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Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
Reconstituted filamentous actin networks with myosin motor proteins form active gels, in which motor proteins generate forces that drive the network far from equilibrium. This motor activity can also strongly affect the network elasticity;…
Machine learning force fields possess unprecedented potential in achieving both accuracy and efficiency in molecular simulations. Nevertheless, their application in organic systems is often hindered by structural collapse during simulation…
Substitution of well-grounded theoretical models by data-driven predictions is not as simple in engineering and sciences as it is in social and economic fields. Scientific problems suffer most times from paucity of data, while they may…
The emergence of a body axis is a fundamental step in the development of multicellular organisms. In simple systems such as $\textit{Hydra}$, growing evidence suggests that mechanical forces generated by collective cellular activity play a…
Discovery of the molecular candidates for applications in drug targets, biomolecular systems, catalysts, photovoltaics, organic electronics, and batteries, necessitates development of machine learning algorithms capable of rapid exploration…
The mechanics of animal cells is strongly determined by stress fibers, which are contractile filament bundles that form dynamically in response to extracellular cues. Stress fibers allow the cell to adapt its mechanics to environmental…
Cells self-organize into functional, ordered structures during tissue morphogenesis, a process that is evocative of colloidal self-assembly into engineered soft materials. Understanding how inter-cellular mechanical interactions may drive…
We discuss several continuum cell-cell adhesion models based on the underlying microscopic assumptions. We propose an improvement on these models leading to sharp fronts and intermingling invasion fronts between different cell type…
Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…
To understand cell migration, it is crucial to gain knowledge on how cells exert and integrate forces on/from their environment. A quantity of prime interest for biophysicists interested in cell movements modeling is the intracellular…
Neural control is an exciting mystery which we instinctively master. Yet, researchers have a hard time explaining the motor control trajectories. Physiologically accurate biomechanical simulations can, to some extent, mimic live subjects…
The ability of cells to sense and respond to the mechanical properties of their environments is fundamental to a range of cellular behaviours, with substrate stiffness increasingly being found to be a key signalling factor. Although active…
This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…
The mechanical properties within living cells play a critical role in the adaptive regulation of their biological functions upon environmental and internal stimuli. While these properties exhibit nonequilibrium dynamics due to the thermal…
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…
Recent biological experiments have shown that certain types of cells are able to move in structured and confined environment even without the activation of focal adhesion. Focusing on this particular phenomenon and based on previous works,…
We present a simple, modular graph-based convolutional neural network that takes structural information from protein-ligand complexes as input to generate models for activity and binding mode prediction. Complex structures are generated by…
Biochemistry and mechanics are closely coupled in cell adhesion. At sites of cell-matrix adhesion, mechanical force triggers signaling through the Rho-pathway, which leads to structural reinforcement and increased contractility in the actin…
Cell migration plays a fundamental role in numerous physiological processes, including embryonic development, wound healing, and cancer metastasis. While cell-cell adhesion is known to regulate motion by shaping cell morphology and…