TY  - JOUR
AU  - Popović, Marko
AU  - Stevanović, Maja
AU  - Mihailović, Marija
PY  - 2024
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7518
AB  - Breaking news are usually disturbing. Natural disasters, wars, epidemics etc. are reported as breaking news. This paper reports a decreased danger of spreading of epidemics caused by the JN.1 variant, since analyses indicate that (a) infectivity of the new variant is decreased compared to most earlier variants, which is confirmed by the number of cases (7500 daily in USA). Moreover, JN.1 despite the great number of mutations has not been able to achieve the values of Gibbs energy of biosynthesis (and thus virus multiplication rate) of the Hu-1 wild type. The research shows that infectivity and pathogenicity of the JN.1 variant has not reached worrying size, which means that there is no reason to expect a worsening of the epidemiologic situation.
AB  - Ударне вести су обично узнемирујуће. О природним катастрофама, ратовима, епидемијама итд. се извештава као ударним вестима. У овом раду је приказана смањена опасност од ширења епидемија изазваних варијантом JN.1, јер анализе показују да је (а) инфективност нове варијанте смањена у односу на већину ранијих варијанти, што потврђује и број случајева (7500 дневно у САД). Штавише, JN.1 упркос великом броју мутација није успео да постигне вредности Гибсове енергије биосинтезе (а самим тим и стопе размножавања вируса) дивљег типа Hu.1. Истраживање показује да инфективност и патогеност варијанте JN.1 није достигла забрињавајућу величину, што значи да нема разлога за очекивање погоршање епидемиолошке ситуације.
PB  - Serbian Chemical Society
T2  - Journal of the Serbian Chemical Society
T1  - Breaking news: Empirical formulas, molar masses, biosynthesis reactions, and thermodynamic properties of virus particles, biosynthesis and binding of Omicron JN.1 variant of SARS-CoV-2
T1  - Ударне вести: емпиријске формуле, моларне масе, реакције биосинтезе и термодинамичке особине вирусних честица, биосинтезе и везивања Omicron JN.1 варијанте SARS-CoV-2
DO  - 10.2298/JSC240119019P
ER  - 

@article{
author = "Popović, Marko and Stevanović, Maja and Mihailović, Marija",
year = "2024",
abstract = "Breaking news are usually disturbing. Natural disasters, wars, epidemics etc. are reported as breaking news. This paper reports a decreased danger of spreading of epidemics caused by the JN.1 variant, since analyses indicate that (a) infectivity of the new variant is decreased compared to most earlier variants, which is confirmed by the number of cases (7500 daily in USA). Moreover, JN.1 despite the great number of mutations has not been able to achieve the values of Gibbs energy of biosynthesis (and thus virus multiplication rate) of the Hu-1 wild type. The research shows that infectivity and pathogenicity of the JN.1 variant has not reached worrying size, which means that there is no reason to expect a worsening of the epidemiologic situation., Ударне вести су обично узнемирујуће. О природним катастрофама, ратовима, епидемијама итд. се извештава као ударним вестима. У овом раду је приказана смањена опасност од ширења епидемија изазваних варијантом JN.1, јер анализе показују да је (а) инфективност нове варијанте смањена у односу на већину ранијих варијанти, што потврђује и број случајева (7500 дневно у САД). Штавише, JN.1 упркос великом броју мутација није успео да постигне вредности Гибсове енергије биосинтезе (а самим тим и стопе размножавања вируса) дивљег типа Hu.1. Истраживање показује да инфективност и патогеност варијанте JN.1 није достигла забрињавајућу величину, што значи да нема разлога за очекивање погоршање епидемиолошке ситуације.",
publisher = "Serbian Chemical Society",
journal = "Journal of the Serbian Chemical Society",
title = "Breaking news: Empirical formulas, molar masses, biosynthesis reactions, and thermodynamic properties of virus particles, biosynthesis and binding of Omicron JN.1 variant of SARS-CoV-2, Ударне вести: емпиријске формуле, моларне масе, реакције биосинтезе и термодинамичке особине вирусних честица, биосинтезе и везивања Omicron JN.1 варијанте SARS-CoV-2",
doi = "10.2298/JSC240119019P"
}

Popović, M., Stevanović, M.,& Mihailović, M.. (2024). Breaking news: Empirical formulas, molar masses, biosynthesis reactions, and thermodynamic properties of virus particles, biosynthesis and binding of Omicron JN.1 variant of SARS-CoV-2. in Journal of the Serbian Chemical Society
Serbian Chemical Society..
https://doi.org/10.2298/JSC240119019P

Popović M, Stevanović M, Mihailović M. Breaking news: Empirical formulas, molar masses, biosynthesis reactions, and thermodynamic properties of virus particles, biosynthesis and binding of Omicron JN.1 variant of SARS-CoV-2. in Journal of the Serbian Chemical Society. 2024;.
doi:10.2298/JSC240119019P .

Popović, Marko, Stevanović, Maja, Mihailović, Marija, "Breaking news: Empirical formulas, molar masses, biosynthesis reactions, and thermodynamic properties of virus particles, biosynthesis and binding of Omicron JN.1 variant of SARS-CoV-2" in Journal of the Serbian Chemical Society (2024),
https://doi.org/10.2298/JSC240119019P . .

TY  - JOUR
AU  - Popović, Marko
PY  - 2024
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7516
AB  - 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.
PB  - Elsevier
T2  - Zoology
T1  - Animal bioenergetics: Thermodynamic and kinetic analysis of growth and metabolism of Anguilla anguilla
VL  - 163
SP  - 126158
DO  - 10.1016/j.zool.2024.126158
ER  - 

@article{
author = "Popović, Marko",
year = "2024",
abstract = "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.",
publisher = "Elsevier",
journal = "Zoology",
title = "Animal bioenergetics: Thermodynamic and kinetic analysis of growth and metabolism of Anguilla anguilla",
volume = "163",
pages = "126158",
doi = "10.1016/j.zool.2024.126158"
}

Popović, M.. (2024). Animal bioenergetics: Thermodynamic and kinetic analysis of growth and metabolism of Anguilla anguilla. in Zoology
Elsevier., 163, 126158.
https://doi.org/10.1016/j.zool.2024.126158

Popović M. Animal bioenergetics: Thermodynamic and kinetic analysis of growth and metabolism of Anguilla anguilla. in Zoology. 2024;163:126158.
doi:10.1016/j.zool.2024.126158 .

Popović, Marko, "Animal bioenergetics: Thermodynamic and kinetic analysis of growth and metabolism of Anguilla anguilla" in Zoology, 163 (2024):126158,
https://doi.org/10.1016/j.zool.2024.126158 . .

TY  - JOUR
AU  - Popović, Marko
AU  - Šekularac, Gavrilo
AU  - Mihailović, Marija
PY  - 2024
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7474
AB  - For thousands of years, medicine has made efforts to study and heal infectious diseases. For centuries, medicine and biology have attempted to study the mechanisms of development of infectious diseases. For 100 years, virology has tried to understand and describe different viruses and reveal the secrets of pathophysiology of infections. Several decades ago, the efforts of biomedical scientists were joined by chemists. Since then viruses have been explored not only as biological systems, but also as chemical systems. With the beginning of the COVID-19 pandemic, biothermodynamics has made its contribution to the research on driving forces and mechanisms of lifecycles of viruses, the virus-host interaction. Since then, viruses have been analyzed as biological, chemical and thermodynamic systems. After reporting of chemical and thermodynamic properties of SARS-CoV, MERS-CoV, SARS-CoV-2, Ebola, Mpox, West Nile virus and bacteriophages, this paper reports for the first time the empirical formulas (unit carbon formulas) of Rotavirus A, as well as its thermodynamic properties of virus-host interaction at the membrane (antigen-receptor binding) and virus-host interaction in the cytoplasm (virus multiplication). The virus-host interactions are essentially chemical reactions, the driving force of which is Gibbs energy (of binding and biosynthesis).
PB  - Elsevier
T2  - Microbial Risk Analysis
T1  - Like a summer storm: Biothermodynamic analysis of Rotavirus A - Empirical formula, biosynthesis reaction and driving force of virus multiplication and antigen-receptor binding
VL  - 26
SP  - 100291
DO  - 10.1016/j.mran.2024.100291
ER  - 

@article{
author = "Popović, Marko and Šekularac, Gavrilo and Mihailović, Marija",
year = "2024",
abstract = "For thousands of years, medicine has made efforts to study and heal infectious diseases. For centuries, medicine and biology have attempted to study the mechanisms of development of infectious diseases. For 100 years, virology has tried to understand and describe different viruses and reveal the secrets of pathophysiology of infections. Several decades ago, the efforts of biomedical scientists were joined by chemists. Since then viruses have been explored not only as biological systems, but also as chemical systems. With the beginning of the COVID-19 pandemic, biothermodynamics has made its contribution to the research on driving forces and mechanisms of lifecycles of viruses, the virus-host interaction. Since then, viruses have been analyzed as biological, chemical and thermodynamic systems. After reporting of chemical and thermodynamic properties of SARS-CoV, MERS-CoV, SARS-CoV-2, Ebola, Mpox, West Nile virus and bacteriophages, this paper reports for the first time the empirical formulas (unit carbon formulas) of Rotavirus A, as well as its thermodynamic properties of virus-host interaction at the membrane (antigen-receptor binding) and virus-host interaction in the cytoplasm (virus multiplication). The virus-host interactions are essentially chemical reactions, the driving force of which is Gibbs energy (of binding and biosynthesis).",
publisher = "Elsevier",
journal = "Microbial Risk Analysis",
title = "Like a summer storm: Biothermodynamic analysis of Rotavirus A - Empirical formula, biosynthesis reaction and driving force of virus multiplication and antigen-receptor binding",
volume = "26",
pages = "100291",
doi = "10.1016/j.mran.2024.100291"
}

Popović, M., Šekularac, G.,& Mihailović, M.. (2024). Like a summer storm: Biothermodynamic analysis of Rotavirus A - Empirical formula, biosynthesis reaction and driving force of virus multiplication and antigen-receptor binding. in Microbial Risk Analysis
Elsevier., 26, 100291.
https://doi.org/10.1016/j.mran.2024.100291

Popović M, Šekularac G, Mihailović M. Like a summer storm: Biothermodynamic analysis of Rotavirus A - Empirical formula, biosynthesis reaction and driving force of virus multiplication and antigen-receptor binding. in Microbial Risk Analysis. 2024;26:100291.
doi:10.1016/j.mran.2024.100291 .

Popović, Marko, Šekularac, Gavrilo, Mihailović, Marija, "Like a summer storm: Biothermodynamic analysis of Rotavirus A - Empirical formula, biosynthesis reaction and driving force of virus multiplication and antigen-receptor binding" in Microbial Risk Analysis, 26 (2024):100291,
https://doi.org/10.1016/j.mran.2024.100291 . .

TY  - JOUR
AU  - Popović, Marko
AU  - Šekularac, Gavrilo
AU  - Popović, Marta
PY  - 2024
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7434
AB  - A question is often asked about what tomorrow brings. During the last 4 years of the COVID-19 pandemic, this question was asked with every appearance of a new SARS-CoV-2 variant. It seems that science has an ability to offer a relatively reliable answer. Theoretical and experimental research have allowed a deep insight into structure and function of SARS-CoV-2. Moreover, the developed mechanistic models allow prediction of virus-host interactions. In August 2023, the Omicron BA.2.86 Pirola variant was detected. Taught by the bad experience from 2019 to 2023, when every new variant that appeared during SARS-CoV-2 evolution has caused a new pandemic wave, the question was raised whether this will be the case with the new variant. Research presented in this paper shows that the driving force for antigen-receptor binding of the Omicron BA.2.86 variant is lower than that of the BN.1 and similar to that of the other variants. Based on the presented research, it seems that the new variant will not be more aggressive relative to the previous variants. The movement in the number of newly infected cases in USA in the period between August and mid-October 2023 is in favor of this prediction.
PB  - Elsevier
T2  - Microbial Risk Analysis
T1  - The wind of change: Gibbs energy of binding and infectivity evolution of Omicron BA.2.86 Pirola, EG.5.1, XBB.1.16 Arcturus, CH.1.1 and BN.1 variants of SARS-CoV-2
VL  - 26
SP  - 100290
DO  - 10.1016/j.mran.2024.100290
ER  - 

@article{
author = "Popović, Marko and Šekularac, Gavrilo and Popović, Marta",
year = "2024",
abstract = "A question is often asked about what tomorrow brings. During the last 4 years of the COVID-19 pandemic, this question was asked with every appearance of a new SARS-CoV-2 variant. It seems that science has an ability to offer a relatively reliable answer. Theoretical and experimental research have allowed a deep insight into structure and function of SARS-CoV-2. Moreover, the developed mechanistic models allow prediction of virus-host interactions. In August 2023, the Omicron BA.2.86 Pirola variant was detected. Taught by the bad experience from 2019 to 2023, when every new variant that appeared during SARS-CoV-2 evolution has caused a new pandemic wave, the question was raised whether this will be the case with the new variant. Research presented in this paper shows that the driving force for antigen-receptor binding of the Omicron BA.2.86 variant is lower than that of the BN.1 and similar to that of the other variants. Based on the presented research, it seems that the new variant will not be more aggressive relative to the previous variants. The movement in the number of newly infected cases in USA in the period between August and mid-October 2023 is in favor of this prediction.",
publisher = "Elsevier",
journal = "Microbial Risk Analysis",
title = "The wind of change: Gibbs energy of binding and infectivity evolution of Omicron BA.2.86 Pirola, EG.5.1, XBB.1.16 Arcturus, CH.1.1 and BN.1 variants of SARS-CoV-2",
volume = "26",
pages = "100290",
doi = "10.1016/j.mran.2024.100290"
}

Popović, M., Šekularac, G.,& Popović, M.. (2024). The wind of change: Gibbs energy of binding and infectivity evolution of Omicron BA.2.86 Pirola, EG.5.1, XBB.1.16 Arcturus, CH.1.1 and BN.1 variants of SARS-CoV-2. in Microbial Risk Analysis
Elsevier., 26, 100290.
https://doi.org/10.1016/j.mran.2024.100290

Popović M, Šekularac G, Popović M. The wind of change: Gibbs energy of binding and infectivity evolution of Omicron BA.2.86 Pirola, EG.5.1, XBB.1.16 Arcturus, CH.1.1 and BN.1 variants of SARS-CoV-2. in Microbial Risk Analysis. 2024;26:100290.
doi:10.1016/j.mran.2024.100290 .

Popović, Marko, Šekularac, Gavrilo, Popović, Marta, "The wind of change: Gibbs energy of binding and infectivity evolution of Omicron BA.2.86 Pirola, EG.5.1, XBB.1.16 Arcturus, CH.1.1 and BN.1 variants of SARS-CoV-2" in Microbial Risk Analysis, 26 (2024):100290,
https://doi.org/10.1016/j.mran.2024.100290 . .

TY  - JOUR
AU  - Popović, Marko
AU  - Šekularac, Gavrilo
AU  - Stevanović, Maja
PY  - 2024
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6906
AB  - 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.
PB  - Elsevier
T2  - Journal of Biotechnology
T1  - 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
VL  - 379
SP  - 6
EP  - 17
DO  - 10.1016/j.jbiotec.2023.11.001
ER  - 

@article{
author = "Popović, Marko and Šekularac, Gavrilo and Stevanović, Maja",
year = "2024",
abstract = "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.",
publisher = "Elsevier",
journal = "Journal of Biotechnology",
title = "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",
volume = "379",
pages = "6-17",
doi = "10.1016/j.jbiotec.2023.11.001"
}

Popović, M., Šekularac, G.,& Stevanović, M.. (2024). 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. in Journal of Biotechnology
Elsevier., 379, 6-17.
https://doi.org/10.1016/j.jbiotec.2023.11.001

Popović M, Šekularac G, Stevanović M. 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. in Journal of Biotechnology. 2024;379:6-17.
doi:10.1016/j.jbiotec.2023.11.001 .

Popović, Marko, Šekularac, Gavrilo, Stevanović, Maja, "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" in Journal of Biotechnology, 379 (2024):6-17,
https://doi.org/10.1016/j.jbiotec.2023.11.001 . .

TY  - JOUR
AU  - Popović, Marko
AU  - Pantović Pavlović, Marijana
AU  - Pavlović, Miroslav
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6180
AB  - From the perspectives of molecular biology, genetics and biothermodynamics, SARS-CoV-2 is the among the best characterized viruses. Research on SARS-CoV-2 has shed a new light onto driving forces and molecular mechanisms of viral evolution. This paper reports results on empirical formulas, biosynthesis reactions and thermodynamic properties of biosynthesis (multiplication) for the Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2. Thermodynamic analysis has shown that the physical driving forces for evolution of SARS-CoV-2 are Gibbs energy of biosynthesis and Gibbs energy of binding. The driving forces have led SARS-CoV-2 through the evolution process from the original Hu-1 to the newest variants in accordance with the expectations of the evolution theory.
PB  - Elsevier
T2  - Microbial Risk Analysis
T1  - Ghosts of the past: Elemental composition, biosynthesis reactions and thermodynamic properties of Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2
VL  - 24
SP  - 100263
DO  - 10.1016/j.mran.2023.100263
ER  - 

@article{
author = "Popović, Marko and Pantović Pavlović, Marijana and Pavlović, Miroslav",
year = "2023",
abstract = "From the perspectives of molecular biology, genetics and biothermodynamics, SARS-CoV-2 is the among the best characterized viruses. Research on SARS-CoV-2 has shed a new light onto driving forces and molecular mechanisms of viral evolution. This paper reports results on empirical formulas, biosynthesis reactions and thermodynamic properties of biosynthesis (multiplication) for the Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2. Thermodynamic analysis has shown that the physical driving forces for evolution of SARS-CoV-2 are Gibbs energy of biosynthesis and Gibbs energy of binding. The driving forces have led SARS-CoV-2 through the evolution process from the original Hu-1 to the newest variants in accordance with the expectations of the evolution theory.",
publisher = "Elsevier",
journal = "Microbial Risk Analysis",
title = "Ghosts of the past: Elemental composition, biosynthesis reactions and thermodynamic properties of Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2",
volume = "24",
pages = "100263",
doi = "10.1016/j.mran.2023.100263"
}

Popović, M., Pantović Pavlović, M.,& Pavlović, M.. (2023). Ghosts of the past: Elemental composition, biosynthesis reactions and thermodynamic properties of Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2. in Microbial Risk Analysis
Elsevier., 24, 100263.
https://doi.org/10.1016/j.mran.2023.100263

Popović M, Pantović Pavlović M, Pavlović M. Ghosts of the past: Elemental composition, biosynthesis reactions and thermodynamic properties of Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2. in Microbial Risk Analysis. 2023;24:100263.
doi:10.1016/j.mran.2023.100263 .

Popović, Marko, Pantović Pavlović, Marijana, Pavlović, Miroslav, "Ghosts of the past: Elemental composition, biosynthesis reactions and thermodynamic properties of Zeta P.2, Eta B.1.525, Theta P.3, Kappa B.1.617.1, Iota B.1.526, Lambda C.37 and Mu B.1.621 variants of SARS-CoV-2" in Microbial Risk Analysis, 24 (2023):100263,
https://doi.org/10.1016/j.mran.2023.100263 . .

TY  - JOUR
AU  - Popović, Marko
AU  - Pantović Pavlović, Marijana
AU  - Popović, Marta
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6981
AB  - Since 2019, when it appeared in Wuhan, in the wild type form later labeled Hu-1, SARS-CoV-2 mutated dozens of times and evolved towards increase in infectivity and decrease or maintenance of constant pathogenicity through dozens of variants. The last of them are Omicron EG.5 and EG.5.1. Until 2019, an empirical formula was known only for the poliovirus. Until now empirical formulas and thermodynamic properties were reported for all variants of SARS-CoV-2 and some other viruses. Also, models were developed that describe the biothermodynamic background of SARS-CoV-2 interaction with its human host. With every new mutation in SARS-CoV-2, the question is raised about the further evolution of the virus. This paper reports for the first time empirical formulas and molar masses of Omicron EG.5 and EG.5.1 variants, as well as thermodynamic properties (enthalpy, entropy and Gibbs energy) of formation and biosynthesis. Moreover, the driving force of virus multiplication was analyzed, as well as multiplication rate and pathogenicity of Omicron EG.5 and EG.5.1.
PB  - Elsevier
T2  - Microbial Risk Analysis
T1  - Eris - another brick in the wall: Empirical formulas, molar masses, biosynthesis reactions, enthalpy, entropy and Gibbs energy of Omicron EG.5 Eris and EG.5.1 variants of SARS-CoV-2
VL  - 25
SP  - 100280
DO  - 10.1016/j.mran.2023.100280
ER  - 

@article{
author = "Popović, Marko and Pantović Pavlović, Marijana and Popović, Marta",
year = "2023",
abstract = "Since 2019, when it appeared in Wuhan, in the wild type form later labeled Hu-1, SARS-CoV-2 mutated dozens of times and evolved towards increase in infectivity and decrease or maintenance of constant pathogenicity through dozens of variants. The last of them are Omicron EG.5 and EG.5.1. Until 2019, an empirical formula was known only for the poliovirus. Until now empirical formulas and thermodynamic properties were reported for all variants of SARS-CoV-2 and some other viruses. Also, models were developed that describe the biothermodynamic background of SARS-CoV-2 interaction with its human host. With every new mutation in SARS-CoV-2, the question is raised about the further evolution of the virus. This paper reports for the first time empirical formulas and molar masses of Omicron EG.5 and EG.5.1 variants, as well as thermodynamic properties (enthalpy, entropy and Gibbs energy) of formation and biosynthesis. Moreover, the driving force of virus multiplication was analyzed, as well as multiplication rate and pathogenicity of Omicron EG.5 and EG.5.1.",
publisher = "Elsevier",
journal = "Microbial Risk Analysis",
title = "Eris - another brick in the wall: Empirical formulas, molar masses, biosynthesis reactions, enthalpy, entropy and Gibbs energy of Omicron EG.5 Eris and EG.5.1 variants of SARS-CoV-2",
volume = "25",
pages = "100280",
doi = "10.1016/j.mran.2023.100280"
}

Popović, M., Pantović Pavlović, M.,& Popović, M.. (2023). Eris - another brick in the wall: Empirical formulas, molar masses, biosynthesis reactions, enthalpy, entropy and Gibbs energy of Omicron EG.5 Eris and EG.5.1 variants of SARS-CoV-2. in Microbial Risk Analysis
Elsevier., 25, 100280.
https://doi.org/10.1016/j.mran.2023.100280

Popović M, Pantović Pavlović M, Popović M. Eris - another brick in the wall: Empirical formulas, molar masses, biosynthesis reactions, enthalpy, entropy and Gibbs energy of Omicron EG.5 Eris and EG.5.1 variants of SARS-CoV-2. in Microbial Risk Analysis. 2023;25:100280.
doi:10.1016/j.mran.2023.100280 .

Popović, Marko, Pantović Pavlović, Marijana, Popović, Marta, "Eris - another brick in the wall: Empirical formulas, molar masses, biosynthesis reactions, enthalpy, entropy and Gibbs energy of Omicron EG.5 Eris and EG.5.1 variants of SARS-CoV-2" in Microbial Risk Analysis, 25 (2023):100280,
https://doi.org/10.1016/j.mran.2023.100280 . .

TY  - JOUR
AU  - Popović, Marko E.
AU  - Pantović-Pavlović, Marijana
AU  - Šekularac, Gavrilo
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6847
AB  - Biothermodynamics is a discipline which has developed intensely during the last 50 years. Thermodynamic properties have been reported for humans, animals, plants and microorganisms. However, this paper reports for the first time the empirical formula and thermodynamic properties for insects. Thermodynamic properties can be applied in research on thermodynamic interactions between organisms and their environment, as well as between organisms themselves. This paper reports for the first time the empirical formula and reactions of catabolism, biosynthesis and entire metabolism are formulated for Bombyx mori (domestic silk moth), as well as the thermodynamic properties of B. mori. It is shown that growth of B. mori is tightly related to catabolism of carbohydrates and lipids, which represents the driving force for the entire metabolism.
PB  - Society of Thermal Engineers of Serbia
T2  - Thermal Science
T1  - Chemical and thermodynamic properties of Bombyx mori (domestic silk moth): Empirical formula, driving force, and biosynthesis, catabolism and metabolism reactions
VL  - 27
IS  - 6 Part B
SP  - 4893
EP  - 4910
DO  - 10.2298/TSCI230901242P
ER  - 

@article{
author = "Popović, Marko E. and Pantović-Pavlović, Marijana and Šekularac, Gavrilo",
year = "2023",
abstract = "Biothermodynamics is a discipline which has developed intensely during the last 50 years. Thermodynamic properties have been reported for humans, animals, plants and microorganisms. However, this paper reports for the first time the empirical formula and thermodynamic properties for insects. Thermodynamic properties can be applied in research on thermodynamic interactions between organisms and their environment, as well as between organisms themselves. This paper reports for the first time the empirical formula and reactions of catabolism, biosynthesis and entire metabolism are formulated for Bombyx mori (domestic silk moth), as well as the thermodynamic properties of B. mori. It is shown that growth of B. mori is tightly related to catabolism of carbohydrates and lipids, which represents the driving force for the entire metabolism.",
publisher = "Society of Thermal Engineers of Serbia",
journal = "Thermal Science",
title = "Chemical and thermodynamic properties of Bombyx mori (domestic silk moth): Empirical formula, driving force, and biosynthesis, catabolism and metabolism reactions",
volume = "27",
number = "6 Part B",
pages = "4893-4910",
doi = "10.2298/TSCI230901242P"
}

Popović, M. E., Pantović-Pavlović, M.,& Šekularac, G.. (2023). Chemical and thermodynamic properties of Bombyx mori (domestic silk moth): Empirical formula, driving force, and biosynthesis, catabolism and metabolism reactions. in Thermal Science
Society of Thermal Engineers of Serbia., 27(6 Part B), 4893-4910.
https://doi.org/10.2298/TSCI230901242P

Popović ME, Pantović-Pavlović M, Šekularac G. Chemical and thermodynamic properties of Bombyx mori (domestic silk moth): Empirical formula, driving force, and biosynthesis, catabolism and metabolism reactions. in Thermal Science. 2023;27(6 Part B):4893-4910.
doi:10.2298/TSCI230901242P .

Popović, Marko E., Pantović-Pavlović, Marijana, Šekularac, Gavrilo, "Chemical and thermodynamic properties of Bombyx mori (domestic silk moth): Empirical formula, driving force, and biosynthesis, catabolism and metabolism reactions" in Thermal Science, 27, no. 6 Part B (2023):4893-4910,
https://doi.org/10.2298/TSCI230901242P . .

TY  - JOUR
AU  - Popović, Marko E.
AU  - Pantović-Pavlović, Marijana
AU  - Šekularac, Gavrilo
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7406
AB  - Biothermodynamics is a discipline which has developed intensely during the last 50 years. Thermodynamic properties have been reported for humans, animals, plants and microorganisms. However, this paper reports for the first time the empirical formula and thermodynamic properties for insects. Thermodynamic properties can be applied in research on thermodynamic interactions between organisms and their environment, as well as between organisms themselves. This paper reports for the first time the empirical formula and reactions of catabolism, biosynthesis and entire metabolism are formulated for Bombyx mori (domestic silk moth), as well as the thermodynamic properties of B. mori. It is shown that growth of B. mori is tightly related to catabolism of carbohydrates and lipids, which represents the driving force for the entire metabolism.
PB  - Society of Thermal Engineers of Serbia
T2  - Thermal Science
T1  - Chemical and thermodynamic properties of Bombyx mori (domestic silk moth): Empirical formula, driving force, and biosynthesis, catabolism and metabolism reactions
VL  - 27
IS  - 6 Part B
SP  - 4893
EP  - 4910
DO  - 10.2298/TSCI230901242P
ER  - 

@article{
author = "Popović, Marko E. and Pantović-Pavlović, Marijana and Šekularac, Gavrilo",
year = "2023",
abstract = "Biothermodynamics is a discipline which has developed intensely during the last 50 years. Thermodynamic properties have been reported for humans, animals, plants and microorganisms. However, this paper reports for the first time the empirical formula and thermodynamic properties for insects. Thermodynamic properties can be applied in research on thermodynamic interactions between organisms and their environment, as well as between organisms themselves. This paper reports for the first time the empirical formula and reactions of catabolism, biosynthesis and entire metabolism are formulated for Bombyx mori (domestic silk moth), as well as the thermodynamic properties of B. mori. It is shown that growth of B. mori is tightly related to catabolism of carbohydrates and lipids, which represents the driving force for the entire metabolism.",
publisher = "Society of Thermal Engineers of Serbia",
journal = "Thermal Science",
title = "Chemical and thermodynamic properties of Bombyx mori (domestic silk moth): Empirical formula, driving force, and biosynthesis, catabolism and metabolism reactions",
volume = "27",
number = "6 Part B",
pages = "4893-4910",
doi = "10.2298/TSCI230901242P"
}

Popović, M. E., Pantović-Pavlović, M.,& Šekularac, G.. (2023). Chemical and thermodynamic properties of Bombyx mori (domestic silk moth): Empirical formula, driving force, and biosynthesis, catabolism and metabolism reactions. in Thermal Science
Society of Thermal Engineers of Serbia., 27(6 Part B), 4893-4910.
https://doi.org/10.2298/TSCI230901242P

Popović ME, Pantović-Pavlović M, Šekularac G. Chemical and thermodynamic properties of Bombyx mori (domestic silk moth): Empirical formula, driving force, and biosynthesis, catabolism and metabolism reactions. in Thermal Science. 2023;27(6 Part B):4893-4910.
doi:10.2298/TSCI230901242P .

Popović, Marko E., Pantović-Pavlović, Marijana, Šekularac, Gavrilo, "Chemical and thermodynamic properties of Bombyx mori (domestic silk moth): Empirical formula, driving force, and biosynthesis, catabolism and metabolism reactions" in Thermal Science, 27, no. 6 Part B (2023):4893-4910,
https://doi.org/10.2298/TSCI230901242P . .

TY  - GEN
AU  - Popović, Marko
PY  - 2023
UR  - https://encyclopedia.pub/entry/39911
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6402
AB  - 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. Biothermodynamics of viruses has suggested a physicochemical mechanism of how viruses can hijack host cell metabolism.
T2  - Encyclopedia Platform
T1  - Biothermodynamics of Viruses
UR  - https://hdl.handle.net/21.15107/rcub_cer_6402
ER  - 

@misc{
author = "Popović, Marko",
year = "2023",
abstract = "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. Biothermodynamics of viruses has suggested a physicochemical mechanism of how viruses can hijack host cell metabolism.",
journal = "Encyclopedia Platform",
title = "Biothermodynamics of Viruses",
url = "https://hdl.handle.net/21.15107/rcub_cer_6402"
}

Popović, M.. (2023). Biothermodynamics of Viruses. in Encyclopedia Platform.
https://hdl.handle.net/21.15107/rcub_cer_6402

Popović M. Biothermodynamics of Viruses. in Encyclopedia Platform. 2023;.
https://hdl.handle.net/21.15107/rcub_cer_6402 .

Popović, Marko, "Biothermodynamics of Viruses" in Encyclopedia Platform (2023),
https://hdl.handle.net/21.15107/rcub_cer_6402 .

TY  - JOUR
AU  - Popović, Marko
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6094
AB  - RNA viruses exhibit a great tendency to mutate. Mutations occur in the parts of the genome that encode the spike glycoprotein and less often in the rest of the genome. This is why Gibbs energy of binding changes more than that of biosynthesis. Starting from 2019, the wild type that was labeled Hu-1 has during the last 3 years evolved to produce several dozen new variants, as a consequence of mutations. Mutations cause changes in empirical formulas of new virus strains, which lead to change in thermodynamic properties of biosynthesis and binding. These changes cause changes in the rate of reactions of binding of virus antigen to the host cell receptor and the rate of virus multiplication in the host cell. Changes in thermodynamic and kinetic parameters lead to changes in biological parameters of infectivity and pathogenicity. Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has been evolving towards increase in infectivity and maintaining constant pathogenicity, or for some variants a slight decrease in pathogenicity. In the case of Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants pathogenicity is identical as in the Omicron BA.2.75 variant. On the other hand, infectivity of the Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants is greater than those of previous variants. This will most likely result in the phenomenon of asymmetric coinfection, that is circulation of several variants in the population, some being dominant.
PB  - Elsevier
T2  - Microbial Risk Analysis
T1  - Never ending story? Evolution of SARS-CoV-2 monitored through Gibbs energies of biosynthesis and antigen-receptor binding of Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants
VL  - 23
SP  - 100250
DO  - 10.1016/j.mran.2023.100250
ER  - 

@article{
author = "Popović, Marko",
year = "2023",
abstract = "RNA viruses exhibit a great tendency to mutate. Mutations occur in the parts of the genome that encode the spike glycoprotein and less often in the rest of the genome. This is why Gibbs energy of binding changes more than that of biosynthesis. Starting from 2019, the wild type that was labeled Hu-1 has during the last 3 years evolved to produce several dozen new variants, as a consequence of mutations. Mutations cause changes in empirical formulas of new virus strains, which lead to change in thermodynamic properties of biosynthesis and binding. These changes cause changes in the rate of reactions of binding of virus antigen to the host cell receptor and the rate of virus multiplication in the host cell. Changes in thermodynamic and kinetic parameters lead to changes in biological parameters of infectivity and pathogenicity. Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has been evolving towards increase in infectivity and maintaining constant pathogenicity, or for some variants a slight decrease in pathogenicity. In the case of Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants pathogenicity is identical as in the Omicron BA.2.75 variant. On the other hand, infectivity of the Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants is greater than those of previous variants. This will most likely result in the phenomenon of asymmetric coinfection, that is circulation of several variants in the population, some being dominant.",
publisher = "Elsevier",
journal = "Microbial Risk Analysis",
title = "Never ending story? Evolution of SARS-CoV-2 monitored through Gibbs energies of biosynthesis and antigen-receptor binding of Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants",
volume = "23",
pages = "100250",
doi = "10.1016/j.mran.2023.100250"
}

Popović, M.. (2023). Never ending story? Evolution of SARS-CoV-2 monitored through Gibbs energies of biosynthesis and antigen-receptor binding of Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants. in Microbial Risk Analysis
Elsevier., 23, 100250.
https://doi.org/10.1016/j.mran.2023.100250

Popović M. Never ending story? Evolution of SARS-CoV-2 monitored through Gibbs energies of biosynthesis and antigen-receptor binding of Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants. in Microbial Risk Analysis. 2023;23:100250.
doi:10.1016/j.mran.2023.100250 .

Popović, Marko, "Never ending story? Evolution of SARS-CoV-2 monitored through Gibbs energies of biosynthesis and antigen-receptor binding of Omicron BQ.1, BQ.1.1, XBB and XBB.1 variants" in Microbial Risk Analysis, 23 (2023):100250,
https://doi.org/10.1016/j.mran.2023.100250 . .

TY  - JOUR
AU  - Popović, Marko
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6095
AB  - SARS-CoV-2 resembles the ancient mythical creature Hydra. Just like with the Hydra, when one head is cut, it is followed by appearance of two more heads, suppression of one SARS-CoV-2 variant causes appearance of newer variants. Unlike Hydra that grows identical heads, newer SARS-CoV-2 variants are usually more infective, which can be observed as time evolution of the virus at hand, which occurs through acquisition of mutations during time. The appearance of new variants is followed by appearance of new COVID-19 pandemic waves. With the appearance of new pandemic waves and determining of sequences, in the scientific community and general public the question is always raised of whether the new variant will be more virulent and more pathogenic. The two variants characterized in this paper, BA.5.2 and BF.7, have caused a pandemic wave during the late 2022. This paper gives full chemical and thermodynamic characterization of the BA.5.2 and BF.7 variants of SARS-CoV-2. Having in mind that Gibbs energy of binding and biosynthesis represent the driving forces for the viral life cycle, based on the calculated thermodynamic properties we can conclude that the newer variants are more infective than earlier ones, but that their pathogenicity has not changed.
PB  - Elsevier
T2  - Microbial Risk Analysis
T1  - The SARS-CoV-2 Hydra, a tiny monster from the 21st century: Thermodynamics of the BA.5.2 and BF.7 variants
VL  - 23
SP  - 100249
DO  - 10.1016/j.mran.2023.100249
ER  - 

@article{
author = "Popović, Marko",
year = "2023",
abstract = "SARS-CoV-2 resembles the ancient mythical creature Hydra. Just like with the Hydra, when one head is cut, it is followed by appearance of two more heads, suppression of one SARS-CoV-2 variant causes appearance of newer variants. Unlike Hydra that grows identical heads, newer SARS-CoV-2 variants are usually more infective, which can be observed as time evolution of the virus at hand, which occurs through acquisition of mutations during time. The appearance of new variants is followed by appearance of new COVID-19 pandemic waves. With the appearance of new pandemic waves and determining of sequences, in the scientific community and general public the question is always raised of whether the new variant will be more virulent and more pathogenic. The two variants characterized in this paper, BA.5.2 and BF.7, have caused a pandemic wave during the late 2022. This paper gives full chemical and thermodynamic characterization of the BA.5.2 and BF.7 variants of SARS-CoV-2. Having in mind that Gibbs energy of binding and biosynthesis represent the driving forces for the viral life cycle, based on the calculated thermodynamic properties we can conclude that the newer variants are more infective than earlier ones, but that their pathogenicity has not changed.",
publisher = "Elsevier",
journal = "Microbial Risk Analysis",
title = "The SARS-CoV-2 Hydra, a tiny monster from the 21st century: Thermodynamics of the BA.5.2 and BF.7 variants",
volume = "23",
pages = "100249",
doi = "10.1016/j.mran.2023.100249"
}

Popović, M.. (2023). The SARS-CoV-2 Hydra, a tiny monster from the 21st century: Thermodynamics of the BA.5.2 and BF.7 variants. in Microbial Risk Analysis
Elsevier., 23, 100249.
https://doi.org/10.1016/j.mran.2023.100249

Popović M. The SARS-CoV-2 Hydra, a tiny monster from the 21st century: Thermodynamics of the BA.5.2 and BF.7 variants. in Microbial Risk Analysis. 2023;23:100249.
doi:10.1016/j.mran.2023.100249 .

Popović, Marko, "The SARS-CoV-2 Hydra, a tiny monster from the 21st century: Thermodynamics of the BA.5.2 and BF.7 variants" in Microbial Risk Analysis, 23 (2023):100249,
https://doi.org/10.1016/j.mran.2023.100249 . .

TY  - CONF
AU  - Barros, Nieves
AU  - Popović, Marko
AU  - Pérez-Cruzado, César
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6130
AB  - Thermodynamic characterization of soils is a developing field that involves the calculation of the enthalpies, Gibbs energy, and entropy of the soil organic matter, SOM. Its achievement would contribute to the development of the bioenergetics of soil systems beyond the existing theoretical models.

This work shows different experimental procedures and theoretical models for the complete thermodynamic characterization of SOM. It was applied to a total of 31 samples representing different soil horizons from different locations.

Thermodynamic characterization of SOM was achieved through the calculation of empirical formulae for SOM from the SOM elemental composition, application of Patel-Erickson, Sandler-Orbey, and Battley methods, as well as direct measurements of the energy content by simultaneous TG-DSC.

The used computational methods belong to a group of approaches modeling thermodynamic properties of SOM as a sum of contributions from its constituent elements. The first computational approaches were those from the Patel-Erickson and Battley equations. Patel-Erickson equation was used to find the standard enthalpy of combustion, ΔCH⁰PE, of SOM based on its elemental composition:

ΔCH⁰PE(SOM) = –111.14 kJ/mol ∙ (4nC + nH – 2nO – 0nN + 5nP + 6nS)

where nJ is the number of atoms of element J in the empirical formula of SOM. The Battley equation gives the standard molar entropy, S⁰m, of SOM:

S⁰m(SOM) = 0.187 ∑J [ S⁰m(J) / aJ ] nJ

where S⁰m(J) and aJ are standard molar entropy and the number of atoms of element J in its standard state elemental form. The enthalpy from the Patel-Erickson equation is combined with entropy from the Battley equation, to find the Gibbs energy of SOM.

The second computational approach handled equations proposed by Sandler and Orbey that allow finding standard enthalpy of combustion ΔCH⁰SO and standard Gibbs energy of combustion, ΔCG⁰, of SOM:

ΔCH⁰SO(SOM) = –109.04 kJ/C-mol ∙ (4nC + nH – 2nO – 0nN + 5nP + 6nS)

ΔCG⁰(SOM) = –110.23 kJ/C-mol ∙ (4nC + nH – 2nO – 0nN + 5nP + 6nS)

The enthalpy and Gibbs energy obtained using the Sandler-Orbey method were combined to find entropy.  

Results obtained by the application of Patel-Erickson and Sandler-Orbey methods to calculate the enthalpy of SOM combustion did not significantly differ when comparing data given by the TG-DSC with those obtained from the SOM empirical formulation. The same results were obtained when comparing the Gibbs energy. These results enabled the calculation of the entropy of SOM and the comparison of those values among different soil layers and sampling sites.
PB  - European Geosciences Union
C3  - Proceedings of the EGU General Assembly 2023
T1  - Complete thermodynamic characterization of the soil organic matter from forest ecosystems.
DO  - 10.5194/egusphere-egu23-1389
ER  - 

@conference{
author = "Barros, Nieves and Popović, Marko and Pérez-Cruzado, César",
year = "2023",
abstract = "Thermodynamic characterization of soils is a developing field that involves the calculation of the enthalpies, Gibbs energy, and entropy of the soil organic matter, SOM. Its achievement would contribute to the development of the bioenergetics of soil systems beyond the existing theoretical models.

This work shows different experimental procedures and theoretical models for the complete thermodynamic characterization of SOM. It was applied to a total of 31 samples representing different soil horizons from different locations.

Thermodynamic characterization of SOM was achieved through the calculation of empirical formulae for SOM from the SOM elemental composition, application of Patel-Erickson, Sandler-Orbey, and Battley methods, as well as direct measurements of the energy content by simultaneous TG-DSC.

The used computational methods belong to a group of approaches modeling thermodynamic properties of SOM as a sum of contributions from its constituent elements. The first computational approaches were those from the Patel-Erickson and Battley equations. Patel-Erickson equation was used to find the standard enthalpy of combustion, ΔCH⁰PE, of SOM based on its elemental composition:

ΔCH⁰PE(SOM) = –111.14 kJ/mol ∙ (4nC + nH – 2nO – 0nN + 5nP + 6nS)

where nJ is the number of atoms of element J in the empirical formula of SOM. The Battley equation gives the standard molar entropy, S⁰m, of SOM:

S⁰m(SOM) = 0.187 ∑J [ S⁰m(J) / aJ ] nJ

where S⁰m(J) and aJ are standard molar entropy and the number of atoms of element J in its standard state elemental form. The enthalpy from the Patel-Erickson equation is combined with entropy from the Battley equation, to find the Gibbs energy of SOM.

The second computational approach handled equations proposed by Sandler and Orbey that allow finding standard enthalpy of combustion ΔCH⁰SO and standard Gibbs energy of combustion, ΔCG⁰, of SOM:

ΔCH⁰SO(SOM) = –109.04 kJ/C-mol ∙ (4nC + nH – 2nO – 0nN + 5nP + 6nS)

ΔCG⁰(SOM) = –110.23 kJ/C-mol ∙ (4nC + nH – 2nO – 0nN + 5nP + 6nS)

The enthalpy and Gibbs energy obtained using the Sandler-Orbey method were combined to find entropy.  

Results obtained by the application of Patel-Erickson and Sandler-Orbey methods to calculate the enthalpy of SOM combustion did not significantly differ when comparing data given by the TG-DSC with those obtained from the SOM empirical formulation. The same results were obtained when comparing the Gibbs energy. These results enabled the calculation of the entropy of SOM and the comparison of those values among different soil layers and sampling sites.",
publisher = "European Geosciences Union",
journal = "Proceedings of the EGU General Assembly 2023",
title = "Complete thermodynamic characterization of the soil organic matter from forest ecosystems.",
doi = "10.5194/egusphere-egu23-1389"
}

Barros, N., Popović, M.,& Pérez-Cruzado, C.. (2023). Complete thermodynamic characterization of the soil organic matter from forest ecosystems.. in Proceedings of the EGU General Assembly 2023
European Geosciences Union..
https://doi.org/10.5194/egusphere-egu23-1389

Barros N, Popović M, Pérez-Cruzado C. Complete thermodynamic characterization of the soil organic matter from forest ecosystems.. in Proceedings of the EGU General Assembly 2023. 2023;.
doi:10.5194/egusphere-egu23-1389 .

Barros, Nieves, Popović, Marko, Pérez-Cruzado, César, "Complete thermodynamic characterization of the soil organic matter from forest ecosystems." in Proceedings of the EGU General Assembly 2023 (2023),
https://doi.org/10.5194/egusphere-egu23-1389 . .

TY  - JOUR
AU  - Popović, Marko
PY  - 2023
UR  - https://life-insilico.com/index.php/pub/article/view/2
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6136
AB  - HIV-1, like other viruses, represents an open thermodynamic system. This is why it is important to know its thermodynamic properties. Virus-host interactions are performed at the membrane as antigen-receptor binding. Antigen-receptor binding represents a chemical reaction, similar to protein-ligand interactions. The driving force for antigen-receptor binding is Gibbs energy of binding. Knowing Gibbs energy of binding, it is possible to estimate the rate of virus binding and entry into host cells. In this paper, binding equilibrium constants and standard Gibbs energies of binding between the HIV-1 gp120 antigen and the CD4 receptor have been reported at 4 °C, 22 °C and 37 °C.
PB  - Bektas Tepe Publications
T2  - Life in Silico
T1  - Closer look into HIV-host interactions: Standard Gibbs energy of binding of the gp120 antigen of HIV-1 to the CD4 receptor and monoclonal antibodies
VL  - 1
IS  - 1
SP  - 8
EP  - 12
UR  - https://hdl.handle.net/21.15107/rcub_cer_6136
ER  - 

@article{
author = "Popović, Marko",
year = "2023",
abstract = "HIV-1, like other viruses, represents an open thermodynamic system. This is why it is important to know its thermodynamic properties. Virus-host interactions are performed at the membrane as antigen-receptor binding. Antigen-receptor binding represents a chemical reaction, similar to protein-ligand interactions. The driving force for antigen-receptor binding is Gibbs energy of binding. Knowing Gibbs energy of binding, it is possible to estimate the rate of virus binding and entry into host cells. In this paper, binding equilibrium constants and standard Gibbs energies of binding between the HIV-1 gp120 antigen and the CD4 receptor have been reported at 4 °C, 22 °C and 37 °C.",
publisher = "Bektas Tepe Publications",
journal = "Life in Silico",
title = "Closer look into HIV-host interactions: Standard Gibbs energy of binding of the gp120 antigen of HIV-1 to the CD4 receptor and monoclonal antibodies",
volume = "1",
number = "1",
pages = "8-12",
url = "https://hdl.handle.net/21.15107/rcub_cer_6136"
}

Popović, M.. (2023). Closer look into HIV-host interactions: Standard Gibbs energy of binding of the gp120 antigen of HIV-1 to the CD4 receptor and monoclonal antibodies. in Life in Silico
Bektas Tepe Publications., 1(1), 8-12.
https://hdl.handle.net/21.15107/rcub_cer_6136

Popović M. Closer look into HIV-host interactions: Standard Gibbs energy of binding of the gp120 antigen of HIV-1 to the CD4 receptor and monoclonal antibodies. in Life in Silico. 2023;1(1):8-12.
https://hdl.handle.net/21.15107/rcub_cer_6136 .

Popović, Marko, "Closer look into HIV-host interactions: Standard Gibbs energy of binding of the gp120 antigen of HIV-1 to the CD4 receptor and monoclonal antibodies" in Life in Silico, 1, no. 1 (2023):8-12,
https://hdl.handle.net/21.15107/rcub_cer_6136 .

TY  - JOUR
AU  - Popović, Marko
AU  - Martin, Jennifer
AU  - Head, Richard
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6255
AB  - We have developed a mechanistic model of SARS-CoV-2 and SARS-CoV infection, exploring the relationship between the viral diffusion in the mucosa and viral affinity for the angiotensin converting enzyme 2 (ACE2) target. Utilising the structural similarity of SARS-CoV and SARS-CoV-2 and a shared viral target receptor (ACE2), but a dramatic difference in upper or lower respiratory tract infectivity, we were able to generate insights into the linkage of mucosal diffusion and target receptor affinity in determining the pathophysiological pathways of these two viruses.
Our analysis reveals that for SARS-CoV-2 the higher affinity of ACE2 binding, the faster and more complete the mucosal diffusion in its transport from the upper airway to the region of the ACE2 target on the epithelium. This diffusional process is essential for the presentation of this virus to the furin catalysed highly efficient entry and infection process in the upper respiratory tract epithelial cells. A failure of SARS-CoV to follow this path is associated with lower respiratory tract infection and decreased infectivity. Thus, our analysis supports the view that through tropism SARS-CoV-2 has evolved a highly efficient membrane entry process that can act in concert with a high binding affinity of this virus and its variants for its ACE2 which in turn promotes enhanced movement of the virus from airway to epithelium. In this way ongoing mutations yielding higher affinities of SARS-CoV-2 for the ACE2 target becomes the basis for higher upper respiratory tract infectivity and greater viral spread. It is concluded that SARS-CoV-2 is constrained in the extent of its activities by the fundamental laws of physics and thermodynamics. Laws that describe diffusion and molecular binding. Moreover it can be speculated that the very earliest contact of this virus with the human mucosa defines the pathogenesis of this infection.
PB  - Elsevier
T2  - Heliyon
T1  - COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease
VL  - 9
IS  - 6
SP  - E17174
DO  - 10.1016/j.heliyon.2023.e17174
ER  - 

@article{
author = "Popović, Marko and Martin, Jennifer and Head, Richard",
year = "2023",
abstract = "We have developed a mechanistic model of SARS-CoV-2 and SARS-CoV infection, exploring the relationship between the viral diffusion in the mucosa and viral affinity for the angiotensin converting enzyme 2 (ACE2) target. Utilising the structural similarity of SARS-CoV and SARS-CoV-2 and a shared viral target receptor (ACE2), but a dramatic difference in upper or lower respiratory tract infectivity, we were able to generate insights into the linkage of mucosal diffusion and target receptor affinity in determining the pathophysiological pathways of these two viruses.
Our analysis reveals that for SARS-CoV-2 the higher affinity of ACE2 binding, the faster and more complete the mucosal diffusion in its transport from the upper airway to the region of the ACE2 target on the epithelium. This diffusional process is essential for the presentation of this virus to the furin catalysed highly efficient entry and infection process in the upper respiratory tract epithelial cells. A failure of SARS-CoV to follow this path is associated with lower respiratory tract infection and decreased infectivity. Thus, our analysis supports the view that through tropism SARS-CoV-2 has evolved a highly efficient membrane entry process that can act in concert with a high binding affinity of this virus and its variants for its ACE2 which in turn promotes enhanced movement of the virus from airway to epithelium. In this way ongoing mutations yielding higher affinities of SARS-CoV-2 for the ACE2 target becomes the basis for higher upper respiratory tract infectivity and greater viral spread. It is concluded that SARS-CoV-2 is constrained in the extent of its activities by the fundamental laws of physics and thermodynamics. Laws that describe diffusion and molecular binding. Moreover it can be speculated that the very earliest contact of this virus with the human mucosa defines the pathogenesis of this infection.",
publisher = "Elsevier",
journal = "Heliyon",
title = "COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease",
volume = "9",
number = "6",
pages = "E17174",
doi = "10.1016/j.heliyon.2023.e17174"
}

Popović, M., Martin, J.,& Head, R.. (2023). COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease. in Heliyon
Elsevier., 9(6), E17174.
https://doi.org/10.1016/j.heliyon.2023.e17174

Popović M, Martin J, Head R. COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease. in Heliyon. 2023;9(6):E17174.
doi:10.1016/j.heliyon.2023.e17174 .

Popović, Marko, Martin, Jennifer, Head, Richard, "COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease" in Heliyon, 9, no. 6 (2023):E17174,
https://doi.org/10.1016/j.heliyon.2023.e17174 . .

TY  - DATA
AU  - Popović, Marko
AU  - Martin, Jennifer
AU  - Head, Richard
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6256
AB  - We have developed a mechanistic model of SARS-CoV-2 and SARS-CoV infection, exploring the relationship between the viral diffusion in the mucosa and viral affinity for the angiotensin converting enzyme 2 (ACE2) target. Utilising the structural similarity of SARS-CoV and SARS-CoV-2 and a shared viral target receptor (ACE2), but a dramatic difference in upper or lower respiratory tract infectivity, we were able to generate insights into the linkage of mucosal diffusion and target receptor affinity in determining the pathophysiological pathways of these two viruses.Our analysis reveals that for SARS-CoV-2 the higher affinity of ACE2 binding, the faster and more complete the mucosal diffusion in its transport from the upper airway to the region of the ACE2 target on the epithelium. This diffusional process is essential for the presentation of this virus to the furin catalysed highly efficient entry and infection process in the upper respiratory tract epithelial cells. A failure of SARS-CoV to follow this path is associated with lower respiratory tract infection and decreased infectivity. Thus, our analysis supports the view that through tropism SARS-CoV-2 has evolved a highly efficient membrane entry process that can act in concert with a high binding affinity of this virus and its variants for its ACE2 which in turn promotes enhanced movement of the virus from airway to epithelium. In this way ongoing mutations yielding higher affinities of SARS-CoV-2 for the ACE2 target becomes the basis for higher upper respiratory tract infectivity and greater viral spread. It is concluded that SARS-CoV-2 is constrained in the extent of its activities by the fundamental laws of physics and thermodynamics. Laws that describe diffusion and molecular binding. Moreover it can be speculated that the very earliest contact of this virus with the human mucosa defines the pathogenesis of this infection.
PB  - Elsevier
T1  - Supplementary data for: "COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease"
UR  - https://hdl.handle.net/21.15107/rcub_cer_6256
ER  - 

@misc{
author = "Popović, Marko and Martin, Jennifer and Head, Richard",
year = "2023",
abstract = "We have developed a mechanistic model of SARS-CoV-2 and SARS-CoV infection, exploring the relationship between the viral diffusion in the mucosa and viral affinity for the angiotensin converting enzyme 2 (ACE2) target. Utilising the structural similarity of SARS-CoV and SARS-CoV-2 and a shared viral target receptor (ACE2), but a dramatic difference in upper or lower respiratory tract infectivity, we were able to generate insights into the linkage of mucosal diffusion and target receptor affinity in determining the pathophysiological pathways of these two viruses.Our analysis reveals that for SARS-CoV-2 the higher affinity of ACE2 binding, the faster and more complete the mucosal diffusion in its transport from the upper airway to the region of the ACE2 target on the epithelium. This diffusional process is essential for the presentation of this virus to the furin catalysed highly efficient entry and infection process in the upper respiratory tract epithelial cells. A failure of SARS-CoV to follow this path is associated with lower respiratory tract infection and decreased infectivity. Thus, our analysis supports the view that through tropism SARS-CoV-2 has evolved a highly efficient membrane entry process that can act in concert with a high binding affinity of this virus and its variants for its ACE2 which in turn promotes enhanced movement of the virus from airway to epithelium. In this way ongoing mutations yielding higher affinities of SARS-CoV-2 for the ACE2 target becomes the basis for higher upper respiratory tract infectivity and greater viral spread. It is concluded that SARS-CoV-2 is constrained in the extent of its activities by the fundamental laws of physics and thermodynamics. Laws that describe diffusion and molecular binding. Moreover it can be speculated that the very earliest contact of this virus with the human mucosa defines the pathogenesis of this infection.",
publisher = "Elsevier",
title = "Supplementary data for: "COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease"",
url = "https://hdl.handle.net/21.15107/rcub_cer_6256"
}

Popović, M., Martin, J.,& Head, R.. (2023). Supplementary data for: "COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease". 
Elsevier..
https://hdl.handle.net/21.15107/rcub_cer_6256

Popović M, Martin J, Head R. Supplementary data for: "COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease". 2023;.
https://hdl.handle.net/21.15107/rcub_cer_6256 .

Popović, Marko, Martin, Jennifer, Head, Richard, "Supplementary data for: "COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease"" (2023),
https://hdl.handle.net/21.15107/rcub_cer_6256 .

TY  - JOUR
AU  - Popović, Marko
AU  - Mihailović, Marija
AU  - Panić, Stefan
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6464
AB  - COVID-19 and SARS-CoV-2 from the perspectives of medicine, biology, molecular biology, chemistry and biothermodynamics represent probably the best studied virus-host interaction until now. Empirical formula of SARS-CoV-2 is the second reported in history, immediately after the poliovirus. Empirical formulas of all SARS-CoV-2 variants have been reported in the literature. This paper reports empirical formulas, biosynthesis reactions and thermodynamic properties (enthalpy, entropy and Gibbs energy) for the XBB.1.9.1, XBF and XBB.1.16 variants of SARS-CoV-2. Since Gibbs energy of biosynthesis represents the driving force for virus multiplication, a conclusion was made that multiplication rate of the new SARS-CoV-2 variants is not significantly different than that of the other Omicron variants. Since multiplication rate determines the damage level to host cells, a conclusion was drawn that there is no increase in the degree of damage to host tissues. Thus, pathogenicity of the new variants did not significantly change. In that case, it can be expected that the number of severe cases should not increase. Therefore, it seems that the health risk for the society should not change.
PB  - Elsevier
T2  - Microbial Risk Analysis
T1  - Upcoming epidemic storm: Empirical formulas, biosynthesis reactions, thermodynamic properties and driving forces of multiplication of the omicron XBB.1.9.1, XBF and XBB.1.16 (Arcturus) variants of SARS-CoV-2
VL  - 25
SP  - 100273
DO  - 10.1016/j.mran.2023.100273
ER  - 

@article{
author = "Popović, Marko and Mihailović, Marija and Panić, Stefan",
year = "2023",
abstract = "COVID-19 and SARS-CoV-2 from the perspectives of medicine, biology, molecular biology, chemistry and biothermodynamics represent probably the best studied virus-host interaction until now. Empirical formula of SARS-CoV-2 is the second reported in history, immediately after the poliovirus. Empirical formulas of all SARS-CoV-2 variants have been reported in the literature. This paper reports empirical formulas, biosynthesis reactions and thermodynamic properties (enthalpy, entropy and Gibbs energy) for the XBB.1.9.1, XBF and XBB.1.16 variants of SARS-CoV-2. Since Gibbs energy of biosynthesis represents the driving force for virus multiplication, a conclusion was made that multiplication rate of the new SARS-CoV-2 variants is not significantly different than that of the other Omicron variants. Since multiplication rate determines the damage level to host cells, a conclusion was drawn that there is no increase in the degree of damage to host tissues. Thus, pathogenicity of the new variants did not significantly change. In that case, it can be expected that the number of severe cases should not increase. Therefore, it seems that the health risk for the society should not change.",
publisher = "Elsevier",
journal = "Microbial Risk Analysis",
title = "Upcoming epidemic storm: Empirical formulas, biosynthesis reactions, thermodynamic properties and driving forces of multiplication of the omicron XBB.1.9.1, XBF and XBB.1.16 (Arcturus) variants of SARS-CoV-2",
volume = "25",
pages = "100273",
doi = "10.1016/j.mran.2023.100273"
}

Popović, M., Mihailović, M.,& Panić, S.. (2023). Upcoming epidemic storm: Empirical formulas, biosynthesis reactions, thermodynamic properties and driving forces of multiplication of the omicron XBB.1.9.1, XBF and XBB.1.16 (Arcturus) variants of SARS-CoV-2. in Microbial Risk Analysis
Elsevier., 25, 100273.
https://doi.org/10.1016/j.mran.2023.100273

Popović M, Mihailović M, Panić S. Upcoming epidemic storm: Empirical formulas, biosynthesis reactions, thermodynamic properties and driving forces of multiplication of the omicron XBB.1.9.1, XBF and XBB.1.16 (Arcturus) variants of SARS-CoV-2. in Microbial Risk Analysis. 2023;25:100273.
doi:10.1016/j.mran.2023.100273 .

Popović, Marko, Mihailović, Marija, Panić, Stefan, "Upcoming epidemic storm: Empirical formulas, biosynthesis reactions, thermodynamic properties and driving forces of multiplication of the omicron XBB.1.9.1, XBF and XBB.1.16 (Arcturus) variants of SARS-CoV-2" in Microbial Risk Analysis, 25 (2023):100273,
https://doi.org/10.1016/j.mran.2023.100273 . .

TY  - JOUR
AU  - Popović, Marko
AU  - Tadić, Vojin
AU  - Mihailović, Marija
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6813
AB  - Insulin was discovered 100 years ago and has been well studied from the perspectives of life and biomedical sciences. This paper reports chemical and biothermodynamic properties of biosynthesis of insulin. This paper reports for the first time the molecular and empirical formulas, biosynthesis reactions, and thermodynamic properties of molecules and their biosynthesis for human preproinsulin, proinsulin, insulin chain A, insulin chain B, insulin, signal peptide and intermediate peptide (C-peptide). Based on these, metabolic reactions were formulated for conversion of preproinsulin to insulin and their thermodynamic feasibility was analyzed.
PB  - Taylor & Francis
T2  - Journal of Biomolecular Structure and Dynamics
T1  - From genotype to phenotype with biothermodynamics: Empirical formulas, biosynthesis reactions and thermodynamic properties of preproinsulin, proinsulin and insulin molecules
DO  - 10.1080/07391102.2023.2256880
ER  - 

@article{
author = "Popović, Marko and Tadić, Vojin and Mihailović, Marija",
year = "2023",
abstract = "Insulin was discovered 100 years ago and has been well studied from the perspectives of life and biomedical sciences. This paper reports chemical and biothermodynamic properties of biosynthesis of insulin. This paper reports for the first time the molecular and empirical formulas, biosynthesis reactions, and thermodynamic properties of molecules and their biosynthesis for human preproinsulin, proinsulin, insulin chain A, insulin chain B, insulin, signal peptide and intermediate peptide (C-peptide). Based on these, metabolic reactions were formulated for conversion of preproinsulin to insulin and their thermodynamic feasibility was analyzed.",
publisher = "Taylor & Francis",
journal = "Journal of Biomolecular Structure and Dynamics",
title = "From genotype to phenotype with biothermodynamics: Empirical formulas, biosynthesis reactions and thermodynamic properties of preproinsulin, proinsulin and insulin molecules",
doi = "10.1080/07391102.2023.2256880"
}

Popović, M., Tadić, V.,& Mihailović, M.. (2023). From genotype to phenotype with biothermodynamics: Empirical formulas, biosynthesis reactions and thermodynamic properties of preproinsulin, proinsulin and insulin molecules. in Journal of Biomolecular Structure and Dynamics
Taylor & Francis..
https://doi.org/10.1080/07391102.2023.2256880

Popović M, Tadić V, Mihailović M. From genotype to phenotype with biothermodynamics: Empirical formulas, biosynthesis reactions and thermodynamic properties of preproinsulin, proinsulin and insulin molecules. in Journal of Biomolecular Structure and Dynamics. 2023;.
doi:10.1080/07391102.2023.2256880 .

Popović, Marko, Tadić, Vojin, Mihailović, Marija, "From genotype to phenotype with biothermodynamics: Empirical formulas, biosynthesis reactions and thermodynamic properties of preproinsulin, proinsulin and insulin molecules" in Journal of Biomolecular Structure and Dynamics (2023),
https://doi.org/10.1080/07391102.2023.2256880 . .

TY  - JOUR
AU  - Popović, Marko
AU  - Popović, Marta
AU  - Šekularac, Gavrilo
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6819
AB  - From July to October, West Nile virus is the leading cause of mosquito born disease in Europe and North America. This paper reports for the first time a chemical and thermodynamic analysis of the West Nile virus particles, genome and proteins, as well as interactions with its host organism. The empirical formula of mature West Nile virus particles was found through the atom counting method. Based on the empirical formula, biosynthesis reactions were formulated, which describe the formation of new virus live matter. Based on the biosynthesis reactions, Gibbs energy of biosynthesis was determined, which represents the physical driving force for the production of viral and host cell components. Gibbs energy of biosynthesis of the West Nile virus was found to be several times more negative than that of its host tissues. Due to the more negative Gibbs energy of biosynthesis, the West Nile virus components are produced much faster than those of its host cells. This allows the virus to hijack the host cell metabolism. Therefore, the virus-host interactions of the West Nile virus were explained through chemical and thermodynamic analysis.
PB  - Elsevier
T2  - Microbial Risk Analysis
T1  - Death from the Nile: Empirical formula, molar mass, biosynthesis reaction and Gibbs energy of biosynthesis of the West Nile virus
VL  - 25
SP  - 100281
DO  - 10.1016/j.mran.2023.100281
ER  - 

@article{
author = "Popović, Marko and Popović, Marta and Šekularac, Gavrilo",
year = "2023",
abstract = "From July to October, West Nile virus is the leading cause of mosquito born disease in Europe and North America. This paper reports for the first time a chemical and thermodynamic analysis of the West Nile virus particles, genome and proteins, as well as interactions with its host organism. The empirical formula of mature West Nile virus particles was found through the atom counting method. Based on the empirical formula, biosynthesis reactions were formulated, which describe the formation of new virus live matter. Based on the biosynthesis reactions, Gibbs energy of biosynthesis was determined, which represents the physical driving force for the production of viral and host cell components. Gibbs energy of biosynthesis of the West Nile virus was found to be several times more negative than that of its host tissues. Due to the more negative Gibbs energy of biosynthesis, the West Nile virus components are produced much faster than those of its host cells. This allows the virus to hijack the host cell metabolism. Therefore, the virus-host interactions of the West Nile virus were explained through chemical and thermodynamic analysis.",
publisher = "Elsevier",
journal = "Microbial Risk Analysis",
title = "Death from the Nile: Empirical formula, molar mass, biosynthesis reaction and Gibbs energy of biosynthesis of the West Nile virus",
volume = "25",
pages = "100281",
doi = "10.1016/j.mran.2023.100281"
}

Popović, M., Popović, M.,& Šekularac, G.. (2023). Death from the Nile: Empirical formula, molar mass, biosynthesis reaction and Gibbs energy of biosynthesis of the West Nile virus. in Microbial Risk Analysis
Elsevier., 25, 100281.
https://doi.org/10.1016/j.mran.2023.100281

Popović M, Popović M, Šekularac G. Death from the Nile: Empirical formula, molar mass, biosynthesis reaction and Gibbs energy of biosynthesis of the West Nile virus. in Microbial Risk Analysis. 2023;25:100281.
doi:10.1016/j.mran.2023.100281 .

Popović, Marko, Popović, Marta, Šekularac, Gavrilo, "Death from the Nile: Empirical formula, molar mass, biosynthesis reaction and Gibbs energy of biosynthesis of the West Nile virus" in Microbial Risk Analysis, 25 (2023):100281,
https://doi.org/10.1016/j.mran.2023.100281 . .

TY  - JOUR
AU  - Popović, Marko
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6049
AB  - SARS-CoV-2 has during the last 3 years mutated several dozen times. Most mutations in the newly formed variants have been chemically and thermodynamically characterized. New variants have been declared as variants under monitoring. The European Centre for Disease Prevention and Control has suggested the hypothesis that the new BN.1, CH.1.1 and XBC variants could have properties similar to those of VOC. Thermodynamic properties of new variants have been reported in this manuscript for the first time. Gibbs energy of biosynthesis, as the driving force for viral multiplication, is less negative for the new variants than for the earlier variants. This indicates that the virus has evolved towards decrease in pathogenicity, which leads to less severe forms of COVID-19.
PB  - Elsevier
T2  - Microbial Risk Analysis
T1  - SARS-CoV-2 strain wars continues: Chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants
VL  - 24
SP  - 100260
DO  - 10.1016/j.mran.2023.100260
ER  - 

@article{
author = "Popović, Marko",
year = "2023",
abstract = "SARS-CoV-2 has during the last 3 years mutated several dozen times. Most mutations in the newly formed variants have been chemically and thermodynamically characterized. New variants have been declared as variants under monitoring. The European Centre for Disease Prevention and Control has suggested the hypothesis that the new BN.1, CH.1.1 and XBC variants could have properties similar to those of VOC. Thermodynamic properties of new variants have been reported in this manuscript for the first time. Gibbs energy of biosynthesis, as the driving force for viral multiplication, is less negative for the new variants than for the earlier variants. This indicates that the virus has evolved towards decrease in pathogenicity, which leads to less severe forms of COVID-19.",
publisher = "Elsevier",
journal = "Microbial Risk Analysis",
title = "SARS-CoV-2 strain wars continues: Chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants",
volume = "24",
pages = "100260",
doi = "10.1016/j.mran.2023.100260"
}

Popović, M.. (2023). SARS-CoV-2 strain wars continues: Chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants. in Microbial Risk Analysis
Elsevier., 24, 100260.
https://doi.org/10.1016/j.mran.2023.100260

Popović M. SARS-CoV-2 strain wars continues: Chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants. in Microbial Risk Analysis. 2023;24:100260.
doi:10.1016/j.mran.2023.100260 .

Popović, Marko, "SARS-CoV-2 strain wars continues: Chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants" in Microbial Risk Analysis, 24 (2023):100260,
https://doi.org/10.1016/j.mran.2023.100260 . .

TY  - JOUR
AU  - Popović, Marko
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6050
AB  - The SARS-CoV-2 Hydra with many heads (variants) has been causing the COVID-19 pandemic for 3 years. The appearance of every new head (SARS-CoV-2 variant) causes a new pandemic wave. The last in the series is the XBB.1.5 “Kraken” variant. In the general public (social media) and in the scientific community (scientific journals), during the last several weeks since the variant has appeared, the question was raised of whether the infectivity of the new variant will be greater. This article attempts to provide the answer. Analysis of thermodynamic driving forces of binding and biosynthesis leads to the conclusion that infectivity of the XBB.1.5 variant could be increased to a certain extent. The pathogenicity of the XBB.1.5 variant seems to be unchanged compared to the other Omicron variants.
PB  - Elsevier
T2  - Microbiological Research
T1  - XBB.1.5 Kraken cracked: Gibbs energies of binding and biosynthesis of the XBB.1.5 variant of SARS-CoV-2
VL  - 270
SP  - 127337
DO  - 10.1016/j.micres.2023.127337
ER  - 

@article{
author = "Popović, Marko",
year = "2023",
abstract = "The SARS-CoV-2 Hydra with many heads (variants) has been causing the COVID-19 pandemic for 3 years. The appearance of every new head (SARS-CoV-2 variant) causes a new pandemic wave. The last in the series is the XBB.1.5 “Kraken” variant. In the general public (social media) and in the scientific community (scientific journals), during the last several weeks since the variant has appeared, the question was raised of whether the infectivity of the new variant will be greater. This article attempts to provide the answer. Analysis of thermodynamic driving forces of binding and biosynthesis leads to the conclusion that infectivity of the XBB.1.5 variant could be increased to a certain extent. The pathogenicity of the XBB.1.5 variant seems to be unchanged compared to the other Omicron variants.",
publisher = "Elsevier",
journal = "Microbiological Research",
title = "XBB.1.5 Kraken cracked: Gibbs energies of binding and biosynthesis of the XBB.1.5 variant of SARS-CoV-2",
volume = "270",
pages = "127337",
doi = "10.1016/j.micres.2023.127337"
}

Popović, M.. (2023). XBB.1.5 Kraken cracked: Gibbs energies of binding and biosynthesis of the XBB.1.5 variant of SARS-CoV-2. in Microbiological Research
Elsevier., 270, 127337.
https://doi.org/10.1016/j.micres.2023.127337

Popović M. XBB.1.5 Kraken cracked: Gibbs energies of binding and biosynthesis of the XBB.1.5 variant of SARS-CoV-2. in Microbiological Research. 2023;270:127337.
doi:10.1016/j.micres.2023.127337 .

Popović, Marko, "XBB.1.5 Kraken cracked: Gibbs energies of binding and biosynthesis of the XBB.1.5 variant of SARS-CoV-2" in Microbiological Research, 270 (2023):127337,
https://doi.org/10.1016/j.micres.2023.127337 . .

TY  - JOUR
AU  - Popović, Marko
AU  - Popović, Marta
PY  - 2022
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6074
AB  - Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has mutated several times into new strains, with an increased infectivity. Infectivity of SARS-CoV-2 strains depends on binding affinity of the virus to its host cell receptor. In this paper, we quantified the binding affinity using Gibbs energy of binding and analyzed the competition between SARS-CoV-2 strains as an interference phenomenon. Gibbs energies of binding were calculated for several SARS-SoV-2 strains, including Hu-1 (wild type), B.1.1.7 (alpha), B.1.351 (beta), P.1 (Gamma), B.1.36 and B.1.617 (Delta). The least negative Gibbs energy of binding is that of Hu-1 strain, -37.97 kJ/mol. On the other hand, the most negative Gibbs energy of binding is that of the Delta strain, -49.50 kJ/mol. We used the more negative Gibbs energy of binding to explain the increased infectivity of newer SARS-CoV-2 strains compared to the wild type. Gibbs energies of binding was found to decrease chronologically, with appearance of new strains. The ratio of Gibbs energies of binding of mutated strains and wild type was used to define a susceptibility coefficient, which is an indicator of viral interference, where a virus can prevent or partially inhibit infection with another virus.
PB  - Elsevier
T2  - Microbial Risk Analysis
T1  - Strain Wars: Competitive interactions between SARS-CoV-2 strains are explained by Gibbs energy of antigen-receptor binding
VL  - 21
SP  - 100202
DO  - 10.1016/j.mran.2022.100202
ER  - 

@article{
author = "Popović, Marko and Popović, Marta",
year = "2022",
abstract = "Since the beginning of the COVID-19 pandemic, SARS-CoV-2 has mutated several times into new strains, with an increased infectivity. Infectivity of SARS-CoV-2 strains depends on binding affinity of the virus to its host cell receptor. In this paper, we quantified the binding affinity using Gibbs energy of binding and analyzed the competition between SARS-CoV-2 strains as an interference phenomenon. Gibbs energies of binding were calculated for several SARS-SoV-2 strains, including Hu-1 (wild type), B.1.1.7 (alpha), B.1.351 (beta), P.1 (Gamma), B.1.36 and B.1.617 (Delta). The least negative Gibbs energy of binding is that of Hu-1 strain, -37.97 kJ/mol. On the other hand, the most negative Gibbs energy of binding is that of the Delta strain, -49.50 kJ/mol. We used the more negative Gibbs energy of binding to explain the increased infectivity of newer SARS-CoV-2 strains compared to the wild type. Gibbs energies of binding was found to decrease chronologically, with appearance of new strains. The ratio of Gibbs energies of binding of mutated strains and wild type was used to define a susceptibility coefficient, which is an indicator of viral interference, where a virus can prevent or partially inhibit infection with another virus.",
publisher = "Elsevier",
journal = "Microbial Risk Analysis",
title = "Strain Wars: Competitive interactions between SARS-CoV-2 strains are explained by Gibbs energy of antigen-receptor binding",
volume = "21",
pages = "100202",
doi = "10.1016/j.mran.2022.100202"
}

Popović, M.,& Popović, M.. (2022). Strain Wars: Competitive interactions between SARS-CoV-2 strains are explained by Gibbs energy of antigen-receptor binding. in Microbial Risk Analysis
Elsevier., 21, 100202.
https://doi.org/10.1016/j.mran.2022.100202

Popović M, Popović M. Strain Wars: Competitive interactions between SARS-CoV-2 strains are explained by Gibbs energy of antigen-receptor binding. in Microbial Risk Analysis. 2022;21:100202.
doi:10.1016/j.mran.2022.100202 .

Popović, Marko, Popović, Marta, "Strain Wars: Competitive interactions between SARS-CoV-2 strains are explained by Gibbs energy of antigen-receptor binding" in Microbial Risk Analysis, 21 (2022):100202,
https://doi.org/10.1016/j.mran.2022.100202 . .

TY  - JOUR
AU  - Popović, Marko
PY  - 2022
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6091
AB  - Quantitative physicochemical perspective on life processes has been a great asset, in bioengineering and biotechnology. The quantitative physicochemical approach can be applied to practically all organisms, including viruses, if their chemical composition and thermodynamic properties are known. In this paper, a new method is suggested for determining elemental composition of viruses, based on atom counting. The atom counting method requires knowledge of genetic sequence, protein sequences and protein copy numbers. An algorithm was suggested for a program that finds elemental composition of various viruses (DNA or RNA, enveloped or non-enveloped). Except for the nucleic acid, capsid proteins, lipid bilayer and carbohydrates, this method includes membrane proteins, as well as spike proteins. The atom counting method has been compared with the existing molecular composition and geometric methods on 5 viruses of different morphology, as well as experimentally determined composition of the poliovirus. The atom counting method was found to be more accurate in most cases. The three methods were found to be complementary, since they require different kind of input information. Moreover, since the 3 methods rest on different assumptions, results of one model can be compared to those of the other two.
PB  - Elsevier
T2  - Computational Biology and Chemistry
T1  - Atom counting method for determining elemental composition of viruses and its applications in biothermodynamics and environmental science
VL  - 96
SP  - 107621
DO  - 10.1016/j.compbiolchem.2022.107621
ER  - 

@article{
author = "Popović, Marko",
year = "2022",
abstract = "Quantitative physicochemical perspective on life processes has been a great asset, in bioengineering and biotechnology. The quantitative physicochemical approach can be applied to practically all organisms, including viruses, if their chemical composition and thermodynamic properties are known. In this paper, a new method is suggested for determining elemental composition of viruses, based on atom counting. The atom counting method requires knowledge of genetic sequence, protein sequences and protein copy numbers. An algorithm was suggested for a program that finds elemental composition of various viruses (DNA or RNA, enveloped or non-enveloped). Except for the nucleic acid, capsid proteins, lipid bilayer and carbohydrates, this method includes membrane proteins, as well as spike proteins. The atom counting method has been compared with the existing molecular composition and geometric methods on 5 viruses of different morphology, as well as experimentally determined composition of the poliovirus. The atom counting method was found to be more accurate in most cases. The three methods were found to be complementary, since they require different kind of input information. Moreover, since the 3 methods rest on different assumptions, results of one model can be compared to those of the other two.",
publisher = "Elsevier",
journal = "Computational Biology and Chemistry",
title = "Atom counting method for determining elemental composition of viruses and its applications in biothermodynamics and environmental science",
volume = "96",
pages = "107621",
doi = "10.1016/j.compbiolchem.2022.107621"
}

Popović, M.. (2022). Atom counting method for determining elemental composition of viruses and its applications in biothermodynamics and environmental science. in Computational Biology and Chemistry
Elsevier., 96, 107621.
https://doi.org/10.1016/j.compbiolchem.2022.107621

Popović M. Atom counting method for determining elemental composition of viruses and its applications in biothermodynamics and environmental science. in Computational Biology and Chemistry. 2022;96:107621.
doi:10.1016/j.compbiolchem.2022.107621 .

Popović, Marko, "Atom counting method for determining elemental composition of viruses and its applications in biothermodynamics and environmental science" in Computational Biology and Chemistry, 96 (2022):107621,
https://doi.org/10.1016/j.compbiolchem.2022.107621 . .

TY  - JOUR
AU  - Popović, Marko
PY  - 2022
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6096
AB  - The model of T4 phage, Lambda phage, and E. coli is often used in research on virus-host interactions. This paper reports for the first time the thermodynamic driving force of biosynthesis, catabolism and metabolism for the three organisms, on the M9 medium. Moreover, the influence of activities of nutrients and metabolic products is analyzed. All three organisms were found to have very similar Gibbs energies of metabolism. Moreover, since they share the same catabolism, their Gibbs energies of catabolism are identical. However, Gibbs energies of biosynthesis differ. The calculated thermodynamic properties have been used to explain the coexistence of both bacteria and phages in a dynamic equilibrium in natural ecosystems.
PB  - Society of Thermal Engineers of Serbia
T2  - Thermal Science
T1  - Thermodynamics of bacteria-phage interactions T4 and Lambda bacteriophages, and E. coli can coexist in natural ecosystems due to the ratio of their Gibbs energies of biosynthesis
VL  - 27
IS  - 1A
SP  - 411
EP  - 431
DO  - 10.2298/TSCI2301411P
ER  - 

@article{
author = "Popović, Marko",
year = "2022",
abstract = "The model of T4 phage, Lambda phage, and E. coli is often used in research on virus-host interactions. This paper reports for the first time the thermodynamic driving force of biosynthesis, catabolism and metabolism for the three organisms, on the M9 medium. Moreover, the influence of activities of nutrients and metabolic products is analyzed. All three organisms were found to have very similar Gibbs energies of metabolism. Moreover, since they share the same catabolism, their Gibbs energies of catabolism are identical. However, Gibbs energies of biosynthesis differ. The calculated thermodynamic properties have been used to explain the coexistence of both bacteria and phages in a dynamic equilibrium in natural ecosystems.",
publisher = "Society of Thermal Engineers of Serbia",
journal = "Thermal Science",
title = "Thermodynamics of bacteria-phage interactions T4 and Lambda bacteriophages, and E. coli can coexist in natural ecosystems due to the ratio of their Gibbs energies of biosynthesis",
volume = "27",
number = "1A",
pages = "411-431",
doi = "10.2298/TSCI2301411P"
}

Popović, M.. (2022). Thermodynamics of bacteria-phage interactions T4 and Lambda bacteriophages, and E. coli can coexist in natural ecosystems due to the ratio of their Gibbs energies of biosynthesis. in Thermal Science
Society of Thermal Engineers of Serbia., 27(1A), 411-431.
https://doi.org/10.2298/TSCI2301411P

Popović M. Thermodynamics of bacteria-phage interactions T4 and Lambda bacteriophages, and E. coli can coexist in natural ecosystems due to the ratio of their Gibbs energies of biosynthesis. in Thermal Science. 2022;27(1A):411-431.
doi:10.2298/TSCI2301411P .

Popović, Marko, "Thermodynamics of bacteria-phage interactions T4 and Lambda bacteriophages, and E. coli can coexist in natural ecosystems due to the ratio of their Gibbs energies of biosynthesis" in Thermal Science, 27, no. 1A (2022):411-431,
https://doi.org/10.2298/TSCI2301411P . .

TY  - JOUR
AU  - Popović, Marko
PY  - 2022
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6108
AB  - Today, the World Health Organization has declared a global health emergency, caused by the Monkeypox outbreak. In the monthly analysis for June, 3500 cases have been reported in 50 countries around the world. In the analysis for July, more than 30000 cases have been reported in 75 countries. Thus, in the circumstances of the continuing COVID-19 pandemic, the appearance and dynamics of spreading of Monkeypox is alarming. In this paper, for the first time, elemental composition of Poxvirus, Monkeypox virus, and Vaccinia virus have been reported. Additionally, thermodynamic properties have been reported for nucleic acids, nucleocapsids, and entire virus particles. The similarity in chemical composition and thermodynamic properties of the analyzed viruses has been used to explain the crossed immunity to Poxviruses. Finally, binding thermodynamic properties have been reported for the Vaccinia virus.
PB  - Society of Thermal Engineers of Serbia
T2  - Thermal Science
T1  - Formulas for death and life: Chemical composition and biothermodynamic properties of Monkeypox (MPV, MPXV, HMPXV) and Vaccinia (VACV) viruses
VL  - 26
IS  - 6A
SP  - 4855
EP  - 4868
DO  - 10.2298/TSCI220524142P
ER  - 

@article{
author = "Popović, Marko",
year = "2022",
abstract = "Today, the World Health Organization has declared a global health emergency, caused by the Monkeypox outbreak. In the monthly analysis for June, 3500 cases have been reported in 50 countries around the world. In the analysis for July, more than 30000 cases have been reported in 75 countries. Thus, in the circumstances of the continuing COVID-19 pandemic, the appearance and dynamics of spreading of Monkeypox is alarming. In this paper, for the first time, elemental composition of Poxvirus, Monkeypox virus, and Vaccinia virus have been reported. Additionally, thermodynamic properties have been reported for nucleic acids, nucleocapsids, and entire virus particles. The similarity in chemical composition and thermodynamic properties of the analyzed viruses has been used to explain the crossed immunity to Poxviruses. Finally, binding thermodynamic properties have been reported for the Vaccinia virus.",
publisher = "Society of Thermal Engineers of Serbia",
journal = "Thermal Science",
title = "Formulas for death and life: Chemical composition and biothermodynamic properties of Monkeypox (MPV, MPXV, HMPXV) and Vaccinia (VACV) viruses",
volume = "26",
number = "6A",
pages = "4855-4868",
doi = "10.2298/TSCI220524142P"
}

Popović, M.. (2022). Formulas for death and life: Chemical composition and biothermodynamic properties of Monkeypox (MPV, MPXV, HMPXV) and Vaccinia (VACV) viruses. in Thermal Science
Society of Thermal Engineers of Serbia., 26(6A), 4855-4868.
https://doi.org/10.2298/TSCI220524142P

Popović M. Formulas for death and life: Chemical composition and biothermodynamic properties of Monkeypox (MPV, MPXV, HMPXV) and Vaccinia (VACV) viruses. in Thermal Science. 2022;26(6A):4855-4868.
doi:10.2298/TSCI220524142P .

Popović, Marko, "Formulas for death and life: Chemical composition and biothermodynamic properties of Monkeypox (MPV, MPXV, HMPXV) and Vaccinia (VACV) viruses" in Thermal Science, 26, no. 6A (2022):4855-4868,
https://doi.org/10.2298/TSCI220524142P . .