REGULATED BIOLOGICAL SYSTEMS

2000 ◽  
Vol 08 (02) ◽  
pp. 141-149 ◽  
Author(s):  
MICHEL CABANAC ◽  
MAURICIO RUSSEK
Keyword(s):  
Control Theory ◽  
Open Systems ◽  
Block Diagram ◽  
Biological Systems ◽  
Fundamental Difference ◽  
Living Systems ◽  
Regulation Process

Control theory is concerned mainly with the treatment of signals. This article takes into account that living beings not only treat information, but they are open systems traversed by flows of energy and mass. A new block diagram of the regulation process is proposed, taking into account this fundamental difference between engineered and living systems. This new diagram possesses both didactic and heuristic advantages.

scholarly journals Nonequilibrium Thermodynamics in Biochemical Systems and Its Application

Entropy ◽  
2021 ◽  
Vol 23 (3) ◽  
pp. 271
Author(s):  
Dongliang Zhang ◽  
Qi Ouyang
Keyword(s):  
Nonequilibrium Thermodynamics ◽  
Open Systems ◽  
Biological Systems ◽  
Nonequilibrium Thermodynamic ◽  
Point Of View ◽  
Living Systems ◽  
Biochemical Reaction Networks ◽  
Stochastic Thermodynamics ◽  
Biochemical Systems ◽  
Jarzynski Equality

Living systems are open systems, where the laws of nonequilibrium thermodynamics play the important role. Therefore, studying living systems from a nonequilibrium thermodynamic aspect is interesting and useful. In this review, we briefly introduce the history and current development of nonequilibrium thermodynamics, especially that in biochemical systems. We first introduce historically how people realized the importance to study biological systems in the thermodynamic point of view. We then introduce the development of stochastic thermodynamics, especially three landmarks: Jarzynski equality, Crooks’ fluctuation theorem and thermodynamic uncertainty relation. We also summarize the current theoretical framework for stochastic thermodynamics in biochemical reaction networks, especially the thermodynamic concepts and instruments at nonequilibrium steady state. Finally, we show two applications and research paradigms for thermodynamic study in biological systems.

Bottom-Up Synthetic Biology: Engineering in a Tinkerer’s World

Science ◽  
2011 ◽  
Vol 333 (6047) ◽  
pp. 1252-1254 ◽  
Author(s):  
Petra Schwille
Keyword(s):  
Synthetic Biology ◽  
Life Science ◽  
Biological Systems ◽  
Living Systems ◽  
Design Features ◽  
Literal Interpretation ◽  
Bottom Up ◽  
Systematic Construction ◽  
Science Discipline ◽  
Recent Developments

How synthetic can “synthetic biology” be? A literal interpretation of the name of this new life science discipline invokes expectations of the systematic construction of biological systems with cells being built module by module—from the bottom up. But can this possibly be achieved, taking into account the enormous complexity and redundancy of living systems, which distinguish them quite remarkably from design features that characterize human inventions? There are several recent developments in biology, in tight conjunction with quantitative disciplines, that may bring this literal perspective into the realm of the possible. However, such bottom-up engineering requires tools that were originally designed by nature’s greatest tinkerer: evolution.

Symbols as constraints

2009 ◽  
Vol 17 (3) ◽  
pp. 653-676 ◽  
Author(s):  
Joanna Raczaszek-Leonardi
Keyword(s):  
Natural Language ◽  
Information Transmission ◽  
Time Scales ◽  
Biological Systems ◽  
Living Systems ◽  
Self Organization ◽  
Language Structure ◽  
Phenomenological Experience ◽  
Hierarchical Levels ◽  
Specialized System

The paper draws a parallel between natural language symbols and the symbolic mode in living systems. The inextricability of symbols and the dynamics with which they are functionally related shows that much of their structuring is due to dynamics and self-organization. It is also stressed that important factors that determine the shape of language structure lie outside individual mind/brains and they draw on time-scales quite different from those of phenomenological experience. Analysis of language into units and subsystems is thus not straightforward, since they show functionality on many levels and many time-scales. Finally it is recognized that, as a specific and specialized system of inter-individual coordination, natural language is many hierarchical levels away form simpler forms of information transmission in biological systems.

scholarly journals REPLICATION AND EVOLUTION OF QUANTUM SPECIES

2004 ◽  
Vol 04 (03) ◽  
pp. R27-R38 ◽  
Author(s):  
ARUN K. PATI
Keyword(s):  
Quantum Information ◽  
Artificial Life ◽  
Biological Systems ◽  
Living System ◽  
Living Systems ◽  
Closed Universe ◽  
Basic Features

We dwell upon the physicist's conception of 'life' since Schrödinger and Wigner through to the modern-day language of living systems in the light of quantum information. We discuss some basic features of a living system such as ordinary replication and evolution in terms of quantum bio-information. We also discuss the principle of no-culling of living replicas. We show that in a collection of identical species there can be no entanglement between one of the mutated copies and the rest of the species in a closed universe. Even though these discussions revolve around 'artificial life' they may still be applicable in real biological systems under suitable conditions.

A roadmap for Living Machines research

2018 ◽  
Author(s):  
Nathan F. Lepora ◽  
Paul F. M. J. Verschure ◽  
Tony J. Prescott
Keyword(s):  
Biological Systems ◽  
Living Systems ◽  
Future Research ◽  
Scientific Policy ◽  
Biologically Inspired ◽  
Policy Makers ◽  
Research And Innovation ◽  
Current Trends

This roadmap identifies current trends in biomimetic and biohybrid systems together with their implications for future research and innovation. Important questions include the scale at which these systems are defined, the types of biological systems addressed, the kind of principles sought, the differences between biologically based and biologically inspired approaches, the role in the understanding of living systems, relevant application domains, common benchmarks, the relation to other fields, and developments on the horizon. We interviewed and collated answers from experts who have been involved a series of events organized by the Convergent Science Network. These answers were then collated into themes of research. Overall, we see a field rapidly expanding in influence and impact. As such, this report will provide information to researchers and scientific policy makers on contemporary biomimetics and its future, together with pointers to further reading on relevant topics within this handbook.

Living Machines

2018 ◽  
Author(s):  
Tony J. Prescott ◽  
Paul F. M. J. Verschure
Keyword(s):  
Biological Systems ◽  
Deep Understanding ◽  
Living System ◽  
Living Systems ◽  
Novel Technologies ◽  
Biological Component

Biomimetics is the development of novel technologies through the distillation of principles from the study of biological systems. Biohybrid systems are formed by at least one biological component—an already existing living system—and at least one artificial, newly engineered component. The development of either biomimetic or biohybrid systems requires a deep understanding of the operation of living systems, and the two fields are united under the theme of “living machines”—the idea that we can construct artifacts that not only mimic life but share some of the same fundamental principles. This chapter sets out the philosophy and history underlying this Living Machines approach and sets the scene for the remainder of this book.

scholarly journals A modified Ising model of Barabási–Albert network with gene-type spins

2020 ◽  
Vol 81 (3) ◽  
pp. 769-798
Author(s):  
Jeyashree Krishnan ◽  
Reza Torabi ◽  
Andreas Schuppert ◽  
Edoardo Di Napoli
Keyword(s):  
Phase Transitions ◽  
Ising Model ◽  
Large Scale ◽  
Biological Systems ◽  
Ising Models ◽  
Network Size ◽  
Living Systems ◽  
Computational Techniques ◽  
Solid State Physics ◽  
Gene Type

Abstract The central question of systems biology is to understand how individual components of a biological system such as genes or proteins cooperate in emerging phenotypes resulting in the evolution of diseases. As living cells are open systems in quasi-steady state type equilibrium in continuous exchange with their environment, computational techniques that have been successfully applied in statistical thermodynamics to describe phase transitions may provide new insights to the emerging behavior of biological systems. Here we systematically evaluate the translation of computational techniques from solid-state physics to network models that closely resemble biological networks and develop specific translational rules to tackle problems unique to living systems. We focus on logic models exhibiting only two states in each network node. Motivated by the apparent asymmetry between biological states where an entity exhibits boolean states i.e. is active or inactive, we present an adaptation of symmetric Ising model towards an asymmetric one fitting to living systems here referred to as the modified Ising model with gene-type spins. We analyze phase transitions by Monte Carlo simulations and propose a mean-field solution of a modified Ising model of a network type that closely resembles a real-world network, the Barabási–Albert model of scale-free networks. We show that asymmetric Ising models show similarities to symmetric Ising models with the external field and undergoes a discontinuous phase transition of the first-order and exhibits hysteresis. The simulation setup presented herein can be directly used for any biological network connectivity dataset and is also applicable for other networks that exhibit similar states of activity. The method proposed here is a general statistical method to deal with non-linear large scale models arising in the context of biological systems and is scalable to any network size.

The Potential for Systems Theory Application to Studies of Motor Performance

1974 ◽  
Vol 16 (5) ◽  
pp. 514-519
Author(s):  
L. Daniel Metz
Keyword(s):  
Control Theory ◽  
Systems Theory ◽  
Motor Performance ◽  
Biological Systems ◽  
Systems And Control ◽  
Theory Application ◽  
And Behavior ◽  
And Control

Motor performance calls into play a number of complex physiological and biological systems. An understanding of the function and behavior of such systems is necessary if motor performance is to be properly analyzed and helpful if it is to be improved. The concepts of systems and control theory offer a powerful (though sometimes not fully exploited) methodological technique for achieving such an understanding. This paper discusses some of the elementary concepts of systems theory as applied to motor performance and presents qualitative discussions of its usefulness in that field.

The Early Development of Control Theory

1976 ◽  
Vol 98 (2) ◽  
pp. 109-118 ◽  
Author(s):  
A. T. Fuller
Keyword(s):  
Control Theory ◽  
Closed Loop ◽  
Block Diagram ◽  
Feedback System ◽  
Nyquist Diagram ◽  
System A ◽  
Integral Action ◽  
History Of ◽  
History Of Control ◽  
Diagram Techniques

The early history of control theory is explored, beginning with the contributions of Hooke and Huygens in the seventeenth century, and ending with Airy’s papers of 1840 and 1851. It is argued that, despite appearances to the contrary, Huygens’ speed control system is actually a feedback system. A proof is given that the Huygens-Hooke parabolic governor has integral action, thus eliminating offset. A detailed exposition of Airy’s techniques is given. It is shown that he used a disguised form of linearization. Airy’s system is also investigated using block diagram and Nyquist diagram techniques. The centrifugal governor is shown to have a tendency to resonance which adversely affects closed-loop stability; in agreement with Airy’s findings. Biographical notes on the main contributors are included in order to bring out the background and motivations of their theories.

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