arXiv subjects

Ana-Sunčana Smith

Publications and source records attributed to Ana-Sunčana Smith.

At least 19 recordsLinked to original sources

arXiv2025

Diversity in emergent cell locomotion from the coupling cytosolic and cortical Marangoni flows with reaction-diffusion dynamics

Cell migration is a fundamental process underlying the survival and function of both unicellular and multicellular organisms. Crawling motility in eukaryotic cells arises from cyclic protrusion and retraction driven by the cytoskeleton, whose organization is regulated by reaction-diffusion (RD) dynamics of Rho GTPases between the cytosol and the cortex. These dynamics generate spatial membrane patterning and establish front-rear polarity through the coupling of biochemical signalling and mechanical feedback. We develop a cross-scale mean-field framework that integrates RD signalling with cytosolic and cortical hydrodynamics to capture emergent cellular locomotion. Our model reproduces diverse experimentally observed shape and motility phenotypes with small parameter changes, indicating that these behaviours correspond to self-organized limit cycles. Phase-space analysis reveals that coupling to both cytosolic flow and spatially varying surface tension is essential to recover the full spectrum of motility modes, providing a theoretical foundation for understanding amoeboid migration.

physics.bio-ph↗

arXiv2024

Criticality in an imidazolium ionic liquid fully wetting a sapphire support

Hypothesis: Ionic liquids have various applications in catalytic reaction environments. In those systems, their interaction with interfaces is key to their performance as a liquid phase. We hypothesize that the way a monolayer ionic liquid phase interacts with interfaces like a sapphire substrate is significantly dependent on temperature and that critical behavior can be observed in the structural properties of the liquid film. Methods and simulations: We perform molecular dynamics simulations of imidazolium-based ionic liquid monolayers deposited on a sapphire substrate at temperatures from 200K to 400K. We develop computational tools to analyze structural properties of molecular arrangement in the monolayer, the structure of the film and the defects spontaneously forming and healing. Findings: We observe a clear structural phase transition at around 300K from a solid-like to a liquid-like behavior of a film. Below the critical point an alternating crystalline structure of cations and anions with alignment of periodic vectors with the underlying substrate grid is observed, with frozen defects. Above the critical temperature, the pattern becomes isotropic within the contact layer that displays dynamic defects of a characteristic size. Our results highlight the importance of confinement to the phase behavior of the system.

cond-mat.soft↗

arXiv2023

Metachronal coordination at the mesoscale

In nature, metachronal coordination is an efficient strategy for fluid pumping and self-propulsion. Yet, mimetic systems for this type of organization are scarce. Recently, metachronal motion was observed in a bead-based magnetocapillary mesoswimmer, but the mechanism of such device's behavior remained unclear. Here, we combine theory and experiments to explain two swimming regimes that we identify by modulation of the driving frequency. In the linear, low-frequency regime, the swimmer motion originates from individual bead rotations. However, the high-frequency, metachronal regime is dominated by deformations of the device near a mechanical resonance, which highlights the role of bead inertia for optimized self-propulsion.

cond-mat.soft↗

arXiv2023

The Stokes-Einstein-Sutherland equation at the nanoscale revisited

The Stokes-Einstein-Sutherland (SES) equation is at the foundation of statistical physics, relating a particle's diffusion coefficient and size with the fluid viscosity, temperature and the boundary condition for the particle-solvent interface. It is assumed that it relies on the separation of scales between the particle and the solvent, hence it is expected to break down for diffusive transport on the molecular scale. This assumption is however challenged by a number of experimental studies showing a remarkably small, if any, violation, while simulations systematically report the opposite. To understand these discrepancies, analytical ultracentrifugation experiments are combined with molecular simulations, both performed at unprecedented accuracies, to study the transport of buckminsterfullerene C60 in toluene at infinite dilution. This system is demonstrated to clearly violate the conditions of slow momentum relaxation. Yet, through a linear response to a constant force, the SES equation can be recovered in the long time limit with no more than 4% uncertainty both in experiments and in simulations. This nonetheless requires partial slip on the particle interface, extracted consistently from all the data. These results, thus, resolve a long-standing discussion on the validity and limits of the SES equation at the molecular scale.

cond-mat.mes-hall↗

arXiv2023

Anisotropic molecular diffusion in confinement I: Transport of small particles in potential and density gradients

Hypothesis: Diffusion in confinement is an important fundamental problem with significant implications for applications of supported liquid phases. However, resolving the spatially dependent diffusion coefficient, parallel and perpendicular to interfaces, has been a standing issue. In the vicinity of interfaces, density fluctuations as a consequence of layering locally impose statistical drift, which impedes the analysis of spatially dependent diffusion coefficients even further. We hypothesise, that we can derive a model to spatially resolve interface-perpendicular diffusion coefficients based on local lifetime statistics with an extension to explicitly account for the effect of local drift using the Smoluchowski equation, that allows us to resolve anisotropic and spatially dependent diffusivity landscapes at interfaces. Methods and simulations: An analytic relation between local crossing times in system slices and diffusivity as well as an explicit term for calculating drift-induced systematic errors is presented. The method is validated on Molecular Dynamics simulations of bulk water and applied to simulations of water in slit pores. Findings: After validation on bulk liquids, we clearly demonstrate the anisotropic nature of diffusion coefficients at interfaces. Significant spatial variations in the diffusivities correlate with interface-induced structuring but cannot be solely attributed to the drift induced by local density fluctuations.

cond-mat.soft↗

arXiv2023

Anisotropic molecular diffusion in confinement II: A model for structurally complex particles applied to transport in thin ionic liquid films

Hypothesis:Diffusion in confinement is an important fundamental problem with significant implications for applications of supported liquid phases. However, resolving the spatially dependent diffusion coefficient, parallel and perpendicular to interfaces, has been a standing issue and for objects of nanometric size, which structurally fluctuate on a similar time scale as they diffuse, no methodology has been established so far. We hypothesise that the complex, coupled dynamics can be captured and analysed by using a model built on the $2$-dimensional Smoluchowski equation and systematic coarse-graining. Methods and simulations: For large, flexible species, a universal approach is offered that does not make any assumptions about the separation of time scales between translation and other degrees of freedom. The method is validated on Molecular Dynamics simulations of bulk systems of a family of ionic liquids with increasing cation sizes where internal degrees of freedom have little to major effects. Findings: After validation on bulk liquids, where we provide an interpretation of two diffusion constants for each species found experimentally, we clearly demonstrate the anisotropic nature of diffusion coefficients at interfaces. Spatial variations in the diffusivities relate to interface-induced structuring of the ionic liquids. Notably, the length scales in strongly confined ionic liquids vary consistently but differently at the solid-liquid and liquid-vapour interfaces.

cond-mat.soft↗

arXiv2022

Mesoscopic modelling of epithelial tissues

Over the last two decades, scientific literature has been blooming with various means of simulating epithelial cell colonies. Each of these simulations can be separated by their respective efficiency (expressed in terms of consumed computational resources), the amount of cells/the size of tissues that can be simulated, the time scale of the simulated dynamics and the coarse grained level of precision. Choosing the right algorithm for the simulation of epithelial cells and tissues is a compromise between each of these key elements. Irrespective of the method, each algorithm includes part, or all, of the following features: short-range membrane-mediated attraction between cells, soft-core repulsion between cells, cell proliferation, cell death, cell motility, fluctuations, etc. We will first give a non-exhaustive overview of commonly used modeling approaches for tissues at a mesoscopic level, giving a rough idea of the coarse-graining decisions made for every one of them. Then we will dive into greater detail on how to implement a relaxation procedure according to the Vertex Model, refreshing aspects of the theoretical groundwork, describing required data structures and simulation steps and pointing out details of the simulation that can present pitfalls to a first-time implementation of the model.

physics.comp-ph↗

arXiv2022

Protein-lipid domains in heterogeneous membranes beyond spontaneous curvature effects

We study a model of a lipid bilayer membrane described by two order parameters: the chemical composition described using the Gaussian model and the spatial configuration described with the elastic deformation model of a membrane with a finite thickness, or equivalently, for an adherent membrane. We assume and explain on physical grounds the linear coupling between the two order parameters. Using the exact solution, we calculate the correlation functions and order parameters profiles. We also study the domains that form around inclusions on the membrane. We propose and compare six distinct ways to quantify the size of such domains. Despite of its simplicity, the model has many interesting features like Fisher-Widom line or two distinct critical regions.

cond-mat.soft↗

arXiv2021

Hydrodynamic particle interactions in linear and radial viscosity gradients

We present a versatile perturbative calculation scheme to determine the mobility matrix for two and more particles in a low Reynolds number fluid with spatially variant viscosity. Assuming an asymptotic non-constant viscosity perturbation superimposed on a constant viscosity background, we exploit the Lorentz reciprocal theorem and a reflection method to obtain the leading order correction to the mobility matrix. We apply our approach firstly to an interface-like linear viscosity gradient with an extension much larger than the length scale of the particle separation. We find that the viscosity gradient gives rise to additional long-range flow fields, for both particle translation and rotation, which decay by one order slower than their constant-viscosity counterparts. Also, we reveal that the relative positioning of two interacting particles in finite-size gradients, a natural precondition to avoid pathological negative viscosity, affects the mobilities of and interaction between both particles. Secondly, we apply our result to two interacting particles with temperatures different from that of the surrounding fluid, which alters both the fluid temperature and viscosity field. We find that both, the self-mobilities of the particles as well as their interactions, increase for hot particles and decrease for cold particles.

physics.flu-dyn↗

arXiv2021

Protein induced lipid demixing in homogeneous membranes

Specific lipid environments are necessary for the establishment of protein signalling platforms in membranes, yet their origin has been highly debated. We present a continuum, exactly solvable model of protein induced local demixing of lipid membranes. The coupling between a local composition and a local thickness of the membrane induces lipid domains around inclusions with hydrophobic mismatch, even for temperatures above the miscibility critical point of the membrane. The model qualitatively explains the experimentally observed formation of lipid domains induced by anchoring of reconstituted actin in flat supported lipid bilayers.

physics.bio-ph↗

arXiv2021

Crowding competes with trapping to enhance interfacial diffusion

Diffusion in the crowded environments of the biological membranes or materials interfaces often involves intermittent binding to surface proteins or defects. To account for this situation we study a 2-dimensional lattice gas in a field of immobilized traps. Using kinetic Monte Carlo simulations, we calculate the effective diffusion coefficient in the long-time limit as a function of the traps and particle densities. We find a remarkable result - an increase of the diffusion coefficient with particle density, an effect that we coin as crowding-enhanced diffusion. We rationalize this result using scaling arguments and the master equation approach.

cond-mat.soft↗

arXiv2021

Theoretical framework for pairwise microswimmer interactions

Hydrodynamic interactions are crucial for determining the cooperative behavior of microswimmers at low Reynolds numbers. Here we provide a comprehensive analysis of the scaling and strength of the interactions in the case of a pair of three-sphere swimmers with intrinsic elasticity. Both stroke-based and force-based microswimmers are analyzed using an analytic perturbative approach. Following a detailed analysis of the passive interactions, as well as active translations and rotations, we find that the mapping between the stroke-based and force-based swimmers is only possible in a low driving frequency regime where the characteristic time scale is smaller than the viscous one. Furthermore, we find that for swimmers separated by up to hundreds of swimmer lengths, swimming in pairs speeds up the self propulsion, due to the dominant quadrupolar hydrodynamic interactions. Finally, we find that the long term behavior of the swimmers, while sensitive to initial relative positioning, does not depend on the pusher or puller nature of the swimmer.

cond-mat.soft↗

arXiv2020

Recent Advances and Prospects in the Research of Nascent Adhesions

Nascent adhesions are submicron transient structures promoting the early adhesion of cells to the extracellular matrix. Nascent adhesions typically consist of several tens of integrins, and serve as platforms for the recruitment and activation of proteins to build mature focal adhesions. They are also associated with early stage signalling and the mechanoresponse. Despite their crucial role in sampling the local extracellular matrix, very little is known about the mechanism of their formation. Consequently, there is a strong scientific activity focused on elucidating the physical and biochemical foundation of their development and function. Precisely the results of this effort will be summarized in this article.

q-bio.SC↗

arXiv2020

Catalytic flow with a coupled Finite Difference -- Lattice Boltzmann scheme

Many catalyst devices employ flow through porous structures, which leads to a complex macroscopic mass and heat transport. To unravel the detailed dynamics of the reactive gas flow, we present an all-encompassing model, consisting of thermal lattice Boltzmann model by Kang et al., used to solve the heat and mass transport in the gas domain, coupled to a finite differences solver for the heat equation in the solid via thermal reactive boundary conditions for a consistent treatment of the reaction enthalpy. The chemical surface reactions are incorporated in a flexible fashion through flux boundary conditions at the gas-solid interface. We scrutinize the thermal FD-LBM by benchmarking the macroscopic transport in the gas domain as well as conservation of the enthalpy across the solid-gas interface. We exemplify the applicability of our model by simulating the reactive gas flow through a microporous material catalysing the so-called water-gas-shift reaction.

physics.flu-dyn↗

arXiv2019

Geometric effects in random assemblies of ellipses

Assemblies of anisotropic particles commonly appear in studies of active many-body systems. However, in two dimensions, the geometric ramifications of the finite density of such objects are not entirely understood. To fully characterize these effects, we perform an in-depth study of random assemblies generated by a slow compression of frictionless elliptical particles. The obtained configurations are then analysed using the Set Voronoi tessellation which takes the particle shape into the account. Not only that we analyse most scalar and vectorial morphological measures, which are commonly discussed in the literature or which have been recently addressed in experiments, but also systematically explore the correlations between them. While in a limited range of parameters similarities with findings in 3D assemblies could be identified, important differences are found when a broad range of aspect ratios and packing fractions are considered. The data discussed in this study should thus provide a unique reference set such that geometric effects and differences from random assemblies could be clearly identified in more complex systems, including ones with soft and active particles that are typically found in biological systems.

physics.bio-ph↗

arXiv2019

Water in an electric field does not dance alone: The relation between equilibrium structure, time dependent viscosity and molecular motions

Dynamic structuring of water is a key player in a large class of processes underlying biochemical and technological developments today, the latter often involving electric fields. However, the anisotropic coupling between the water structure and the field has not been understood on a molecular level so far. Here we perform extensive molecular dynamics simulations to explore the influence of an externally imposed electric field on liquid water under ambient conditions. Using self-developed analysis tools and rigorous statistical analysis, we unambiguously show that water hydration shells break into subcompartments, which were hitherto not observed due to radial averaging. The shape of subcompartments is sensitive to the field magnitude, and affects excitations of the hydrogen bond network including the femtosecond stretching and the sub-picosecond restructuring of hydrogen bonds. Furthermore, by analysing the reorientational dynamics of water molecules, we ascertain the existence of cooperative excitations of small water clusters. Enabled by the interplay between hydrogen bonding, and the coupling of water dipoles to the field, these coordinated motions, occurring on the picosecond time scale, are associated with fluctuations between torque-free states of water dipoles. We show that unlike the coupling between translation and reorientation of water molecules, which takes place on even longer time scales, these coordinated motions are the key for understanding the emergent anisotropy of diffusion and viscosity of water. Particular effort is invested to provide an analysis that allows for future experimental validation.

cond-mat.soft↗

arXiv2019

Statistical mechanics of an elastically pinned membrane: Static profile and correlations

The relation between thermal fluctuations and the mechanical response of a free membrane has been explored in great detail, both theoretically and experimentally. However, understanding this relationship for membranes, locally pinned by proteins, is significantly more challenging. Given that the coupling of the membrane to the cell cytoskeleton, the extracellular matrix and to other internal structures is crucial for the regulation of a number of cellular processes, understanding the role of the pinning is of great interest. In this manuscript we consider a single protein (elastic spring of a finite rest length) pinning a membrane modelled in the Monge gauge. First, we determine the Green$'$s function for the system and complement this approach by the calculation of the mode coupling coefficients for the plane wave expansion, and the orthonormal fluctuation modes, in turn building a set of tools for numerical and analytic studies of a pinned membrane. Furthermore, we explore static correlations of the free and the pinned membrane, as well as the membrane shape, showing that all three are mutually interdependent and have an identical long-range behaviour characterised by the correlation length. Interestingly, the latter displays a non-monotonic behaviour as a function of membrane tension. Importantly, exploiting these relations allows for the experimental determination of the elastic parameters of the pinning. Last but not least, we calculate the interaction potential between two pinning sites and show that, even in the absence of the membrane deformation, the pinnings will be subject to an attractive force due to changes in membrane fluctuations.

physics.bio-ph↗

arXiv2018

Two Heads Are (Sometimes) Better Than One: How Rate Formulations Impact Molecular Motor Dynamics

Cells are complex structures which require considerable amounts of organization via transport of large intracellular cargo. While passive diffusion is often sufficiently fast for the transport of smaller cargo, active transport is necessary to organize large structures on short timescales. The main mechanism of this transport is by cargo attachment to motors which walk in a directed fashion along intracellular filaments. There are a number of models which seek to describe the motion of motors with attached cargo, from detailed microscopic to coarse phenomenological descriptions. We focus on the intermediate-detailed discrete stochastic hopping models, and explore how cargo transport changes depending on the number of motors, motor interaction, system constraints and rate formulations which are derived from common thermodynamic assumptions. We find that, despite obeying the same detailed balance constraint, the choice of rate formulation considerably affects the characteristics of the overall motion of the system, with one rate formulation exhibiting novel behavior of loaded motor groups moving faster than a single unloaded motor.

q-bio.BM↗