arXiv subjects

Fernanda Pérez-Verdugo

Publications and source records attributed to Fernanda Pérez-Verdugo.

5 recordsLinked to original sources

arXiv2026

Beads, springs and fields: particle-based vs continuum models in cell biophysics

Quantitative modeling has become an essential tool in modern biophysics, driven by advances in both experimental techniques and theoretical frameworks. Powerful high-resolution techniques now provide detailed datasets spanning molecular to tissue scales, allowing to visualize cellular structures with unprecedented detail. In parallel, developments in soft and active matter physics have established a robust theoretical basis for describing biological systems. In this context, two main modeling paradigms have emerged: particle-based models, which explicitly represent discrete components and their interactions, and continuum models, which describe systems through spatially varying fields. We compare these approaches across biological scales, highlighting their respective strengths, limitations, and domains of applicability. To keep our discussion biologically relevant, we focus on five systems of fundamental importance: the cytoskeleton, membranes, chromatin, biomolecular condensates and tissues. With this Review, we thus aim to provide a framework for both theorists and experimentalists to select appropriate modeling strategies, and highlight future directions in biophysical modeling.

cond-mat.soft↗

arXiv2023

Tension Remodeling Controls Topological Transitions in Epithelial Tissues

Cell neighbor exchanges play a critical role in regulating tissue fluidity during epithelial morphogenesis and repair. In vivo, these neighbor exchanges are often hindered by the formation of transiently stable four-fold vertices, which can develop into complex multicellular rosettes where five or more cell junctions meet. Despite their importance, the mechanical origins of multicellular rosettes have remained elusive, and current cellular models lack the ability to explain their formation and maintenance. Here we present a dynamic vertex model of epithelial tissues with strain-dependent tension remodeling and mechanical memory dissipation. We show that an increase in cell junction tension upon contraction and reduction in tension upon extension can stabilize higher-order vertices, temporarily stalling cell rearrangements. On the other hand, inducing mechanical memory dissipation via relaxation of junction strain and stress promotes the resolution of higher-order vertices, facilitating cell neighbor exchanges. We demonstrate that by tuning the rates of tension remodeling and mechanical memory dissipation, we can control topological transitions and tissue material properties, recapitulating complex cellular topologies seen in developing organisms.

physics.bio-ph↗

arXiv2023

Excitable dynamics driven by mechanical feedback in biological tissues

Pulsatory activity patterns, driven by mechanochemical feedback, are prevalent in many biological systems. Here we present a theoretical framework to elucidate the mechanical origin and regulation of pulsatile activity patterns within multicellular tissues. We show that a simple mechanical feedback at the level of individual cells - activation of contractility upon stretch and subsequent inactivation upon turnover of active elements - is sufficient to explain the emergence of quiescent states, long-range wave propagation, and traveling activity pulse at the tissue-level. We find that the transition between a propagating pulse and a wave is driven by the competition between timescales associated with cellular mechanical response and geometrical disorder in the tissue. This sheds light on the fundamental role of cell packing geometry on tissue excitability and spatial propagation of activity patterns.

physics.bio-ph↗

arXiv2023

Continuum description of confluent tissues with spatial heterogeneous activity

A continuum description is built to characterize the stationary and transient deformations of confluent tissues subject to heterogeneous activities. By defining a coarse-grained texture matrix field to represent the shape and size of cells, we derive the coarse-grained stress tensor for the vertex model. Activity in the tissue takes the form of inhomogeneous apical contractions, which can be modeled as reductions of the vertex model reference areas or perimeters representing activity in the medial and perimeter regions of the cells, respectively. For medial activity, the extra stress is just an isotropic pressure, while for perimeter activity, it also has a deviatoric component, which is aligned with the texture matrix. The predictions of the continuum description are compared with the average spatiotemporal deformations obtained in simulations of the vertex model subject to localized apical contractions, showing an excellent agreement, even if the active patch is as small as one cell. The fluctuations around the average are more prominent when the activity is in the medial region due to the lack of negative active shape feedback, which, coupled with the confluent property, increases cellular shape and size variations.

physics.bio-ph↗

arXiv2021

Modelling of active contraction pulses in epithelial cells using the vertex model

Several models have been proposed to describe the dynamics of epithelial tissues undergoing morphogenetic changes driven by apical constriction pulses, which differ in where the constriction is applied, either at the perimeter or medial regions. To help discriminate between these models, using the vertex model for epithelial dynamics, we analysed the impact of where the constriction is applied on the final geometry of the active cell that is reducing its apical size. We find that medial activity, characterised by a reduction in the reference area in the vertex model, induces symmetry breaking and generates anisotropic cell shapes, while isotropic cell shapes and larger contractions occur when the reference perimeter in the model is reduced. When plasticity is included, sufficiently slow processes of medial contractile activity, compared with typical apical constriction pulses, can also achieve significant cell contraction. Finally, we apply the model to describe the active apical contractile pulses observed during cellular mitotic events within the epithelial enveloping cell layer in the developing annual killifish Austrolebias nigripinnis, being able to quantitatively describe the temporal evolution of cell shape changes when perimeter activity and area plasticity are included. A global fit of all parameters of the vertex model is provided.

cond-mat.soft↗