Research

Malaria is an ancient disease that still causes more than half a million deaths every year, mostly among children and almost exclusively in low-income countries. As a pharmacometrics scientist at the Medicines for Malaria Venture (MMV), I use mathematical modeling and pharmacometrics to tackle a range of problems in drug development, from recommending first in human doses to modeling the activity of the immune system.

Collaborators: scientists and medical doctors of MMV and its partners.

Figure: Electron micrograph of red blood cells infected with Plasmodium falciparum. From NIH Image Gallery

Publications:
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We are interested in the spontaneous waves observed in the actin cortex of animal cells. These waves emerge from the coupling of active mechanical forces with cell signaling networks. We study these waves in both adherent cells, in vitro, and developing Drosophila embryos, in vivo. In adherent cells, these waves have been argued to play a role during migration, whereas in embryos they contribute to cell and tissue morphogenesis.

Collaborators: Daniel Riveline, Olivier Pertz, Damian Brunner and Karsten Kruse

Figure: Myosin-II oscillations on the surface of a Drosophila embryo’s yolk cell, from Selvaggi et al (2022)

Publications:
Barberi, Sarantseva, Brunner & Kruse, in preparation

We have theoretically shown that active fluids coupled to chemical reaction networks support a rich variety of localized states (aka dissipative solitons). These states emerge via a homoclinic snaking instability and are structurally stable. They can be stationary as well as dynamic, in particular they can develop internal oscillations, either periodic or chaotic. Our results provide the first theoretical framework for the localized dynamics often observed in the actin cortex of animal cells, with implications in our understanding of phenomena such as cell migration and cancer invasion.

Collaborators: Karsten Kruse and Alan Champneys

Figure: Localized spatiotemporal dynamics in a 2D active fluid. Adapted from Barberi & Kruse (2024).

Publications:
Localized spatiotemporal dynamics in active fluids (2024)
Localized states in active fluids (2023)

In viruses and cells, DNA is closely packed and tightly curved thanks to polyvalent cations inducing an effective attraction between its negatively charged filaments. Our understanding of this effective attraction remains very incomplete, mainly because it results from multiple microscopic mechanisms that are hard to predict starting from first principles. We study this fundamental attraction by combining structural data of DNA condensates realized in vitro with effective equilibrium theories, where inter-helical forces compete with DNA elasticity.

Collaborators: Amélie Leforestier, Françoise Livolant and Martin Lenz

Figure: math. model of a twisted DNA toroid.

Publications:
Twist-induced local curvature of filaments in DNA toroids (2021)
Local structure of DNA toroids reveals curvature-dependent intermolecular forces (2021)

ESCRT-III polymers are responsible for membrane remodeling in many cellular processes, ranging from the maturation of retroviruses (like HIV and Ebola) to the constriction of the cytokinetic bridge. Despite its ubiquitous biological role, many aspects of ESCRT-mediated membrane remodeling are still unclear. Recent in vitro experiments revealed that ESCRT polymers can reshape spherical vesicles into helical tubes. Inspired by structural insights from such experiments, we develop generic theories on the competition between ESCRT and membrane elasticity to shed light on the ESCRT-membrane interactions responsible of membrane remodeling in vivo.

Collaborators: Joachim Moser Von Filseck, Aurélien Roux and Martin Lenz

Figure: exptal image vs. math. model of a helical membrane tube.

Publication:
Anisotropic ESCRT-III architecture governs helical membrane tube formation (2020)