TY  - JOUR
AU  - Čevizović, Dalibor
AU  - Zdravković, Slobodan
AU  - Chizhov, Alexei V.
AU  - Ivić, Zoran
PY  - 2023
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/10752
AB  - We investigate the properties of the excess charge (electron, hole) introduced into a two-strand biomolecule. We consider the possibility that the stable soliton excitation can be formed due to interaction of excess charge with the phonon subsystem. The influence of overlap of the molecular orbitals between adjacent structure elements of the macromolecular chain on the soliton properties is discussed. Special attention is paid to the influence of the overlapping of the molecular orbitals between structure elements placed on the different chains. Using the literature values of the basic energy parameters of the two-chain biomolecular structures, possible types of soliton solutions are discussed. © 2023 Chinese Physical Society and IOP Publishing Ltd.
T2  - Chinese Physics B
T1  - Charge self-trapping in two strand biomolecules: Adiabatic polaron approach
VL  - 32
IS  - 1
SP  - 010506
DO  - 10.1088/1674-1056/ac70bc
ER  - 

@article{
author = "Čevizović, Dalibor and Zdravković, Slobodan and Chizhov, Alexei V. and Ivić, Zoran",
year = "2023",
abstract = "We investigate the properties of the excess charge (electron, hole) introduced into a two-strand biomolecule. We consider the possibility that the stable soliton excitation can be formed due to interaction of excess charge with the phonon subsystem. The influence of overlap of the molecular orbitals between adjacent structure elements of the macromolecular chain on the soliton properties is discussed. Special attention is paid to the influence of the overlapping of the molecular orbitals between structure elements placed on the different chains. Using the literature values of the basic energy parameters of the two-chain biomolecular structures, possible types of soliton solutions are discussed. © 2023 Chinese Physical Society and IOP Publishing Ltd.",
journal = "Chinese Physics B",
title = "Charge self-trapping in two strand biomolecules: Adiabatic polaron approach",
volume = "32",
number = "1",
pages = "010506",
doi = "10.1088/1674-1056/ac70bc"
}

Čevizović, D., Zdravković, S., Chizhov, A. V.,& Ivić, Z.. (2023). Charge self-trapping in two strand biomolecules: Adiabatic polaron approach. in Chinese Physics B, 32(1), 010506.
https://doi.org/10.1088/1674-1056/ac70bc

Čevizović D, Zdravković S, Chizhov AV, Ivić Z. Charge self-trapping in two strand biomolecules: Adiabatic polaron approach. in Chinese Physics B. 2023;32(1):010506.
doi:10.1088/1674-1056/ac70bc .

Čevizović, Dalibor, Zdravković, Slobodan, Chizhov, Alexei V., Ivić, Zoran, "Charge self-trapping in two strand biomolecules: Adiabatic polaron approach" in Chinese Physics B, 32, no. 1 (2023):010506,
https://doi.org/10.1088/1674-1056/ac70bc . .

TY  - JOUR
AU  - Satarić, Miljko V.
AU  - Nemeš, Tomas
AU  - Zdravković, Slobodan
PY  - 2023
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/11445
AB  - Calcium is one of the most versatile messengers for intracellular signaling. In the case of cilia and flagella calcium has the central role in transfer of communications between extracellular stimuli and intracellular formation of frequency modulated signal and their deciphering by target proteins. In this paper, the diffusion of fluorescently or otherwise tagged and un-tagged Ca2＋ particles is analyzed by solving the system of pertaining reaction–diffusion equations. We used Fourier transform tools to get asymptotic eigenfunctions for tagged (un-tagged) free and buffered Ca2＋ ions. We made some numerical estimations for diffusion coefficients corroborating the fact that messages diffuse faster than Ca2＋ messengers. From the best of our knowledge, this is the first time that Ca2＋ signaling in living cells is biophysically elaborated within the framework of model presented here. We suggest the experimental assay on the basis of radioactive Ca2＋ as tagged probe.
T2  - Biosystems
T1  - Calcium messages in flagella are faster than messenger particles
VL  - 232
SP  - 105003
DO  - 10.1016/j.biosystems.2023.105003
ER  - 

@article{
author = "Satarić, Miljko V. and Nemeš, Tomas and Zdravković, Slobodan",
year = "2023",
abstract = "Calcium is one of the most versatile messengers for intracellular signaling. In the case of cilia and flagella calcium has the central role in transfer of communications between extracellular stimuli and intracellular formation of frequency modulated signal and their deciphering by target proteins. In this paper, the diffusion of fluorescently or otherwise tagged and un-tagged Ca2＋ particles is analyzed by solving the system of pertaining reaction–diffusion equations. We used Fourier transform tools to get asymptotic eigenfunctions for tagged (un-tagged) free and buffered Ca2＋ ions. We made some numerical estimations for diffusion coefficients corroborating the fact that messages diffuse faster than Ca2＋ messengers. From the best of our knowledge, this is the first time that Ca2＋ signaling in living cells is biophysically elaborated within the framework of model presented here. We suggest the experimental assay on the basis of radioactive Ca2＋ as tagged probe.",
journal = "Biosystems",
title = "Calcium messages in flagella are faster than messenger particles",
volume = "232",
pages = "105003",
doi = "10.1016/j.biosystems.2023.105003"
}

Satarić, M. V., Nemeš, T.,& Zdravković, S.. (2023). Calcium messages in flagella are faster than messenger particles. in Biosystems, 232, 105003.
https://doi.org/10.1016/j.biosystems.2023.105003

Satarić MV, Nemeš T, Zdravković S. Calcium messages in flagella are faster than messenger particles. in Biosystems. 2023;232:105003.
doi:10.1016/j.biosystems.2023.105003 .

Satarić, Miljko V., Nemeš, Tomas, Zdravković, Slobodan, "Calcium messages in flagella are faster than messenger particles" in Biosystems, 232 (2023):105003,
https://doi.org/10.1016/j.biosystems.2023.105003 . .

TY  - JOUR
AU  - Ranković, Dragana
AU  - Sivčević, Vladimir
AU  - Batova, Anna
AU  - Zdravković, Slobodan
PY  - 2023
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/10856
AB  - In the present article we investigate the nonlinear dynamics of microtubules, the basic components of the eukaryotic cytoskeleton, relying on the known general model. We introduce the W-potential energy, describing a crucial interaction among constitutive particles within the microtubule. Three kinds of this potential are studied, one symmetrical and two non-symmetrical. We demonstrate an advantage of the latter ones. Solutions of crucial differential equations are solitary waves. The stability of the solutions having physical sense is studied. We show that only subsonic solitary waves are stable, while supersonic ones are not.
T2  - Chaos, Solitons and Fractals
T1  - Three kinds of W-potentials in nonlinear biophysics of microtubules
VL  - 170
SP  - 113345
DO  - 10.1016/j.chaos.2023.113345
ER  - 

@article{
author = "Ranković, Dragana and Sivčević, Vladimir and Batova, Anna and Zdravković, Slobodan",
year = "2023",
abstract = "In the present article we investigate the nonlinear dynamics of microtubules, the basic components of the eukaryotic cytoskeleton, relying on the known general model. We introduce the W-potential energy, describing a crucial interaction among constitutive particles within the microtubule. Three kinds of this potential are studied, one symmetrical and two non-symmetrical. We demonstrate an advantage of the latter ones. Solutions of crucial differential equations are solitary waves. The stability of the solutions having physical sense is studied. We show that only subsonic solitary waves are stable, while supersonic ones are not.",
journal = "Chaos, Solitons and Fractals",
title = "Three kinds of W-potentials in nonlinear biophysics of microtubules",
volume = "170",
pages = "113345",
doi = "10.1016/j.chaos.2023.113345"
}

Ranković, D., Sivčević, V., Batova, A.,& Zdravković, S.. (2023). Three kinds of W-potentials in nonlinear biophysics of microtubules. in Chaos, Solitons and Fractals, 170, 113345.
https://doi.org/10.1016/j.chaos.2023.113345

Ranković D, Sivčević V, Batova A, Zdravković S. Three kinds of W-potentials in nonlinear biophysics of microtubules. in Chaos, Solitons and Fractals. 2023;170:113345.
doi:10.1016/j.chaos.2023.113345 .

Ranković, Dragana, Sivčević, Vladimir, Batova, Anna, Zdravković, Slobodan, "Three kinds of W-potentials in nonlinear biophysics of microtubules" in Chaos, Solitons and Fractals, 170 (2023):113345,
https://doi.org/10.1016/j.chaos.2023.113345 . .

TY  - JOUR
PY  - 2022
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/10816
AB  - From the very beginning of the twentieth century, a crucial question in physics research has been whether to use classical or quantum mechanics. Some physical systems are predominantly classical, while some of them are quantum in nature. There are a variety of examples where a system has been studied using both classical and quantum mechanics. However, there has been one more choice, and that is linear versus nonlinear. From a mathematical point of view, linear systems are described by linear, while nonlinear ones require nonlinear differential equations.
T2  - Nonlinear Dynamics of Nanobiophysics
T1  - Introduction
SP  - 1
EP  - 6
DO  - 10.1007/978-981-19-5323-1_1
ER  - 

@article{
editor = "Zdravković, Slobodan, Čevizović, Dalibor",
year = "2022",
abstract = "From the very beginning of the twentieth century, a crucial question in physics research has been whether to use classical or quantum mechanics. Some physical systems are predominantly classical, while some of them are quantum in nature. There are a variety of examples where a system has been studied using both classical and quantum mechanics. However, there has been one more choice, and that is linear versus nonlinear. From a mathematical point of view, linear systems are described by linear, while nonlinear ones require nonlinear differential equations.",
journal = "Nonlinear Dynamics of Nanobiophysics",
title = "Introduction",
pages = "1-6",
doi = "10.1007/978-981-19-5323-1_1"
}

Zdravković, S.,& Čevizović, D.. (2022). Introduction. in Nonlinear Dynamics of Nanobiophysics, 1-6.
https://doi.org/10.1007/978-981-19-5323-1_1

Zdravković S, Čevizović D. Introduction. in Nonlinear Dynamics of Nanobiophysics. 2022;:1-6.
doi:10.1007/978-981-19-5323-1_1 .

Zdravković, Slobodan, Čevizović, Dalibor, "Introduction" in Nonlinear Dynamics of Nanobiophysics (2022):1-6,
https://doi.org/10.1007/978-981-19-5323-1_1 . .

TY  - BOOK
PY  - 2022
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/10818
AB  - Highlights important aspects of nonlinear dynamics of biophysical nanosystems- DNA, microtubes, and alpha helix

Presents useful read for students and researchers in the field, with chapters containing exercises

Includes computational methods in nonlinear nanobiophysics
T1  - Nonlinear Dynamics of Nanobiophysics
DO  - 10.1007/978-981-19-5323-1
ER  - 

@book{
editor = "Zdravković, Slobodan, Čevizović, Dalibor",
year = "2022",
abstract = "Highlights important aspects of nonlinear dynamics of biophysical nanosystems- DNA, microtubes, and alpha helix

Presents useful read for students and researchers in the field, with chapters containing exercises

Includes computational methods in nonlinear nanobiophysics",
title = "Nonlinear Dynamics of Nanobiophysics",
doi = "10.1007/978-981-19-5323-1"
}

Zdravković, S.,& Čevizović, D.. (2022). Nonlinear Dynamics of Nanobiophysics. .
https://doi.org/10.1007/978-981-19-5323-1

Zdravković S, Čevizović D. Nonlinear Dynamics of Nanobiophysics. 2022;.
doi:10.1007/978-981-19-5323-1 .

Zdravković, Slobodan, Čevizović, Dalibor, "Nonlinear Dynamics of Nanobiophysics" (2022),
https://doi.org/10.1007/978-981-19-5323-1 . .

TY  - JOUR
AU  - Ranković, Dragana
AU  - Zdravković, Slobodan
PY  - 2022
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/10442
AB  - This work represents a contribution to modelling nonlinear dynamics of microtubules, the basic components of the eukaryotic cytoskeleton. Their dynamics can be explained in terms of kink and antikink solitary waves. Special attention was paid to the stability of solitonic solutions of differential equations describing the dynamics of microtubules. It is shown that subsonic solitons are stable, while supersonic ones are not.
T2  - Chaos, Solitons and Fractals
T1  - Two component model of microtubules – subsonic and supersonic solitary waves
VL  - 164
SP  - 112693
DO  - 10.1016/j.chaos.2022.112693
ER  - 

@article{
author = "Ranković, Dragana and Zdravković, Slobodan",
year = "2022",
abstract = "This work represents a contribution to modelling nonlinear dynamics of microtubules, the basic components of the eukaryotic cytoskeleton. Their dynamics can be explained in terms of kink and antikink solitary waves. Special attention was paid to the stability of solitonic solutions of differential equations describing the dynamics of microtubules. It is shown that subsonic solitons are stable, while supersonic ones are not.",
journal = "Chaos, Solitons and Fractals",
title = "Two component model of microtubules – subsonic and supersonic solitary waves",
volume = "164",
pages = "112693",
doi = "10.1016/j.chaos.2022.112693"
}

Ranković, D.,& Zdravković, S.. (2022). Two component model of microtubules – subsonic and supersonic solitary waves. in Chaos, Solitons and Fractals, 164, 112693.
https://doi.org/10.1016/j.chaos.2022.112693

Ranković D, Zdravković S. Two component model of microtubules – subsonic and supersonic solitary waves. in Chaos, Solitons and Fractals. 2022;164:112693.
doi:10.1016/j.chaos.2022.112693 .

Ranković, Dragana, Zdravković, Slobodan, "Two component model of microtubules – subsonic and supersonic solitary waves" in Chaos, Solitons and Fractals, 164 (2022):112693,
https://doi.org/10.1016/j.chaos.2022.112693 . .

TY  - CHAP
AU  - Zdravković, Slobodan
PY  - 2022
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/10815
AB  - Deoxyribonucleic acid (DNA) is found in all prokaryotic and eukaryotic cells and many viruses. This complex molecular structure is certainly one of the most interesting molecules. Interest in its structure and dynamics is primarily due to the important role that this molecule plays in life processes. The molecule was first identified in the 1860s by the Swiss chemist Johann Friedrich Miescher. He discovered a substance that had unexpected properties, different from those of the other proteins he had been familiar with. He did not know he had discovered the molecular basis of life, which he called nuclein.
T2  - Nonlinear Dynamics of Nanobiophysics
T1  - Nonlinear Dynamics of DNA Chain
SP  - 29
EP  - 65
DO  - 10.1007/978-981-19-5323-1_3
ER  - 

@inbook{
author = "Zdravković, Slobodan",
year = "2022",
abstract = "Deoxyribonucleic acid (DNA) is found in all prokaryotic and eukaryotic cells and many viruses. This complex molecular structure is certainly one of the most interesting molecules. Interest in its structure and dynamics is primarily due to the important role that this molecule plays in life processes. The molecule was first identified in the 1860s by the Swiss chemist Johann Friedrich Miescher. He discovered a substance that had unexpected properties, different from those of the other proteins he had been familiar with. He did not know he had discovered the molecular basis of life, which he called nuclein.",
journal = "Nonlinear Dynamics of Nanobiophysics",
booktitle = "Nonlinear Dynamics of DNA Chain",
pages = "29-65",
doi = "10.1007/978-981-19-5323-1_3"
}

Zdravković, S.. (2022). Nonlinear Dynamics of DNA Chain. in Nonlinear Dynamics of Nanobiophysics, 29-65.
https://doi.org/10.1007/978-981-19-5323-1_3

Zdravković S. Nonlinear Dynamics of DNA Chain. in Nonlinear Dynamics of Nanobiophysics. 2022;:29-65.
doi:10.1007/978-981-19-5323-1_3 .

Zdravković, Slobodan, "Nonlinear Dynamics of DNA Chain" in Nonlinear Dynamics of Nanobiophysics (2022):29-65,
https://doi.org/10.1007/978-981-19-5323-1_3 . .

TY  - CHAP
AU  - Zdravković, Slobodan
PY  - 2022
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/10817
AB  - Microtubules (MTs) were discovered by biologists more than 50 years ago. This great breakthrough was made whilst trying to isolate, purify, and characterize the colchicine-binding protein, as explained in a review paper (Borisy et al. in Nat Rev Mol Cell Bio 17:322, 2016 [1]). There are two kinds of cells, eukaryotic and prokaryotic ones. Eukaryotes are usually larger and much more sophisticated than prokaryotic cells. Plant and animal cells are eukaryotic, whilst bacterial cells are prokaryotic.
T2  - Nonlinear Dynamics of Nanobiophysics
T1  - Nonlinear Dynamics of Microtubules
SP  - 263
EP  - 305
DO  - 10.1007/978-981-19-5323-1_10
ER  - 

@inbook{
author = "Zdravković, Slobodan",
year = "2022",
abstract = "Microtubules (MTs) were discovered by biologists more than 50 years ago. This great breakthrough was made whilst trying to isolate, purify, and characterize the colchicine-binding protein, as explained in a review paper (Borisy et al. in Nat Rev Mol Cell Bio 17:322, 2016 [1]). There are two kinds of cells, eukaryotic and prokaryotic ones. Eukaryotes are usually larger and much more sophisticated than prokaryotic cells. Plant and animal cells are eukaryotic, whilst bacterial cells are prokaryotic.",
journal = "Nonlinear Dynamics of Nanobiophysics",
booktitle = "Nonlinear Dynamics of Microtubules",
pages = "263-305",
doi = "10.1007/978-981-19-5323-1_10"
}

Zdravković, S.. (2022). Nonlinear Dynamics of Microtubules. in Nonlinear Dynamics of Nanobiophysics, 263-305.
https://doi.org/10.1007/978-981-19-5323-1_10

Zdravković S. Nonlinear Dynamics of Microtubules. in Nonlinear Dynamics of Nanobiophysics. 2022;:263-305.
doi:10.1007/978-981-19-5323-1_10 .

Zdravković, Slobodan, "Nonlinear Dynamics of Microtubules" in Nonlinear Dynamics of Nanobiophysics (2022):263-305,
https://doi.org/10.1007/978-981-19-5323-1_10 . .

TY  - JOUR
AU  - Zdravković, Slobodan
AU  - Zeković, Slobodan
AU  - Bugay, Aleksandr Nikolaevich
AU  - Petrović, Jovana S.
PY  - 2021
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/9918
AB  - In the present work, we study the nonlinear dynamics of microtubules, the basic components of the eukaryotic cytoskeleton. We introduce a two-component model describing tangential oscillations of dimers. A crucial nonlinear differential equation is solved using continuum approximation. We show that the dynamics of microtubules can be explained in terms of kink and antikink solitary waves. We used two mathematical procedures, that is the tangent hyperbolic function method and, more general, the simplest equation method. It is shown that both procedures bring about equal solutions. © 2021
T2  - Chaos, Solitons and Fractals
T1  - Two component model of microtubules and continuum approximation
VL  - 152
SP  - 111352
DO  - 10.1016/j.chaos.2021.111352
ER  - 

@article{
author = "Zdravković, Slobodan and Zeković, Slobodan and Bugay, Aleksandr Nikolaevich and Petrović, Jovana S.",
year = "2021",
abstract = "In the present work, we study the nonlinear dynamics of microtubules, the basic components of the eukaryotic cytoskeleton. We introduce a two-component model describing tangential oscillations of dimers. A crucial nonlinear differential equation is solved using continuum approximation. We show that the dynamics of microtubules can be explained in terms of kink and antikink solitary waves. We used two mathematical procedures, that is the tangent hyperbolic function method and, more general, the simplest equation method. It is shown that both procedures bring about equal solutions. © 2021",
journal = "Chaos, Solitons and Fractals",
title = "Two component model of microtubules and continuum approximation",
volume = "152",
pages = "111352",
doi = "10.1016/j.chaos.2021.111352"
}

Zdravković, S., Zeković, S., Bugay, A. N.,& Petrović, J. S.. (2021). Two component model of microtubules and continuum approximation. in Chaos, Solitons and Fractals, 152, 111352.
https://doi.org/10.1016/j.chaos.2021.111352

Zdravković S, Zeković S, Bugay AN, Petrović JS. Two component model of microtubules and continuum approximation. in Chaos, Solitons and Fractals. 2021;152:111352.
doi:10.1016/j.chaos.2021.111352 .

Zdravković, Slobodan, Zeković, Slobodan, Bugay, Aleksandr Nikolaevich, Petrović, Jovana S., "Two component model of microtubules and continuum approximation" in Chaos, Solitons and Fractals, 152 (2021):111352,
https://doi.org/10.1016/j.chaos.2021.111352 . .

TY  - JOUR
AU  - Zdravković, Slobodan
AU  - Sivčević, Vladimir
PY  - 2021
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/9893
AB  - In this work, we study nonlinear dynamics of microtubules. An important interaction among constitutive particles is modeled using W-potential. We compare a symmetric potential with two kinds of non-symmetric ones. An advantage of the latter ones is demonstrated. © 2021, Education and Upbringing Publishing. All rights reserved.
T2  - Nonlinear Phenomena in Complex Systems
T1  - Non-symmetrical w-potential in nonlinear biophysics of microtubules
VL  - 24
IS  - 2
SP  - 198
EP  - 202
DO  - 10.33581/1561-4085-2021-24-2-198-202
ER  - 

@article{
author = "Zdravković, Slobodan and Sivčević, Vladimir",
year = "2021",
abstract = "In this work, we study nonlinear dynamics of microtubules. An important interaction among constitutive particles is modeled using W-potential. We compare a symmetric potential with two kinds of non-symmetric ones. An advantage of the latter ones is demonstrated. © 2021, Education and Upbringing Publishing. All rights reserved.",
journal = "Nonlinear Phenomena in Complex Systems",
title = "Non-symmetrical w-potential in nonlinear biophysics of microtubules",
volume = "24",
number = "2",
pages = "198-202",
doi = "10.33581/1561-4085-2021-24-2-198-202"
}

Zdravković, S.,& Sivčević, V.. (2021). Non-symmetrical w-potential in nonlinear biophysics of microtubules. in Nonlinear Phenomena in Complex Systems, 24(2), 198-202.
https://doi.org/10.33581/1561-4085-2021-24-2-198-202

Zdravković S, Sivčević V. Non-symmetrical w-potential in nonlinear biophysics of microtubules. in Nonlinear Phenomena in Complex Systems. 2021;24(2):198-202.
doi:10.33581/1561-4085-2021-24-2-198-202 .

Zdravković, Slobodan, Sivčević, Vladimir, "Non-symmetrical w-potential in nonlinear biophysics of microtubules" in Nonlinear Phenomena in Complex Systems, 24, no. 2 (2021):198-202,
https://doi.org/10.33581/1561-4085-2021-24-2-198-202 . .

TY  - JOUR
AU  - Čevizović, Dalibor
AU  - Michieletto, Davide
AU  - Mvogo, Alain
AU  - ZakirYanov, Farit Kabirovich
AU  - Zdravković, Slobodan
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/9787
AB  - The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard-Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of 'self-trapping' of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo, possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field. © 2020 The Authors.
T2  - Royal Society Open Science
T1  - A review on nonlinear DNA physics
VL  - 7
IS  - 11
SP  - 200774
DO  - 10.1098/rsos.200774
ER  - 

@article{
author = "Čevizović, Dalibor and Michieletto, Davide and Mvogo, Alain and ZakirYanov, Farit Kabirovich and Zdravković, Slobodan",
year = "2020",
abstract = "The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard-Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of 'self-trapping' of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo, possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field. © 2020 The Authors.",
journal = "Royal Society Open Science",
title = "A review on nonlinear DNA physics",
volume = "7",
number = "11",
pages = "200774",
doi = "10.1098/rsos.200774"
}

Čevizović, D., Michieletto, D., Mvogo, A., ZakirYanov, F. K.,& Zdravković, S.. (2020). A review on nonlinear DNA physics. in Royal Society Open Science, 7(11), 200774.
https://doi.org/10.1098/rsos.200774

Čevizović D, Michieletto D, Mvogo A, ZakirYanov FK, Zdravković S. A review on nonlinear DNA physics. in Royal Society Open Science. 2020;7(11):200774.
doi:10.1098/rsos.200774 .

Čevizović, Dalibor, Michieletto, Davide, Mvogo, Alain, ZakirYanov, Farit Kabirovich, Zdravković, Slobodan, "A review on nonlinear DNA physics" in Royal Society Open Science, 7, no. 11 (2020):200774,
https://doi.org/10.1098/rsos.200774 . .

TY  - JOUR
AU  - Justin, Mibaile
AU  - Zdravković, Slobodan
AU  - Hubert, Malwe Boudoue
AU  - Betchewe, Gambo
AU  - Doka, Serge Yamigno
AU  - Kofane, Timoleon Crepin
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/9610
AB  - A new nonlinear phenomenon has been studied theoretically on one of the main cytoskeletal element of eukaryotic cells, namely chaos in microtubules vibrations. The general model of microtubules is used to draw phase portraits and Lyapunov spectra. The examination of numerical results reveals that the velocity of the chaotic wave could be the physical parameter that governs chaos. The energy released after the hydrolysation of guanosine triphosphate is converted to active turbulence leading to chaos. The high values of the Lyapunov exponents give hints that there are strong dissipations yielding in the lessening of the velocity of chaotic wave propagation in the microtubules. Moreover, the role of chaos in information processing has been established in microtubules. The energy coming from hydrolysis of guanosine triphosphate stimulates the tubulin leading it to probe its environment and collect information. The net sum of Lyapunov exponents is found to be positive in this stage of the process. Also, the collected information is compressed with a negative sum of Lyapunov exponents. Eventually, the compressibility rate has been estimated to be η=67.2%, and 1.11 bit is lost. © 2020 Elsevier B.V.
T2  - Biosystems
T1  - Chaotic vibration of microtubules and biological information processing
VL  - 198
SP  - 104230
DO  - 10.1016/j.biosystems.2020.104230
ER  - 

@article{
author = "Justin, Mibaile and Zdravković, Slobodan and Hubert, Malwe Boudoue and Betchewe, Gambo and Doka, Serge Yamigno and Kofane, Timoleon Crepin",
year = "2020",
abstract = "A new nonlinear phenomenon has been studied theoretically on one of the main cytoskeletal element of eukaryotic cells, namely chaos in microtubules vibrations. The general model of microtubules is used to draw phase portraits and Lyapunov spectra. The examination of numerical results reveals that the velocity of the chaotic wave could be the physical parameter that governs chaos. The energy released after the hydrolysation of guanosine triphosphate is converted to active turbulence leading to chaos. The high values of the Lyapunov exponents give hints that there are strong dissipations yielding in the lessening of the velocity of chaotic wave propagation in the microtubules. Moreover, the role of chaos in information processing has been established in microtubules. The energy coming from hydrolysis of guanosine triphosphate stimulates the tubulin leading it to probe its environment and collect information. The net sum of Lyapunov exponents is found to be positive in this stage of the process. Also, the collected information is compressed with a negative sum of Lyapunov exponents. Eventually, the compressibility rate has been estimated to be η=67.2%, and 1.11 bit is lost. © 2020 Elsevier B.V.",
journal = "Biosystems",
title = "Chaotic vibration of microtubules and biological information processing",
volume = "198",
pages = "104230",
doi = "10.1016/j.biosystems.2020.104230"
}

Justin, M., Zdravković, S., Hubert, M. B., Betchewe, G., Doka, S. Y.,& Kofane, T. C.. (2020). Chaotic vibration of microtubules and biological information processing. in Biosystems, 198, 104230.
https://doi.org/10.1016/j.biosystems.2020.104230

Justin M, Zdravković S, Hubert MB, Betchewe G, Doka SY, Kofane TC. Chaotic vibration of microtubules and biological information processing. in Biosystems. 2020;198:104230.
doi:10.1016/j.biosystems.2020.104230 .

Justin, Mibaile, Zdravković, Slobodan, Hubert, Malwe Boudoue, Betchewe, Gambo, Doka, Serge Yamigno, Kofane, Timoleon Crepin, "Chaotic vibration of microtubules and biological information processing" in Biosystems, 198 (2020):104230,
https://doi.org/10.1016/j.biosystems.2020.104230 . .

TY  - JOUR
AU  - Satarić, Miljko V.
AU  - Nemeš, Tomas
AU  - Satarić, Bogdan
AU  - Sekulić, Dalibor
AU  - Zdravković, Slobodan
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/9059
AB  - The cytoskeleton of cilia and flagella is so called axoneme a stable cylindrical architecture of nine microtubule doublets. Axoneme performs periodic bending motion by utilizing specific dynein motor family powered by ATP hydrolysis. It is still unclear how this highly organized “ciliary beat” is being initiated and strongly coordinated by the combined action of hundreds dynein motors. Based on the experimental evidences we here elaborate a plausible scenario in which actually calcium ions play the roles of catalytic activators and coordinators of dynein attachments doing it in superposition with already known mechanical control tools of “ciliary beat”. Polyelectrolyte properties of microtubules incorporated in axoneme doublets enable the formation and propagation of soliton-like “ionic clouds” of Ca2+ ions along these “coaxial nanocables”. The sliding speed of such Ca2+ “clouds” along microtubule doublets is comparable with the speed of propagation of “ciliary beat” itself. We elaborated the interplay between influx of Ca2+ ions in ciliary based body and the sliding of microtubule triplets therein. In second segment we considered how the dynein motors activated by Ca2+ ions contained within solitonic “ionic clouds” in competition with axoneme curvature regulate ciliary and flagellar beating.
T2  - Biosystems
T1  - Calcium ions tune the beats of cilia and flagella
VL  - 196
SP  - 104172
DO  - 10.1016/j.biosystems.2020.104172
ER  - 

@article{
author = "Satarić, Miljko V. and Nemeš, Tomas and Satarić, Bogdan and Sekulić, Dalibor and Zdravković, Slobodan",
year = "2020",
abstract = "The cytoskeleton of cilia and flagella is so called axoneme a stable cylindrical architecture of nine microtubule doublets. Axoneme performs periodic bending motion by utilizing specific dynein motor family powered by ATP hydrolysis. It is still unclear how this highly organized “ciliary beat” is being initiated and strongly coordinated by the combined action of hundreds dynein motors. Based on the experimental evidences we here elaborate a plausible scenario in which actually calcium ions play the roles of catalytic activators and coordinators of dynein attachments doing it in superposition with already known mechanical control tools of “ciliary beat”. Polyelectrolyte properties of microtubules incorporated in axoneme doublets enable the formation and propagation of soliton-like “ionic clouds” of Ca2+ ions along these “coaxial nanocables”. The sliding speed of such Ca2+ “clouds” along microtubule doublets is comparable with the speed of propagation of “ciliary beat” itself. We elaborated the interplay between influx of Ca2+ ions in ciliary based body and the sliding of microtubule triplets therein. In second segment we considered how the dynein motors activated by Ca2+ ions contained within solitonic “ionic clouds” in competition with axoneme curvature regulate ciliary and flagellar beating.",
journal = "Biosystems",
title = "Calcium ions tune the beats of cilia and flagella",
volume = "196",
pages = "104172",
doi = "10.1016/j.biosystems.2020.104172"
}

Satarić, M. V., Nemeš, T., Satarić, B., Sekulić, D.,& Zdravković, S.. (2020). Calcium ions tune the beats of cilia and flagella. in Biosystems, 196, 104172.
https://doi.org/10.1016/j.biosystems.2020.104172

Satarić MV, Nemeš T, Satarić B, Sekulić D, Zdravković S. Calcium ions tune the beats of cilia and flagella. in Biosystems. 2020;196:104172.
doi:10.1016/j.biosystems.2020.104172 .

Satarić, Miljko V., Nemeš, Tomas, Satarić, Bogdan, Sekulić, Dalibor, Zdravković, Slobodan, "Calcium ions tune the beats of cilia and flagella" in Biosystems, 196 (2020):104172,
https://doi.org/10.1016/j.biosystems.2020.104172 . .

TY  - JOUR
AU  - Satarić, Miljko V.
AU  - Zdravković, Slobodan
AU  - Nemeš, Tomas
AU  - Satarić, Bogdan M.
PY  - 2020
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/9719
AB  - To adapt to changing environments cells must signal and signaling requires messengers whose concentration varies with time in space. We here consider the messenger role of calcium ions implicated in regulation of the wave-like bending dynamics of cilia and flagella. The emphasis is on microtubules as polyelectrolytes serving as transmission lines for the flow of Ca2+ signals in the axoneme. This signaling is superimposed with a geometric clutch mechanism for the regulation of flagella bending dynamics and our modeling produces results in agreement with experimental data.
T2  - European Biophysics Journal
T1  - Calcium signaling modulates the dynamics of cilia and flagella
VL  - 49
IS  - 7
SP  - 619
EP  - 631
DO  - 10.1007/s00249-020-01471-8
ER  - 

@article{
author = "Satarić, Miljko V. and Zdravković, Slobodan and Nemeš, Tomas and Satarić, Bogdan M.",
year = "2020",
abstract = "To adapt to changing environments cells must signal and signaling requires messengers whose concentration varies with time in space. We here consider the messenger role of calcium ions implicated in regulation of the wave-like bending dynamics of cilia and flagella. The emphasis is on microtubules as polyelectrolytes serving as transmission lines for the flow of Ca2+ signals in the axoneme. This signaling is superimposed with a geometric clutch mechanism for the regulation of flagella bending dynamics and our modeling produces results in agreement with experimental data.",
journal = "European Biophysics Journal",
title = "Calcium signaling modulates the dynamics of cilia and flagella",
volume = "49",
number = "7",
pages = "619-631",
doi = "10.1007/s00249-020-01471-8"
}

Satarić, M. V., Zdravković, S., Nemeš, T.,& Satarić, B. M.. (2020). Calcium signaling modulates the dynamics of cilia and flagella. in European Biophysics Journal, 49(7), 619-631.
https://doi.org/10.1007/s00249-020-01471-8

Satarić MV, Zdravković S, Nemeš T, Satarić BM. Calcium signaling modulates the dynamics of cilia and flagella. in European Biophysics Journal. 2020;49(7):619-631.
doi:10.1007/s00249-020-01471-8 .

Satarić, Miljko V., Zdravković, Slobodan, Nemeš, Tomas, Satarić, Bogdan M., "Calcium signaling modulates the dynamics of cilia and flagella" in European Biophysics Journal, 49, no. 7 (2020):619-631,
https://doi.org/10.1007/s00249-020-01471-8 . .

TY  - JOUR
AU  - Zdravković, Slobodan
AU  - Čevizović, Dalibor
AU  - Bugay, Aleksandr N.
AU  - Maluckov, Aleksandra
PY  - 2019
UR  - http://aip.scitation.org/doi/10.1063/1.5090962
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8207
AB  - We study nonlinear dynamics of the DNA molecule relying on a helicoidal Peyrard-Bishop model. We look for traveling wave solutions and show that a continuum approximation brings about kink solitons moving along the chain. This statement is supported by the numerical solution of a relevant dynamical equation of motion. Finally, we argue that an existence of both kinks and localized modulated solitons (breathers) could be a useful tool to describe DNA-RNA transcription. © 2019 Author(s).
T2  - Chaos
T1  - Stationary solitary and kink solutions in the helicoidal Peyrard-Bishop model of DNA molecule
VL  - 29
IS  - 5
SP  - 053118
DO  - 10.1063/1.5090962
ER  - 

@article{
author = "Zdravković, Slobodan and Čevizović, Dalibor and Bugay, Aleksandr N. and Maluckov, Aleksandra",
year = "2019",
abstract = "We study nonlinear dynamics of the DNA molecule relying on a helicoidal Peyrard-Bishop model. We look for traveling wave solutions and show that a continuum approximation brings about kink solitons moving along the chain. This statement is supported by the numerical solution of a relevant dynamical equation of motion. Finally, we argue that an existence of both kinks and localized modulated solitons (breathers) could be a useful tool to describe DNA-RNA transcription. © 2019 Author(s).",
journal = "Chaos",
title = "Stationary solitary and kink solutions in the helicoidal Peyrard-Bishop model of DNA molecule",
volume = "29",
number = "5",
pages = "053118",
doi = "10.1063/1.5090962"
}

Zdravković, S., Čevizović, D., Bugay, A. N.,& Maluckov, A.. (2019). Stationary solitary and kink solutions in the helicoidal Peyrard-Bishop model of DNA molecule. in Chaos, 29(5), 053118.
https://doi.org/10.1063/1.5090962

Zdravković S, Čevizović D, Bugay AN, Maluckov A. Stationary solitary and kink solutions in the helicoidal Peyrard-Bishop model of DNA molecule. in Chaos. 2019;29(5):053118.
doi:10.1063/1.5090962 .

Zdravković, Slobodan, Čevizović, Dalibor, Bugay, Aleksandr N., Maluckov, Aleksandra, "Stationary solitary and kink solutions in the helicoidal Peyrard-Bishop model of DNA molecule" in Chaos, 29, no. 5 (2019):053118,
https://doi.org/10.1063/1.5090962 . .

TY  - JOUR
AU  - Zdravković, Slobodan
AU  - Satarić, Miljko V.
AU  - Parkhomenko, Aleksandr Yu.
AU  - Bugay, Aleksandr N.
PY  - 2018
UR  - http://aip.scitation.org/doi/10.1063/1.5046772
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/7940
AB  - Nonlinear dynamics of DNA molecule at segments where DNA-RNA transcription occurs is studied. Our basic idea is that the solitary wave, moving along the chain, transforms into a demodulated one at these segments. The second idea is that the wave becomes a standing one due to interaction with DNA surrounding, e.g., RNA polymerase molecules. We explain why this is biologically convenient and show that our results match the experimental ones. In addition, we suggest how to experimentally determine crucial constant describing covalent bonds within DNA. © 2018 Author(s).
T2  - Chaos
T1  - Demodulated standing solitary wave and DNA-RNA transcription
VL  - 28
IS  - 11
SP  - 113103
DO  - 10.1063/1.5046772
ER  - 

@article{
author = "Zdravković, Slobodan and Satarić, Miljko V. and Parkhomenko, Aleksandr Yu. and Bugay, Aleksandr N.",
year = "2018",
abstract = "Nonlinear dynamics of DNA molecule at segments where DNA-RNA transcription occurs is studied. Our basic idea is that the solitary wave, moving along the chain, transforms into a demodulated one at these segments. The second idea is that the wave becomes a standing one due to interaction with DNA surrounding, e.g., RNA polymerase molecules. We explain why this is biologically convenient and show that our results match the experimental ones. In addition, we suggest how to experimentally determine crucial constant describing covalent bonds within DNA. © 2018 Author(s).",
journal = "Chaos",
title = "Demodulated standing solitary wave and DNA-RNA transcription",
volume = "28",
number = "11",
pages = "113103",
doi = "10.1063/1.5046772"
}

Zdravković, S., Satarić, M. V., Parkhomenko, A. Yu.,& Bugay, A. N.. (2018). Demodulated standing solitary wave and DNA-RNA transcription. in Chaos, 28(11), 113103.
https://doi.org/10.1063/1.5046772

Zdravković S, Satarić MV, Parkhomenko AY, Bugay AN. Demodulated standing solitary wave and DNA-RNA transcription. in Chaos. 2018;28(11):113103.
doi:10.1063/1.5046772 .

Zdravković, Slobodan, Satarić, Miljko V., Parkhomenko, Aleksandr Yu., Bugay, Aleksandr N., "Demodulated standing solitary wave and DNA-RNA transcription" in Chaos, 28, no. 11 (2018):113103,
https://doi.org/10.1063/1.5046772 . .

TY  - JOUR
AU  - Zdravković, Slobodan
AU  - Satarić, Miljko V.
AU  - Sivčević, Vladimir
PY  - 2018
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/7652
AB  - In the present work, we deal with nonlinear dynamics of microtubules. A new model, describing nonlinear dynamics of microtubules, is introduced. Its advantages over two existing models are demonstrated. We show that dynamics of microtubules can be explained in terms of kink solitons. Also, circumstances yielding to either subsonic or supersonic solitons are discussed.
T2  - Nonlinear Dynamics
T1  - General model of microtubules
VL  - 92
IS  - 2
SP  - 479
EP  - 486
DO  - 10.1007/s11071-018-4069-5
ER  - 

@article{
author = "Zdravković, Slobodan and Satarić, Miljko V. and Sivčević, Vladimir",
year = "2018",
abstract = "In the present work, we deal with nonlinear dynamics of microtubules. A new model, describing nonlinear dynamics of microtubules, is introduced. Its advantages over two existing models are demonstrated. We show that dynamics of microtubules can be explained in terms of kink solitons. Also, circumstances yielding to either subsonic or supersonic solitons are discussed.",
journal = "Nonlinear Dynamics",
title = "General model of microtubules",
volume = "92",
number = "2",
pages = "479-486",
doi = "10.1007/s11071-018-4069-5"
}

Zdravković, S., Satarić, M. V.,& Sivčević, V.. (2018). General model of microtubules. in Nonlinear Dynamics, 92(2), 479-486.
https://doi.org/10.1007/s11071-018-4069-5

Zdravković S, Satarić MV, Sivčević V. General model of microtubules. in Nonlinear Dynamics. 2018;92(2):479-486.
doi:10.1007/s11071-018-4069-5 .

Zdravković, Slobodan, Satarić, Miljko V., Sivčević, Vladimir, "General model of microtubules" in Nonlinear Dynamics, 92, no. 2 (2018):479-486,
https://doi.org/10.1007/s11071-018-4069-5 . .

TY  - JOUR
AU  - Tuszynski, Jack A.
AU  - Satarić, Miljko V.
AU  - Sekulić, Dalibor L.
AU  - Satarić, Bogdan M.
AU  - Zdravković, Slobodan
PY  - 2018
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/8397
AB  - Calcium ions (Ca2+) tune and control numerous diverse aspects of cochlear and vestibular physiological processes. This paper is focused on the Ca2+ control of mechanotransduction in sensory hair cells in the context of polyelectrolyte properties of actin filaments within the hair–bundles of inner ear. These actin filaments appear to serve as efficient pathways for the flow of Ca2+ ions inside stereocilia. We showed how this can be utilized for tuning of force–generating myosin motors. In an established model, we unified the Ca2+ nonlinear dynamics involved in the control of myosin adaptation motors with mechanical displacements of hair–bundles. The model shows that the characteristic time scales fit reasonably well with the available experimental data for spontaneous oscillations in the inner ear. This scenario promises to fill a gap in our understanding of the role of Ca2+ ions in the regulation of processes in the auditory cells of the inner ear. © 2018 Elsevier B.V.
T2  - Biosystems
T1  - Nonlinear calcium ion waves along actin filaments control active hair–bundle motility
VL  - 173
SP  - 181
EP  - 190
DO  - 10.1016/j.biosystems.2018.08.006
ER  - 

@article{
author = "Tuszynski, Jack A. and Satarić, Miljko V. and Sekulić, Dalibor L. and Satarić, Bogdan M. and Zdravković, Slobodan",
year = "2018",
abstract = "Calcium ions (Ca2+) tune and control numerous diverse aspects of cochlear and vestibular physiological processes. This paper is focused on the Ca2+ control of mechanotransduction in sensory hair cells in the context of polyelectrolyte properties of actin filaments within the hair–bundles of inner ear. These actin filaments appear to serve as efficient pathways for the flow of Ca2+ ions inside stereocilia. We showed how this can be utilized for tuning of force–generating myosin motors. In an established model, we unified the Ca2+ nonlinear dynamics involved in the control of myosin adaptation motors with mechanical displacements of hair–bundles. The model shows that the characteristic time scales fit reasonably well with the available experimental data for spontaneous oscillations in the inner ear. This scenario promises to fill a gap in our understanding of the role of Ca2+ ions in the regulation of processes in the auditory cells of the inner ear. © 2018 Elsevier B.V.",
journal = "Biosystems",
title = "Nonlinear calcium ion waves along actin filaments control active hair–bundle motility",
volume = "173",
pages = "181-190",
doi = "10.1016/j.biosystems.2018.08.006"
}

Tuszynski, J. A., Satarić, M. V., Sekulić, D. L., Satarić, B. M.,& Zdravković, S.. (2018). Nonlinear calcium ion waves along actin filaments control active hair–bundle motility. in Biosystems, 173, 181-190.
https://doi.org/10.1016/j.biosystems.2018.08.006

Tuszynski JA, Satarić MV, Sekulić DL, Satarić BM, Zdravković S. Nonlinear calcium ion waves along actin filaments control active hair–bundle motility. in Biosystems. 2018;173:181-190.
doi:10.1016/j.biosystems.2018.08.006 .

Tuszynski, Jack A., Satarić, Miljko V., Sekulić, Dalibor L., Satarić, Bogdan M., Zdravković, Slobodan, "Nonlinear calcium ion waves along actin filaments control active hair–bundle motility" in Biosystems, 173 (2018):181-190,
https://doi.org/10.1016/j.biosystems.2018.08.006 . .

TY  - JOUR
AU  - Petrović, Suzana
AU  - Gaković, Biljana M.
AU  - Zamfirescu, M.
AU  - Radu, C.
AU  - Peruško, Davor
AU  - Radak, Bojan
AU  - Ristoscu, Carmen
AU  - Zdravković, Slobodan
AU  - Luculescu, C. L.
AU  - Mihailescu, Ion N.
PY  - 2017
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/7164
AB  - Modification of single and complex nickel-palladium samples by laser processing in the femtosecond time domain was studied. The samples were processed by focused Ti:Sapphire laser beam (Clark CPA-2101) with 775 nm laser wavelength, 2 kHz repetition rate, 200 fs pulse duration. The laser-induced morphological modifications have shown dependence on the applied fluences and number of laser pulses. The formed surface nanostructures on the single NiPd/Si and multilayer 5x(Ni/Pd)/Si systems are compared with individual Ni and Pd thin films. The results show an increase in surface roughness, formation of parallel periodic surface structures, appearance of hydrodynamic features and ablation of surface material. At low number of pulses (less than 10 pulses) and low pulse energies range (not over 1.7 mu J), the two types of laser-induced periodic surface structure (LIPSS) can be observed: low and high spatial frequency LIPSS (HSFL and LSFL). For all samples, the measured LSFL periods were 720 nm for the ripples created solely on thin film surfaces during the single pulse action. In the case of the multi-pulse irradiation, the periodicities of created LSFLs on the all investigated thin films have shown tendency to reduction with increasing of pulse energies. (C) 2016 Elsevier B.V. All rights reserved.
T2  - Applied Surface Science
T1  - Femtosecond laser processing of NiPd single and 5x(Ni/Pd) multilayer thin films
VL  - 417
SP  - 16
EP  - 22
DO  - 10.1016/j.apsusc.2016.12.142
ER  - 

@article{
author = "Petrović, Suzana and Gaković, Biljana M. and Zamfirescu, M. and Radu, C. and Peruško, Davor and Radak, Bojan and Ristoscu, Carmen and Zdravković, Slobodan and Luculescu, C. L. and Mihailescu, Ion N.",
year = "2017",
abstract = "Modification of single and complex nickel-palladium samples by laser processing in the femtosecond time domain was studied. The samples were processed by focused Ti:Sapphire laser beam (Clark CPA-2101) with 775 nm laser wavelength, 2 kHz repetition rate, 200 fs pulse duration. The laser-induced morphological modifications have shown dependence on the applied fluences and number of laser pulses. The formed surface nanostructures on the single NiPd/Si and multilayer 5x(Ni/Pd)/Si systems are compared with individual Ni and Pd thin films. The results show an increase in surface roughness, formation of parallel periodic surface structures, appearance of hydrodynamic features and ablation of surface material. At low number of pulses (less than 10 pulses) and low pulse energies range (not over 1.7 mu J), the two types of laser-induced periodic surface structure (LIPSS) can be observed: low and high spatial frequency LIPSS (HSFL and LSFL). For all samples, the measured LSFL periods were 720 nm for the ripples created solely on thin film surfaces during the single pulse action. In the case of the multi-pulse irradiation, the periodicities of created LSFLs on the all investigated thin films have shown tendency to reduction with increasing of pulse energies. (C) 2016 Elsevier B.V. All rights reserved.",
journal = "Applied Surface Science",
title = "Femtosecond laser processing of NiPd single and 5x(Ni/Pd) multilayer thin films",
volume = "417",
pages = "16-22",
doi = "10.1016/j.apsusc.2016.12.142"
}

Petrović, S., Gaković, B. M., Zamfirescu, M., Radu, C., Peruško, D., Radak, B., Ristoscu, C., Zdravković, S., Luculescu, C. L.,& Mihailescu, I. N.. (2017). Femtosecond laser processing of NiPd single and 5x(Ni/Pd) multilayer thin films. in Applied Surface Science, 417, 16-22.
https://doi.org/10.1016/j.apsusc.2016.12.142

Petrović S, Gaković BM, Zamfirescu M, Radu C, Peruško D, Radak B, Ristoscu C, Zdravković S, Luculescu CL, Mihailescu IN. Femtosecond laser processing of NiPd single and 5x(Ni/Pd) multilayer thin films. in Applied Surface Science. 2017;417:16-22.
doi:10.1016/j.apsusc.2016.12.142 .

Petrović, Suzana, Gaković, Biljana M., Zamfirescu, M., Radu, C., Peruško, Davor, Radak, Bojan, Ristoscu, Carmen, Zdravković, Slobodan, Luculescu, C. L., Mihailescu, Ion N., "Femtosecond laser processing of NiPd single and 5x(Ni/Pd) multilayer thin films" in Applied Surface Science, 417 (2017):16-22,
https://doi.org/10.1016/j.apsusc.2016.12.142 . .

TY  - JOUR
AU  - Zdravković, Slobodan
AU  - Zeković, Slobodan
PY  - 2017
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/1856
AB  - Microtubules (MTs) are the most important part of cytoskeleton. In this paper we deal with two basic nonlinear differential equations coming from the two known models describing nonlinear dynamics of MTs. These equations are solved using the series expansion unknown function method (SEUFM). Trying to recognize the most general mathematical procedure for solving these equations the solutions are compared with those obtained earlier using the tangent hyperbolic function method (THFM) and the simplest equation method (SEM). In all these three approaches we express the solutions of these equations as series expansions. In the cases of THFM and SEM the functions existing in the series are known while SEUFM assumes unknown function.
T2  - Chinese Journal of Physics
T1  - Nonlinear dynamics of microtubules and series expansion unknown function method
VL  - 55
IS  - 6
SP  - 2400
EP  - 2406
DO  - 10.1016/j.cjph.2017.10.009
ER  - 

@article{
author = "Zdravković, Slobodan and Zeković, Slobodan",
year = "2017",
abstract = "Microtubules (MTs) are the most important part of cytoskeleton. In this paper we deal with two basic nonlinear differential equations coming from the two known models describing nonlinear dynamics of MTs. These equations are solved using the series expansion unknown function method (SEUFM). Trying to recognize the most general mathematical procedure for solving these equations the solutions are compared with those obtained earlier using the tangent hyperbolic function method (THFM) and the simplest equation method (SEM). In all these three approaches we express the solutions of these equations as series expansions. In the cases of THFM and SEM the functions existing in the series are known while SEUFM assumes unknown function.",
journal = "Chinese Journal of Physics",
title = "Nonlinear dynamics of microtubules and series expansion unknown function method",
volume = "55",
number = "6",
pages = "2400-2406",
doi = "10.1016/j.cjph.2017.10.009"
}

Zdravković, S.,& Zeković, S.. (2017). Nonlinear dynamics of microtubules and series expansion unknown function method. in Chinese Journal of Physics, 55(6), 2400-2406.
https://doi.org/10.1016/j.cjph.2017.10.009

Zdravković S, Zeković S. Nonlinear dynamics of microtubules and series expansion unknown function method. in Chinese Journal of Physics. 2017;55(6):2400-2406.
doi:10.1016/j.cjph.2017.10.009 .

Zdravković, Slobodan, Zeković, Slobodan, "Nonlinear dynamics of microtubules and series expansion unknown function method" in Chinese Journal of Physics, 55, no. 6 (2017):2400-2406,
https://doi.org/10.1016/j.cjph.2017.10.009 . .

TY  - JOUR
AU  - Zdravković, Slobodan
AU  - Bugay, Aleksandr N.
AU  - Parkhomenko, Aleksandr Yu.
PY  - 2017
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/1824
AB  - We here present a model of nonlinear dynamics of microtubules using modified extended tanh-function method as a mathematical tool. Interaction between neighbouring dimers belonging to a single protofilament is commonly modelled by a harmonic potential. In this paper, we introduce a more realistic Morse potential energy instead. We obtained three solitary waves as before, when the harmonic potential was used. However, the Morse potential allows transition from the state when elastic term in the expression for total energy is bigger than the inertial one to the state when the inertial potential is bigger. Also, three new solutions were obtained.
T2  - Nonlinear Dynamics
T1  - Application of Morse potential in nonlinear dynamics of microtubules
VL  - 90
IS  - 4
SP  - 2841
EP  - 2849
DO  - 10.1007/s11071-017-3845-y
ER  - 

@article{
author = "Zdravković, Slobodan and Bugay, Aleksandr N. and Parkhomenko, Aleksandr Yu.",
year = "2017",
abstract = "We here present a model of nonlinear dynamics of microtubules using modified extended tanh-function method as a mathematical tool. Interaction between neighbouring dimers belonging to a single protofilament is commonly modelled by a harmonic potential. In this paper, we introduce a more realistic Morse potential energy instead. We obtained three solitary waves as before, when the harmonic potential was used. However, the Morse potential allows transition from the state when elastic term in the expression for total energy is bigger than the inertial one to the state when the inertial potential is bigger. Also, three new solutions were obtained.",
journal = "Nonlinear Dynamics",
title = "Application of Morse potential in nonlinear dynamics of microtubules",
volume = "90",
number = "4",
pages = "2841-2849",
doi = "10.1007/s11071-017-3845-y"
}

Zdravković, S., Bugay, A. N.,& Parkhomenko, A. Yu.. (2017). Application of Morse potential in nonlinear dynamics of microtubules. in Nonlinear Dynamics, 90(4), 2841-2849.
https://doi.org/10.1007/s11071-017-3845-y

Zdravković S, Bugay AN, Parkhomenko AY. Application of Morse potential in nonlinear dynamics of microtubules. in Nonlinear Dynamics. 2017;90(4):2841-2849.
doi:10.1007/s11071-017-3845-y .

Zdravković, Slobodan, Bugay, Aleksandr N., Parkhomenko, Aleksandr Yu., "Application of Morse potential in nonlinear dynamics of microtubules" in Nonlinear Dynamics, 90, no. 4 (2017):2841-2849,
https://doi.org/10.1007/s11071-017-3845-y . .

TY  - JOUR
AU  - Zdravković, Slobodan
PY  - 2017
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/1690
AB  - In the present paper we deal with nonlinear dynamics of microtubules. The structure and role of microtubules in cells are explained as well as one of models explaining their dynamics. Solutions of the crucial nonlinear differential equation depend on used mathematical methods. Two commonly used procedures, continuum and semi-discrete approximations, are explained. These solutions are solitary waves usually called as kink solitons, breathers and bell-type solitons.
T2  - Journal of the Serbian Chemical Society
T1  - Microtubules: a network for solitary waves
VL  - 82
IS  - 5
SP  - 469
EP  - 481
DO  - 10.2298/JSC161118020Z
ER  - 

@article{
author = "Zdravković, Slobodan",
year = "2017",
abstract = "In the present paper we deal with nonlinear dynamics of microtubules. The structure and role of microtubules in cells are explained as well as one of models explaining their dynamics. Solutions of the crucial nonlinear differential equation depend on used mathematical methods. Two commonly used procedures, continuum and semi-discrete approximations, are explained. These solutions are solitary waves usually called as kink solitons, breathers and bell-type solitons.",
journal = "Journal of the Serbian Chemical Society",
title = "Microtubules: a network for solitary waves",
volume = "82",
number = "5",
pages = "469-481",
doi = "10.2298/JSC161118020Z"
}

Zdravković, S.. (2017). Microtubules: a network for solitary waves. in Journal of the Serbian Chemical Society, 82(5), 469-481.
https://doi.org/10.2298/JSC161118020Z

Zdravković S. Microtubules: a network for solitary waves. in Journal of the Serbian Chemical Society. 2017;82(5):469-481.
doi:10.2298/JSC161118020Z .

Zdravković, Slobodan, "Microtubules: a network for solitary waves" in Journal of the Serbian Chemical Society, 82, no. 5 (2017):469-481,
https://doi.org/10.2298/JSC161118020Z . .

TY  - JOUR
AU  - Satarić, Miljko V.
AU  - Sekulić, Dalibor L.
AU  - Zdravković, Slobodan
AU  - Ralević, Nebojša M.
PY  - 2017
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/1560
AB  - It appears that so called post translational modifications of tubulin heterodimers are mostly focussed at positions of amino acid sequences of carboxy terminal tails. These changes have very profound effects on microtubule functions especially in connection with cellular traffic in terms of motor proteins. In this study, we elaborated the biophysical model aimed to explain the strategy governing these subtle interplays between structural and functional properties of microtubules. We relied onto Langevin equations including fluctuation dissipation processes. In that context we found out that small interaction between a charged motor neck domain and oppositely charged carboxy terminal tail of the a tubulin plays the decisive role in tuning kinesin-1 motor processivity along microtubules.
T2  - Journal of Theoretical Biology
T1  - A biophysical model of how alpha-tubulin carboxy-terminal tails tune kinesin-1 processivity along microtubule
VL  - 420
SP  - 152
EP  - 157
DO  - 10.1016/j.jtbi.2017.03.012
ER  - 

@article{
author = "Satarić, Miljko V. and Sekulić, Dalibor L. and Zdravković, Slobodan and Ralević, Nebojša M.",
year = "2017",
abstract = "It appears that so called post translational modifications of tubulin heterodimers are mostly focussed at positions of amino acid sequences of carboxy terminal tails. These changes have very profound effects on microtubule functions especially in connection with cellular traffic in terms of motor proteins. In this study, we elaborated the biophysical model aimed to explain the strategy governing these subtle interplays between structural and functional properties of microtubules. We relied onto Langevin equations including fluctuation dissipation processes. In that context we found out that small interaction between a charged motor neck domain and oppositely charged carboxy terminal tail of the a tubulin plays the decisive role in tuning kinesin-1 motor processivity along microtubules.",
journal = "Journal of Theoretical Biology",
title = "A biophysical model of how alpha-tubulin carboxy-terminal tails tune kinesin-1 processivity along microtubule",
volume = "420",
pages = "152-157",
doi = "10.1016/j.jtbi.2017.03.012"
}

Satarić, M. V., Sekulić, D. L., Zdravković, S.,& Ralević, N. M.. (2017). A biophysical model of how alpha-tubulin carboxy-terminal tails tune kinesin-1 processivity along microtubule. in Journal of Theoretical Biology, 420, 152-157.
https://doi.org/10.1016/j.jtbi.2017.03.012

Satarić MV, Sekulić DL, Zdravković S, Ralević NM. A biophysical model of how alpha-tubulin carboxy-terminal tails tune kinesin-1 processivity along microtubule. in Journal of Theoretical Biology. 2017;420:152-157.
doi:10.1016/j.jtbi.2017.03.012 .

Satarić, Miljko V., Sekulić, Dalibor L., Zdravković, Slobodan, Ralević, Nebojša M., "A biophysical model of how alpha-tubulin carboxy-terminal tails tune kinesin-1 processivity along microtubule" in Journal of Theoretical Biology, 420 (2017):152-157,
https://doi.org/10.1016/j.jtbi.2017.03.012 . .

TY  - JOUR
AU  - Kavitha, L.
AU  - Parasuraman, E.
AU  - Muniyappan, A.
AU  - Gopi, D.
AU  - Zdravković, Slobodan
PY  - 2017
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/1582
AB  - We made an attempt to provide a realistic picture of the localization of energy in microtubules (MTs), and we intend to model the nonlinear dynamics of MTs using the double-well form of the potential describing the dipole-dipole interactions. We investigate the modulational instability (MI) of the nonlinear plane wave solutions by considering both the wave vector (q) of the basic states and the wave vector (Q) of the perturbations as free parameters. A set of explicit criteria of MI is derived, and under the plane-wave perturbation, the constant amplitude solution becomes unstable and localized discrete breathers (DBs) solutions appear. We show numerically that MI is also an indicator of the presence of discrete breathers. We suggest that an electric field favourably leads the DB excitations towards the properly aligned end triggering a dissembly of the protofilament due to the energy release. These DBs could catalyse MT-associated proteins attachment/detachment and promote or inhibit the kinesin walk. We establish that the electromechanical vibrations in MTs can generate an electromagnetic field in the form of an electric pulse (breathers) which propagates along MT serving as signalling pathway in neuronal cells. The DBs in MT can be viewed as a bit of information whose propagation can be controlled by an electric filed. They might perform the role of elementary logic gates, thus implementing a subneuronal mode of computation. The generated DBs present us with novel possibilities for the direct interaction between the local electromagnetic field and the cytoskeletal structures in neurons. Thus, we emphasize that the effect of discreteness and electric field plays a significant role in MTs.
T2  - Nonlinear Dynamics
T1  - Localized discrete breather modes in neuronal microtubules
VL  - 88
IS  - 3
SP  - 2013
EP  - 2033
DO  - 10.1007/s11071-017-3359-7
ER  - 

@article{
author = "Kavitha, L. and Parasuraman, E. and Muniyappan, A. and Gopi, D. and Zdravković, Slobodan",
year = "2017",
abstract = "We made an attempt to provide a realistic picture of the localization of energy in microtubules (MTs), and we intend to model the nonlinear dynamics of MTs using the double-well form of the potential describing the dipole-dipole interactions. We investigate the modulational instability (MI) of the nonlinear plane wave solutions by considering both the wave vector (q) of the basic states and the wave vector (Q) of the perturbations as free parameters. A set of explicit criteria of MI is derived, and under the plane-wave perturbation, the constant amplitude solution becomes unstable and localized discrete breathers (DBs) solutions appear. We show numerically that MI is also an indicator of the presence of discrete breathers. We suggest that an electric field favourably leads the DB excitations towards the properly aligned end triggering a dissembly of the protofilament due to the energy release. These DBs could catalyse MT-associated proteins attachment/detachment and promote or inhibit the kinesin walk. We establish that the electromechanical vibrations in MTs can generate an electromagnetic field in the form of an electric pulse (breathers) which propagates along MT serving as signalling pathway in neuronal cells. The DBs in MT can be viewed as a bit of information whose propagation can be controlled by an electric filed. They might perform the role of elementary logic gates, thus implementing a subneuronal mode of computation. The generated DBs present us with novel possibilities for the direct interaction between the local electromagnetic field and the cytoskeletal structures in neurons. Thus, we emphasize that the effect of discreteness and electric field plays a significant role in MTs.",
journal = "Nonlinear Dynamics",
title = "Localized discrete breather modes in neuronal microtubules",
volume = "88",
number = "3",
pages = "2013-2033",
doi = "10.1007/s11071-017-3359-7"
}

Kavitha, L., Parasuraman, E., Muniyappan, A., Gopi, D.,& Zdravković, S.. (2017). Localized discrete breather modes in neuronal microtubules. in Nonlinear Dynamics, 88(3), 2013-2033.
https://doi.org/10.1007/s11071-017-3359-7

Kavitha L, Parasuraman E, Muniyappan A, Gopi D, Zdravković S. Localized discrete breather modes in neuronal microtubules. in Nonlinear Dynamics. 2017;88(3):2013-2033.
doi:10.1007/s11071-017-3359-7 .

Kavitha, L., Parasuraman, E., Muniyappan, A., Gopi, D., Zdravković, Slobodan, "Localized discrete breather modes in neuronal microtubules" in Nonlinear Dynamics, 88, no. 3 (2017):2013-2033,
https://doi.org/10.1007/s11071-017-3359-7 . .

TY  - JOUR
AU  - Sekulić, Dalibor L.
AU  - Satarić, Bogdan M.
AU  - Zdravković, Slobodan
AU  - Bugay, Aleksandr N.
AU  - Satarić, Miljko V.
PY  - 2016
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/1225
AB  - The mechanical and electrical properties, and information processing capabilities of microtubules are the permanent subject of interest for carrying out experiments in vitro and in silico, as well as for theoretical attempts to elucidate the underlying processes. In this paper, we developed a new model of the mechano-electrical waves elicited in the rows of very flexible C-terminal tails which decorate the outer surface of each microtubule. The fact that C-terminal tails play very diverse roles in many cellular functions, such as recruitment of motor proteins and microtubule-associated proteins, motivated us to consider their collective dynamics as the source of localized waves aimed for communication between microtubule and associated proteins. Our approach is based on the ferroelectric liquid crystal model and it leads to the effective asymmetric double-well potential which brings about the conditions for the appearance of kink-waves conducted by intrinsic electric fields embedded in microtubules. These kinks can serve as the signals for control and regulation of intracellular traffic along microtubules performed by processive motions of motor proteins, primarly from kinesin and dynein families. On the other hand, they can be precursors for initiation of dynamical instability of microtubules by recruiting the proper proteins responsible for the depolymerization process. Published by AIP Publishing.
T2  - Chaos
T1  - Nonlinear dynamics of C-terminal tails in cellular microtubules
VL  - 26
IS  - 7
DO  - 10.1063/1.4959802
ER  - 

@article{
author = "Sekulić, Dalibor L. and Satarić, Bogdan M. and Zdravković, Slobodan and Bugay, Aleksandr N. and Satarić, Miljko V.",
year = "2016",
abstract = "The mechanical and electrical properties, and information processing capabilities of microtubules are the permanent subject of interest for carrying out experiments in vitro and in silico, as well as for theoretical attempts to elucidate the underlying processes. In this paper, we developed a new model of the mechano-electrical waves elicited in the rows of very flexible C-terminal tails which decorate the outer surface of each microtubule. The fact that C-terminal tails play very diverse roles in many cellular functions, such as recruitment of motor proteins and microtubule-associated proteins, motivated us to consider their collective dynamics as the source of localized waves aimed for communication between microtubule and associated proteins. Our approach is based on the ferroelectric liquid crystal model and it leads to the effective asymmetric double-well potential which brings about the conditions for the appearance of kink-waves conducted by intrinsic electric fields embedded in microtubules. These kinks can serve as the signals for control and regulation of intracellular traffic along microtubules performed by processive motions of motor proteins, primarly from kinesin and dynein families. On the other hand, they can be precursors for initiation of dynamical instability of microtubules by recruiting the proper proteins responsible for the depolymerization process. Published by AIP Publishing.",
journal = "Chaos",
title = "Nonlinear dynamics of C-terminal tails in cellular microtubules",
volume = "26",
number = "7",
doi = "10.1063/1.4959802"
}

Sekulić, D. L., Satarić, B. M., Zdravković, S., Bugay, A. N.,& Satarić, M. V.. (2016). Nonlinear dynamics of C-terminal tails in cellular microtubules. in Chaos, 26(7).
https://doi.org/10.1063/1.4959802

Sekulić DL, Satarić BM, Zdravković S, Bugay AN, Satarić MV. Nonlinear dynamics of C-terminal tails in cellular microtubules. in Chaos. 2016;26(7).
doi:10.1063/1.4959802 .

Sekulić, Dalibor L., Satarić, Bogdan M., Zdravković, Slobodan, Bugay, Aleksandr N., Satarić, Miljko V., "Nonlinear dynamics of C-terminal tails in cellular microtubules" in Chaos, 26, no. 7 (2016),
https://doi.org/10.1063/1.4959802 . .