scholarly journals Differences and implications in biogeochemistry from maximizing entropy production locally versus globally

2011 ◽  
Vol 2 (1) ◽  
pp. 1-44
Author(s):  
J. J. Vallino
Keyword(s):  
Entropy Production ◽  
Biological Systems ◽  
Biogeochemical Processes ◽  
Biological Structure ◽  
Transient Conditions ◽  
Entropy Maximization ◽  
Planetary Scale ◽  
Modeling Systems ◽  
Spatial Dimensions ◽  
Multiple Levels

Abstract. In this manuscript we investigate the use of the maximum entropy production (MEP) principle for modeling biogeochemical processes that are catalyzed by living systems. Because of novelties introduced by the MEP approach, many questions need to be answered and techniques developed in the application of MEP to describe biological systems that are responsible for energy and mass transformations on a planetary scale. In previous work we introduce the importance of integrating entropy production over time to distinguish abiotic from biotic processes under transient conditions. Here we investigate the ramifications of modeling biological systems involving one or more spatial dimensions. When modeling systems with spatial dimensions, entropy production can be maximized either locally at each point in space asynchronously or globally over the system domain synchronously. We use a simple two-box model inspired by two-layer ocean models to illustrate the differences in local versus global entropy maximization. Synthesis and oxidation of biological structure is modeled using two autocatalytic reactions that account for changes in community kinetics using a single parameter each. Our results show that entropy production can be increased if maximized over the system domain rather than locally, which has important implications regarding how biological systems organize and supports the hypothesis for multiple levels of selection and cooperation in biology for the dissipation of free energy.

scholarly journals Differences and implications in biogeochemistry from maximizing entropy production locally versus globally

2011 ◽  
Vol 2 (1) ◽  
pp. 69-85 ◽  
Author(s):  
J. J. Vallino
Keyword(s):  
Entropy Production ◽  
Biological Systems ◽  
Biogeochemical Processes ◽  
Biological Structure ◽  
Transient Conditions ◽  
Entropy Maximization ◽  
Planetary Scale ◽  
Modeling Systems ◽  
Spatial Dimensions ◽  
Multiple Levels

Abstract. In this manuscript we investigate the use of the maximum entropy production (MEP) principle for modeling biogeochemical processes that are catalyzed by living systems. Because of novelties introduced by the MEP approach, many questions need to be answered and techniques developed in the application of MEP to describe biological systems that are responsible for energy and mass transformations on a planetary scale. In previous work we introduce the importance of integrating entropy production over time to distinguish abiotic from biotic processes under transient conditions. Here we investigate the ramifications of modeling biological systems involving one or more spatial dimensions. When modeling systems over space, entropy production can be maximized either locally at each point in space asynchronously or globally over the system domain synchronously. We use a simple two-box model inspired by two-layer ocean models to illustrate the differences in local versus global entropy maximization. Synthesis and oxidation of biological structure is modeled using two autocatalytic reactions that account for changes in community kinetics using a single parameter each. Our results show that entropy production can be increased if maximized over the system domain rather than locally, which has important implications regarding how biological systems organize and supports the hypothesis for multiple levels of selection and cooperation in biology for the dissipation of free energy.

scholarly journals Modeling Biological Systems Using Crowdsourcing

2018 ◽  
Vol 43 (3) ◽  
pp. 219-243 ◽  
Author(s):  
Szymon Wasik
Keyword(s):  
Systems Biology ◽  
Serious Games ◽  
Domain Knowledge ◽  
Biological Systems ◽  
Effective Technique ◽  
Design Models ◽  
Modeling Systems ◽  
Vast Network

Abstract Crowdsourcing is a very effective technique for outsourcing work to a vast network usually comprising anonymous people. In this study, we review the application of crowdsourcing to modeling systems originating from systems biology. We consider a variety of verified approaches, including well-known projects such as EyeWire, FoldIt, and DREAM Challenges, as well as novel projects conducted at the European Center for Bioinformatics and Genomics. The latter projects utilized crowdsourced serious games to design models of dynamic biological systems, and it was demonstrated that these models could be used successfully to involve players without domain knowledge. We conclude the review of these systems by providing 10 guidelines to facilitate the efficient use of crowdsourcing.

scholarly journals Hierarchically embedded interaction networks represent a missing link in the study of behavioral and community ecology

2019 ◽  
Vol 31 (2) ◽  
pp. 279-286 ◽  
Author(s):  
P O Montiglio ◽  
K M Gotanda ◽  
C F Kratochwil ◽  
K L Laskowski ◽  
D R Farine
Keyword(s):  
Community Ecology ◽  
Evolutionary Theory ◽  
Biological Systems ◽  
Ecological Effects ◽  
Interaction Networks ◽  
Biological Organization ◽  
Embedded Networks ◽  
Biological Phenomena ◽  
Embedded Structure ◽  
Multiple Levels

Abstract Because genes and phenotypes are embedded within individuals, and individuals within populations, interactions within one level of biological organization are inherently linked to interactors at others. Here, we expand the network paradigm to consider that nodes can be embedded within other nodes, and connections (edges) between nodes at one level of organization form “bridges” for connections between nodes embedded within them. Such hierarchically embedded networks highlight two central properties of biological systems: 1) processes occurring across multiple levels of organization shape connections among biological units at any given level of organization and 2) ecological effects occurring at a given level of organization can propagate up or down to additional levels. Explicitly considering the embedded structure of evolutionary and ecological networks can capture otherwise hidden feedbacks and generate new insights into key biological phenomena, ultimately promoting a broader understanding of interactions in evolutionary theory.

scholarly journals Improved bounds on entropy production in living systems

2021 ◽  
Vol 118 (18) ◽  
pp. e2024300118
Author(s):  
Dominic J. Skinner ◽  
Jörn Dunkel
Keyword(s):  
Entropy Production ◽  
Biological Systems ◽  
Detailed Balance ◽  
Calcium Oscillations ◽  
Living Systems ◽  
Entropy Production Rate ◽  
Local Order ◽  
Nonequilibrium Processes ◽  
Diverse Range ◽  
Human Embryonic Kidney Cells

Living systems maintain or increase local order by working against the second law of thermodynamics. Thermodynamic consistency is restored as they consume free energy, thereby increasing the net entropy of their environment. Recently introduced estimators for the entropy production rate have provided major insights into the efficiency of important cellular processes. In experiments, however, many degrees of freedom typically remain hidden to the observer, and, in these cases, existing methods are not optimal. Here, by reformulating the problem within an optimization framework, we are able to infer improved bounds on the rate of entropy production from partial measurements of biological systems. Our approach yields provably optimal estimates given certain measurable transition statistics. In contrast to prevailing methods, the improved estimator reveals nonzero entropy production rates even when nonequilibrium processes appear time symmetric and therefore may pretend to obey detailed balance. We demonstrate the broad applicability of this framework by providing improved bounds on the energy consumption rates in a diverse range of biological systems including bacterial flagella motors, growing microtubules, and calcium oscillations within human embryonic kidney cells.

scholarly journals Ecosystem biogeochemistry considered as a distributed metabolic network ordered by maximum entropy production

2010 ◽  
Vol 365 (1545) ◽  
pp. 1417-1427 ◽  
Author(s):  
Joseph J. Vallino
Keyword(s):  
Metabolic Network ◽  
Entropy Production ◽  
Maximum Entropy ◽  
Biological Systems ◽  
Reaction Pathways ◽  
Maximum Entropy Production ◽  
Biological Structures ◽  
Temporal Averaging ◽  
Ecosystem Level ◽  
Spatio Temporal

We examine the application of the maximum entropy production principle for describing ecosystem biogeochemistry. Since ecosystems can be functionally stable despite changes in species composition, we use a distributed metabolic network for describing biogeochemistry, which synthesizes generic biological structures that catalyse reaction pathways, but is otherwise organism independent. Allocation of biological structure and regulation of biogeochemical reactions is determined via solution of an optimal control problem in which entropy production is maximized. However, because synthesis of biological structures cannot occur if entropy production is maximized instantaneously, we propose that information stored within the metagenome allows biological systems to maximize entropy production when averaged over time. This differs from abiotic systems that maximize entropy production at a point in space–time, which we refer to as the steepest descent pathway. It is the spatio-temporal averaging that allows biological systems to outperform abiotic processes in entropy production, at least in many situations. A simulation of a methanotrophic system is used to demonstrate the approach. We conclude with a brief discussion on the implications of viewing ecosystems as self-organizing molecular machines that function to maximize entropy production at the ecosystem level of organization.

The Geometry of Health

2021 ◽  
pp. 93-109
Author(s):  
Manish Arora ◽  
Paul Curtin ◽  
Austen Curtin ◽  
Christine Austin ◽  
Alessandro Giuliani
Keyword(s):  
Clinical Application ◽  
Biological Systems ◽  
Epidemiological Methods ◽  
Biological Structure ◽  
Dynamic Nature ◽  
Independent Dimension ◽  
Functional Dynamics ◽  
As If

Chapter 5 examines the dynamic nature of interfaces and starts examining their characteristics. The authors posit that just as we might derive a multitude of dimensions to describe biological structure, so too are there many dimensions that describe the functional dynamics in how biological systems vary over time. Current environmental epidemiological methods used in analyzing data on our environment and our physiology treat each measure as if it were an independent dimension, much like a carpenter measuring the height, width, or length of a piece of furniture. However, because there are processes underlying our physiological development, constraints are applied to the forms that we and our environment can take. Knowledge of these can be harnessed to identify the primary dimensions along which we must characterize the systems under study. By doing this we were able to take an important first step in operationalizing Environmental Biodynamics for clinical application.

scholarly journals Entropy production and entropic attractors in black hole fusion and fission

2020 ◽  
Vol 2020 (8) ◽  
Author(s):  
Tomás Andrade ◽  
Roberto Emparan ◽  
Aron Jansen ◽  
David Licht ◽  
Raimon Luna ◽  
...  
Keyword(s):  
Black Holes ◽  
Black Hole ◽  
Entropy Production ◽  
Black Hole Entropy ◽  
Effective Theory ◽  
Small Subset ◽  
Entropy Maximization ◽  
Good Guide ◽  
Black Strings ◽  
The Stability

Abstract We study how black hole entropy is generated and the role it plays in several highly dynamical processes: the decay of unstable black strings and ultraspinning black holes; the fusion of two rotating black holes; and the subsequent fission of the merged system into two black holes that fly apart (which can occur in dimension D ≥ 6, with a mild violation of cosmic censorship). Our approach uses the effective theory of black holes at D → ∞, but we expect our main conclusions to hold at finite D. Black hole fusion is highly irreversible, while fission, which follows the pattern of the decay of black strings, generates comparatively less entropy. In 2 → 1 → 2 black hole collisions an intermediate, quasi-thermalized state forms that then fissions. This intermediate state erases much of the memory of the initial states and acts as an attractor funneling the evolution of the collision towards a small subset of outgoing parameters, which is narrower the closer the total angular momentum is to the critical value for fission. Entropy maximization provides a very good guide for predicting the final outgoing states. Along our study, we clarify how entropy production and irreversibility appear in the large D effective theory. We also extend the study of the stability of new black hole phases (black bars and dumbbells). Finally, we discuss entropy production through charge diffusion in collisions of charged black holes.

Observation of biological macromolecules using various electron microscopic methods

1978 ◽  
Vol 36 (2) ◽  
pp. 170-171
Author(s):  
Mitsuo Ohtsuki ◽  
Michael Sogard
Keyword(s):  
Electron Microscope ◽  
Phase Contrast ◽  
Image Interpretation ◽  
Density Lipoprotein ◽  
Biological Macromolecules ◽  
Contrast Effects ◽  
Biological Structure ◽  
Electron Microscopic ◽  
Structural Investigations ◽  
Staining Techniques

Structural investigations of biological macromolecules commonly employ CTEM with negative staining techniques. Difficulties in valid image interpretation arise, however, due to problems such as variability in thickness and degree of penetration of the staining agent, noise from the supporting film, and artifacts from defocus phase contrast effects. In order to determine the effects of these variables on biological structure, as seen by the electron microscope, negative stained macromolecules of high density lipoprotein-3 (HDL3) from human serum were analyzed with both CTEM and STEM, and results were then compared with CTEM micrographs of freeze-etched HDL3. In addition, we altered the structure of this molecule by digesting away its phospholipid component with phospholipase A2 and look for consistent changes in structure.

Transmission Electron Microscopy of Protein Macromolecules

1971 ◽  
Vol 29 ◽  
pp. 424-425
Author(s):  
Henry S. Slayter
Keyword(s):  
Biological Systems ◽  
Metal Vapor ◽  
Resolving Power ◽  
Electron Microscopic ◽  
Chemical Methods ◽  
Molecular Weights ◽  
The Past ◽  
Physical Chemical ◽  
Transmission Electron

Electron microscopic methods have been applied increasingly during the past fifteen years, to problems in structural molecular biology. Used in conjunction with physical chemical methods and/or Fourier methods of analysis, they constitute powerful tools for determining sizes, shapes and modes of aggregation of biopolymers with molecular weights greater than 50, 000. However, the application of the e.m. to the determination of very fine structure approaching the limit of instrumental resolving power in biological systems has not been productive, due to various difficulties such as the destructive effects of dehydration, damage to the specimen by the electron beam, and lack of adequate and specific contrast. One of the most satisfactory methods for contrasting individual macromolecules involves the deposition of heavy metal vapor upon the specimen. We have investigated this process, and present here what we believe to be the more important considerations for optimizing it. Results of the application of these methods to several biological systems including muscle proteins, fibrinogen, ribosomes and chromatin will be discussed.

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