scholarly journals Energy flows, metabolism and translation

2011 ◽  
Vol 366 (1580) ◽  
pp. 2949-2958 ◽  
Author(s):  
Robert Pascal ◽  
Laurent Boiteau
Keyword(s):  
Free Energy ◽  
Carbon Metabolism ◽  
Energy Levels ◽  
Self Organization ◽  
Discrete Events ◽  
Covalent Bonds ◽  
Biochemical Processes ◽  
Energy Flows ◽  
Living Organisms ◽  
Complex Chemistry

Thermodynamics provides an essential approach to understanding how living organisms survive in an organized state despite the second law. Exchanges with the environment constantly produce large amounts of entropy compensating for their own organized state. In addition to this constraint on self-organization, the free energy delivered to the system, in terms of potential, is essential to understand how a complex chemistry based on carbon has emerged. Accordingly, the amount of free energy brought about through discrete events must reach the strength needed to induce chemical changes in which covalent bonds are reorganized. The consequence of this constraint was scrutinized in relation to both the development of a carbon metabolism and that of translation. Amino acyl adenylates involved as aminoacylation intermediates of the latter process reach one of the higher free energy levels found in biochemistry, which may be informative on the range in which energy was exchanged in essential early biochemical processes. The consistency of this range with the amount of energy needed to weaken covalent bonds involving carbon may not be accidental but the consequence of the abovementioned thermodynamic constraints. This could be useful in building scenarios for the emergence and early development of translation.

scholarly journals Self-replication of a quantum artificial organism driven by single-photon pulses

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Daniel Valente
Keyword(s):  
Self Assembly ◽  
Artificial Life ◽  
Single Photon ◽  
Self Organization ◽  
Physical Systems ◽  
Self Organized ◽  
Living Organisms ◽  
A Chain ◽  
Thermodynamic Mechanism ◽  
Self Replication

AbstractImitating the transition from inanimate to living matter is a longstanding challenge. Artificial life has achieved computer programs that self-replicate, mutate, compete and evolve, but lacks self-organized hardwares akin to the self-assembly of the first living cells. Nonequilibrium thermodynamics has achieved lifelike self-organization in diverse physical systems, but has not yet met the open-ended evolution of living organisms. Here, I look for the emergence of an artificial-life code in a nonequilibrium physical system undergoing self-organization. I devise a toy model where the onset of self-replication of a quantum artificial organism (a chain of lambda systems) is owing to single-photon pulses added to a zero-temperature environment. I find that spontaneous mutations during self-replication are unavoidable in this model, due to rare but finite absorption of off-resonant photons. I also show that the replication probability is proportional to the absorbed work from the photon, thereby fulfilling a dissipative adaptation (a thermodynamic mechanism underlying lifelike self-organization). These results hint at self-replication as the scenario where dissipative adaptation (pointing towards convergence) coexists with open-ended evolution (pointing towards divergence).

Metabolic and energy correlates of intracellular pH in progressive fatigue of squid (L. brevis) mantle muscle

1996 ◽  
Vol 271 (5) ◽  
pp. R1403-R1414 ◽  
Author(s):  
H. O. Portner ◽  
E. Finke ◽  
P. G. Lee
Keyword(s):  
Free Energy ◽  
Critical Velocity ◽  
Energy Levels ◽  
High Energy ◽  
Swimming Velocity ◽  
High Energy Phosphates ◽  
Energy Status ◽  
Intracellular Acidosis ◽  
Model Calculations

Squid (Lolliguncula brevis) were exercised at increasing swimming speeds to allow us to analyze the correlated changes in intracellular metabolic, acid-base, and energy status of the mantle musculature. Beyond a critical swimming velocity of 1.5 mantle lengths/s, an intracellular acidosis developed that was caused by an initial base loss from the cells, the onset of respiratory acidification, and, predominantly, octopine formation. The acidosis was correlated with decreasing levels of phospho-L-arginine and, thus, supported ATP buffering at the expense of the phosphagen. Monohydrogenphosphate, the actual substrate of glycogen phosphorylase accumulated, enabling glycogen degradation, despite progressive acidosis. In addition to octopine, succinate, and glycerophosphate accumulation, the onset of acidosis characterizes the critical velocity and indicates the transition to a non-steady-state time-limited situation. Accordingly, swimming above the critical velocity caused cellular energy levels (in vivo Gibbs free energy change of ATP hydrolysis) to fall. A minimal value was reached at about -45 kJ/mol. Model calculations demonstrate that changes in free Mg2+ levels only minimally affect ATP free energy, but minimum levels are relevant in maintaining functional concentrations of Mg(2+)-complexed adenylates. Model calculations also reveal that phosphagen breakdown enabled L. brevis to reach swimming speeds about three times higher than the critical velocity. Comparison of two offshore squid species (Loligo pealei and Illex illecebrosus) with the estuarine squid L.brevis indicates that the latter uses a strategy to delay the exploitation of high-energy phosphates and protect energy levels at higher than the minimum levels (-42 kJ/mol) characterizing fatigue in the other species. A more economical use of anaerobic resources and an early reduction in performance may enable L. brevis to tolerate more extreme environmental conditions in shallow estuarine waters and even hypoxic environments and to prevent a fatal depletion of energy stores.

scholarly journals Emergence and Self-Organisation of Complex Systems: the role of energy flows and information a philosophical approach

2018 ◽  
Vol 2 (1) ◽  
pp. 31 ◽  
Author(s):  
Norbert Fenzl
Keyword(s):  
Complex Systems ◽  
Driving Forces ◽  
Open Systems ◽  
Structural Information ◽  
Self Organization ◽  
Specific Information ◽  
Philosophical Approach ◽  
Energy Flows ◽  
Energy And Material Flows

How order emerges from noise? How higher complexity arises from lower complexity? For what reason a certain number of open systems start interacting in a coherent way, producing new structures, building up cohesion and new structural boundaries? To answer these questions we need to precise the concepts we use to describe open and complex systems and the basic driving forces of self-organization.   We assume that self-organization processes are related to the flow and throughput of Energy and Matter and the production of system-specific Information. These two processes are intimately linked together: Energy and Material flows are the fundamental carriers of signs, which are processed by the internal structure of the system to produce system-specific structural Information (Is). So far, the present theoretical reflections are focused on the emergence of open systems and on the role of Energy Flows and Information in a self-organizing process. Based on the assumption that Energy, Mass and Information are intrinsically linked together and are fundamental aspects of the Universe, we discuss how they might be related to each other and how they are able to produce the emergence of new structures and systems. 

5. Robots and artificial life

2018 ◽  
Author(s):  
Margaret A. Boden
Keyword(s):  
Artificial Life ◽  
Biological Systems ◽  
Evolutionary Programming ◽  
Self Organization ◽  
Big Business ◽  
Practical Applications ◽  
Living Organisms ◽  
Self Organizing

Artificial life (A-Life) models biological systems. Like AI, it has both technological and scientific aims. ‘Robots and artificial life’ explains that A-Life is integral to AI, because all the intelligence we know about is found in living organisms. AI technologists turn to biology in developing practical applications of many kinds, including robots, evolutionary programming, and self-organizing devices. Robots are quintessential examples of AI, having high visibility and being hugely ingenious—and very big business, too. Evolutionary AI, although widely used, is less well known. Self-organizing machines are even less familiar. Nevertheless, in the quest to understand self-organization, AI has been as useful to biology as biology has been to AI.

Dangling Bonds in Amorphous Silicon Nitride Alloys: Predictions of the Free Energy Model

1992 ◽  
Vol 284 ◽  
Author(s):  
F. W. Smith ◽  
H. Efstathiadis ◽  
Z. Yin
Keyword(s):  
Free Energy ◽  
Energy Gap ◽  
Energy Levels ◽  
Experimental Studies ◽  
Energy Model ◽  
Paramagnetic Defect ◽  
Amorphous Network ◽  
Energy Of Mixing ◽  
Free Energy Model ◽  
Free Energy Of Mixing

ABSTRACTThe free energy model (FEM) for bonding in a-SixNyHz alloys has been extended to include the contributions of neutral and charged Si and N defects to the free energy of mixing of the amorphous alloy. The FEM predicts that the dominant defects in N-rich alloys are N2o, N2-, and either S3+ or N2+, in contrast to the results of experimental studies that find the dominant neutral, paramagnetic defect to be Si3o. It is concluded that either the observed Si3o defects are not in thermodynamic equilibrium with the amorphous network or the N2o defects have energy levels which lie much higher in the energy gap than currently believed.

scholarly journals Self-Organization of Motor-Propelled Cytoskeletal Filaments at Topographically Defined Borders

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Alf Månsson ◽  
Richard Bunk ◽  
Mark Sundberg ◽  
Lars Montelius
Keyword(s):  
Molecular Motor ◽  
Direct Consequence ◽  
Self Organization ◽  
Test Model ◽  
Structured Surfaces ◽  
Microstructured Surfaces ◽  
Living Organisms ◽  
Edge Tracing ◽  
Motor Density

Self-organization phenomena are of critical importance in living organisms and of great interest to exploit in nanotechnology. Here we describe in vitro self-organization of molecular motor-propelled actin filaments, manifested as a tendency of the filaments to accumulate in high density close to topographically defined edges on nano- and microstructured surfaces. We hypothesized that this “edge-tracing” effect either (1) results from increased motor density along the guiding edges or (2) is a direct consequence of the asymmetric constraints on stochastic changes in filament sliding direction imposed by the edges. The latter hypothesis is well captured by a model explicitly defining the constraints of motility on structured surfaces in combination with Monte-Carlo simulations [cf. Nitta et al. (2006)] of filament sliding. In support of hypothesis 2 we found that the model reproduced the edge tracing effect without the need to assume increased motor density at the edges. We then used model simulations to elucidate mechanistic details. The results are discussed in relation to nanotechnological applications and future experiments to test model predictions.

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