the controlling parameter for ignition.

Inspired by the classical Plateau-Douglas problem for soap films bounded by two closed curves, we solve an analogous problem for fluid interfaces with fixed surface area and resistance to out-of-plane bending. The boundaries are planar but need not be symmetric or concentric. The equilibrium surfaces minimize the Willmore bending energy and generalize minimal surfaces such as the catenoid while also exhibiting characteristic features of confined elastic interfaces such as buckling. We systematically classify all possible buckling modes and solution branches by performing a weakly nonlinear analysis and developing a fully nonlinear spectral solver. Our mathematical framework provides insight into the forces and torques required to stabilize cellular membranes and other soft materials and shows that physically relevant asymmetric states can arise even in symmetric systems.

We report a study of the emergent dynamics arising in two-dimensional suspensions of semi-flexible chains whose tip is chemically active, generating a phoretic field. By varying the chain length (number of monomers per chain $N_{pc}$), the area fraction $\phi$, and the sign of the phoretic coupling $J_0$, we map out a rich non-equilibrium phase diagram in the presence of phoretic interactions. For repulsive phoretic interactions ($J_0 > 0$) between the chains, we find that short chains ($N_{pc} = 2$) develop a transient chaotic flow state that crosses over at long times to a global polar flock with super-diffusive mean-squared displacement and long-ranged velocity correlations. Surprisingly, we find this state to have suppressed density fluctuations, indicating the emergence of hyperuniformity. At intermediate chain lengths ($N_{pc} \sim 4$-$8$), the repulsive chemical field drives chaotic mesoscale flows – a dry route to active turbulence – without the need for hydrodynamic interactions or steric alignment interactions. For attractive phoretic interactions ($J_0 < 0$), chains self-organise into hedgehog-like micellar aggregates with heads forming the core and flexible tails radiating outward, in structural analogy with amphiphile micellisation but driven entirely by non-equilibrium self-propulsion. A coarse-grained theory of a tip-emitting active rod predicts the onset of the flocking of dimers, though overestimates the presence of polar order for longer chains. Our results establish phoretic tip activity as a minimal, experimentally realisable mechanism for a spectrum of collective states hitherto attributed to hydrodynamic interactions or steric alignment.

We present a generic solution for the relative motion of two diffusiophoretic prey-predator particles of arbitrary chemical activity Ai and radius Ri, where i = 1;2 refers to the predator and prey, respectively. Using the Lorentz reciprocal theorem, we investigate the impact of radius ratios and chemical reaction rates on the interaction between the particles. Our study reveals four distinct regimes of interaction, similar to the findings of Nasouri & Ramin (Phys. Rev. Lett., vol. 124, 2020, pp. 168003) for particles of identical sizes: (i) the prey particle escapes; (ii) two particles reach a stable equilibrium distance; (iii) two particles reach an unstable equilibrium distance where the prey is captured below it and escapes above it; (iv) the prey particle is captured. Unlike previous work, we differentiate between regimes with near-field and far-field interactions, which can be either attractive or repulsive, and find that the boundary between (i, iii) and (ii, iv) represents the transition from the attraction to repulsion in the far field, given by jA1=A2j = (R2=R1)2, while the transition between (i, ii) and (iii, iv) represents the interaction transition for particles in close proximity. We also perform three-dimensional simulations of prey-predator systems, which validate our theoretical predictions. Our study extends the applicability of the Lorentz reciprocal theorem to prey-predator system and quantitatively obtains interaction regime transition curves by distinguishing near-field and far-field interactions.

Ion channels and pumps drive ion-selective currents through cell membranes at localized sites, yet a cell's electrical state is routinely summarized by a single transmembrane voltage. Combining theory and numerical simulations, we resolve the spatiotemporal dynamics of charge reorganization driven by a localized current on a spherical membrane vesicle. At early times, the response is insensitive to membrane geometry: as in the case of a flat membrane (arXiv:2407.11947; arXiv:2508.14001), the transmembrane voltage decays in a monopolar fashion, varying inversely with distance from the source, and crosses over to a dipolar tail that scales as the inverse cube of distance. Under sustained current, this monopolar response spreads outward from the source. Because the vesicle is closed, this response cannot persist indefinitely; once the monopolar front traverses the entire vesicle, the subsequent charging dynamics is dominated by a spatially uniform mode corresponding to capacitive charging of the membrane. We further decompose the bulk potentials into an electrostatic image-charge component that generates the bulk electric fields and a spatially uniform capacitive mode that can be represented as an equivalent circuit. We also derive a nonlocal cable equation governing the transmembrane voltage dynamics and show that the uniform mode is its long-time solution. This work provides a first-principles basis for the electrophysiological simplification of an electrotonically compact cell.

We present a kinetic Monte Carlo (KMC) modeling approach to describe the stochastic dynamics of a peptide molecule spanning nanosecond to second timescales. The dynamics of protein conformational changes is interpreted at a local level in terms of dihedral transitions. Taking Trp-cage miniprotein as an example, the KMC model "learns" about the transitions from multiple MD trajectories. Training is based on local divide-and-conquer strategy that identifies the discretized backbone dihedral states as building blocks for the conformational space, along with associated transition rates of dihedral flips to describe the conformational state-to-state dynamics. A key feature in our approach is the incorporation of backbone correlations, such that rates are conditioned on the local environment and steric coupling. We show that with the correlations built-in, the KMC model closely matches MD. Such an approach is shown to reach second timescales in a few CPU hours on a standard desktop computer, and can easily yield multiple stochastic realizations of the conformational dynamics. Our KMC model construction scheme should be generally applicable to a wide range of proteins, and can be used for bridging local flexibility to protein-wide dynamics.

We present a reduced-order semi-analytical model for reorientational nonlinearity in chiral nematic liquid crystals, showing that the chiral pitch acts as the dominant physical length scale governing the onset of nonlinear self-focusing and soliton formation. Starting from the full Frank-Oseen equation, we derive a closed-form expression for the optically induced molecular rotation that captures the essential saturable response of the medium while reducing computational cost by more than two orders of magnitude compared with standard relaxation-method solvers. Despite its simplicity, the model reproduces the essential features of the numerically obtained nonlinear refractive index, the onset of self-localization, and the transition from discrete to continuous solitons in one and two dimensions. It further predicts the formation of fully localized astigmatic nematicons with only minor shifts in the self-localization threshold due to the neglect of nonlocal effects. The proposed model provides direct physical insight into light-matter interactions with soft matter media and offers a computationally efficient tool for the design and optimization of nonlinear photonic devices.

Localized forcing in the fluid inside or outside a viscous drop can drive drop translation. Using the Lorentz reciprocal theorem, we derive an integral expression for the translational velocity of a spherical Newtonian drop subject to localized force and source distributions in either fluid and to interfacial traction. For a clean drop, we obtain explicit responses to Stokeslets, force dipoles, rotlets, general second force moments, and source dipoles as functions of position, orientation, and viscosity ratio. Interior forcing obeys a finite selection rule: only force moments through second order and the first source moment contribute directly to translation. Exterior forcing can couple to multipoles of all orders and produces distance-dependent responses. Although different enclosed singularities can produce the same drop velocity, resolving their exterior flows in drop-centered spherical Stokes modes provides additional constraints on the underlying forcing. We also distinguish regularized force distributions, governed by prescribed kernel moments, from resolved rigid particles, governed by low-order surface-traction moments and prescribed slip. The framework unifies these representations and shows how exterior-flow measurements provide information beyond drop translation, laying the foundation for constructing squirmer-like viscous drop solutions with controllable far-field behaviors.

We investigate the impact of charge regulation (CR) on the non-uniform swelling behavior of polyelectrolyte hydrogels. The Poisson-Boltzmann theory with electro-elastic coupling between the local polymer density and elastic deformation is considered. We investigate the spatial distributions of the elastic displacement and polymer density under different salt concentrations and compare charge-regulated gels with fixed-charge (non-CR) gels of the same net charge. Our results show that the CR induces spatially varying charge fractions, which strengthen the electro-elastic response and lead to stronger non-uniform swelling compared with non-CR gels. These findings provide a theoretical basis for understanding and controlling non-uniform swelling in responsive polyelectrolyte hydrogels.