arXiv subjects

Miguel Amaral

Publications and source records attributed to Miguel Amaral.

3 recordsLinked to original sources

arXiv2026

A non-reciprocal model for morphogenesis in symbiosis

The shape of a cell influences, and it is influenced by its interactions with its neighbours. Here, we introduce a coarse-grained computational model of non-reciprocal interactions between single-cell organisms to study emergent morphologies during symbiotic association. We show that the cell membrane can be remodelled into branched protrusions, invaginations, transient blebs and other dynamical morphologies that depend on the number of interacting partners, the asymmetry, and the magnitude of partnership activity. Our model finds a dynamical feedback between the local deformation of the membrane and its driving force, leading to membrane morphologies not reported in reciprocal systems with constant activity.

cond-mat.soft↗

arXiv2026

Cracking donuts and sorting lipids: Geometry controls archaeal membrane stability and lipid organization

Cells are defined by lipid membranes that differ in their structure across the tree of life. While the membranes of most bacteria and eukaryotes consist of single-headed bilayer lipids, the membranes of archaea are composed of mixtures of single-headed bilayer lipids and double-headed bolalipids. Archaeal bolalipids can adopt straight or u-shaped conformations, enabling them - together with bilayer lipids - to control whether membranes form bilayer or monolayer structures. Yet, the physical principles governing archaeal membranes remain largely unexplored, especially how membrane structure couples to externally imposed curvature during membrane remodeling. Here, we perform coarse-grained molecular dynamics simulations of toroidal vesicles to systematically probe the effects of all relevant combinations of mean and Gaussian curvatures on shape stability and lipid organization. We find that soft bilayer membranes can sustain all curvatures induced, whereas rigid bolalipid monolayer membranes either transition to different vesicle shapes or rupture. Bilayer-mimicking u-shaped bolalipids and bilayer lipids are spatially accumulated in regions of high mean membrane curvature independent of Gaussian curvature. Our work identifies curvature-composition coupling as a physical signature of archaeal membrane remodeling.

cond-mat.soft↗

arXiv2025

A tutorial for mesoscale computer simulations of lipid membranes: tether pulling, tubulation and fluctuation

Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting up and using membrane simulations can come with barriers due to the multidisciplinary effort involved and the vast choice of existing simulations models. In this review, we introduce the non-expert reader to coarse-grained membrane simulations (CGMS) at the mesoscale. Firstly, we give a concise overview of the modelling approaches to study fluid membranes, together with guidance to more specialized references. Secondly, we provide a conceptual guide on how to develop CGMS. Lastly, we construct a hands-on tutorial on how to apply CGMS, by providing a pedagogical examination of tether pulling, tubulation and fluctuations with three different membrane models, and discussing them in terms of their scope and how resource-intensive they are. To ease the reader's venture into the field, we provide a repository with ready-to-run tutorials.

physics.bio-ph↗