Related papers: bcd mRNA active transport: 3D agent-based modeling
For a two-dimensional system of agents modeled by molecular dynamics, we simulate epidemics spreading, which was recently studied on complex networks. Our resulting network model is time-evolving. We study the transitions to spreading as…
Modelling and computational methods have been essential in advancing quantitative science, especially in the past two decades with the availability of vast amount of complex, voluminous, and heterogeneous data. In particular, there has been…
This paper presents our methodology to simulate the behavior of the DeLend Platform. Such simulations are important to verify if the system is able to connect the different sets of agents linked to the platform in a functional manner. They…
This work introduces a diffusion model for molecule generation in 3D that is equivariant to Euclidean transformations. Our E(3) Equivariant Diffusion Model (EDM) learns to denoise a diffusion process with an equivariant network that jointly…
We propose a calibrated two-dimensional cellular automaton model to simulate pedestrian motion behavior. It is a v=4 (3) model with exclusion statistics and random shuffled dynamics. The underlying regular grid structure results in a…
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
This paper deals with the cellular biological network analysis of the tumor-growth model, consisting of multiple spaces and time scales. In this paper, we present a model in graph simulation using ABM for tumor growth. In particular, we…
n this work, we propose a latent molecular diffusion model that can make the generated 3D molecules rich in diversity and maintain rich geometric features. The model captures the information of the forces and local constraints between atoms…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…
Agent-Based Models are very useful for simulation of physical or social processes, such as the spreading of a pandemic in a city. Such models proceed by specifying the behavior of individuals (agents) and their interactions, and…
Agent-based modeling is indispensable for studying complex systems across many domains. However, existing simulation platforms exhibit two major issues: performance and modularity. Low performance prevents simulations with a large number of…
Active gel theory has recently been very successful in describing biologically active materials such as actin filaments or moving bacteria in temporally fixed and simple geometries such as cubes or spheres. Here we develop a computational…
Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models it is not always…
Device-to-device (D2D) communications is one of the key emerging technologies for the fifth generation (5G) networks and beyond. It enables direct communication between mobile users and thereby extends coverage for devices lacking direct…
Agent modeling is a critical component in developing effective policies within multi-agent systems, as it enables agents to form beliefs about the behaviors, intentions, and competencies of others. Many existing approaches assume access to…
Equivariant diffusion models have achieved impressive performance in 3D molecule generation. These models incorporate Euclidean symmetries of 3D molecules by utilizing an SE(3)-equivariant denoising network. However, specialized equivariant…
We discuss a theoretical model for bidirectional cargo transport in biological cells, which is driven by teams of molecular motors and subject to thermal fluctuations. The model describes explicitly the directed motion of the molecular…
Molecular dynamics (MD) simulation is a powerful tool for studying biomolecular structural changes, molecular recognition, transmembrane transport, and functional mechanisms. However, its practical bottleneck lies not only in software…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…