Related papers: Simulating Organogenesis in COMSOL: Parameter Opti…
We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the…
A wide range of modern science and engineering applications are formulated as optimization problems with a system of partial differential equations (PDEs) as constraints. These PDE-constrained optimization problems are typically solved in a…
Simulating in silico cellular responses to interventions is a promising direction to accelerate high-content image-based assays, critical for advancing drug discovery and gene editing. To support this, we introduce MorphGen, a…
Morphogen transport is a biological process, occurring in the tissue of living organisms, which is a determining step in cell differentiation. We present rigorous analysis of a simple model of this process, which is a system coupling…
In recent years, there has been a growing interest in understanding complex microstructures and their effect on macroscopic properties. In general, it is difficult to derive an effective constitutive law for such microstructures with…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Mesoscale simulations of woven composites using parameterized analytical geometries offer a way to connect constituent material properties and their geometric arrangement to effective composite properties and performance. However, the…
We develop a mathematical and numerical framework to solve state estimation problems for applications that present variations in the shape of the spatial domain. This situation arises typically in a biomedical context where inverse problems…
Modeling the spontaneous evolution of morphology in natural systems and its preservation by proportionate growth remains a major scientific challenge. Yet, it is conceivable that if the basic mechanisms of growth and the coupled kinetic…
Parametric model order reduction (pMOR) is a powerful tool for accelerating finite element (FE) simulations while maintaining parametric dependencies. For geometric parameters, pMOR by matrix interpolation is a well-suited approach because…
In material science, models are derived to predict emergent material properties (e.g. elasticity, strength, conductivity) and their relations to processing conditions. A major drawback is the calibration of model parameters that depend on…
This study presents an internalized morphogenesis model for autonomous systems, such as swarm robotics and micro-nanomachines, that eliminates the need for external spatial computation. Traditional self-organizing models often require…
In this paper we propose a data-driven methodology to gain insight into the formation of different types of pseudopalisade structures. To this end, we start from a state of the art macroscopic model for the dynamics of GBM, that is coupled…
Many organs of higher organisms are heavily branched structures and arise by an at first sight similar process of branching morphogenesis. Yet the regulatory components and local interactions that have been identified differ greatly in…
This paper presents a methodological framework for training, self-optimising, and self-organising surrogate models to approximate and speed up multiobjective optimisation of technical systems based on multiphysics simulations. At the hand…
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular…
This paper describes a class of shape optimization problems for optical metamaterials comprised of periodic microscale inclusions composed of a dielectric, low-dimensional material suspended in a non-magnetic bulk dielectric. The shape…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…