Standard Thermodynamic Properties, Biosynthesis Rates, and the Driving Force of Growth of Five Agricultural Plants

Unravelling the thermodynamic properties of soil ecosystems in mature beech forests

Thermodynamics is a vast area of knowledge with a debatable role in explaining the evolution of ecosystems. In the case of soil ecosystems, this role is still unclear due to difficulties in determining the thermodynamic functions that are involved in the survival and evolution of soils as living systems. The existing knowledge is largely based on theoretical approaches and has never been applied to soils using thermodynamic functions that have been experimentally determined. In this study, we present a method for the complete experimental thermodynamic characterization of soil organic matter. This method quantifies all the thermodynamic functions for combustion and formation reactions which are involved in the thermodynamic principles governing the evolution of the universe. We applied them to track the progress of soil organic matter with soil depth in mature beech forests. Our results show that soil organic matter evolves to a higher degree of reduction as it is mineralized, yielding products with lower carbon but higher energy content than the original organic matter used as reference. These products have higher entropy than the original one, demonstrating how the soil ecosystem evolves with depth, in accordance with the second law of thermodynamics. The results were sensitive to soil organic matter transformation in forests under different management, indicating potential applicability in elucidating the energy strategies for evolution and survival of soil systems as well as in settling their evolutionary states.

Animal bioenergetics: Thermodynamic and kinetic analysis of growth and metabolism of Anguilla anguilla

Bioenergetics and biothermodynamics are valuable tools in research on growth and metabolic processes of a wide range of organisms, including viruses, bacteria, fungi, algae and plants, as is shown by the many publications on this topic in the literature. These studies provide insight into growth and metabolism of individual species, as well as interactions between species, like the virus-host interaction (infection) and virus-virus interaction (competition). However, this approach has not yet been applied to animal species. The universality of biothermodynamics and bioenergetics provides a good motive to apply them in analysis of animals. In this research, we made a bioenergetic, biothermodynamic and kinetic characterization for the first time for an animal species - Anguilla anguilla L. (European eel). We made a comparative analysis on yellow (young adult) and silver (mature adult) phases. Metabolic processes were modeled as chemical reactions with characteristic thermodynamic properties: enthalpy, entropy and Gibbs energy. Moreover, Gibbs energy explained growth rates, through phenomenological equations. This analysis of animal metabolism and growth explained metabolic properties of yellow and silver A. anguilla, including the bioenergetic aspect of life history. Moreover, we compared thermodynamic properties of A. anguilla with those of its main macromolecular components and other organisms. The thermodynamic properties were explained by the structural properties of organisms. This research extends the bioenergetic and biothermodynamic approaches to zoology, which should allow analysis of the energetic aspect of animal metabolic processes, interactions with their environment and interactions with other organisms. Furthermore, it connects the macroscopic perspective of zoology with the microscopic perspectives of biochemistry, bioenergetics and biothermodynamics. This will provide a basis for development of mechanistic models of animal growth and metabolism.

Thermodynamics of microbial consortia: Enthalpies and Gibbs energies of microorganism live matter and macromolecules of E. coli, G. oxydans, P. fluorescens, S. thermophilus and P. chrysogenum

Every microorganism represents a biothermodynamic system, characterized by an empirical formula and thermodynamic properties of biosynthesis. Gibbs energy of biosynthesis influences the multiplication rate of a microorganism. In case of a mixed culture (microbial consortia) biosynthesis processes of microbial species are competitive. This is why Gibbs energy of biosynthesis determines the growth in a mixed culture. This paper gives a mechanistic model that explains growth of microorganisms in mixed culture and ability to grow in microbial consortia. Detailed biosynthesis reactions were formulated for the first time for five microorganism species, which include metallic elements. Moreover, thermodynamic properties of live matter and biosynthesis were calculated for the first time for five microorganism species and macromolecules.

Nutrient recovery and pollutant removal during renewable fuel production: opportunities and challenges

Stimulated by the desire to achieve a Net Zero energy economy, the demand for renewable fuels is growing rapidly. The production of toxic waste streams that accompanies the transition from fossil fuels to renewable fuels is often overlooked. These waste streams include, among others, thiols and ammonia, and benzene, toluene, and xylene (BTX). When suitable treatment technologies are available, these compounds can be converted to valuable nutrients. In this opinion article, we provide an overview of expected waste streams and their characteristics. We indicate future challenges for associated waste streams, such as the lag in developing resource recovery technologies. Furthermore, we discuss unexploited opportunities to recover valuable nutrients from these waste streams.

Biothermodynamics of Viruses from Absolute Zero (1950) to Virothermodynamics (2022)

Biothermodynamics of viruses is among the youngest but most rapidly developing scientific disciplines. During the COVID-19 pandemic, it closely followed the results published by molecular biologists. Empirical formulas were published for 50 viruses and thermodynamic properties for multiple viruses and virus variants, including all variants of concern of SARS-CoV-2, SARS-CoV, MERS-CoV, Ebola virus, Vaccinia and Monkeypox virus. A review of the development of biothermodynamics of viruses during the last several decades and intense development during the last 3 years is described in this paper.

Why doesn't Ebola virus cause pandemics like SARS-CoV-2?

Ebola virus is among the most dangerous, contagious and deadly etiological causes of viral diseases. However, Ebola virus has never extensively spread in human population and never have led to a pandemic. Why? The mechanistic biophysical model revealing the biothermodynamic background of virus-host interaction) could help us to understand pathogenesis of Ebola virus disease (earlier known as the Ebola hemorrhagic fever). In this paper for the first time the empirical formula, thermodynamic properties of biosynthesis (including the driving force of virus multiplication in the susceptible host), binding constant and thermodynamic properties of binding are reported. Thermodynamic data for Ebola virus were compared with data for SARS-CoV-2 to explain why SARS-CoV-2 has caused a pandemic, while Ebola remains on local epidemic level. The empirical formula of the Ebola virus was found to be CH_1.569O_0.3281N_0.2786P_0.00173S_0.00258. Standard Gibbs energy of biosynthesis of the Ebola virus nucleocapsid is -151.59 kJ/C-mol.

Strain wars 3: Differences in infectivity and pathogenicity between Delta and Omicron strains of SARS-CoV-2 can be explained by thermodynamic and kinetic parameters of binding and growth

In this paper, for the first time, empirical formulas have been reported of the Delta and Omicron strains of SARS-CoV-2. The empirical formula of the Delta strain entire virion was found to be CH1.6383O0.2844N0.2294P0.0064S0.0042, while its nucleocapsid has the formula CH1.5692O0.3431N0.3106P0.0060S0.0043. The empirical formula of the Omicron strain entire virion was found to be CH1.6404O0.2842N0.2299P0.0064S0.0038, while its nucleocapsid has the formula CH1.5734O0.3442N0.3122P0.0060S0.0033. Based on the empirical formulas, standard thermodynamic properties of formation and growth have been calculated and reported for the Delta and Omicron strains. Moreover, standard thermodynamic properties of binding have been reported for Wild type (Hu-1), Alpha, Beta, Gamma, Delta and Omicron strains. For all the strains, binding phenomenological coefficients and antigen-receptor (SGP-ACE2) binding rates have been determined and compared, which are proportional to infectivity. The results show that the binding rate of the Omicron strain is between 1.5 and 2.5 times greater than that of the Delta strain. The Omicron strain is characterized by a greater infectivity, based on the epidemiological data available in the literature. The increased infectivity was explained in this paper using Gibbs energy of binding. However, no indications exist for decreased pathogenicity of the Omicron strain. Pathogenicity is proportional to the virus multiplication rate, while Gibbs energies of multiplication are very similar for the Delta and Omicron strains. Thus, multiplication rate and pathogenicity are similar for the Delta and Omicron strains. The lower number of severe cases caused by the Omicron strain can be explained by increased number of immunized people. Immunization does not influence the possibility of occurrence of infection, but influences the rate of immune response, which is much more efficient in immunized people. This leads to prevention of more severe Omicron infection cases.

Omicron BA.2.75 Sublineage (Centaurus) Follows the Expectations of the Evolution Theory: Less Negative Gibbs Energy of Biosynthesis Indicates Decreased Pathogenicity

SARS-CoV-2 belongs to the group of RNA viruses with a pronounced tendency to mutate. Omicron BA.2.75 is a subvariant believed to be able to suppress the currently dominant BA.5 and cause a new winter wave of the COVID-19 pandemic. Omicron BA.2.75 is characterized by a greater infectivity compared to earlier Omicron variants. However, the Gibbs energy of the biosynthesis of virus particles is slightly less negative compared to those of other variants. Thus, the multiplication rate of Omicron BA.2.75 is lower than that of other SARS-CoV-2 variants. This leads to slower accumulation of newly formed virions and less damage to host cells, indicating evolution of SARS-CoV-2 toward decreasing pathogenicity.