Related papers: Intracellular Measurement-Informed Multiscale Mode…
Three-dimensional molecular generators based on diffusion models can now reach near-crystallographic accuracy, yet they remain fragmented across tasks. SMILES-only inputs, two-stage pretrain-finetune pipelines, and one-task-one-model…
Bone remodeling involves the coordinated removal of bone by osteoclasts and addition of bone by osteoblasts, a process that is modulated by the prevailing mechanical environment. In this paper a fully coupled model of bone remodeling is…
The membrane curvature of cells and intracellular compartments continuously adapts to enable cells to perform vital functions, from cell division to signal trafficking. Understanding how membrane geometry affects these processes in vivo is…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
From bird flocks and fish schools to migrating cell sheets, collective motion is a ubiquitous biological phenomenon that inspires quantitative modeling through self-propelled particle (SPP) frameworks. Conventional SPP models prescribe…
A long-standing challenge is designing multi-scale structures with good connectivity between cells while optimizing each cell to reach close to the theoretical performance limit. We propose a new method for direct multi-scale topology…
Derivation of macroscopic models for advection-diffusion processes in the presence of dominant heterogeneous (e.g., surface) reactions using homogenisation theory or volume averaging is often deemed unfeasible due to the strong coupling…
Materials exhibit geometric structures across mesoscopic to microscopic scales, influencing macroscale properties such as appearance, mechanical strength, and thermal behavior. Capturing and modeling these multiscale structures is…
The aim of this chapter is to convey the importance and usefulness of mathematical modelling as a tool to achieve a deeper understanding of stem cell biology. We introduce key mathematical concepts (random walk theory, differential…
The development of complex multicellular organisms from a single parent cell is a highly orchestrated process that cells conduct collectively without central guidance, creating intricate dynamic patterns essential for development and…
Robotic Manipulation Surfaces (RMS) manipulate objects by deforming the surface on which they rest, offering safe, parallel handling of diverse and fragile items. However, existing designs face a fundamental tradeoff: achieving fine control…
In this paper homogenization of a mathematical model for plant tissue biomechanics is presented. The microscopic model constitutes a strongly coupled system of reaction-diffusion-convection equations for chemical processes in plant cells,…
Multiphase field models have emerged as an important computational tool for understanding biological tissue while resolving single-cell properties. While they have successfully reproduced many experimentally observed behaviors of living…
Computational modeling of multicellular systems may aid in untangling cellular dynamics and emergent properties of biological cell populations. A key challenge is to balance the level of model detail and the computational efficiency, while…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
Highly multiplexed microscopy enables rich spatial characterization of tissues at single-cell resolution, yet most analyses rely on two-dimensional sections despite inherently three-dimensional tissue organization. Acquiring dense…
Protein structure generative models excel at predicting single protein static structures from sequence, but routinely fail to capture the correct conformational state of protein complexes, critical for protein design and induced proximity…
We construct a model of cell reprogramming (the conversion of fully differentiated cells to a state of pluripotency, known as induced pluripotent stem cells, or iPSCs) which builds on key elements of cell biology viz. cell cycles and cell…
Bioprocess mechanistic modeling is essential for advancing intelligent digital twin representation of biomanufacturing, yet challenges persist due to complex intracellular regulation, stochastic system behavior, and limited experimental…
Metamaterials exhibit materials response deviation from conventional elasticity. This phenomenon is captured by the generalized elasticity as a result of extending the theory at the expense of introducing additional parameters. These…