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  - Kavitha, L.
AU  - Muniyappan, A.
AU  - Zdravković, Slobodan
AU  - Satarić, Miljko V.
AU  - Marlewski, A.
AU  - Dhamayanthi, S.
AU  - Gopi, D.
PY  - 2014
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/182
AB  - Among many types of proteinaceous filaments, microtubules (MTs) constitute the most rigid components of the cellular cytoskeleton. Microtubule dynamics is essential for many vital cellular processes such as intracellular transport, metabolism, and cell division. We investigate the nonlinear dynamics of inhomogeneous microtubulin systems and the MT dynamics is found to be governed by a perturbed sine-Gordon equation. In the presence of various competing nonlinear inhomogeneities, it is shown that this nonlinear model can lead to the existence of kink and antikink solitons moving along MTs. We demonstrate kink-antikink pair collision in the framework of Hirotas bilinearization method. We conjecture that the collisions of the quanta of energy propagating in the form of kinks and antikinks may offer a new view of the mechanism of the retrograde and anterograde transport direction regulation of motor proteins in microtubulin systems.
T2  - Chinese Physics B
T1  - Propagation of kink-antikink pair along microtubules as a control mechanism for polymerization and depolymerization processes
VL  - 23
IS  - 9
DO  - 10.1088/1674-1056/23/9/098703
ER  - 

@article{
author = "Kavitha, L. and Muniyappan, A. and Zdravković, Slobodan and Satarić, Miljko V. and Marlewski, A. and Dhamayanthi, S. and Gopi, D.",
year = "2014",
abstract = "Among many types of proteinaceous filaments, microtubules (MTs) constitute the most rigid components of the cellular cytoskeleton. Microtubule dynamics is essential for many vital cellular processes such as intracellular transport, metabolism, and cell division. We investigate the nonlinear dynamics of inhomogeneous microtubulin systems and the MT dynamics is found to be governed by a perturbed sine-Gordon equation. In the presence of various competing nonlinear inhomogeneities, it is shown that this nonlinear model can lead to the existence of kink and antikink solitons moving along MTs. We demonstrate kink-antikink pair collision in the framework of Hirotas bilinearization method. We conjecture that the collisions of the quanta of energy propagating in the form of kinks and antikinks may offer a new view of the mechanism of the retrograde and anterograde transport direction regulation of motor proteins in microtubulin systems.",
journal = "Chinese Physics B",
title = "Propagation of kink-antikink pair along microtubules as a control mechanism for polymerization and depolymerization processes",
volume = "23",
number = "9",
doi = "10.1088/1674-1056/23/9/098703"
}

Kavitha, L., Muniyappan, A., Zdravković, S., Satarić, M. V., Marlewski, A., Dhamayanthi, S.,& Gopi, D.. (2014). Propagation of kink-antikink pair along microtubules as a control mechanism for polymerization and depolymerization processes. in Chinese Physics B, 23(9).
https://doi.org/10.1088/1674-1056/23/9/098703

Kavitha L, Muniyappan A, Zdravković S, Satarić MV, Marlewski A, Dhamayanthi S, Gopi D. Propagation of kink-antikink pair along microtubules as a control mechanism for polymerization and depolymerization processes. in Chinese Physics B. 2014;23(9).
doi:10.1088/1674-1056/23/9/098703 .

Kavitha, L., Muniyappan, A., Zdravković, Slobodan, Satarić, Miljko V., Marlewski, A., Dhamayanthi, S., Gopi, D., "Propagation of kink-antikink pair along microtubules as a control mechanism for polymerization and depolymerization processes" in Chinese Physics B, 23, no. 9 (2014),
https://doi.org/10.1088/1674-1056/23/9/098703 . .

TY  - JOUR
AU  - Kavitha, L.
AU  - Muniyappan, A.
AU  - Prabhu, A.
AU  - Zdravković, Slobodan
AU  - Jayanthi, S.
AU  - Gopi, D.
PY  - 2013
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/5231
AB  - Non-linear localization phenomena in biological lattices have attracted a steadily growing interest and their existence has been predicted in a wide range of physical settings. We investigate the non-linear proton dynamics of a hydrogen-bonded chain in a semi-classical limit using the coherent state method combined with a Holstein-Primakoff bosonic representation. We demonstrate that even a weak inherent discreteness in the hydrogen-bonded (HB) chain may drastically modify the dynamics of the non-linear system, leading to instabilities that have no analog in the continuum limit. We suggest a possible localization mechanism of polarization oscillations of protons in a hydrogen-bonded chain through modulational instability analysis. This mechanism arises due to the neighboring proton-proton interaction and coherent tunneling of protons along hydrogen bonds and/or around heavy atoms. We present a detailed analysis of modulational instability, and highlight the role of the interaction strength of neighboring protons in the process of bioenergy localization. We perform molecular dynamics simulations and demonstrate the existence of nanoscale discrete breather (DB) modes in the hydrogen-bonded chain. These highly localized and long-lived non-linear breather modes may play a functional role in targeted energy transfer in biological systems.
T2  - Journal of Biological Physics
T1  - Nano breathers and molecular dynamics simulations in hydrogen-bonded chains
VL  - 39
IS  - 1
SP  - 15
EP  - 35
DO  - 10.1007/s10867-012-9283-7
ER  - 

@article{
author = "Kavitha, L. and Muniyappan, A. and Prabhu, A. and Zdravković, Slobodan and Jayanthi, S. and Gopi, D.",
year = "2013",
abstract = "Non-linear localization phenomena in biological lattices have attracted a steadily growing interest and their existence has been predicted in a wide range of physical settings. We investigate the non-linear proton dynamics of a hydrogen-bonded chain in a semi-classical limit using the coherent state method combined with a Holstein-Primakoff bosonic representation. We demonstrate that even a weak inherent discreteness in the hydrogen-bonded (HB) chain may drastically modify the dynamics of the non-linear system, leading to instabilities that have no analog in the continuum limit. We suggest a possible localization mechanism of polarization oscillations of protons in a hydrogen-bonded chain through modulational instability analysis. This mechanism arises due to the neighboring proton-proton interaction and coherent tunneling of protons along hydrogen bonds and/or around heavy atoms. We present a detailed analysis of modulational instability, and highlight the role of the interaction strength of neighboring protons in the process of bioenergy localization. We perform molecular dynamics simulations and demonstrate the existence of nanoscale discrete breather (DB) modes in the hydrogen-bonded chain. These highly localized and long-lived non-linear breather modes may play a functional role in targeted energy transfer in biological systems.",
journal = "Journal of Biological Physics",
title = "Nano breathers and molecular dynamics simulations in hydrogen-bonded chains",
volume = "39",
number = "1",
pages = "15-35",
doi = "10.1007/s10867-012-9283-7"
}

Kavitha, L., Muniyappan, A., Prabhu, A., Zdravković, S., Jayanthi, S.,& Gopi, D.. (2013). Nano breathers and molecular dynamics simulations in hydrogen-bonded chains. in Journal of Biological Physics, 39(1), 15-35.
https://doi.org/10.1007/s10867-012-9283-7

Kavitha L, Muniyappan A, Prabhu A, Zdravković S, Jayanthi S, Gopi D. Nano breathers and molecular dynamics simulations in hydrogen-bonded chains. in Journal of Biological Physics. 2013;39(1):15-35.
doi:10.1007/s10867-012-9283-7 .

Kavitha, L., Muniyappan, A., Prabhu, A., Zdravković, Slobodan, Jayanthi, S., Gopi, D., "Nano breathers and molecular dynamics simulations in hydrogen-bonded chains" in Journal of Biological Physics, 39, no. 1 (2013):15-35,
https://doi.org/10.1007/s10867-012-9283-7 . .