Related papers: bcd mRNA active transport: 3D agent-based modeling
Molecular signalling in living cells occurs at low copy numbers and is thereby inherently limited by the noise imposed by thermal diffusion. The precision at which biochemical receptors can count signalling molecules is intimately related…
We investigate in detail a recent model of colliding mobile agents [Phys. Rev. Lett.~96, 088702], used as an alternative approach to construct evolving networks of interactions formed by the collisions governed by suitable dynamical rules.…
Investigation of dynamic processes in cell biology very often relies on the observation in two dimensions of 3D biological processes. Consequently, the data are partial and statistical methods and models are required to recover the…
This paper reports a case study of an application of high-resolution agent-based modeling and simulation to pandemic response planning on a university campus. In the summer of 2020, we were tasked with a COVID-19 pandemic response project…
This paper presents a molecular mechanics study using a molecular dynamics software (NAMD) coupled to virtual reality (VR) techniques for intuitive Bio-NanoRobotic prototyping. Using simulated Bio-Nano environments in VR, the operator can…
Diffusion-based models have shown great promise in molecular generation but often require a large number of sampling steps to generate valid samples. In this paper, we introduce a novel Straight-Line Diffusion Model (SLDM) to tackle this…
In this paper, we deploy a Lattice Boltzmann - Particle Dynamics (LBPD) method to dissect the transport properties within arterioles and venules. First, the numerical approach is applied to study the transport of Red Blood Cells (RBC)…
A complex system is made up of many components with many interactions. So the design of systems such as simulation systems, cooperative systems or assistance systems includes a very accurate modelling of interactional and communicational…
Complex scheduling problems require a large amount computation power and innovative solution methods. The objective of this paper is the conception and implementation of a multi-agent system that is applicable in various problem domains.…
Simulation serves as a third way of doing science, in contrast to both induction and deduction. The web based modeling may considerably facilitate the execution of simulations by other people. We present examples of agent-based and…
It has long been asserted that proteins like transcription factors may locate their target in DNA sequences at rates that surpass by several orders of magnitude the three-dimensional diffusion limit thank to facilitated diffusion, that is…
Domain decomposition is a technique used to reduce memory overhead on large neutron transport problems. Currently, the optimal load-balanced processor allocation for these domains is typically determined through small-scale simulations of…
As society paves its way towards device miniaturization and precision medicine, micro-scale actuation and guided transport become increasingly prominent research fields with high impact in both technological and clinical contexts. In order…
Agent-based models (ABMs) simulate the formation and evolution of social processes at a fundamental level by decoupling agent behavior from global observations. In the case where ABM networks evolve over time as a result of (or in…
We study the spreading of excitations in 2D systems of mobile agents where the excitation is transmitted when a quiescent agent keeps contact with an excited one during a non-vanishing time. We show that the steady states strongly depend on…
There is a growing body of work considering the use of representations based upon genetic regulatory networks. This paper uses a recently presented abstract, tunable Boolean regulatory network model to explore aspects of mobile DNA, such as…
A new upscaling procedure that provides 1D representations of 2D mixing-limited reactive transport systems is developed and applied. A key complication with upscaled models in this setting is that the procedure must differentiate between…
We develop a simulation framework for studying misinformation spread within online social networks that blends agent-based modeling and natural language processing techniques. While many other agent-based simulations exist in this space,…
This paper presents a distributed optimization scheme over a network of agents in the presence of cost uncertainties and over switching communication topologies. Inspired by recent advances in distributed convex optimization, we propose a…
This paper develops a dynamic agent-based model for rural-urban migration, based on the previous relevant works. The model conforms to the typical dynamic linear multi-agent systems model concerned extensively in systems science, in which…