Dataset Information

Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework.

ABSTRACT: Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. The rationale behind this new tool is the necessity to describe interactions at the molecular level to be able to grasp emergent and meaningful biological behaviour. We are particularly interested in characterising and quantifying the various effects that facilitate biocatalysis. Enzymes may display high specificity for their substrates and this information is crucial to the engineering and optimisation of bioprocesses. Simulation results demonstrate that molecule distributions, reaction rate parameters, and structural parameters can be adjusted separately in the simulation allowing a comprehensive study of individual effects in the context of realistic cell environments. While higher percentage of collisions with occurrence of reaction increases the affinity of the enzyme to the substrate, a faster reaction (i.e., turnover number) leads to a smaller number of time steps. Slower diffusion rates and molecular crowding (physical hurdles) decrease the collision rate of reactants, hence reducing the reaction rate, as expected. Also, the random distribution of molecules affects the results significantly.

SUBMITTER: Perez-Rodriguez G

PROVIDER: S-EPMC4385633 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework.

Pérez-Rodríguez Gael G Pérez-Pérez Martín M Glez-Peña Daniel D Fdez-Riverola Florentino F Azevedo Nuno F NF Lourenço Anália A

BioMed research international 20150322

Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. The rationale behind this new tool is the necessity to describe interactions at the molecular level to be able to grasp emergent and meaningful biological behaviour. We are particularly interested in characterising and quantifying the v ...[more]

PMID: 25874228

Similar Datasets

Project description:A lot of hard work and years of research are still needed for developing successful Blockchain (BC) applications. Although it is not yet standardized, BC technology was proven as to be an enhancement factor for security, decentralization, and reliability, leading to be successfully implemented in cryptocurrency industries. Fog computing (FC) is one of the recently emerged paradigms that needs to be improved to serve Internet of Things (IoT) environments of the future. As hundreds of projects, ideas, and systems were proposed, one can find a great R&D potential for integrating BC and FC technologies. Examples of organizations contributing to the R&D of these two technologies, and their integration, include Linux, IBM, Google, Microsoft, and others. To validate an integrated Fog-Blockchain protocol or method implementation, before the deployment phase, a suitable and accurate simulation environment is needed. Such validation should save a great deal of costs and efforts on researchers and companies adopting this integration. Current available simulation environments facilitate Fog simulation, or BC simulation, but not both. In this paper, we introduce a Fog-Blockchain simulator, namely FoBSim, with the main goal to ease the experimentation and validation of integrated Fog-Blockchain approaches. According to our proposed workflow of simulation, we implement different Consensus Algorithms (CA), different deployment options of the BC in the FC architecture, and different functionalities of the BC in the simulation. Furthermore, technical details and algorithms on the simulated integration are provided. We validate FoBSim by describing the technologies used within FoBSim, highlighting FoBSim's novelty compared to the state-of-the-art, discussing the event validity in FoBSim, and providing a clear walk-through validation. Finally, we simulate case studies, then present and analyze the obtained results, where deploying the BC network in the fog layer shows enhanced efficiency in terms of total run time and total storage cost.

Project description:Virtual representations of the knee joint can provide clinicians, scientists, and engineers the tools to explore mechanical functions of the knee and its tissue structures in health and disease. Modeling and simulation approaches such as finite element analysis also provide the possibility to understand the influence of surgical procedures and implants on joint stresses and tissue deformations. A large number of knee joint models are described in the biomechanics literature. However, freely accessible, customizable, and easy-to-use models are scarce. Availability of such models can accelerate clinical translation of simulations, where labor-intensive reproduction of model development steps can be avoided. Interested parties can immediately utilize readily available models for scientific discovery and clinical care. Motivated by this gap, this study aims to describe an open source and freely available finite element representation of the tibiofemoral joint, namely Open Knee, which includes the detailed anatomical representation of the joint's major tissue structures and their nonlinear mechanical properties and interactions. Three use cases illustrate customization potential of the model, its predictive capacity, and its scientific and clinical utility: prediction of joint movements during passive flexion, examining the role of meniscectomy on contact mechanics and joint movements, and understanding anterior cruciate ligament mechanics. A summary of scientific and clinically directed studies conducted by other investigators are also provided. The utilization of this open source model by groups other than its developers emphasizes the premise of model sharing as an accelerator of simulation-based medicine. Finally, the imminent need to develop next-generation knee models is noted. These are anticipated to incorporate individualized anatomy and tissue properties supported by specimen-specific joint mechanics data for evaluation, all acquired in vitro from varying age groups and pathological states.

Dataset Information

Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework.

Publications

Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets