TY  - JOUR
AU  - Tadić, Bosiljka
AU  - Anđelković, Miroslav
AU  - Šuvakov, Milovan
PY  - 2018
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/1953
AB  - Hyperbolicity or negative curvature of complex networks is the intrinsic geometric proximity of nodes in the graph metric space, which implies an improved network function. Here, we investigate hidden combinatorial geometries in brain-to-brain coordination networks arising through social communications. The networks originate from correlations among EEG signals previously recorded during spoken communications comprising of 14 individuals with 24 speaker-listener pairs. We find that the corresponding networks are delta-hyperbolic with delta(max) = 1 and the graph diameter D = 3 in each brain. While the emergent hyperbolicity in the two-brain networks varies satisfying delta(max)/D/2 LT = 1 and can be attributed to the topology of the subgraph formed around the cross-brains linking channels. We identify these subgraphs in each studied two-brain network and decompose their structure into simple geometric descriptors ( triangles, tetrahedra and cliques of higher orders) that contribute to hyperbolicity. Considering topologies that exceed two separate brain networks as a measure of coordination synergy between the brains, we identify different neural correlation patterns ranging from weak coordination to super-brain structure. These topology features are in qualitative agreement with the listeners self-reported ratings of own experience and quality of the speaker, suggesting that studies of the cross-brain connector networks can reveal new insight into the neural mechanisms underlying human social behavior.
T2  - Frontiers in Physics
T1  - Origin of Hyperbolicity in Brain-to-Brain Coordination Networks
VL  - 6
DO  - 10.3389/fphy.2018.00007
ER  - 

@article{
author = "Tadić, Bosiljka and Anđelković, Miroslav and Šuvakov, Milovan",
year = "2018",
abstract = "Hyperbolicity or negative curvature of complex networks is the intrinsic geometric proximity of nodes in the graph metric space, which implies an improved network function. Here, we investigate hidden combinatorial geometries in brain-to-brain coordination networks arising through social communications. The networks originate from correlations among EEG signals previously recorded during spoken communications comprising of 14 individuals with 24 speaker-listener pairs. We find that the corresponding networks are delta-hyperbolic with delta(max) = 1 and the graph diameter D = 3 in each brain. While the emergent hyperbolicity in the two-brain networks varies satisfying delta(max)/D/2 LT = 1 and can be attributed to the topology of the subgraph formed around the cross-brains linking channels. We identify these subgraphs in each studied two-brain network and decompose their structure into simple geometric descriptors ( triangles, tetrahedra and cliques of higher orders) that contribute to hyperbolicity. Considering topologies that exceed two separate brain networks as a measure of coordination synergy between the brains, we identify different neural correlation patterns ranging from weak coordination to super-brain structure. These topology features are in qualitative agreement with the listeners self-reported ratings of own experience and quality of the speaker, suggesting that studies of the cross-brain connector networks can reveal new insight into the neural mechanisms underlying human social behavior.",
journal = "Frontiers in Physics",
title = "Origin of Hyperbolicity in Brain-to-Brain Coordination Networks",
volume = "6",
doi = "10.3389/fphy.2018.00007"
}

Tadić, B., Anđelković, M.,& Šuvakov, M.. (2018). Origin of Hyperbolicity in Brain-to-Brain Coordination Networks. in Frontiers in Physics, 6.
https://doi.org/10.3389/fphy.2018.00007

Tadić B, Anđelković M, Šuvakov M. Origin of Hyperbolicity in Brain-to-Brain Coordination Networks. in Frontiers in Physics. 2018;6.
doi:10.3389/fphy.2018.00007 .

Tadić, Bosiljka, Anđelković, Miroslav, Šuvakov, Milovan, "Origin of Hyperbolicity in Brain-to-Brain Coordination Networks" in Frontiers in Physics, 6 (2018),
https://doi.org/10.3389/fphy.2018.00007 . .

TY  - JOUR
AU  - Šuvakov, Milovan
AU  - Anđelković, Miroslav
AU  - Tadić, Bosiljka
PY  - 2018
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/1931
AB  - Multilevel self-assembly involving small structured groups of nano-particles provides new routes to development of functional materials with a sophisticated architecture. Apart from the inter-particle forces, the geometrical shapes and compatibility of the building blocks are decisive factors. Therefore, a comprehensive understanding of these processes is essential for the design of assemblies of desired properties. Here, we introduce a computational model for cooperative self-assembly with the simultaneous attachment of structured groups of particles, which can be described by simplexes (connected pairs, triangles, tetrahedrons and higher order cliques) to a growing network. The model incorporates geometric rules that provide suitable nesting spaces for the new group and the chemical affinity of the system to accept excess particles. For varying chemical affinity, we grow different classes of assemblies by binding the cliques of distributed sizes. Furthermore, we characterize the emergent structures by metrics of graph theory and algebraic topology of graphs, and 4-point test for the intrinsic hyperbolicity of the networks. Our results show that higher Q-connectedness of the appearing simplicial complexes can arise due to only geometric factors and that it can be efficiently modulated by changing the chemical potential and the polydispersity of the binding simplexes.
T2  - Scientific Reports
T1  - Hidden geometries in networks arising from cooperative self-assembly
VL  - 8
IS  - 1
SP  - 1987
DO  - 10.1038/s41598-018-20398-x
ER  - 

@article{
author = "Šuvakov, Milovan and Anđelković, Miroslav and Tadić, Bosiljka",
year = "2018",
abstract = "Multilevel self-assembly involving small structured groups of nano-particles provides new routes to development of functional materials with a sophisticated architecture. Apart from the inter-particle forces, the geometrical shapes and compatibility of the building blocks are decisive factors. Therefore, a comprehensive understanding of these processes is essential for the design of assemblies of desired properties. Here, we introduce a computational model for cooperative self-assembly with the simultaneous attachment of structured groups of particles, which can be described by simplexes (connected pairs, triangles, tetrahedrons and higher order cliques) to a growing network. The model incorporates geometric rules that provide suitable nesting spaces for the new group and the chemical affinity of the system to accept excess particles. For varying chemical affinity, we grow different classes of assemblies by binding the cliques of distributed sizes. Furthermore, we characterize the emergent structures by metrics of graph theory and algebraic topology of graphs, and 4-point test for the intrinsic hyperbolicity of the networks. Our results show that higher Q-connectedness of the appearing simplicial complexes can arise due to only geometric factors and that it can be efficiently modulated by changing the chemical potential and the polydispersity of the binding simplexes.",
journal = "Scientific Reports",
title = "Hidden geometries in networks arising from cooperative self-assembly",
volume = "8",
number = "1",
pages = "1987",
doi = "10.1038/s41598-018-20398-x"
}

Šuvakov, M., Anđelković, M.,& Tadić, B.. (2018). Hidden geometries in networks arising from cooperative self-assembly. in Scientific Reports, 8(1), 1987.
https://doi.org/10.1038/s41598-018-20398-x

Šuvakov M, Anđelković M, Tadić B. Hidden geometries in networks arising from cooperative self-assembly. in Scientific Reports. 2018;8(1):1987.
doi:10.1038/s41598-018-20398-x .

Šuvakov, Milovan, Anđelković, Miroslav, Tadić, Bosiljka, "Hidden geometries in networks arising from cooperative self-assembly" in Scientific Reports, 8, no. 1 (2018):1987,
https://doi.org/10.1038/s41598-018-20398-x . .

TY  - JOUR
AU  - Lazović, Saša
AU  - Leskovac, Andreja
AU  - Petrović, Sandra
AU  - Senerović, Lidija
AU  - Krivokapić, Nevena
AU  - Mitrović, Tatjana
AU  - Božović, Nikola
AU  - Vasić, Vesna M.
AU  - Nikodinović-Runić, Jasmina
PY  - 2017
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/1370
AB  - It is known that some bacterial species are more resilient to different kinds of irradiation due to the naturally developed protective mechanisms and compounds such as pigments. On the other hand, reasoned tissue engineering using plasma remains a critical task and requires very precise control of plasma parameters in order to mitigate its potential detrimental effects. Here we isolated a natural protective agent, microbially produced undecylprodigiosin ((52)-4-methoxy-5-[(5-undecy1-1H-pyrrol2-yl)methylenel-1H,5H-2,2-bipyrrole), and investigated its effects on human blood cells independently and in combination with plasma. Two apprOaches were applied; the first, undecylprodigiosin (UP pigment) was added to the blood cultures, which then were exposed to plasma (pre-treatment); and the second- the blood cultures were exposed to plasma and then treated with pigment (post-treatment). The interactions of plasma and UP pigment with blood cells were investigated by conducting a series of biological tests providing the information regarding their genotoxicity, cytotoxicity and redox modulating activities. The exposure of cells to plasma induced oxidative stress as well as certain genotoxic and cytotoxic effects seen as elevated micronuclei incidence, decreased cell proliferation and enhanced apoptosis. In blood cultures treated with UP pigment alone, we found that both cytotoxic and protective effects could be induced depending on the concentration used. The highest UP pigment concentration increased lipid peroxidation and the incidence of micronuclei by more than 70% with maximal suppression of cell proliferation. On the contrary, we found that the lowest UP pigment concentration displayed protective effects. In combined treatments with plasma and UP pigment, we found that UP pigment could provide spatial shielding to plasma exposure. In the pre-treatment approach, the incidence of micronuclei was reduced by 35.52% compared to control while malondialdehyde level decreased by 36% indicating a significant mitigation of membrane damage induced by plasma. These results open perspectives for utilizing UP pigment for protection against overexposures in the field of plasma medicine. (C) 2016 Elsevier GmbH. All rights reserved.
T2  - Experimental and Toxicologic Pathology
T1  - Biological effects of bacterial pigment undecylprodigiosin on human blood cells treated with atmospheric gas plasma in vitro
VL  - 69
IS  - 1
SP  - 55
EP  - 62
DO  - 10.1016/j.etp.2016.11.003
ER  - 

@article{
author = "Lazović, Saša and Leskovac, Andreja and Petrović, Sandra and Senerović, Lidija and Krivokapić, Nevena and Mitrović, Tatjana and Božović, Nikola and Vasić, Vesna M. and Nikodinović-Runić, Jasmina",
year = "2017",
abstract = "It is known that some bacterial species are more resilient to different kinds of irradiation due to the naturally developed protective mechanisms and compounds such as pigments. On the other hand, reasoned tissue engineering using plasma remains a critical task and requires very precise control of plasma parameters in order to mitigate its potential detrimental effects. Here we isolated a natural protective agent, microbially produced undecylprodigiosin ((52)-4-methoxy-5-[(5-undecy1-1H-pyrrol2-yl)methylenel-1H,5H-2,2-bipyrrole), and investigated its effects on human blood cells independently and in combination with plasma. Two apprOaches were applied; the first, undecylprodigiosin (UP pigment) was added to the blood cultures, which then were exposed to plasma (pre-treatment); and the second- the blood cultures were exposed to plasma and then treated with pigment (post-treatment). The interactions of plasma and UP pigment with blood cells were investigated by conducting a series of biological tests providing the information regarding their genotoxicity, cytotoxicity and redox modulating activities. The exposure of cells to plasma induced oxidative stress as well as certain genotoxic and cytotoxic effects seen as elevated micronuclei incidence, decreased cell proliferation and enhanced apoptosis. In blood cultures treated with UP pigment alone, we found that both cytotoxic and protective effects could be induced depending on the concentration used. The highest UP pigment concentration increased lipid peroxidation and the incidence of micronuclei by more than 70% with maximal suppression of cell proliferation. On the contrary, we found that the lowest UP pigment concentration displayed protective effects. In combined treatments with plasma and UP pigment, we found that UP pigment could provide spatial shielding to plasma exposure. In the pre-treatment approach, the incidence of micronuclei was reduced by 35.52% compared to control while malondialdehyde level decreased by 36% indicating a significant mitigation of membrane damage induced by plasma. These results open perspectives for utilizing UP pigment for protection against overexposures in the field of plasma medicine. (C) 2016 Elsevier GmbH. All rights reserved.",
journal = "Experimental and Toxicologic Pathology",
title = "Biological effects of bacterial pigment undecylprodigiosin on human blood cells treated with atmospheric gas plasma in vitro",
volume = "69",
number = "1",
pages = "55-62",
doi = "10.1016/j.etp.2016.11.003"
}

Lazović, S., Leskovac, A., Petrović, S., Senerović, L., Krivokapić, N., Mitrović, T., Božović, N., Vasić, V. M.,& Nikodinović-Runić, J.. (2017). Biological effects of bacterial pigment undecylprodigiosin on human blood cells treated with atmospheric gas plasma in vitro. in Experimental and Toxicologic Pathology, 69(1), 55-62.
https://doi.org/10.1016/j.etp.2016.11.003

Lazović S, Leskovac A, Petrović S, Senerović L, Krivokapić N, Mitrović T, Božović N, Vasić VM, Nikodinović-Runić J. Biological effects of bacterial pigment undecylprodigiosin on human blood cells treated with atmospheric gas plasma in vitro. in Experimental and Toxicologic Pathology. 2017;69(1):55-62.
doi:10.1016/j.etp.2016.11.003 .

Lazović, Saša, Leskovac, Andreja, Petrović, Sandra, Senerović, Lidija, Krivokapić, Nevena, Mitrović, Tatjana, Božović, Nikola, Vasić, Vesna M., Nikodinović-Runić, Jasmina, "Biological effects of bacterial pigment undecylprodigiosin on human blood cells treated with atmospheric gas plasma in vitro" in Experimental and Toxicologic Pathology, 69, no. 1 (2017):55-62,
https://doi.org/10.1016/j.etp.2016.11.003 . .

TY  - JOUR
AU  - Tadić, Bosiljka
AU  - Anđelković, Miroslav
AU  - Šuvakov, Milovan
PY  - 2016
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/1243
AB  - Charge transport in the Coulomb blockade regime of two-dimensional nanoparticle arrays exhibits nonlinear I-V characteristics, where the level of nonlinearity strongly associates with the arrays architecture. Here, we use different mathematical techniques to investigate the collective behavior of the charge transport and quantify its relationship to the structure of the nanoparticle assembly. First, we simulate single-electron tunneling conduction in a class of nanoparticle networks with a controlled variation of the structural characteristics (branching, extended linear segments) which influence the local communication among the conducting paths between the electrodes. Further, by applying an innovative approach based on the algebraic topology of graphs, we analyze the structure of connections in the manifolds, which map the fractal time series of charge fluctuations in the phase space. By tracking the I-V curves in different nanoparticle networks together with the indicators of collective dynamics and the topology of the phase space manifolds, we show that the increased I-V nonlinearity is fully consistent with the enhanced aggregate fluctuations and higher connection complexity among the participating states. Also, by determining shifts in the topology and cooperative transport features, we explore the impact of the size of electrodes and local charge disorder. The results are relevant for designing the nanoparticle devices with improved conduction; they also highlight the significance of topological descriptions for a broader understanding of the nature of fluctuations at the nanoscale.
T2  - Journal of Coupled Systems and Multiscale Dynamics
T1  - The influence of architecture of nanoparticle networks on collective charge transport revealed by the fractal time series and topology of phase space manifolds
VL  - 4
IS  - 1
SP  - 30
EP  - 42
DO  - 10.1166/jcsmd.2016.1094
ER  - 

@article{
author = "Tadić, Bosiljka and Anđelković, Miroslav and Šuvakov, Milovan",
year = "2016",
abstract = "Charge transport in the Coulomb blockade regime of two-dimensional nanoparticle arrays exhibits nonlinear I-V characteristics, where the level of nonlinearity strongly associates with the arrays architecture. Here, we use different mathematical techniques to investigate the collective behavior of the charge transport and quantify its relationship to the structure of the nanoparticle assembly. First, we simulate single-electron tunneling conduction in a class of nanoparticle networks with a controlled variation of the structural characteristics (branching, extended linear segments) which influence the local communication among the conducting paths between the electrodes. Further, by applying an innovative approach based on the algebraic topology of graphs, we analyze the structure of connections in the manifolds, which map the fractal time series of charge fluctuations in the phase space. By tracking the I-V curves in different nanoparticle networks together with the indicators of collective dynamics and the topology of the phase space manifolds, we show that the increased I-V nonlinearity is fully consistent with the enhanced aggregate fluctuations and higher connection complexity among the participating states. Also, by determining shifts in the topology and cooperative transport features, we explore the impact of the size of electrodes and local charge disorder. The results are relevant for designing the nanoparticle devices with improved conduction; they also highlight the significance of topological descriptions for a broader understanding of the nature of fluctuations at the nanoscale.",
journal = "Journal of Coupled Systems and Multiscale Dynamics",
title = "The influence of architecture of nanoparticle networks on collective charge transport revealed by the fractal time series and topology of phase space manifolds",
volume = "4",
number = "1",
pages = "30-42",
doi = "10.1166/jcsmd.2016.1094"
}

Tadić, B., Anđelković, M.,& Šuvakov, M.. (2016). The influence of architecture of nanoparticle networks on collective charge transport revealed by the fractal time series and topology of phase space manifolds. in Journal of Coupled Systems and Multiscale Dynamics, 4(1), 30-42.
https://doi.org/10.1166/jcsmd.2016.1094

Tadić B, Anđelković M, Šuvakov M. The influence of architecture of nanoparticle networks on collective charge transport revealed by the fractal time series and topology of phase space manifolds. in Journal of Coupled Systems and Multiscale Dynamics. 2016;4(1):30-42.
doi:10.1166/jcsmd.2016.1094 .

Tadić, Bosiljka, Anđelković, Miroslav, Šuvakov, Milovan, "The influence of architecture of nanoparticle networks on collective charge transport revealed by the fractal time series and topology of phase space manifolds" in Journal of Coupled Systems and Multiscale Dynamics, 4, no. 1 (2016):30-42,
https://doi.org/10.1166/jcsmd.2016.1094 . .

TY  - JOUR
AU  - Lazovic, S.
AU  - Maletić, Dimitrije
AU  - Leskovac, Andreja
AU  - Filipović, Jelena G.
AU  - Puac, N.
AU  - Malović, Gordana N.
AU  - Joksić, Gordana
AU  - Petrović, Z. Lj.
PY  - 2014
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/154
AB  - We use human primary fibroblasts for comparing plasma and gamma rays induced DNA damage. In both cases, DNA strand breaks occur, but of fundamentally different nature. Unlike gamma exposure, contact with plasma predominantly leads to single strand breaks and base-damages, while double strand breaks are mainly consequence of the cell repair mechanisms. Different cell signaling mechanisms are detected confirming this (ataxia telangiectasia mutated - ATM and ataxia telangiectasia and Rad3 related - ATR, respectively). The effective plasma doses can be tuned to match the typical therapeutic doses of 2Gy. Tailoring the effective dose through plasma power and duration of the treatment enables safety precautions mainly by inducing apoptosis and consequently reduced frequency of micronuclei. (C) 2014 AIP Publishing LLC.
T2  - Applied Physics Letters
T1  - Plasma induced DNA damage: Comparison with the effects of ionizing radiation
VL  - 105
IS  - 12
DO  - 10.1063/1.4896626
ER  - 

@article{
author = "Lazovic, S. and Maletić, Dimitrije and Leskovac, Andreja and Filipović, Jelena G. and Puac, N. and Malović, Gordana N. and Joksić, Gordana and Petrović, Z. Lj.",
year = "2014",
abstract = "We use human primary fibroblasts for comparing plasma and gamma rays induced DNA damage. In both cases, DNA strand breaks occur, but of fundamentally different nature. Unlike gamma exposure, contact with plasma predominantly leads to single strand breaks and base-damages, while double strand breaks are mainly consequence of the cell repair mechanisms. Different cell signaling mechanisms are detected confirming this (ataxia telangiectasia mutated - ATM and ataxia telangiectasia and Rad3 related - ATR, respectively). The effective plasma doses can be tuned to match the typical therapeutic doses of 2Gy. Tailoring the effective dose through plasma power and duration of the treatment enables safety precautions mainly by inducing apoptosis and consequently reduced frequency of micronuclei. (C) 2014 AIP Publishing LLC.",
journal = "Applied Physics Letters",
title = "Plasma induced DNA damage: Comparison with the effects of ionizing radiation",
volume = "105",
number = "12",
doi = "10.1063/1.4896626"
}

Lazovic, S., Maletić, D., Leskovac, A., Filipović, J. G., Puac, N., Malović, G. N., Joksić, G.,& Petrović, Z. Lj.. (2014). Plasma induced DNA damage: Comparison with the effects of ionizing radiation. in Applied Physics Letters, 105(12).
https://doi.org/10.1063/1.4896626

Lazovic S, Maletić D, Leskovac A, Filipović JG, Puac N, Malović GN, Joksić G, Petrović ZL. Plasma induced DNA damage: Comparison with the effects of ionizing radiation. in Applied Physics Letters. 2014;105(12).
doi:10.1063/1.4896626 .

Lazovic, S., Maletić, Dimitrije, Leskovac, Andreja, Filipović, Jelena G., Puac, N., Malović, Gordana N., Joksić, Gordana, Petrović, Z. Lj., "Plasma induced DNA damage: Comparison with the effects of ionizing radiation" in Applied Physics Letters, 105, no. 12 (2014),
https://doi.org/10.1063/1.4896626 . .