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Dynamic Mode Decomposition (DMD) is a powerful data-driven method used to extract spatio-temporal coherent structures that dictate a given dynamical system. The method consists of stacking collected temporal snapshots into a matrix and…
Dynamin is a ubiquitous GTPase that tubulates lipid bilayers and is implicated in many membrane severing processes in eukaryotic cells. Setting the grounds for a better understanding of this biological function, we develop a generalized…
We consider two minimal mathematical models for cancer dynamics and self-adaptation. We aim to capture the interplay between the rapid progression of cancer growth and the possibility to leverage and enhance self-adaptive defense mechanisms…
Two-dimensional (2D) mechanical models of confluent tissues have related the mechanical state of a monolayer of cells to the average perimeter length of the cell cross sections, predicting floppiness or rigidity of the material. For the…
Biological cells utilize membranes and liquid-like droplets, known as biomolecular condensates, to structure their interior. The interaction of droplets and membranes, despite being involved in several key biological processes, is so far…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
We review theoretical results for the adhesion-induced phase behavior of biomembranes. The focus is on models in which the membranes are represented as discretized elastic sheets with embedded adhesion molecules. We present several…
Density-functional theory is a formally exact description of a many-body quantum system in terms of its density; in practice, however, approximations to the universal density functional are required. In this work, a model based on deep…
Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule…
Molecular dynamics (MD) simulations provide atomistic insights into the structure, dynamics, and function of biomolecules by generating time-resolved, high-dimensional trajectories. Analyzing such data benefits from estimating the minimal…
Lipid membranes, the barrier defining living cells and many of their sub-compartments, bind to a wide variety of nano- and micro-meter sized objects. In the presence of strong adhesive forces, membranes can strongly deform and wrap the…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
With the growth of computational resources, the scope of electronic structure simulations has increased greatly. Artificial intelligence and robust data analysis hold the promise to accelerate large-scale simulations and their analysis to…
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these materials, providing insights into their properties that…
Subsystem Density-Functional Theory (DFT) is an emerging technique for calculating the electronic structure of complex molecular and condensed phase systems. In this topical review, we focus on some recent advances in this field related to…
Constancy of life vitally depends on the internalization of particles through biomembranes. Of particular interest, cellular uptake, including phagocytosis, receptor-mediated endocytosis, and membrane fusion, critically depends on the…
Lipid structures exhibit complex and highly dynamic lateral structure; and changes in lipid density and fluidity are believed to play an essential role in membrane targeting and function. The dynamic structure of liquids on the molecular…
The dynamics of cellular pattern formation is crucial for understanding embryonic development and tissue morphogenesis. Recent studies have shown that human dermal fibroblasts cultured on liquid crystal elastomers can exhibit an increase in…