Systematic Reverse Engineering of Biological Systems

2007 ◽  
Author(s):  
Jamal O. Wilson ◽  
David Rosen
Keyword(s):  
Reverse Engineering ◽  
Biological Systems ◽  
Variable Stiffness ◽  
Design Principles ◽  
Efficient Solutions ◽  
Engineering Systems ◽  
Biological Design ◽  
Engineering Problems ◽  
Airplane Wing ◽  
Current Engineering

The duality between biological systems and engineering systems exists in the pursuit of economical and efficient solutions. By adapting biological design principles, nature’s technology can be harnessed. In this paper, we present a systematic method for reverse engineering biological systems to assist the designer in searching for solutions in nature to current engineering problems. Specifically, we present methods for decomposing the physical and functional biological architectures, representing dynamic functions, and abstracting biological design principles to guide conceptual design. We illustrate this method with an example of the design of a variable stiffness skin for a morphable airplane wing based on the mutable connective tissue of the sea cucumber.

scholarly journals Synthetic Biology: Integrated Gene Circuits

Science ◽  
2011 ◽  
Vol 333 (6047) ◽  
pp. 1244-1248 ◽  
Author(s):  
Nagarajan Nandagopal ◽  
Michael B. Elowitz
Keyword(s):  
Synthetic Biology ◽  
Biological Systems ◽  
Design Principles ◽  
Genetic Circuits ◽  
Major Goal ◽  
Gene Circuits ◽  
Biological Design ◽  
Cellular Processes ◽  
Regulatory Architecture ◽  
New Generation

A major goal of synthetic biology is to develop a deeper understanding of biological design principles from the bottom up, by building circuits and studying their behavior in cells. Investigators initially sought to design circuits “from scratch” that functioned as independently as possible from the underlying cellular system. More recently, researchers have begun to develop a new generation of synthetic circuits that integrate more closely with endogenous cellular processes. These approaches are providing fundamental insights into the regulatory architecture, dynamics, and evolution of genetic circuits and enabling new levels of control across diverse biological systems.

Finding Approximate Shape Regularities for Reverse Engineering

2001 ◽  
Vol 1 (4) ◽  
pp. 282-290 ◽  
Author(s):  
F. C. Langbein ◽  
B. I. Mills ◽  
A. D. Marshall ◽  
R. R. Martin
Keyword(s):  
Reverse Engineering ◽  
Small Groups ◽  
Input Data ◽  
Boundary Representation ◽  
Range Data ◽  
Engineering Systems ◽  
Post Processing ◽  
Processing Step ◽  
3D Range Data

Current reverse engineering systems can generate boundary representation (B-rep) models from 3D range data. Such models suffer from inaccuracies caused by noise in the input data and algorithms. The quality of reverse engineered geometric models can be improved by finding candidate shape regularities in such a model, and constraining the model to meet a suitable subset of them, in a post-processing step called beautification. This paper discusses algorithms to detect such approximate regularities in terms of similarities between feature objects describing properties of faces, edges and vertices, and small groups of these elements in a B-rep model with only planar, spherical, cylindrical, conical and toroidal faces. For each group of similar feature objects they also seek special feature objects which may represent the group, e.g. an integer value which approximates the radius of similar cylinders. Experiments show that the regularities found by the algorithms include the desired regularities as well as spurious regularities, which can be limited by an appropriate choice of tolerances.

Biological Design Principles of Complex Feedback Modules in the E. coli Ammonia Assimilation System

2011 ◽  
Vol 18 (1) ◽  
pp. 53-90 ◽  
Author(s):  
Koichi Masaki ◽  
Kazuhiro Maeda ◽  
Hiroyuki Kurata
Keyword(s):  
Feedback Control ◽  
Design Principles ◽  
Cellular Systems ◽  
Fine Tuning ◽  
Ammonia Assimilation ◽  
Control Module ◽  
E Coli ◽  
Biological Design ◽  
Modular Structures ◽  
Assimilation System

To synthesize natural or artificial life, it is critically important to understand the design principles of how biochemical networks generate particular cellular functions and evolve complex systems in comparison with engineering systems. Cellular systems maintain their robustness in the face of perturbations arising from environmental and genetic variations. In analogy to control engineering architectures, the complexity of modular structures within a cell can be attributed to the necessity of achieving robustness. To reveal such biological design, the E. coli ammonia assimilation system is analyzed, which consists of complex but highly structured modules: the glutamine synthetase (GS) activity feedback control module with bifunctional enzyme cascades for catalyzing reversible reactions, and the GS synthesis feedback control module with positive and negative feedback loops. We develop a full-scale dynamic model that unifies the two modules, and we analyze its robustness and fine tuning with respect to internal and external perturbations. The GS activity control is added to the GS synthesis module to improve its transient response to ammonia depletion, compensating the tradeoffs of each module, but its robustness to internal perturbations is lost. These findings suggest some design principles necessary for the synthesis of life.

A Set-Based System for Eliminating Infeasible Designs in Engineering Problems Dominated by Uncertainty

1997 ◽  
Author(s):  
William W. Finch ◽  
Allen C. Ward
Keyword(s):  
Electronic Circuit ◽  
Predicate Logic ◽  
Software Tool ◽  
Design Parameters ◽  
Engineering Systems ◽  
Multiple Sources ◽  
Design Problems ◽  
Engineering Design Problems ◽  
Engineering Problems ◽  
Prototype Software

Abstract This paper gives an overview of a system which eliminates infeasible designs from engineering design problems dominated by multiple sources of uncertainty. It outlines methods for representing constraints on sets of values for design parameters using quantified relations, a special class of predicate logic expressions which express some of the causal information inherent in engineering systems. The paper extends constraint satisfaction techniques and describes elimination algorithms that operate on quantified relations and catalogs of toleranced or adjustable parts. It demonstrates the utility of these tools on a simple electronic circuit, and describes their implementation and test in a prototype software tool.

Organization and Self-Assembly Away from Equilibrium: Toward Thermodynamic Design Principles

2021 ◽  
Vol 12 (1) ◽  
pp. 273-290
Author(s):  
Michael Nguyen ◽  
Yuqing Qiu ◽  
Suriyanarayanan Vaikuntanathan
Keyword(s):  
Energy Dissipation ◽  
Self Assembly ◽  
Biological Systems ◽  
Design Principles ◽  
Nonequilibrium Process ◽  
Nanoscale Materials ◽  
Stochastic Thermodynamics ◽  
Synthetic Materials ◽  
Starting Point

Studies of biological systems and materials, together with recent experimental and theoretical advances in colloidal and nanoscale materials, have shown how nonequilibrium forcing can be used to modulate organization in many novel ways. In this review, we focus on how an accounting of energy dissipation, using the tools of stochastic thermodynamics, can constrain and provide intuition for the correlations and configurations that emerge in a nonequilibrium process. We anticipate that the frameworks reviewed here can provide a starting point to address some of the unique phenomenology seen in biophysical systems and potentially replicate them in synthetic materials.

Optimisation of Engineering Systems With the Bees Algorithm

2018 ◽  
Vol 8 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Duc T Pham ◽  
Luca Baronti ◽  
Biao Zhang ◽  
Marco Castellani
Keyword(s):  
Neural Networks ◽  
Inverse Kinematics ◽  
State Of The Art ◽  
Bees Algorithm ◽  
Engineering Systems ◽  
Standard Formulation ◽  
First Case ◽  
Engineering Problems ◽  
Hydraulic Load ◽  
Optimisation Technique

This article describes the Bees Algorithm in standard formulation and presents two applications to real-world continuous optimisation engineering problems. In the first case, the Bees Algorithm is employed to train three artificial neural networks (ANNs) to model the inverse kinematics of the joints of a three-link manipulator. In the second case, the Bees Algorithm is used to optimise the parameters of a linear model used to approximate the torque output for an electro-hydraulic load system. In both cases, the Bees Algorithm outperformed the state-of-the-art in the literature, proving to be an effective optimisation technique for engineering systems.

scholarly journals Small-molecule fluorescent probes for imaging gaseous signaling molecules: current progress and future implications

2020 ◽  
Vol 11 (20) ◽  
pp. 5127-5141 ◽  
Author(s):  
Mingwang Yang ◽  
Jiangli Fan ◽  
Jianjun Du ◽  
Xiaojun Peng
Keyword(s):  
Small Molecule ◽  
Fluorescent Probes ◽  
Biological Systems ◽  
Design Principles ◽  
Signaling Molecules ◽  
Gaseous Signaling Molecules

This perspective article aims to introduce the design principles and recognition strategies of small-molecule fluorescent probes which are applied for the detection of gas signaling molecules including NO, CO and H2S in biological systems.

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