Multiple Verification in Complex Biological Systems: The Bone Remodelling Case Study

2012 ◽  
pp. 53-76 ◽  
Author(s):  
Ezio Bartocci ◽  
Pietro Liò ◽  
Emanuela Merelli ◽  
Nicola Paoletti
Keyword(s):  
Bone Remodelling ◽  
Biological Systems

A product architecture-based tool for bioinspired function-sharing

2020 ◽  
pp. 1-33 ◽  
Author(s):  
Devesh Bhasin ◽  
Daniel A. McAdams ◽  
Astrid Layton
Keyword(s):  
Engineering Design ◽  
Biological Function ◽  
Biological Systems ◽  
Product Architecture ◽  
Biological Structures ◽  
Structure Tree ◽  
Single Structure ◽  
Function Sharing ◽  
Architectural Characteristics

Abstract In this work, we show that bioinspired function-sharing can be effectively applied in engineering design by abstracting and emulating the product architecture of biological systems that exhibit function-sharing. Systems that leverage function-sharing enable multiple functions to be performed by a single structure. Billions of years of evolution has led to the development of function-sharing adaptations in biological systems. Currently, engineers leverage biological function-sharing by imitating serendipitously encountered biological structures. As a result, utilizing bioinspired function-sharing remains limited to some specific engineering problems. To overcome this limitation, we propose the Function-Behavior-Structure tree as a tool to simultaneously abstract both biological adaptations and the product architecture of biological systems. The tool uses information from an existing bioinspired design abstraction tool and an existing product architecture representation tool. A case study demonstrates the tool's ability to abstract the product architectural characteristics of function-sharing biological systems. The abstracted product architectural characteristics are then shown to facilitate problem-driven bioinspiration of function-sharing. The availability of a problem-driven approach may reduce the need to imitate biological structures to leverage biological function-sharing in engineering design. This work is a step forward in analyzing biological product architectures to inspire engineering design.

Designing Robust Systems Using Bioinspired Product Architecture

2021 ◽  
Author(s):  
Devesh Bhasin ◽  
David Staack ◽  
Daniel A. McAdams
Keyword(s):  
Biological Systems ◽  
Product Architecture ◽  
Engineering Systems ◽  
Modular Product ◽  
Engineered Systems ◽  
Function Sharing ◽  
Robust Systems ◽  
Random Failures

Abstract This work analyzes the role of bioinspired product architecture in facilitating the development of robust engineering systems. Existing studies on bioinspired product architecture largely focus on inspiring biology-like function-sharing in engineering design. This work shows that the guidelines for bioinspired product architecture, originally developed for bioinspiration of function-sharing, may induce robustness to random failures in engineered systems. To quantify such an improvement, this study utilizes Functional Modeling to derive modular equivalents of biological systems. The application of the bioinspired product architecture guidelines is then modeled as a transition from the modular product architecture of the modular equivalents to the actual product architecture of the biological systems. The robustness of the systems to random failures is analyzed after the application of each guideline by modeling the systems as directed networks. A singular robustness metric is then introduced to quantify the degradation in the expected functionality of systems upon increasing severity of random disruptions. Our results show that a system with bioinspired product architecture exhibits a gradual degradation in expected functionality upon increasing the number of failed modules as compared to an equivalent system with a one-to-one mapping of functions to modules. The findings are validated by designing and analyzing a COVID-19 breathalyzer as a case study.

What Makes a Panther a Panther?

2020 ◽  
Vol 15 (1) ◽  
pp. 19-31
Author(s):  
Catherine Macdonald ◽  
Julia Wester
Keyword(s):  
Social Construction ◽  
Puma Concolor ◽  
Biological Systems ◽  
Real Life ◽  
The Social ◽  
Functional Extinction

Species categorizations can involve both scientific input and conservation questions about what should be preserved and how. We present a case study exploring the social construction of species categories using a real-life example of a cougar subspecies (Puma concolor stanleyana) purposefully introduced into Florida to prevent the functional extinction of a related subspecies of panther (P. c. coryi). Participants in an online sample (n = 500) were asked to make categorization decisions and then reflect on those decisions in an open format. Analysis of coded responses suggest people may experience “species” as both a social and biological construct, and that the question of what species people think an animal belongs to cannot be answered in isolation from questions about how that animal fits into larger social and biological systems.

scholarly journals Dynamical Ising model of spatially-coupled ecological oscillators

2020 ◽  
Author(s):  
Vahini Reddy Nareddy ◽  
Jonathan Machta ◽  
Karen C. Abbott ◽  
Shadisadat Esmaeili ◽  
Alan Hastings
Keyword(s):  
Ising Model ◽  
Biological Systems ◽  
Universality Class ◽  
Phase Changes ◽  
Additional Parameter ◽  
Local Dynamics ◽  
Critical Boundary ◽  
Two Parameters ◽  
With Memory

AbstractLong-range synchrony from short-range interactions is a familiar pattern in biological and physical systems, many of which share a common set of “universal” properties at the point of synchronization. Common biological systems of coupled oscillators have been shown to be members of the Ising universality class, meaning that the very simple Ising model replicates certain spatial statistics of these systems at stationarity. This observation is useful because it reveals which aspects of spatial pattern arise independently of the details governing local dynamics, resulting in both deeper understanding of and a simpler baseline model for biological synchrony. However, in many situations a system’s dynamics are of greater interest than their static spatial properties. Here, we ask whether a dynamical Ising model can replicate universal and non-universal features of ecological systems, using noisy coupled metapopulation models with two-cycle dynamics as a case study. The standard Ising model makes unrealistic dynamical predictions, but the Ising model with memory corrects this by using an additional parameter to reflect the tendency for local dynamics to maintain their phase of oscillation. By fitting the two parameters of the Ising model with memory to simulated ecological dynamics, we assess the correspondence between the Ising and ecological models in several of their features (location of the critical boundary in parameter space between synchronous and asynchronous dynamics, probability of local phase changes, and ability to predict future dynamics). We find that the Ising model with memory is reasonably good at representing these properties of ecological metapopulations. The correspondence between these models creates the potential for the simple and well-known Ising class of models to become a valuable tool for understanding complex biological systems.

Modelling fluorescence lifetimes with TD-DFT: a case study with syn-bimanes

RSC Advances ◽  
2016 ◽  
Vol 6 (90) ◽  
pp. 87237-87245 ◽  
Author(s):  
Z. C. Wong ◽  
W. Y. Fan ◽  
T. S. Chwee ◽  
M. B. Sullivan
Keyword(s):  
Biological Systems ◽  
Fluorescence Lifetimes ◽  
Td Dft

Syn-bimanes are a class of fluorophores that are widely used for labelling thiol containing biological systems. We used TD-DFT to study their absorption, emission, solvatochromism, and fluorescence lifetimes.

scholarly journals Hybrid modelling of biological systems using fuzzy continuous Petri nets

2019 ◽  
Author(s):  
Fei Liu ◽  
Wujie Sun ◽  
Monika Heiner ◽  
David Gilbert
Keyword(s):  
Petri Nets ◽  
Kinetic Data ◽  
Fuzzy Inference ◽  
Biological Systems ◽  
Integrated Modelling ◽  
Fuzzy Inference Systems ◽  
Hybrid Modelling ◽  
Continuous Petri Nets ◽  
Inference Systems

Abstract Integrated modelling of biological systems is challenged by composing components with sufficient kinetic data and components with insufficient kinetic data or components built only using experts’ experience and knowledge. Fuzzy continuous Petri nets (FCPNs) combine continuous Petri nets with fuzzy inference systems, and thus offer an hybrid uncertain/certain approach to integrated modelling of such biological systems with uncertainties. In this paper, we give a formal definition and a corresponding simulation algorithm of FCPNs, and briefly introduce the FCPN tool that we have developed for implementing FCPNs. We then present a methodology and workflow utilizing FCPNs to achieve hybrid (uncertain/certain) modelling of biological systems illustrated with a case study of the Mercaptopurine metabolic pathway. We hope this research will promote the wider application of FCPNs and address the uncertain/certain integrated modelling challenge in the systems biology area.

Modeling framework for membrane computing in biological systems: Evaluation with a case study

2014 ◽  
Vol 5 (2) ◽  
pp. 137-143 ◽  
Author(s):  
Ravie Chandren Muniyandi ◽  
Abdullah Mohd Zin
Keyword(s):  
Membrane Computing ◽  
Biological Systems ◽  
Modeling Framework
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