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.

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.

Nonequilibrium Thermodynamics in Cell Biology: Extending Equilibrium Formalism to Cover Living Systems

2020 ◽  
Vol 49 (1) ◽  
pp. 227-246 ◽  
Author(s):  
Xiaona Fang ◽  
Jin Wang
Keyword(s):  
Cell Cycle ◽  
Cell Biology ◽  
Nonequilibrium Thermodynamics ◽  
Driving Forces ◽  
Nonequilibrium Thermodynamic ◽  
Living Systems ◽  
Nonequilibrium Dynamics ◽  
Enzyme Dynamics ◽  
Trade Offs ◽  
Speed Accuracy

We discuss new developments in the nonequilibrium dynamics and thermodynamics of living systems, giving a few examples to demonstrate the importance of nonequilibrium thermodynamics for understanding biological dynamics and functions. We study single-molecule enzyme dynamics, in which the nonequilibrium thermodynamic and dynamic driving forces of chemical potential and flux are crucial for the emergence of non-Michaelis-Menten kinetics. We explore single-gene expression dynamics, in which nonequilibrium dissipation can suppress fluctuations. We investigate the cell cycle and identify the nutrition supply as the energy input that sustains the stability, speed, and coherence of cell cycle oscillation, from which the different vital phases of the cell cycle emerge. We examine neural decision-making processes and find the trade-offs among speed, accuracy, and thermodynamic costs that are important for neural function. Lastly, we consider the thermodynamic cost for specificity in cellular signaling and adaptation.

Open Systems and Consciousness: A Physical Discussion

2002 ◽  
Vol 09 (04) ◽  
pp. 339-369
Author(s):  
Roman S. Ingarden
Keyword(s):  
Biological System ◽  
Open Systems ◽  
Human Person ◽  
Life Time ◽  
Point Of View ◽  
Living Systems ◽  
Decoherence Time ◽  
The Brain ◽  
Cerebral Neocortex

Further discussion of the author's ideas, as well as their confrontation with similar and different concepts of consciousness, have been given in the Introduction. Then the physical and, in lesser degree, also mathematical aspects of open systems, in particular of human person, are sketched in Sec. 2. The quantum concept of the decoherence time is treated as a model for a finite life-time of any composed physical and biological system. In Sec. 3 the role of languages of many types in living and non-living systems is briefly considered, as well as the importance of modality for sentence predicates. In Sec. 4, the structure of the cerebral neocortex and its speech centers is briefly described from the point of view of the mechanism of thinking and the consciousness. The concepts of laterality and dominance (left or right hemispheres of the brain) and their dependence on the type of culture and education are shown on the example of the differences between the Japanese and Western perception of languages (discoveries of Liberman and Tsunoda). In Secs. 5 and 6 the experimental evidence for the connection of consciousness with the speech centers are presented and some questions are posed.

scholarly journals Thermodynamics of Quantum Causal Models: An Inclusive, Hamiltonian Approach

Quantum ◽  
2020 ◽  
Vol 4 ◽  
pp. 240 ◽  
Author(s):  
Philipp Strasberg
Keyword(s):  
Causal Model ◽  
Open Systems ◽  
Natural Extension ◽  
Strong Support ◽  
Causal Models ◽  
Point Of View ◽  
Thermodynamic Quantities ◽  
Stochastic Thermodynamics ◽  
Measurement Results ◽  
Definition Of

Operational quantum stochastic thermodynamics is a recently proposed theory to study the thermodynamics of open systems based on the rigorous notion of a quantum stochastic process or quantum causal model. In there, a stochastic trajectory is defined solely in terms of experimentally accessible measurement results, which serve as the basis to define the corresponding thermodynamic quantities. In contrast to this observer-dependent point of view, a `black box', which evolves unitarily and can simulate a quantum causal model, is constructed here. The quantum thermodynamics of this big isolated system can then be studied using widely accepted arguments from statistical mechanics. It is shown that the resulting definitions of internal energy, heat, work, and entropy have a natural extension to the trajectory level. The canonical choice of them coincides with the proclaimed definitions of operational quantum stochastic thermodynamics, thereby providing strong support in favour of that novel framework. However, a few remaining ambiguities in the definition of stochastic work and heat are also discovered and in light of these findings some other proposals are reconsidered. Finally, it is demonstrated that the first and second law hold for an even wider range of scenarios than previously thought, covering a large class of quantum causal models based solely on a single assumption about the initial system-bath state.

scholarly journals On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 99
Author(s):  
Cristian Privat ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Jaime Rubio-Martínez
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Md Simulations ◽  
Point Of View ◽  
Conformational Space ◽  
Conformational Sampling ◽  
Protonation State ◽  
Constant Ph ◽  
Biochemical Systems ◽  
Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

scholarly journals Comparison of Quantitative Morphology of Layered and Arbitrary Patterns: Contrary to Visual Perception, Binary Arbitrary Patterns Are Layered from a Structural Point of View

2021 ◽  
Vol 11 (14) ◽  
pp. 6300
Author(s):  
Igor Smolyar ◽  
Daniel Smolyar
Keyword(s):  
Boolean Function ◽  
Layer Structure ◽  
Central Element ◽  
Morphological Characteristics ◽  
Building Blocks ◽  
Point Of View ◽  
Living Systems ◽  
Seismic Profiles ◽  
Contour Maps ◽  
Anisotropic Layers

Patterns found among both living systems, such as fish scales, bones, and tree rings, and non-living systems, such as terrestrial and extraterrestrial dunes, microstructures of alloys, and geological seismic profiles, are comprised of anisotropic layers of different thicknesses and lengths. These layered patterns form a record of internal and external factors that regulate pattern formation in their various systems, making it potentially possible to recognize events in the formation history of these systems. In our previous work, we developed an empirical model (EM) of anisotropic layered patterns using an N-partite graph, denoted as G(N), and a Boolean function to formalize the layer structure. The concept of isotropic and anisotropic layers was presented and described in terms of the G(N) and Boolean function. The central element of the present work is the justification that arbitrary binary patterns are made up of such layers. It has been shown that within the frame of the proposed model, it is the isotropic and anisotropic layers themselves that are the building blocks of binary layered and arbitrary patterns; pixels play no role. This is why the EM can be used to describe the morphological characteristics of such patterns. We present the parameters disorder of layer structure, disorder of layer size, and pattern complexity to describe the degree of deviation of the structure and size of an arbitrary anisotropic pattern being studied from the structure and size of a layered isotropic analog. Experiments with arbitrary patterns, such as regular geometric figures, convex and concave polygons, contour maps, the shape of island coastlines, river meanders, historic texts, and artistic drawings are presented to illustrate the spectrum of problems that it may be possible to solve by applying the EM. The differences and similarities between the proposed and existing morphological characteristics of patterns has been discussed, as well as the pros and cons of the suggested method.

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.

scholarly journals Dirac structures in nonequilibrium thermodynamics for simple open systems

2020 ◽  
Vol 61 (9) ◽  
pp. 092701
Author(s):  
François Gay-Balmaz ◽  
Hiroaki Yoshimura
Keyword(s):  
Nonequilibrium Thermodynamics ◽  
Open Systems ◽  
Dirac Structures

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.

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