• dr Marcin Lipowczan
Stanowisko: Adiunkt
Jednostka: Wydział Nauk Przyrodniczych
Adres: 40-032 Katowice, ul. Jagiellońska 28
Piętro: III
Numer pokoju: C-342
Telefon: (32) 2009 579
E-mail: marcin.lipowczan@us.edu.pl
Spis publikacji: Spis wg CINiBA
Spis publikacji: Spis wg OPUS
Scopus Author ID: 8399903200
Publikacje z bazy Scopus
2023
Pietruszka, M. A.; Lipowczan, M.
Phase coherent quasi-particle formation in biological systems Journal Article
In: BioSystems, vol. 233, 2023, ISSN: 03032647.
@article{2-s2.0-85171476080,
title = {Phase coherent quasi-particle formation in biological systems},
author = { M.A. Pietruszka and M. Lipowczan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85171476080&doi=10.1016%2fj.biosystems.2023.105020&partnerID=40&md5=68229d1d4e3f25db51dc0718a0497ece},
doi = {10.1016/j.biosystems.2023.105020},
issn = {03032647},
year = {2023},
date = {2023-01-01},
journal = {BioSystems},
volume = {233},
publisher = {Elsevier Ireland Ltd},
abstract = {The problem of the origin of canonical and aberrant DNA mutations and the contribution of protons to genetic stability is an essential topic in molecular biology. Based on the empirical results, we reconsidered canonical and tautomeric mutations under the two-fluid model of quantum physics. We assumed that the pressure exerted by protons (H+) in the DNA environment, through changes in pH, could alter the concentration ratio of canonical and tautomeric base pairs, which were found to be different at and beyond the criticality level, respectively. We anticipate that the deviation of the cellular system from a specific (critical) temperature at which dynamic entropy reaches a minimum and a critical pH occurs could result in tautomerization and point mutations. © 2023 Elsevier B.V.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The problem of the origin of canonical and aberrant DNA mutations and the contribution of protons to genetic stability is an essential topic in molecular biology. Based on the empirical results, we reconsidered canonical and tautomeric mutations under the two-fluid model of quantum physics. We assumed that the pressure exerted by protons (H+) in the DNA environment, through changes in pH, could alter the concentration ratio of canonical and tautomeric base pairs, which were found to be different at and beyond the criticality level, respectively. We anticipate that the deviation of the cellular system from a specific (critical) temperature at which dynamic entropy reaches a minimum and a critical pH occurs could result in tautomerization and point mutations. © 2023 Elsevier B.V.
2019
Piekarska-Stachowiak, A.; Szymanowska-Pułka, J.; Potocka, I. W.; Lipowczan, M.
Topological traits of a cellular pattern versus growth rate anisotropy in radish roots Journal Article
In: Protoplasma, vol. 256, no. 4, pp. 1037-1049, 2019, ISSN: 0033183X, (2).
@article{2-s2.0-85062693923,
title = {Topological traits of a cellular pattern versus growth rate anisotropy in radish roots},
author = { A. Piekarska-Stachowiak and J. Szymanowska-Pułka and I.W. Potocka and M. Lipowczan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85062693923&doi=10.1007%2fs00709-019-01362-6&partnerID=40&md5=cccf6583996ca648bc09a4c2447b52e2},
doi = {10.1007/s00709-019-01362-6},
issn = {0033183X},
year = {2019},
date = {2019-01-01},
journal = {Protoplasma},
volume = {256},
number = {4},
pages = {1037-1049},
publisher = {Springer-Verlag Wien},
abstract = {The topology of a cellular pattern, which means the spatial arrangement of cells, directly corresponds with cell packing, which is crucial for tissue and organ functioning. The topological features of cells that are typically analyzed are the number of their neighbors and the cell area. To date, the objects of most topological studies have been the growing cells of the surface tissues of plant and animal organs. Some of these researches also provide verification of Lewis’s Law concerning the linear correlation between the number of neighboring cells and the cell area. Our aim was to analyze the cellular topology and applicability of Lewis’s Law to an anisotropically growing plant organ. The object of our study was the root apex of radish. Based on the tensor description of plant organ growth, we specified the level of anisotropy in specific zones (the root proper; the columella of the cap and the lateral parts of the cap) and in specific types of both external (epidermis) and internal tissues (stele and ground tissue) of the apex. The strongest anisotropy occurred in the root proper, while both zones of the cap showed an intermediate level of anisotropy of growth. Some differences in the topology of the cellular pattern in the zones were also detected; in the root proper, six-sided cells predominated, while in the root cap columella and in the lateral parts of the cap, most cells had five neighbors. The correlation coefficient rL between the number of neighboring cells and the cell area was high in the apex as a whole as well as in all of the zones except the root proper and in all of the tissue types except the ground tissue. In general, Lewis’s Law was fulfilled in the anisotropically growing radish root apex. However, the level of the applicability (rL value) of Lewis’s Law was negatively correlated with the level of the anisotropy of growth, which may suggest that in plant organs in the regions of anisotropic growth, the number of neighboring cells is less dependent on the cell size. © 2019, The Author(s).},
note = {2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The topology of a cellular pattern, which means the spatial arrangement of cells, directly corresponds with cell packing, which is crucial for tissue and organ functioning. The topological features of cells that are typically analyzed are the number of their neighbors and the cell area. To date, the objects of most topological studies have been the growing cells of the surface tissues of plant and animal organs. Some of these researches also provide verification of Lewis’s Law concerning the linear correlation between the number of neighboring cells and the cell area. Our aim was to analyze the cellular topology and applicability of Lewis’s Law to an anisotropically growing plant organ. The object of our study was the root apex of radish. Based on the tensor description of plant organ growth, we specified the level of anisotropy in specific zones (the root proper; the columella of the cap and the lateral parts of the cap) and in specific types of both external (epidermis) and internal tissues (stele and ground tissue) of the apex. The strongest anisotropy occurred in the root proper, while both zones of the cap showed an intermediate level of anisotropy of growth. Some differences in the topology of the cellular pattern in the zones were also detected; in the root proper, six-sided cells predominated, while in the root cap columella and in the lateral parts of the cap, most cells had five neighbors. The correlation coefficient rL between the number of neighboring cells and the cell area was high in the apex as a whole as well as in all of the zones except the root proper and in all of the tissue types except the ground tissue. In general, Lewis’s Law was fulfilled in the anisotropically growing radish root apex. However, the level of the applicability (rL value) of Lewis’s Law was negatively correlated with the level of the anisotropy of growth, which may suggest that in plant organs in the regions of anisotropic growth, the number of neighboring cells is less dependent on the cell size. © 2019, The Author(s).
2018
Lipowczan, M.; Borowska-Wykręt, D.; Natonik-Białoń, S.; Kwiatkowska, D.
In: Journal of Experimental Botany, vol. 69, no. 20, pp. 4987-, 2018, ISSN: 00220957.
@article{2-s2.0-85066835305,
title = {Erratum: Growing cell walls show a gradient of elastic strain across their layers (Journal of Experimental Botany Advance (2018) DOI: 10.1093/jxb/ery237)},
author = { M. Lipowczan and D. Borowska-Wykręt and S. Natonik-Białoń and D. Kwiatkowska},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85066835305&doi=10.1093%2fjxb%2fery280&partnerID=40&md5=cb20bdeb54380500da1f0b32475d2cfd},
doi = {10.1093/jxb/ery280},
issn = {00220957},
year = {2018},
date = {2018-01-01},
journal = {Journal of Experimental Botany},
volume = {69},
number = {20},
pages = {4987-},
publisher = {Oxford University Press},
abstract = {Journal of Experimental Botany, Advance Access publication 26 June 2018, doi:10.1093/jxb/ery237 The original online version of this article contained errors in the typesetting of an equation, listed under 'Computation of minimum energy configurations of plates'. This equation, concerning the inward modulus (E) gradient described in part (ii), has now been corrected to read "(E1 > E2 > E3)". The publisher would like to apologise for this error. © 2018 Oxford University Press. All rights reserved.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Journal of Experimental Botany, Advance Access publication 26 June 2018, doi:10.1093/jxb/ery237 The original online version of this article contained errors in the typesetting of an equation, listed under 'Computation of minimum energy configurations of plates'. This equation, concerning the inward modulus (E) gradient described in part (ii), has now been corrected to read "(E1 > E2 > E3)". The publisher would like to apologise for this error. © 2018 Oxford University Press. All rights reserved.
Lipowczan, M.; Borowska-Wykręt, D.; Natonik-Białoń, S.; Kwiatkowska, D.
Growing cell walls show a gradient of elastic strain across their layers Journal Article
In: Journal of Experimental Botany, vol. 69, no. 18, pp. 4349-4362, 2018, ISSN: 00220957, (10).
@article{2-s2.0-85055429118,
title = {Growing cell walls show a gradient of elastic strain across their layers},
author = { M. Lipowczan and D. Borowska-Wykręt and S. Natonik-Białoń and D. Kwiatkowska},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85055429118&doi=10.1093%2fjxb%2fery237&partnerID=40&md5=74f7e7ffc91b4a79053ee8c5db2d4437},
doi = {10.1093/jxb/ery237},
issn = {00220957},
year = {2018},
date = {2018-01-01},
journal = {Journal of Experimental Botany},
volume = {69},
number = {18},
pages = {4349-4362},
publisher = {Oxford University Press},
abstract = {The relatively thick primary walls of epidermal and collenchyma cells often form waviness on the surface that faces the protoplast when they are released from the tensile in-plane stress that operates in situ. This waviness is a manifestation of buckling that results from the heterogeneity of the elastic strain across the wall. In this study, this heterogeneity was confirmed by the spontaneous bending of isolated wall fragments that were initially flat. We combined the empirical data on the formation of waviness in growing cell walls with computations of the buckled wall shapes. We chose cylindrical-shaped organs with a high degree of longitudinal tissue stress because in such organs the surface deformation that accompanies the removal of the stress is strongly anisotropic and leads to the formation of waviness in which wrinkles on the inner wall surface are always transverse to the organ axis. The computations showed that the strain heterogeneity results from individual or overlaid gradients of pre-stress and stiffness across the wall. The computed wall shapes depend on the assumed wall thickness and mechanical gradients. Thus, a quantitative analysis of the wall waviness that forms after stress removal can be used to assess the mechanical heterogeneity of the cell wall. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Experimental Biology.},
note = {10},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The relatively thick primary walls of epidermal and collenchyma cells often form waviness on the surface that faces the protoplast when they are released from the tensile in-plane stress that operates in situ. This waviness is a manifestation of buckling that results from the heterogeneity of the elastic strain across the wall. In this study, this heterogeneity was confirmed by the spontaneous bending of isolated wall fragments that were initially flat. We combined the empirical data on the formation of waviness in growing cell walls with computations of the buckled wall shapes. We chose cylindrical-shaped organs with a high degree of longitudinal tissue stress because in such organs the surface deformation that accompanies the removal of the stress is strongly anisotropic and leads to the formation of waviness in which wrinkles on the inner wall surface are always transverse to the organ axis. The computations showed that the strain heterogeneity results from individual or overlaid gradients of pre-stress and stiffness across the wall. The computed wall shapes depend on the assumed wall thickness and mechanical gradients. Thus, a quantitative analysis of the wall waviness that forms after stress removal can be used to assess the mechanical heterogeneity of the cell wall. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Experimental Biology.
Elsner, J.; Lipowczan, M.; Kwiatkowska, D.
Differential growth of pavement cells of Arabidopsis thaliana leaf epidermis as revealed by microbead labeling Journal Article
In: American Journal of Botany, vol. 105, no. 2, pp. 257-265, 2018, ISSN: 00029122, (20).
@article{2-s2.0-85041997672,
title = {Differential growth of pavement cells of Arabidopsis thaliana leaf epidermis as revealed by microbead labeling},
author = { J. Elsner and M. Lipowczan and D. Kwiatkowska},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85041997672&doi=10.1002%2fajb2.1021&partnerID=40&md5=a8c25e42eb1cfdb5b52acfb3b36e871c},
doi = {10.1002/ajb2.1021},
issn = {00029122},
year = {2018},
date = {2018-01-01},
journal = {American Journal of Botany},
volume = {105},
number = {2},
pages = {257-265},
publisher = {Wiley-Blackwell},
abstract = {Premise of the Study: In numerous vascular plants, pavement cells of the leaf epidermis are shaped like a jigsaw-puzzle piece. Knowledge about the subcellular pattern of growth that accompanies morphogenesis of such a complex shape is crucial for studies of the role of the cytoskeleton, cell wall and phytohormones in plant cell development. Because the detailed growth pattern of the anticlinal and periclinal cell walls remains unknown, our aim was to measure pavement cell growth at a subcellular resolution. Methods: Using fluorescent microbeads applied to the surface of the adaxial leaf epidermis of Arabidopsis thaliana as landmarks for growth computation, we directly assessed the growth rates for the outer periclinal and anticlinal cell walls at a subcellular scale. Key Results: We observed complementary tendencies in the growth pattern of the outer periclinal and anticlinal cell walls. Central portions of periclinal walls were characterized by relatively slow growth, while growth of the other wall portions was heterogeneous. Local growth of the periclinal walls accompanying lobe development after initiation was relatively fast and anisotropic, with maximal extension usually in the direction along the lobe axis. This growth pattern of the periclinal walls was complemented by the extension of the anticlinal walls, which was faster on the lobe sides than at the tips. Conclusions: Growth of the anticlinal and outer periclinal walls of leaf pavement cells is heterogeneous. The growth of the lobes resembles cell elongation via diffuse growth rather than tip growth. © 2018 Botanical Society of America},
note = {20},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Premise of the Study: In numerous vascular plants, pavement cells of the leaf epidermis are shaped like a jigsaw-puzzle piece. Knowledge about the subcellular pattern of growth that accompanies morphogenesis of such a complex shape is crucial for studies of the role of the cytoskeleton, cell wall and phytohormones in plant cell development. Because the detailed growth pattern of the anticlinal and periclinal cell walls remains unknown, our aim was to measure pavement cell growth at a subcellular resolution. Methods: Using fluorescent microbeads applied to the surface of the adaxial leaf epidermis of Arabidopsis thaliana as landmarks for growth computation, we directly assessed the growth rates for the outer periclinal and anticlinal cell walls at a subcellular scale. Key Results: We observed complementary tendencies in the growth pattern of the outer periclinal and anticlinal cell walls. Central portions of periclinal walls were characterized by relatively slow growth, while growth of the other wall portions was heterogeneous. Local growth of the periclinal walls accompanying lobe development after initiation was relatively fast and anisotropic, with maximal extension usually in the direction along the lobe axis. This growth pattern of the periclinal walls was complemented by the extension of the anticlinal walls, which was faster on the lobe sides than at the tips. Conclusions: Growth of the anticlinal and outer periclinal walls of leaf pavement cells is heterogeneous. The growth of the lobes resembles cell elongation via diffuse growth rather than tip growth. © 2018 Botanical Society of America
2017
Kucypera, K.; Lipowczan, M.; Piekarska-Stachowiak, A.; Nakielski, J.
A method to generate the surface cell layer of the 3D virtual shoot apex from apical initials Journal Article
In: Plant Methods, vol. 13, no. 1, 2017, ISSN: 17464811, (4).
@article{2-s2.0-85037706805,
title = {A method to generate the surface cell layer of the 3D virtual shoot apex from apical initials},
author = { K. Kucypera and M. Lipowczan and A. Piekarska-Stachowiak and J. Nakielski},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85037706805&doi=10.1186%2fs13007-017-0262-7&partnerID=40&md5=5852bdccd55c2cb939ad7a084fd7b363},
doi = {10.1186/s13007-017-0262-7},
issn = {17464811},
year = {2017},
date = {2017-01-01},
journal = {Plant Methods},
volume = {13},
number = {1},
publisher = {BioMed Central Ltd.},
abstract = {Background: The development of cell pattern in the surface cell layer of the shoot apex can be investigated in vivo by use of a time-lapse confocal images, showing naked meristem in 3D in successive times. However, how this layer is originated from apical initials and develops as a result of growth and divisions of their descendants, remains unknown. This is an open area for computer modelling. A method to generate the surface cell layer is presented on the example of the 3D paraboloidal shoot apical dome. In the used model the layer originates from three apical initials that meet at the dome summit and develops through growth and cell divisions under the isotropic surface growth, defined by the growth tensor. The cells, which are described by polyhedrons, divide anticlinally with the smallest division plane that passes depending on the used mode through the cell center, or the point found randomly near this center. The formation of the surface cell pattern is described with the attention being paid to activity of the apical initials and fates of their descendants. Results: The computer generated surface layer that included about 350 cells required about 1200 divisions of the apical initials and their derivatives. The derivatives were arranged into three more or less equal clonal sectors composed of cellular clones at different age. Each apical initial renewed itself 7-8 times to produce the sector. In the shape and location and the cellular clones the following divisions of the initial were manifested. The application of the random factor resulted in more realistic cell pattern in comparison to the pure mode. The cell divisions were analyzed statistically on the top view. When all of the division walls were considered, their angular distribution was uniform, whereas in the distribution that was limited to apical initials only, some preferences related to their arrangement at the dome summit were observed. Conclusions: The realistic surface cell pattern was obtained. The present method is a useful tool to generate surface cell layer, study activity of initial cells and their derivatives, and how cell expansion and division are coordinated during growth. We expect its further application to clarify the question of a number and permanence or impermanence of initial cells, and possible relationship between their shape and oriented divisions, both on the ground of the growth tensor approach. © 2017 The Author(s).},
note = {4},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background: The development of cell pattern in the surface cell layer of the shoot apex can be investigated in vivo by use of a time-lapse confocal images, showing naked meristem in 3D in successive times. However, how this layer is originated from apical initials and develops as a result of growth and divisions of their descendants, remains unknown. This is an open area for computer modelling. A method to generate the surface cell layer is presented on the example of the 3D paraboloidal shoot apical dome. In the used model the layer originates from three apical initials that meet at the dome summit and develops through growth and cell divisions under the isotropic surface growth, defined by the growth tensor. The cells, which are described by polyhedrons, divide anticlinally with the smallest division plane that passes depending on the used mode through the cell center, or the point found randomly near this center. The formation of the surface cell pattern is described with the attention being paid to activity of the apical initials and fates of their descendants. Results: The computer generated surface layer that included about 350 cells required about 1200 divisions of the apical initials and their derivatives. The derivatives were arranged into three more or less equal clonal sectors composed of cellular clones at different age. Each apical initial renewed itself 7-8 times to produce the sector. In the shape and location and the cellular clones the following divisions of the initial were manifested. The application of the random factor resulted in more realistic cell pattern in comparison to the pure mode. The cell divisions were analyzed statistically on the top view. When all of the division walls were considered, their angular distribution was uniform, whereas in the distribution that was limited to apical initials only, some preferences related to their arrangement at the dome summit were observed. Conclusions: The realistic surface cell pattern was obtained. The present method is a useful tool to generate surface cell layer, study activity of initial cells and their derivatives, and how cell expansion and division are coordinated during growth. We expect its further application to clarify the question of a number and permanence or impermanence of initial cells, and possible relationship between their shape and oriented divisions, both on the ground of the growth tensor approach. © 2017 The Author(s).
Lipowczan, M.; Pietruszka, M. A.
Frequency-associated transition from single-cell asynchronous motion to monotonic growth Journal Article
In: Journal of Biological Physics, vol. 43, no. 4, pp. 461-470, 2017, ISSN: 00920606.
@article{2-s2.0-85029184821,
title = {Frequency-associated transition from single-cell asynchronous motion to monotonic growth},
author = { M. Lipowczan and M.A. Pietruszka},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85029184821&doi=10.1007%2fs10867-017-9462-7&partnerID=40&md5=194868730293244768a4635f420772a1},
doi = {10.1007/s10867-017-9462-7},
issn = {00920606},
year = {2017},
date = {2017-01-01},
journal = {Journal of Biological Physics},
volume = {43},
number = {4},
pages = {461-470},
publisher = {Springer Netherlands},
abstract = {This paper presents a Fourier analysis of the Ortega equation that examines the growth dynamics of plants, specifically the pollen tubes or non-meristematic zones of elongating coleoptiles. A frequency-induced transition from highly nonlinear (periodical) growth—like the one observed in pollen tubes—to monotonically ascending and asymptotically saturated (sigmoid-like) growth, which is anticipated within the framework of a ‘two-fluid model’, is shown. A dynamic phase diagram is calculated and presented in the form of a live video clip. © 2017, Springer Science+Business Media B.V.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This paper presents a Fourier analysis of the Ortega equation that examines the growth dynamics of plants, specifically the pollen tubes or non-meristematic zones of elongating coleoptiles. A frequency-induced transition from highly nonlinear (periodical) growth—like the one observed in pollen tubes—to monotonically ascending and asymptotically saturated (sigmoid-like) growth, which is anticipated within the framework of a ‘two-fluid model’, is shown. A dynamic phase diagram is calculated and presented in the form of a live video clip. © 2017, Springer Science+Business Media B.V.
Pietruszka, M. A.; Lipowczan, M.
Are water temperature anomalies conjugated to brain functions in microtubules? Journal Article
In: NeuroQuantology, vol. 15, no. 1, pp. 18-21, 2017, ISSN: 13035150, (3).
@article{2-s2.0-85025149317,
title = {Are water temperature anomalies conjugated to brain functions in microtubules?},
author = { M.A. Pietruszka and M. Lipowczan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85025149317&doi=10.14704%2fnq.2017.15.1.984&partnerID=40&md5=b2b2f0290f907d1695cea70041597318},
doi = {10.14704/nq.2017.15.1.984},
issn = {13035150},
year = {2017},
date = {2017-01-01},
journal = {NeuroQuantology},
volume = {15},
number = {1},
pages = {18-21},
publisher = {E-FLOW PDF NeuroQuantology},
abstract = {We considered a system of microtubule(s) (MTs) immersed in a water reservoir in order to investigate its thermodynamic properties and computation (processing) potential. We started with the “double frustration” concept for a single microtubule and next extended our considerations to an MT multi-cluster. We probed the influence of the physical anomalies of water in compressibility and the speed of sound, where acoustic phonons that are conjugated to the stress fluctuations that are produced by changes in symmetry, are possible carriers of information and the cause of ‘calculation’ enhancement at the physiological temperatures of human brain. We showed that the timing of the internal clock can be as high as 117 GHz and that the long-range coherence should be maintained for about 0.1 ms, which is a reasonable dynamical timescale. We advocated that some ‘local’, ‘intermediate’ and ‘extended states’ of our mind could be in relation to water temperature anomalies. We also suggested that the frustration scheme might introduce a direct link to the evolutionary survival paradigm in the case of the slow or fast computations that are performed by elementary systems able to perform basic calculations that can be identified with ‘thinking’. © 2017, E-FLOW PDF NeuroQuantology. All rights reserved.},
note = {3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We considered a system of microtubule(s) (MTs) immersed in a water reservoir in order to investigate its thermodynamic properties and computation (processing) potential. We started with the “double frustration” concept for a single microtubule and next extended our considerations to an MT multi-cluster. We probed the influence of the physical anomalies of water in compressibility and the speed of sound, where acoustic phonons that are conjugated to the stress fluctuations that are produced by changes in symmetry, are possible carriers of information and the cause of ‘calculation’ enhancement at the physiological temperatures of human brain. We showed that the timing of the internal clock can be as high as 117 GHz and that the long-range coherence should be maintained for about 0.1 ms, which is a reasonable dynamical timescale. We advocated that some ‘local’, ‘intermediate’ and ‘extended states’ of our mind could be in relation to water temperature anomalies. We also suggested that the frustration scheme might introduce a direct link to the evolutionary survival paradigm in the case of the slow or fast computations that are performed by elementary systems able to perform basic calculations that can be identified with ‘thinking’. © 2017, E-FLOW PDF NeuroQuantology. All rights reserved.
2015
de Reuille, P. B.; Routier-Kierzkowska, A. L.; Kierzkowski, D.; Bassel, G. W.; Schüpbach, T.; Tauriello, G.; Bajpai, N.; Strauss, S.; Weber, A.; Kiss, A.; Burian, A.; Hofhuis, H.; Sapala, A.; Lipowczan, M.; Heimlicher, M. B.; Robinson, S.; Bayer, E. M.; Basler, K.; Koumoutsakos, P.; Roeder, A. H. K.; Aegerter-Wilmsen, T.; Nakayama, N.; Tsiantis, M.; Hay, A.; Kwiatkowska, D.; Xenarios, I.; Kuhlemeier, C.; Smith, R. S.
MorphoGraphX: A platform for quantifying morphogenesis in 4D Journal Article
In: eLife, vol. 4, no. MAY, pp. 1-20, 2015, ISSN: 2050084X, (267).
@article{2-s2.0-84930640355,
title = {MorphoGraphX: A platform for quantifying morphogenesis in 4D},
author = { P.B. de Reuille and A.L. Routier-Kierzkowska and D. Kierzkowski and G.W. Bassel and T. Schüpbach and G. Tauriello and N. Bajpai and S. Strauss and A. Weber and A. Kiss and A. Burian and H. Hofhuis and A. Sapala and M. Lipowczan and M.B. Heimlicher and S. Robinson and E.M. Bayer and K. Basler and P. Koumoutsakos and A.H.K. Roeder and T. Aegerter-Wilmsen and N. Nakayama and M. Tsiantis and A. Hay and D. Kwiatkowska and I. Xenarios and C. Kuhlemeier and R.S. Smith},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84930640355&doi=10.7554%2feLife.05864&partnerID=40&md5=2bc848f64b00656937202a22152fb707},
doi = {10.7554/eLife.05864},
issn = {2050084X},
year = {2015},
date = {2015-01-01},
journal = {eLife},
volume = {4},
number = {MAY},
pages = {1-20},
publisher = {eLife Sciences Publications Ltd},
abstract = {Morphogenesis emerges from complex multiscale interactions between genetic and mechanical processes. To understand these processes, the evolution of cell shape, proliferation and gene expression must be quantified. This quantification is usually performed either in full 3D, which is computationally expensive and technically challenging, or on 2D planar projections, which introduces geometrical artifacts on highly curved organs. Here we present MorphoGraphX (www.MorphoGraphX.org), a software that bridges this gap by working directly with curved surface images extracted from 3D data. In addition to traditional 3D image analysis, we have developed algorithms to operate on curved surfaces, such as cell segmentation, lineage tracking and fluorescence signal quantification. The software’s modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth. © Barbier de Reuille et al.},
note = {267},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Morphogenesis emerges from complex multiscale interactions between genetic and mechanical processes. To understand these processes, the evolution of cell shape, proliferation and gene expression must be quantified. This quantification is usually performed either in full 3D, which is computationally expensive and technically challenging, or on 2D planar projections, which introduces geometrical artifacts on highly curved organs. Here we present MorphoGraphX (www.MorphoGraphX.org), a software that bridges this gap by working directly with curved surface images extracted from 3D data. In addition to traditional 3D image analysis, we have developed algorithms to operate on curved surfaces, such as cell segmentation, lineage tracking and fluorescence signal quantification. The software’s modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth. © Barbier de Reuille et al.
2014
Szymanowska-Pułka, J.; Lipowczan, M.
Growth rate distribution in the forming lateral root of arabidopsis Journal Article
In: Annals of Botany, vol. 114, no. 5, pp. 913-921, 2014, ISSN: 03057364, (1).
@article{2-s2.0-84922914838,
title = {Growth rate distribution in the forming lateral root of arabidopsis},
author = { J. Szymanowska-Pułka and M. Lipowczan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84922914838&doi=10.1093%2faob%2fmcu159&partnerID=40&md5=d1c8e9d94dd4e29da8d2827146aea7cc},
doi = {10.1093/aob/mcu159},
issn = {03057364},
year = {2014},
date = {2014-01-01},
journal = {Annals of Botany},
volume = {114},
number = {5},
pages = {913-921},
publisher = {Oxford University Press},
abstract = {Background and Aims: Microscopic observations of lateral roots (LRs) in Arabidopsis thaliana reveal that the cross-sectional shape of the organ changes from its basal to its apical region. The founder cells for LRs are elongated along the parent root axis, and thus from the site of initiation the base of LRs resemble an ellipse. The circumference of the apical part of LRs is usually a circle. The objective of this study was to analyse the characteristics of changes in the growth field of LRs possessing various shapes in their basal regions. Methods: The LRs of the wild type (Col-0) and two transgenic arabidopsis lines were analysed. On the basis of measurements of the long and short diameters (DL and DS; respectively) of the ellipse-like figure representing the bases of particular LRs, their asymmetry ratios (DL/DS) were determined. Possible differences between accessions were analysed by applying statistical methods. Key Results: No significant differences between accessions were detected. Comparisons were therefore made of the maximal, minimal and mean value of the ratio of all the LRs analysed. Taking into consideration the lack of circular symmetry of the basal part, rates of growth were determined at selected points on the surface of LRs by the application of the growth tensor method, a mathematical tool previously applied only to describe organs with rotational symmetry. Maps showing the distribution of growth rates were developed for surfaces of LRs of various asymmetry ratios. Conclusions: The maps of growth rates on the surfaces of LRs having various shapes of the basal part show differences in both the geometry and the manner of growth, thus indicating that the manner of growth of the LR primordium is correlated to its shape. This is the first report of a description of growth of an asymmetric plant organ using the growth tensor method. The mathematical modelling adopted in the study provides new insights into plant organ formation and shape. © The Author 2014.},
note = {1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Background and Aims: Microscopic observations of lateral roots (LRs) in Arabidopsis thaliana reveal that the cross-sectional shape of the organ changes from its basal to its apical region. The founder cells for LRs are elongated along the parent root axis, and thus from the site of initiation the base of LRs resemble an ellipse. The circumference of the apical part of LRs is usually a circle. The objective of this study was to analyse the characteristics of changes in the growth field of LRs possessing various shapes in their basal regions. Methods: The LRs of the wild type (Col-0) and two transgenic arabidopsis lines were analysed. On the basis of measurements of the long and short diameters (DL and DS; respectively) of the ellipse-like figure representing the bases of particular LRs, their asymmetry ratios (DL/DS) were determined. Possible differences between accessions were analysed by applying statistical methods. Key Results: No significant differences between accessions were detected. Comparisons were therefore made of the maximal, minimal and mean value of the ratio of all the LRs analysed. Taking into consideration the lack of circular symmetry of the basal part, rates of growth were determined at selected points on the surface of LRs by the application of the growth tensor method, a mathematical tool previously applied only to describe organs with rotational symmetry. Maps showing the distribution of growth rates were developed for surfaces of LRs of various asymmetry ratios. Conclusions: The maps of growth rates on the surfaces of LRs having various shapes of the basal part show differences in both the geometry and the manner of growth, thus indicating that the manner of growth of the LR primordium is correlated to its shape. This is the first report of a description of growth of an asymmetric plant organ using the growth tensor method. The mathematical modelling adopted in the study provides new insights into plant organ formation and shape. © The Author 2014.
Lipowczan, M.; Piekarska-Stachowiak, A.
Comparison of empirical rules describing cell plate formation in 2D computer simulations of apical meristem in plants Journal Article
In: Journal of Biological Systems, vol. 22, no. 1, pp. 61-71, 2014, ISSN: 02183390, (2).
@article{2-s2.0-84896755666,
title = {Comparison of empirical rules describing cell plate formation in 2D computer simulations of apical meristem in plants},
author = { M. Lipowczan and A. Piekarska-Stachowiak},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84896755666&doi=10.1142%2fS021833901450003X&partnerID=40&md5=dd1c32d1b2fce8a2a5ab8eef9b1c2a54},
doi = {10.1142/S021833901450003X},
issn = {02183390},
year = {2014},
date = {2014-01-01},
journal = {Journal of Biological Systems},
volume = {22},
number = {1},
pages = {61-71},
abstract = {There are two families of lines describing the cell wall pattern in root and shoot apices; periclines and anticlines. The lines of these two families are mutually orthogonal and steady during apex growth. They approximate orientation of cell walls in the apices. These lines are preserved in the growing organ. The direction of periclines and anticlines is regulated at the organ level. This paper focuses on the question: how is the pattern of periclines and anticlines maintained? There are a number of rules, which deal with the problem of the orientation of a new cell wall. We test three of them: Errera rule (the smallest possible area of a new cell wall that divides the mother cell into equal portions is chosen), Sachs rule (the new wall is perpendicular to the nearest wall from the geometric center where it is inserted) and Hejnowicz postulate (the new cell wall is perpendicular to one of the principal directions of growth rate). We tested these rules in the computer simulation of the organ growth and cell divisions. © World Scientific Publishing Company.},
note = {2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
There are two families of lines describing the cell wall pattern in root and shoot apices; periclines and anticlines. The lines of these two families are mutually orthogonal and steady during apex growth. They approximate orientation of cell walls in the apices. These lines are preserved in the growing organ. The direction of periclines and anticlines is regulated at the organ level. This paper focuses on the question: how is the pattern of periclines and anticlines maintained? There are a number of rules, which deal with the problem of the orientation of a new cell wall. We test three of them: Errera rule (the smallest possible area of a new cell wall that divides the mother cell into equal portions is chosen), Sachs rule (the new wall is perpendicular to the nearest wall from the geometric center where it is inserted) and Hejnowicz postulate (the new cell wall is perpendicular to one of the principal directions of growth rate). We tested these rules in the computer simulation of the organ growth and cell divisions. © World Scientific Publishing Company.
Pietruszka, M. A.; Lipowczan, M.
Check sum computing in doubly frustrated microtubule clusters Journal Article
In: NeuroQuantology, vol. 12, no. 3, pp. 344-349, 2014, ISSN: 13035150, (2).
@article{2-s2.0-84907454460,
title = {Check sum computing in doubly frustrated microtubule clusters},
author = { M.A. Pietruszka and M. Lipowczan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84907454460&doi=10.14704%2fnq.2014.12.3.760&partnerID=40&md5=712b49290a0e8fc5c06b02b8f4c04082},
doi = {10.14704/nq.2014.12.3.760},
issn = {13035150},
year = {2014},
date = {2014-01-01},
journal = {NeuroQuantology},
volume = {12},
number = {3},
pages = {344-349},
publisher = {E-FLOW PDF NeuroQuantology},
abstract = {The hitherto unexplained presence of 12 or 13 tubulin dimmers forming parallel protofilament subunits in microtubules (MTs) is supposed to ensure sum checking in the system of two MTs, each one being a potential computing ‘core’. The recently proposed, frustration – originated, double well potential is mapped, exclusively for modelling reasons, onto the Ising – type Hamiltonian acting in the rings with an intra-site nearest neighbours interaction. We infer that the final state of energetically favourable 12 qubit ‘calculation’ at physiological temperature is randomly ‘corrected’ by the conjugated nearest 13 qubit ‘core’ (via inter-site; as yet indeterminate; long-range interaction) in the double MT cluster. Helmholtz free energy is calculated to show that such computing cluster lowers the system demands for ATP energy while retaining the possibility of higher accuracy calculations. By performing calculation for two model systems, we find the frustration – originated energy enhancement at physiological temperatures of the human brain for the semi-classical system against the corresponding quantum one. Also, existing studies have not clearly dissociated the neural processes supporting short- and long-duration memories – we propose a possible localization of durable/flash memory in MTs, through introducing a double frustration concept. By extension to double frustration description it may be meaningful to make the next intuitive leap to the question of quantum computing and its possible function in the theory of consciousness. © 2014 NeuroQuantology. All rights reserved.},
note = {2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The hitherto unexplained presence of 12 or 13 tubulin dimmers forming parallel protofilament subunits in microtubules (MTs) is supposed to ensure sum checking in the system of two MTs, each one being a potential computing ‘core’. The recently proposed, frustration – originated, double well potential is mapped, exclusively for modelling reasons, onto the Ising – type Hamiltonian acting in the rings with an intra-site nearest neighbours interaction. We infer that the final state of energetically favourable 12 qubit ‘calculation’ at physiological temperature is randomly ‘corrected’ by the conjugated nearest 13 qubit ‘core’ (via inter-site; as yet indeterminate; long-range interaction) in the double MT cluster. Helmholtz free energy is calculated to show that such computing cluster lowers the system demands for ATP energy while retaining the possibility of higher accuracy calculations. By performing calculation for two model systems, we find the frustration – originated energy enhancement at physiological temperatures of the human brain for the semi-classical system against the corresponding quantum one. Also, existing studies have not clearly dissociated the neural processes supporting short- and long-duration memories – we propose a possible localization of durable/flash memory in MTs, through introducing a double frustration concept. By extension to double frustration description it may be meaningful to make the next intuitive leap to the question of quantum computing and its possible function in the theory of consciousness. © 2014 NeuroQuantology. All rights reserved.
2013
Nakielski, J.; Lipowczan, M.
Spatial and directional variation of growth rates in Arabidopsis root apex: A modelling study Journal Article
In: PLoS ONE, vol. 8, no. 12, 2013, ISSN: 19326203, (6).
@article{2-s2.0-84893203367,
title = {Spatial and directional variation of growth rates in Arabidopsis root apex: A modelling study},
author = { J. Nakielski and M. Lipowczan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84893203367&doi=10.1371%2fjournal.pone.0084337&partnerID=40&md5=942a6ee0c8fc8275ab900604a2f9adaf},
doi = {10.1371/journal.pone.0084337},
issn = {19326203},
year = {2013},
date = {2013-01-01},
journal = {PLoS ONE},
volume = {8},
number = {12},
abstract = {Growth and cellular organization of the Arabidopsis root apex are investigated in various aspects, but still little is known about spatial and directional variation of growth rates in very apical part of the apex, especially in 3D. The present paper aims to fill this gap with the aid of a computer modelling based on the growth tensor method. The root apex with a typical shape and cellular pattern is considered. Previously, on the basis of two types of empirical data: the published velocity profile along the root axis and dimensions of cell packets formed in the lateral part of the root cap, the displacement velocity field for the root apex was determined. Here this field is adopted to calculate the linear growth rate in different points and directions. The results are interpreted taking principal growth directions into account. The root apex manifests a significant anisotropy of the linear growth rate. The directional preferences depend on a position within the root apex. In the root proper the rate in the periclinal direction predominates everywhere, while in the root cap the predominating direction varies with distance from the quiescent centre. The rhizodermis is distinguished from the neighbouring tissues (cortex; root cap) by relatively high contribution of the growth rate in the anticlinal direction. The degree of growth anisotropy calculated for planes defined by principal growth directions and exemplary cell walls may be as high as 25. The changes in the growth rate variation are modelled. © 2013 Nakielski, Lipowczan.},
note = {6},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Growth and cellular organization of the Arabidopsis root apex are investigated in various aspects, but still little is known about spatial and directional variation of growth rates in very apical part of the apex, especially in 3D. The present paper aims to fill this gap with the aid of a computer modelling based on the growth tensor method. The root apex with a typical shape and cellular pattern is considered. Previously, on the basis of two types of empirical data: the published velocity profile along the root axis and dimensions of cell packets formed in the lateral part of the root cap, the displacement velocity field for the root apex was determined. Here this field is adopted to calculate the linear growth rate in different points and directions. The results are interpreted taking principal growth directions into account. The root apex manifests a significant anisotropy of the linear growth rate. The directional preferences depend on a position within the root apex. In the root proper the rate in the periclinal direction predominates everywhere, while in the root cap the predominating direction varies with distance from the quiescent centre. The rhizodermis is distinguished from the neighbouring tissues (cortex; root cap) by relatively high contribution of the growth rate in the anticlinal direction. The degree of growth anisotropy calculated for planes defined by principal growth directions and exemplary cell walls may be as high as 25. The changes in the growth rate variation are modelled. © 2013 Nakielski, Lipowczan.
Lipowczan, M.; Piekarska-Stachowiak, A.; Elsner, J.; Pietrakowski, J.
The tensor-based model of plant growth applied to leaves of Arabidopsis thaliana: A two-dimensional computer model Journal Article
In: Comptes Rendus - Biologies, vol. 336, no. 9, pp. 425-432, 2013, ISSN: 16310691, (3).
@article{2-s2.0-84886726393,
title = {The tensor-based model of plant growth applied to leaves of Arabidopsis thaliana: A two-dimensional computer model},
author = { M. Lipowczan and A. Piekarska-Stachowiak and J. Elsner and J. Pietrakowski},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84886726393&doi=10.1016%2fj.crvi.2013.09.001&partnerID=40&md5=e404b4fe93dc95ae0c5377886c53be45},
doi = {10.1016/j.crvi.2013.09.001},
issn = {16310691},
year = {2013},
date = {2013-01-01},
journal = {Comptes Rendus - Biologies},
volume = {336},
number = {9},
pages = {425-432},
abstract = {Plant organs grow in coordinated and continuous way. Such growth is of a tensor nature, hence there is an infinite number of different directions of growth rate in each point of the growing organ. Three mutually orthogonal directions of growth can be recognized in which growth achieves extreme values (principal directions of growth [PDGs]). Models based on the growth tensor have already been successfully applied to the root and shoot apex. This paper presents the 2D model of growth applied to the arabidopsis leaf. The model employs the growth tensor method with a non-stationary velocity field. The postulated velocity functions are confirmed by growth measurements with the aid of the replica method. © 2013 Académie des sciences.},
note = {3},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Plant organs grow in coordinated and continuous way. Such growth is of a tensor nature, hence there is an infinite number of different directions of growth rate in each point of the growing organ. Three mutually orthogonal directions of growth can be recognized in which growth achieves extreme values (principal directions of growth [PDGs]). Models based on the growth tensor have already been successfully applied to the root and shoot apex. This paper presents the 2D model of growth applied to the arabidopsis leaf. The model employs the growth tensor method with a non-stationary velocity field. The postulated velocity functions are confirmed by growth measurements with the aid of the replica method. © 2013 Académie des sciences.
Pietruszka, M. A.; Lipowczan, M.
Conscious events as possible consequence of topological frustration in microtubules Journal Article
In: NeuroQuantology, vol. 11, no. 3, pp. 426-430, 2013, ISSN: 13035150, (2).
@article{2-s2.0-84885799447,
title = {Conscious events as possible consequence of topological frustration in microtubules},
author = { M.A. Pietruszka and M. Lipowczan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84885799447&doi=10.14704%2fnq.2013.11.3.680&partnerID=40&md5=1e47d7c260abd5fca0abf9e0b11b36dc},
doi = {10.14704/nq.2013.11.3.680},
issn = {13035150},
year = {2013},
date = {2013-01-01},
journal = {NeuroQuantology},
volume = {11},
number = {3},
pages = {426-430},
publisher = {NeuroQuantology},
abstract = {The phenomenon of persistent frustration of pollen tubes led us to recognition of a new form of anharmonic potential, which after a simple transformation may yield a so called 'double well potential'. Because of possible links with conformational changes taking place in microtubules (MT) of human brain neuronal system, to start with, we have calculated the shift of energy levels of a double well potential with respect to the infinite square double well. We conjecture that the dynamic instability of MTs, which has not been elucidated yet, may be the effect of recently proposed mechanism of geometrical frustration, which can also be utilized in case of tubulin dimers forming parallel protofilament subunits in MTs and for modeling the cognitive brain processes.},
note = {2},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The phenomenon of persistent frustration of pollen tubes led us to recognition of a new form of anharmonic potential, which after a simple transformation may yield a so called 'double well potential'. Because of possible links with conformational changes taking place in microtubules (MT) of human brain neuronal system, to start with, we have calculated the shift of energy levels of a double well potential with respect to the infinite square double well. We conjecture that the dynamic instability of MTs, which has not been elucidated yet, may be the effect of recently proposed mechanism of geometrical frustration, which can also be utilized in case of tubulin dimers forming parallel protofilament subunits in MTs and for modeling the cognitive brain processes.
2012
Pietruszka, M. A.; Lipowczan, M.; Geitmann, A.
Persistent Symmetry Frustration in Pollen Tubes Journal Article
In: PLoS ONE, vol. 7, no. 11, 2012, ISSN: 19326203, (8).
@article{2-s2.0-84868353676,
title = {Persistent Symmetry Frustration in Pollen Tubes},
author = { M.A. Pietruszka and M. Lipowczan and A. Geitmann},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84868353676&doi=10.1371%2fjournal.pone.0048087&partnerID=40&md5=b002799cac5d40976d8b8661be86d8e6},
doi = {10.1371/journal.pone.0048087},
issn = {19326203},
year = {2012},
date = {2012-01-01},
journal = {PLoS ONE},
volume = {7},
number = {11},
abstract = {Pollen tubes are extremely rapidly growing plant cells whose morphogenesis is determined by spatial gradients in the biochemical composition of the cell wall. We investigate the hypothesis (MP) that the distribution of the local mechanical properties of the wall, corresponding to the change of the radial symmetry along the axial direction, may lead to growth oscillations in pollen tubes. We claim that the experimentally observed oscillations originate from the symmetry change at the transition zone, where both intervening symmetries (cylindrical and spherical) meet. The characteristic oscillations between resonating symmetries at a given (constant) turgor pressure and a gradient of wall material constants may be identified with the observed growth-cycles in pollen tubes. © 2012 Pietruszka et al.},
note = {8},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pollen tubes are extremely rapidly growing plant cells whose morphogenesis is determined by spatial gradients in the biochemical composition of the cell wall. We investigate the hypothesis (MP) that the distribution of the local mechanical properties of the wall, corresponding to the change of the radial symmetry along the axial direction, may lead to growth oscillations in pollen tubes. We claim that the experimentally observed oscillations originate from the symmetry change at the transition zone, where both intervening symmetries (cylindrical and spherical) meet. The characteristic oscillations between resonating symmetries at a given (constant) turgor pressure and a gradient of wall material constants may be identified with the observed growth-cycles in pollen tubes. © 2012 Pietruszka et al.
Nakielski, J.; Lipowczan, M.
A method to determine the displacement velocity field in the apical region of the Arabidopsis root Journal Article
In: Planta, vol. 236, no. 5, pp. 1547-1557, 2012, ISSN: 00320935, (5).
@article{2-s2.0-84868121277,
title = {A method to determine the displacement velocity field in the apical region of the Arabidopsis root},
author = { J. Nakielski and M. Lipowczan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84868121277&doi=10.1007%2fs00425-012-1707-x&partnerID=40&md5=954a94908c43b614e580b9b56d47f035},
doi = {10.1007/s00425-012-1707-x},
issn = {00320935},
year = {2012},
date = {2012-01-01},
journal = {Planta},
volume = {236},
number = {5},
pages = {1547-1557},
abstract = {In angiosperms, growth of the root apex is determined by the quiescent centre. All tissues of the root proper and the root cap are derived from initial cells that surround this zone. The diversity of cell lineages originated from these initials suggests an interesting variation of the displacement velocity within the root apex. However, little is known about this variation, especially in the most apical region including the root cap. This paper shows a method of determination of velocity field for this region taking the Arabidopsis root apex as example. Assuming the symplastic growth without a rotation around the root axis, the method combines mathematical modelling and two types of empirical data: the published velocity profile along the root axis above the quiescent centre, and dimensions of cell packet originated from the initials of epidermis and lateral root cap. The velocities, calculated for points of the axial section, vary in length and direction. Their length increases with distance from the quiescent centre, in the root cap at least twice slower than in the root proper, if points at similar distance from the quiescent centre are compared. The vector orientation depends on the position of a calculation point, the widest range of angular changes, reaching almost 90°, in the lateral root cap. It is demonstrated how the velocity field is related to both distribution of growth rates and growth-resulted deformation of the cell wall system. Also changes in the field due to cell pattern asymmetry and differences in slope of the velocity profile are modelled. © 2012 The Author(s).},
note = {5},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
In angiosperms, growth of the root apex is determined by the quiescent centre. All tissues of the root proper and the root cap are derived from initial cells that surround this zone. The diversity of cell lineages originated from these initials suggests an interesting variation of the displacement velocity within the root apex. However, little is known about this variation, especially in the most apical region including the root cap. This paper shows a method of determination of velocity field for this region taking the Arabidopsis root apex as example. Assuming the symplastic growth without a rotation around the root axis, the method combines mathematical modelling and two types of empirical data: the published velocity profile along the root axis above the quiescent centre, and dimensions of cell packet originated from the initials of epidermis and lateral root cap. The velocities, calculated for points of the axial section, vary in length and direction. Their length increases with distance from the quiescent centre, in the root cap at least twice slower than in the root proper, if points at similar distance from the quiescent centre are compared. The vector orientation depends on the position of a calculation point, the widest range of angular changes, reaching almost 90°, in the lateral root cap. It is demonstrated how the velocity field is related to both distribution of growth rates and growth-resulted deformation of the cell wall system. Also changes in the field due to cell pattern asymmetry and differences in slope of the velocity profile are modelled. © 2012 The Author(s).
2007
Borgieł, W.; Stysiak, D.; Gonsior, M.; Lipowczan, M.
Influence of the short range order (SRO) on electrical resistivity of the magnetic rare earth metals in the paramagnetic region Journal Article
In: Journal of Alloys and Compounds, vol. 442, no. 1-2 SPEC. ISS., pp. 139-141, 2007, ISSN: 09258388, (1).
@article{2-s2.0-34250819949,
title = {Influence of the short range order (SRO) on electrical resistivity of the magnetic rare earth metals in the paramagnetic region},
author = { W. Borgieł and D. Stysiak and M. Gonsior and M. Lipowczan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34250819949&doi=10.1016%2fj.jallcom.2006.11.217&partnerID=40&md5=eaee36ffc603ed476e39854d4eff6fed},
doi = {10.1016/j.jallcom.2006.11.217},
issn = {09258388},
year = {2007},
date = {2007-01-01},
journal = {Journal of Alloys and Compounds},
volume = {442},
number = {1-2 SPEC. ISS.},
pages = {139-141},
abstract = {The model of the magnetic rare earth metals which contains interacting itinerant electrons and localized spins was considered. The interaction between both kinds of electrons was assumed in the simple local exchange s-f form. The complicated many body problem was reduced to the one particle one with the help of coherent potential approximation (CPA). Itinerant electron self-energy was calculated using standard Green's function technique with taking into account short range order (SRO) within the localized spin system. The magnetic part of the dc electrical conductivity σ in the paramagnetic region, expressed by Kubo-Greenwood formula, was calculated. The resistivity ρ = 1 / σ and its derivative over the temperature shows the structure near TC + 0+. The quantities ρ, ∂ ρ / ∂ T were not constant versus temperatures as it is in the simple models often used. The influence of the important model parameters and single ion anisotropy on the resistivity was calculated and shortly discussed. © 2007 Elsevier B.V. All rights reserved.},
note = {1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The model of the magnetic rare earth metals which contains interacting itinerant electrons and localized spins was considered. The interaction between both kinds of electrons was assumed in the simple local exchange s-f form. The complicated many body problem was reduced to the one particle one with the help of coherent potential approximation (CPA). Itinerant electron self-energy was calculated using standard Green's function technique with taking into account short range order (SRO) within the localized spin system. The magnetic part of the dc electrical conductivity σ in the paramagnetic region, expressed by Kubo-Greenwood formula, was calculated. The resistivity ρ = 1 / σ and its derivative over the temperature shows the structure near TC + 0+. The quantities ρ, ∂ ρ / ∂ T were not constant versus temperatures as it is in the simple models often used. The influence of the important model parameters and single ion anisotropy on the resistivity was calculated and shortly discussed. © 2007 Elsevier B.V. All rights reserved.
2006
Lipowczan, M.; Borgieł, W.; Stysiak, D.
Influence of the short range order (SRO) on electrical resistivity of magnetic alloys Proceedings
vol. 3, no. 1, 2006, ISSN: 16101634, (2).
@proceedings{2-s2.0-31144437832,
title = {Influence of the short range order (SRO) on electrical resistivity of magnetic alloys},
author = { M. Lipowczan and W. Borgieł and D. Stysiak},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-31144437832&doi=10.1002%2fpssc.200562517&partnerID=40&md5=1115b264c54ca653ffb90cff94c9b3f9},
doi = {10.1002/pssc.200562517},
issn = {16101634},
year = {2006},
date = {2006-01-01},
journal = {Physica Status Solidi C: Conferences},
volume = {3},
number = {1},
pages = {36-39},
abstract = {The model of the magnetic binary alloy which contains interacting itinerant electrons and localized spins was considered. The interaction between both kinds of electrons was assumed in the simple local exchange form. The complicated many body problem was reduced to the one particle one with the help of Coherent Potential Approximation (CPA). Itinerant electron selfenergy was calculated using standard Green's function technique with taking into account short range order (SRO) within the localized spin system. Electron's states were strongly affected by the correlations (SRO; when T > TC) within localized moments system. The DC electrical conductivity σ in the paramagnetic region expressed by Kubo-Grennwood alloy formula was calculated. The resistivity ρ = 1/σ and its derivative over the temperature have the structure near TC, which depends on the number of the electrons in the band and the interaction strength between two subsystems. The quantities ρ, ∂ρ/∂T were not constant vs. temperature as it is in the simple models, The influence of the important model parameters on the DC conductivity was also discussed. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA.},
note = {2},
keywords = {},
pubstate = {published},
tppubtype = {proceedings}
}
The model of the magnetic binary alloy which contains interacting itinerant electrons and localized spins was considered. The interaction between both kinds of electrons was assumed in the simple local exchange form. The complicated many body problem was reduced to the one particle one with the help of Coherent Potential Approximation (CPA). Itinerant electron selfenergy was calculated using standard Green's function technique with taking into account short range order (SRO) within the localized spin system. Electron's states were strongly affected by the correlations (SRO; when T > TC) within localized moments system. The DC electrical conductivity σ in the paramagnetic region expressed by Kubo-Grennwood alloy formula was calculated. The resistivity ρ = 1/σ and its derivative over the temperature have the structure near TC, which depends on the number of the electrons in the band and the interaction strength between two subsystems. The quantities ρ, ∂ρ/∂T were not constant vs. temperature as it is in the simple models, The influence of the important model parameters on the DC conductivity was also discussed. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA.
2004
Nolting, W.; Hickel, T.; Ramakanth, A.; Reddy, G. G.; Lipowczan, M.
Carrier-induced ferromagnetism in concentrated and diluted local-moment systems Journal Article
In: Physical Review B - Condensed Matter and Materials Physics, vol. 70, no. 7, pp. 075207-1-075207-8, 2004, ISSN: 01631829, (12).
@article{2-s2.0-19544386293,
title = {Carrier-induced ferromagnetism in concentrated and diluted local-moment systems},
author = { W. Nolting and T. Hickel and A. Ramakanth and G.G. Reddy and M. Lipowczan},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-19544386293&doi=10.1103%2fPhysRevB.70.075207&partnerID=40&md5=b9ecfb09bfd670800a0e386b52e23d8f},
doi = {10.1103/PhysRevB.70.075207},
issn = {01631829},
year = {2004},
date = {2004-01-01},
journal = {Physical Review B - Condensed Matter and Materials Physics},
volume = {70},
number = {7},
pages = {075207-1-075207-8},
publisher = {American Physical Society},
abstract = {For modeling the magnetic properties of concentrated and diluted magnetic semiconductors, we use the Kondo-lattice model. The magnetic phase diagram is derived by inspecting the static susceptibility of itinerant band electrons, which are exchange coupled to localized magnetic moments. It turns out that rather low band occupations favor a ferromagnetic ordering of the local moment systems due to an indirect coupling mediated by a spin polarization of the itinerant charge carriers. The disorder in diluted systems is treated by adding a CPA-type concept to the theory. For almost all moment concentrations x, ferromagnetism is possible, however, only for carrier concentrations n distinctly smaller than x. The charge carrier compensation in real magnetic semiconductors (in Ga1-xMnxAs by; e.g.; antisites) seems to be a necessary condition for getting carrier induced ferromagnetism.},
note = {12},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
For modeling the magnetic properties of concentrated and diluted magnetic semiconductors, we use the Kondo-lattice model. The magnetic phase diagram is derived by inspecting the static susceptibility of itinerant band electrons, which are exchange coupled to localized magnetic moments. It turns out that rather low band occupations favor a ferromagnetic ordering of the local moment systems due to an indirect coupling mediated by a spin polarization of the itinerant charge carriers. The disorder in diluted systems is treated by adding a CPA-type concept to the theory. For almost all moment concentrations x, ferromagnetism is possible, however, only for carrier concentrations n distinctly smaller than x. The charge carrier compensation in real magnetic semiconductors (in Ga1-xMnxAs by; e.g.; antisites) seems to be a necessary condition for getting carrier induced ferromagnetism.
2003
Lipowczan, M.; Deniszczyk, J.; Borgieł, W.
Calculations of the thermoelectric power for the (Gd1-xRx)nMm alloys Journal Article
In: Physica Status Solidi (A) Applied Research, vol. 196, no. 1 SPEC., pp. 336-339, 2003, ISSN: 00318965.
@article{2-s2.0-0038301335,
title = {Calculations of the thermoelectric power for the (Gd1-xRx)nMm alloys},
author = { M. Lipowczan and J. Deniszczyk and W. Borgieł},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0038301335&doi=10.1002%2fpssa.200306422&partnerID=40&md5=b88a1ecf8faa95e1ab5ea88e333994c1},
doi = {10.1002/pssa.200306422},
issn = {00318965},
year = {2003},
date = {2003-01-01},
journal = {Physica Status Solidi (A) Applied Research},
volume = {196},
number = {1 SPEC.},
pages = {336-339},
abstract = {Disordered substitutional alloys (Gd1-xRx)mMn represent a very interesting alloy family showing both well defined (no orbital contribution) randomly distributed localized spins (Gd) and itinerant electron bands with a population depending on the concentration x. Because of the complicated many-body task, only the paramagnetic state was considered. The influence of the external uniform magnetic field was also discussed. The main contribution to the thermoelectric power (TEP) has a magnetic origin and is caused by scattering of the conducting electrons on the stochastic distributions of the large Gd spin (S = 7/2ℏ) over the lattice sites. The many-body approximations used for our models are based on the alloy analogy approximations for the fictitious electronic alloys. Band structure calculations yielding informations on the widths and positions of the itinerant bands were performed. The results on TEP as a function of alloy concentration x fit well the experimental results.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Disordered substitutional alloys (Gd1-xRx)mMn represent a very interesting alloy family showing both well defined (no orbital contribution) randomly distributed localized spins (Gd) and itinerant electron bands with a population depending on the concentration x. Because of the complicated many-body task, only the paramagnetic state was considered. The influence of the external uniform magnetic field was also discussed. The main contribution to the thermoelectric power (TEP) has a magnetic origin and is caused by scattering of the conducting electrons on the stochastic distributions of the large Gd spin (S = 7/2ℏ) over the lattice sites. The many-body approximations used for our models are based on the alloy analogy approximations for the fictitious electronic alloys. Band structure calculations yielding informations on the widths and positions of the itinerant bands were performed. The results on TEP as a function of alloy concentration x fit well the experimental results.
2000
Borgieł, W.; Deniszczyk, J.; Lipowczan, M.; Braun, J.
Resistivity of (Gd1-xYx)2in alloys at high temperatures - Two-band model approach Journal Article
In: Acta Physica Polonica A, vol. 98, no. 5, pp. 547-550, 2000, ISSN: 05874246, (1).
@article{2-s2.0-0037670395,
title = {Resistivity of (Gd1-xYx)2in alloys at high temperatures - Two-band model approach},
author = { W. Borgieł and J. Deniszczyk and M. Lipowczan and J. Braun},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037670395&doi=10.12693%2fAPhysPolA.98.547&partnerID=40&md5=72dc75766dae5a4e0962683b9bc556e8},
doi = {10.12693/APhysPolA.98.547},
issn = {05874246},
year = {2000},
date = {2000-01-01},
journal = {Acta Physica Polonica A},
volume = {98},
number = {5},
pages = {547-550},
publisher = {Polish Academy of Sciences},
abstract = {Two-band model for the substitutionary binary alloy of different rare earth metals with relatively simple 4f multiplet structure placed within the transition metal host matrix was proposed and applied to (Gd1-xYx)2In. The main interaction which causes the magnetic part of the resistivity was assumed in a form of stochastically distributed in space s-f interaction. The calculated high temperature spin disorder resistivity of (Gd1-xYx)2In alloys reproduces well the experimental alloys data.},
note = {1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Two-band model for the substitutionary binary alloy of different rare earth metals with relatively simple 4f multiplet structure placed within the transition metal host matrix was proposed and applied to (Gd1-xYx)2In. The main interaction which causes the magnetic part of the resistivity was assumed in a form of stochastically distributed in space s-f interaction. The calculated high temperature spin disorder resistivity of (Gd1-xYx)2In alloys reproduces well the experimental alloys data.