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Membrane phase-separation is a mechanism that biological membranes often use to locally concentrate specific lipid species in order to organize diverse membrane processes. Phase separation has also been explored as a tool for the design of…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
Spatial transcriptomics methods capture cellular measurements such as gene expression and cell types at specific locations in a cell, helping provide a localized picture of tissue health. Traditional visualization techniques superimpose the…
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
This paper is a first step to chase the ambitious objective of developing a mathmatical theory of living systems. The contents refer modeling large systems of interacting living entities with the aim of describing their collective behaviors…
Although polymerization and curing reactions govern the performance of advanced materials, their simulation remains challenging owing to the need for accurate, transferable potentials and rarity of chemical events. Conventional reactive…
Blended mathematical sensemaking in science (blended MSS) involves deep conceptual understanding of quantitative relationships describing phenomena in science and has been studies in various disciplines. However, no unified characterization…
This work presents a comprehensive three-dimensional third-medium contact framework for modeling complex contact interactions in hyperelastic solids and pneumatically actuated systems. The proposed third-medium formulation embeds a…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
Model merging, typically on Instruct and Thinking models, has shown remarkable performance for efficient reasoning. In this paper, we systematically revisit the simplest merging method that interpolates two weights directly. Particularly,…
During last decade, multi-level agent-based modeling has received significant and dramatically increasing interest. In this article we present a comprehensive and structured review of literature on the subject. We present the main…
We propose a two-scale model to resolve essential features of developmental tissue deformations. The model couples individual cellular behavior to the mechanics at tissue scale. This is realized by a multiphase-field model addressing the…
Biological cells exhibit a hierarchical spatial organization, where various compartments harbor condensates that form by phase separation. Cells can control the emergence of these condensates by affecting compartment size, the amount of the…
This article describes a volumetric approach for procedural shape modeling and a new Procedural Shape Modeling Language (PSML) that facilitates the specification of these models. PSML provides programmers the ability to describe shapes in…
Diffusion probabilistic models have made their way into a number of high-profile applications since their inception. In particular, there has been a wave of research into using diffusion models in the prediction and design of biomolecular…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by…
We consider a multiscale approach based on immersed methods for the efficient computational modeling of tissues composed of an elastic matrix (in two or three-dimensions) and a thin vascular structure (treated as a co-dimension two…