Related papers: How high-resolution agent-based models can improve…

The current economic crisis has provoked an active response from the interdisciplinary scientific community. As a result many papers suggesting what can be improved in understanding of the complex socio-economics systems were published.…

In social sciences, researchers often face challenges when conducting large-scale experiments, particularly due to the simulations' complexity and the lack of technical expertise required to develop such frameworks. Agent-Based Modeling…

Multi-agent simulations enables the modeling and analyses of the dynamic behaviors and interactions of autonomous entities evolving in complex environments. Agent-based models (ABM) are widely used to study emergent phenomena arising from…

Biological cells can exchange messages through soluble molecules or membrane-bound receptors. In particular in the latter case, the interaction is usually located in specific regions of the interacting cells and may depend on or induce…

Computer simulations offer a robust toolset for exploring complex systems across various disciplines. A particularly impactful approach within this realm is Agent-Based Modeling (ABM), which harnesses the interactions of individual agents…

We develop an agent-based model of the motion and pattern formation of vesicles. These intracellular particles can be found in four different modes of (undirected and directed) motion and can fuse with other vesicles. While the size of…

Modeling and control of agent-based models is twice cursed by the dimensionality of the problem, as both the number of agents and their state space dimension can be large. Even though the computational barrier posed by a large ensemble of…

Research in cultural evolution aims at providing causal explanations for the change of culture over time. Over the past decades, this field has generated an important body of knowledge, using experimental, historical, and computational…

This study investigates the spatial integration of agent-based models (ABMs) and compartmental models for infectious disease modeling, presenting a novel hybrid approach and examining its implications. ABMs offer detailed insights by…

Large Intelligent Systems are so complex these days that an urgent need for designing such systems in best available way is evolving. Modeling is the useful technique to show a complex real world system into the form of abstraction, so that…

Multi-modal AI systems will likely become a ubiquitous presence in our everyday lives. A promising approach to making these systems more interactive is to embody them as agents within physical and virtual environments. At present, systems…

Virtual cell modeling aims to predict cellular responses to diverse perturbations but faces challenges from biological complexity, multimodal data heterogeneity, and the need for interdisciplinary expertise. We introduce CellForge, a…

The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…

Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…

Formal modelling provides a toolkit for understanding cultural dynamics, from individual decisions to recurring patterns of change. This chapter explains what models are and why they matter. Using a precise, shared language, they aid…

During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…

A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matter---ranging from molecular motors and cytoskeletal…

Design - especially of physical objects - can be understood as creative acts solving practical problems. In this paper we describe a biologically-inspired developmental model as the basis of a generative form-finding system. Using local…

For the past few years, deep generative models have increasingly been used in biological research for a variety of tasks. Recently, they have proven to be valuable for uncovering subtle cell phenotypic differences that are not directly…

Virtual cell modeling aims to predict cellular responses to perturbations. Existing virtual cell models rely heavily on large-scale single-cell datasets, learning explicit mappings between gene expression and perturbations. Although recent…