High performance computing for three-dimensional agent-based molecular models

Abstract

Agent-based simulations are increasingly popular in exploring and understanding cellular systems, but the natural complexity of these systems and the desire to grasp different modelling levels demand cost-effective simulation strategies and tools. In this context, the present paper introduces novel sequential and distributed approaches for the three-dimensional agent-based simulation of individual molecules in cellular events. These approaches are able to describe the dimensions and position of the molecules with high accuracy and thus, study the critical effect of spatial distribution on cellular events. Moreover, two of the approaches allow multi-thread high performance simulations, distributing the three-dimensional model in a platform independent and computationally efficient way. Evaluation addressed the reproduction of molecular scenarios and different scalability aspects of agent creation and agent interaction. The three approaches simulate common biophysical and biochemical laws faithfully. The distributed approaches show improved performance when dealing with large agent populations while the sequential approach is better suited for small to medium size agent populations. Overall, the main new contribution of the approaches is the ability to simulate three-dimensional agent-based models at the molecular level with reduced implementation effort and moderate-level computational capacity. Since these approaches have a generic design, they have the major potential of being used in any event-driven agent-based tool.

Computational Resources and Strategies to Construct Single-Molecule Models of FISH

“…Hence, computational biologists often resort to coarser approaches to simulate large biological processes [25]. In fact, most research facilities only have access to mid-performance computers and cannot realistically simulate highly-detailed models [26]. As a possible solution, the use of simulation frameworks can reduce some of the burden of implementing ABM.…”

“…Therefore, choosing a modelling platform is not straightforward and should be carefully thought out, based on extensive surveys, experience and programming knowledge [26]. A review of the available simulation platforms is out of the scope of this work, as several reviews on the topic are already published [1,19,24].…”

“…In an attempt to create even more efficient and less-demanding algorithms, Pérez-Rodriguez et. al (2018), developed two alternative approaches [26]. The first alternative is the parallel approach, which introduces only one agent, named the controller, in the scheduler.…”

Application of Agent-Based Modeling to Complex Systems

“…ABM may address these limitations since it offers the ability to completely describe AOP reaction pathways at the molecular (i.e., individual) level and allows for concentration profiles to be produced as an emergent product of the system. Despite the benefits associated with studying AOPs in this fashion, ABM has remained relatively unexplored in the study of AOPs and in the broader field of chemistry, with some limited work done in biochemistry to explore the applications of ABM in the context of intracellular reactions (see [51][52][53]).…”

“…Effectively, the completeness of the reactions used in the ABM is only limited by the overall understanding of the elementary reaction pathways. While the use of ABM is fairly new to chemical modeling, there has been increasing interest in using ABM to explore biochemical systems such as intracellular signaling and reactions [51,52], biomolecular modeling [53], and complex biochemistry [253].…”