scholarly journals Radiation Induced Reactions of Succinic Acid in Aqueous Solution: An Agent-Based Model

2020 ◽  
Vol 7 (2) ◽  
pp. 117-121
Author(s):  
Ana Leonor Rivera ◽  
Sergio Ramos-Beltran ◽  
Alicia Negrón-Mendoza
Keyword(s):  
Gamma Radiation ◽  
Succinic Acid ◽  
Aqueous Media ◽  
Chemical Species ◽  
Reaction Rates ◽  
Product Formation ◽  
Laboratory Model ◽  
Agent Based Model ◽  
Agent Based ◽  
Radiation Induced

An approach to studying the formation of critical bio-organic compounds in the early Earth is to simulate in the laboratory possible processes that may occur in primitive scenarios. In this context, it can be studied the evolution of succinic acid in an aqueous media exposed to gamma radiation, as starting material produced more complex prebiotic molecules. To describe the products generated by the interaction of the different elements under radiation, there is a mathematical model that considers chemical reactions as nonlinear ordinary differential equations based on the mass balance of all the species, that has been implemented here by an agent-based model. In this simulation, each chemical species involved is considered as an agent that can interact with other species with known reaction rates, and the radiation is taken as a factor that promotes product formation. The results from the agentbased model are compared with the molar concentrations of succinic acid, and its products obtained in the lab. Simulation shows the exponential decomposition of succinic acid due to gamma radiation at room temperature in agreement with the laboratory model.

scholarly journals A 3D Agent-Based Model of Lung Fibrosis

Symmetry ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 90
Author(s):  
Nicolò Cogno ◽  
Roman Bauer ◽  
Marco Durante
Keyword(s):  
Lung Fibrosis ◽  
Computational Models ◽  
Multiple Scales ◽  
Inflammatory Diseases ◽  
Cell Damage ◽  
Heterogeneous Systems ◽  
Chronic Obstructive ◽  
Agent Based Model ◽  
Agent Based ◽  
Radiation Induced

Understanding the pathophysiology of lung fibrosis is of paramount importance to elaborate targeted and effective therapies. As it onsets, the randomly accumulating extracellular matrix (ECM) breaks the symmetry of the branching lung structure. Interestingly, similar pathways have been reported for both idiopathic pulmonary fibrosis and radiation-induced lung fibrosis (RILF). Individuals suffering from the disease, the worldwide incidence of which is growing, have poor prognosis and a short mean survival time. In this context, mathematical and computational models have the potential to shed light on key underlying pathological mechanisms, shorten the time needed for clinical trials, parallelize hypotheses testing, and improve personalized drug development. Agent-based modeling (ABM) has proven to be a reliable and versatile simulation tool, whose features make it a good candidate for recapitulating emergent behaviors in heterogeneous systems, such as those found at multiple scales in the human body. In this paper, we detail the implementation of a 3D agent-based model of lung fibrosis using a novel simulation platform, namely, BioDynaMo, and prove that it can qualitatively and quantitatively reproduce published results. Furthermore, we provide additional insights on late-fibrosis patterns through ECM density distribution histograms. The model recapitulates key intercellular mechanisms, while cell numbers and types are embodied by alveolar segments that act as agents and are spatially arranged by a custom algorithm. Finally, our model may hold potential for future applications in the context of lung disorders, ranging from RILF (by implementing radiation-induced cell damage mechanisms) to COVID-19 and inflammatory diseases (such as asthma or chronic obstructive pulmonary disease).

scholarly journals Radiation Induced Oxidation Reactions of Ferrous Ions: An Agent-based Model

2017 ◽  
Vol 5 (1) ◽  
pp. 15-23 ◽  
Author(s):  
A.L. Rivera ◽  
◽  
A.S. Ramos-Bernal ◽  
A. Negrón-Mendoza ◽  
◽  
...  
Keyword(s):  
Oxidation Reactions ◽  
Agent Based Model ◽  
Ferrous Ions ◽  
Agent Based ◽  
Radiation Induced

scholarly journals Connecting actin polymer dynamics across multiple scales

2020 ◽  
Author(s):  
Calina Copos ◽  
Brittany Bannish ◽  
Kelsey Gasior ◽  
Rebecca L. Pinals ◽  
Minghao W. Rostami ◽  
...  
Keyword(s):  
Molecular Level ◽  
Effective Diffusion ◽  
Diffusion Constant ◽  
Reaction Rates ◽  
Actin Dynamics ◽  
Actin Network ◽  
Agent Based Model ◽  
Agent Based ◽  
Cell Functions ◽  
Microscale Model

AbstractActin is an intracellular protein that constitutes a primary component of the cellular cytoskeleton and is accordingly crucial for various cell functions. Actin assembles into semi-flexible filaments that cross-link to form higher order structures within the cytoskeleton. In turn, the actin cytoskeketon regulates cell shape, and participates in cell migration and division. A variety of theoretical models have been proposed to investigate actin dynamics across distinct scales, from the stochastic nature of protein and molecular motor dynamics to the deterministic macroscopic behavior of the cytoskeleton. Yet, the relationship between molecular-level actin processes and cellular-level actin network behavior remains understudied, where prior models do not holistically bridge the two scales together.In this work, we focus on the dynamics of the formation of a branched actin structure as observed at the leading edge of motile eukaryotic cells. We construct a minimal agent-based model for the microscale branching actin dynamics, and a deterministic partial differential equation model for the macroscopic network growth and bulk diffusion. The microscale model is stochastic, as its dynamics are based on molecular level effects. The effective diffusion constant and reaction rates of the deterministic model are calculated from averaged simulations of the microscale model, using the mean displacement of the network front and characteristics of the actin network density. With this method, we design concrete metrics that connect phenomenological parameters in the reaction-diffusion system to the biochemical molecular rates typically measured experimentally. A parameter sensitivity analysis in the stochastic agent-based model shows that the effective diffusion and growth constants vary with branching parameters in a complementary way to ensure that the outward speed of the network remains fixed. These results suggest that perturbations to microscale rates can have significant consequences at the macroscopic level, and these should be taken into account when proposing continuum models of actin network dynamics.

scholarly journals Agent Based Model of the Cytosine Radiation Induced Reaction

2012 ◽  
Vol 6 (1) ◽  
pp. 93-97 ◽  
Author(s):  
A L Rivera ◽  
◽  
S Ramos-Beltran ◽  
A Paredes-Arriaga ◽  
A Negron-Mendoza ◽  
...  
Keyword(s):  
Agent Based Model ◽  
Agent Based ◽  
Radiation Induced ◽  
Induced Reaction

Simulations of an Agent-Based Model that Consists of a Large Number of Agents Moving Stochastically in a Wide Bounded Domain

2001 ◽  
Author(s):  
Minoru Tabata ◽  
Akira Ide ◽  
Nobuoki Eshima ◽  
Kyushu Takagi ◽  
Yasuhiro Takei ◽  
...  
Keyword(s):  
Bounded Domain ◽  
Agent Based Model ◽  
Agent Based
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