Related papers: Computational models for active matter
Understanding active matter has led to new perspectives on biophysics and non-equilibrium dynamics. However, the development of numerical tools for simulating active fluids capable of incorporating non-trivial boundaries or inclusions has…
Active filaments, such as microtubules with attached cargo-carrying motor proteins, are important dynamic structures for fluid transport in and around living cells. The mathematical models of active filaments appearing in the literature…
Mathematical models come in many forms across biological applications. In the case of complex, spatial dynamics and pattern formation, stochastic models also face two main challenges: pattern data is largely qualitative, and model…
We derive a hydrodynamic description of metric-free active matter: starting from self-propelled particles aligning with neighbors defined by "topological" rules, not metric zones, -a situation advocated recently to be relevant for bird…
Computational scientists have investigated swimming performance across a multitude of different systems for decades. Most models depend on numerous model parameters and performance is sensitive to those parameters. In this paper, parameter…
The traditional methods of the biology, based on illustrative descriptions and linear logic explanations, are discussed. This work aims to improve this approach by introducing alternative tools to describe and represent complex biological…
Machine learning models of vastly different modalities and architectures are being trained to predict the behavior of molecules, materials, and proteins. However, it remains unclear whether they learn similar internal representations of…
Model-based approaches for image reconstruction, analysis and interpretation have made significant progress over the last decades. Many of these approaches are based on either mathematical, physical or biological models. A challenge for…
Computational multiscale modeling encompasses a wide range of end-products and a great number of technological applications. This paper provides an overview of the computational multiscale modeling approach based on the utilization of MBN…
Modeling of fluid flows requires corresponding adequate and effective approaches that would account for multiscale nature of the considered physics. Despite the tremendous growth of computational power in the past decades, modeling of fluid…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Quantitative modeling has become an essential tool in modern biophysics, driven by advances in both experimental techniques and theoretical frameworks. Powerful high-resolution techniques now provide detailed datasets spanning molecular to…
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
In this book chapter we describe recent applications of artificial intelligence and in particular machine learning to active matter systems. Active matter is composed of agents, or particles, that are capable of propelling themselves. While…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…
Coupled natural systems are generally modeled at multiple abstraction levels. Both structural scale and behavioral complexity of these models are determinants in the kinds of questions that can be posed and answered. As scale and complexity…
Animals exploit time to survive in the world. Temporal information is required for higher-level cognitive abilities such as planning, decision making, communication, and effective cooperation. Since time is an inseparable part of cognition,…
The modeling of complex systems such as ecological or socio-economic systems can be very challenging. Although various modeling approaches exist, they are generally not compatible and mutually consistent, and empirical data often do not…
Many mathematical models of synaptic plasticity have been proposed to explain the diversity of plasticity phenomena observed in biological organisms. These models range from simple interpretations of Hebb's postulate, which suggests that…
To determine an optimal plan for complex tasks, one often deals with dynamic and hierarchical relationships between several entities. Traditionally, such problems are tackled with optimal control, which relies on the optimization of cost…