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19 results on '"Milan Brumen"'

1. Modelling the mechanical response of two-layered artery using thermomechanical analogy approach

Author

Janez Urevc, Vojko Flis, Milan Brumen, and Boris Štok

Subjects
common carotid artery, finite element method, residual stresses, thermomechanics, Engineering (General). Civil engineering (General), TA1-2040
Abstract

This work deals with the prediction of the mechanical response of a section of a human common carotid artery (CCA). The arterial residual stress state is accounted for using the thermomechanical analogy (TMA) approach, which is applied in this work to model the mechanical response of a two-layered arterial structure. The starting point to model the arterial residual stress state is normally the cut-open section, which is in the case of patient-specific artery not known. With TMA approach, however, instead of using the arterial zero-stress cut-open configuration to predict the arterial residual stress state, a thermomechanical model of the CCA is considered with its zero-stress geometry defined based on the actual CCA in vivo configuration. The approximation to the CCA residual stress state is then obtained by exposing the auxiliary CCA model to a volumetric deformation, enforced via adequate thermal dilatations. The approach is validated on a circular arterial model and by predicting the CCA cut-open zero-stress state.

Published
2017
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2. An approach to consider the arterial residual stresses in modelling of a patient-specific artery

Author

Janez Urevc, Miroslav Halilovič, Milan Brumen, and Boris Štok

Subjects
Mechanical engineering and machinery, TJ1-1570
Abstract

In this work, the residual stress state of a human common carotid artery is predicted using the so-called thermomechanical analogy approach. The purpose of the approach is to enable consistent mapping of residual stresses and the respective configuration from a circular arterial segment to a patient-specific arterial geometry. This is achieved by applying proper volumetric dilatations to the actual arterial stress-free in vivo geometry, which makes use of the analogy that states that the bending stresses can be obtained on an equivalent manner by applying proper thermal dilatations. The common carotid artery data are obtained in vivo from a healthy 28-year-old man using non-invasive methods. The predicted residual stresses of the common carotid artery are in good quantitative agreement with the data from prior work in this field. The approach is validated by predicting the common carotid artery zero-stress state configuration, where a sector-like (cut-open) state is obtained. With this approach, it is thus possible to predict the residual stresses as well as the configuration of patient-specific arterial geometry without the need to model its cut-open zero-stress configuration.

Published
2016
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3. The Maximum Entropy Production Principle and Linear Irreversible Processes

Author

Milan Brumen, Davor Juretić, Dražen Petrov, Željana Bonačić Lošić, Domagoj Kuić, and Paško Županović

Subjects
entropy production, linear nonequilibrium thermodynamics, linearized Boltzmann equation, Science, Astrophysics, QB460-466, Physics, QC1-999
Abstract

It is shown that Onsager’s principle of the least dissipation of energy is equivalent to the maximum entropy production principle. It is known that solutions of the linearized Boltzmann equation make extrema of entropy production. It is argued, in the case of stationary processes, that this extremum is a maximum rather than a minimum.

Published
2010
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4. Dynamic model of eicosanoid production with special reference to non‐steroidal anti‐inflammatory drug‐triggered hypersensitivity

Author

Tadej Emeršič, Dirk Schäfer, Aleš Fajmut, Milan Brumen, Nataša Antić, and Andrej Dobovišek

Subjects
musculoskeletal diseases, Population, Inflammation, Pharmacology, Biology, Drug Hypersensitivity, chemistry.chemical_compound, Genetics, medicine, Humans, Computer Simulation, education, Molecular Biology, Research Articles, chemistry.chemical_classification, education.field_of_study, Aspirin, Anti-Inflammatory Agents, Non-Steroidal, Models, Immunological, Computational Biology, Cell Biology, Kinetics, Metabolic pathway, Enzyme, chemistry, Modeling and Simulation, Immunology, Eicosanoids, lipids (amino acids, peptides, and proteins), Bronchoconstriction, Arachidonic acid, medicine.symptom, Biotechnology, medicine.drug, Eicosanoid Production
Abstract

The authors developed a mathematical model of arachidonic acid (AA) degradation to prostaglandins (PGs) and leukotrienes (LTs), which are implicated in the processes of inflammation and hypersensitivity to non‐steroidal anti‐inflammatory drugs (NSAIDs). The model focuses on two PGs (PGE(2) and PGD(2)) and one LT (LTC(4)), their % increases and their ratios. Results are compared with experimental studies obtained from non‐asthmatics (NAs), and asthmatics tolerant (ATA) or intolerant (AIA) to aspirin. Simulations are carried out for predefined model populations NA, ATA and three AIA, based on the differences of two enzymes, PG E synthase and/or LTC(4)‐synthase in two states, that is, no‐inflammation and inflammation. Their model reveals that the model population with concomitant malfunctions in both enzymes is the most sensitive to NSAIDs, since the duration and the capacity for bronchoconstriction risk are highest after simulated oral dosing of indomethacin. Furthermore, inflammation prolongs the duration of the bronchoconstriction risk in all AIA model populations, and the sensitivity analysis reveals multiple possible scenarios leading to hypersensitivity, especially if inflammatory processes affect the expression of multiple enzymes of the AA metabolic pathway. Their model estimates the expected fold‐changes in enzyme activities and gives valuable information for further targeted transcriptomic/proteomic and metabolomic studies.

Published
2015
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5. The maximum entropy production principle and linear irreversible processes

Author

Milan Brumen, Domagoj Kuić, Zeljana Bonacic Losic, Drazen Petrov, Davor Juretić, and Pasko Zupanovic

Subjects
General Physics and Astronomy, FOS: Physical sciences, lcsh:Astrophysics, 01 natural sciences, entropy production, 010305 fluids & plasmas, udc:536, linear nonequilibrium thermodynamics, linearized Boltzmann equation, linearna neuravnotežena termodinamika, 0103 physical sciences, lcsh:QB460-466, produkcija entropije, Maximum entropy production, Statistical physics, Physics::Chemical Physics, 010306 general physics, lcsh:Science, Condensed Matter - Statistical Mechanics, Physics, Statistical Mechanics (cond-mat.stat-mech), Entropy production, Dissipation, Boltzmann equation, lcsh:QC1-999, Maxima and minima, linearizacija Boltzmannove enačbe, lcsh:Q, Energy (signal processing), lcsh:Physics
Abstract

It is shown that Onsager's principle of the least dissipation of energy is equivalent to the maximum entropy production principle. It is known that solutions of the linearized Boltzmann equation make extrema of entropy production. It is argued, in the case of stationary processes, that this extremum is a maximum rather than a minimum., 12 pages, revtex4

Published
2017

6. Modelling the mechanical response of two-layered artery using thermomechanical analogy approach

Author

Boris Štok, Janez Urevc, Milan Brumen, and Vojko Flis

Subjects
metoda konačnih elemenata, termo-mehanika, zajednička arterija glave, zaostala naprezanja, thermomechanics, lcsh:TA1-2040, residual stresses, parasitic diseases, finite element method, General Engineering, cardiovascular system, cardiovascular diseases, common carotid artery, lcsh:Engineering (General). Civil engineering (General)
Abstract

Ovaj rad obrađuje problem predviđanja mehaničkog odziva dijela zajedničke arterije glave (ZAG). Zaostala naprezanja u arteriji uzeta su u obzir uporabom termo-mehaničke analogije (TMA), koja se primjenjuje u ovom radu za potrebe modeliranja mehaničkog odziva dvoslojne strukture stijenke arterije. Obično se modeliranju zaostalih naprezanja u arteriji pristupi s uzdužno otvorenim modelom arterije, tzv. cut-open section, koji u slučaju bolesnikove arterije nije poznat. S TMA pristupom, umjesto uporabe uzdužno prerezane stijenke arterije, koja doduše osigurava početno stanje bez zaostalih naprezanja, u termo-mehaničkom modelu zajedničke arterije glave također je postignuto početno stanje bez zaostalih naprezanja ali na modelu stvarne, in vivo arterije. Tim pristupom, zaostalo naprezanje u ZAG aproksimirano je podvrgavanjem ZAG modela obujamskom deformacijom, t.j. primjenom odgovarajućih termičkih dilatacija. Takav pristup potvrđen je na modelu arterije kružnog presjeka i postizanjem stanja bez naprezanja u slučaju uzdužnog rezanja stijenke., This work deals with the prediction of the mechanical response of a section of a human common carotid artery (CCA). The arterial residual stress state is accounted for using the thermomechanical analogy (TMA) approach, which is applied in this work to model the mechanical response of a two-layered arterial structure. The starting point to model the arterial residual stress state is normally the cut-open section, which is in the case of patient-specific artery not known. With TMA approach, however, instead of using the arterial zero-stress cut-open configuration to predict the arterial residual stress state, a thermomechanical model of the CCA is considered with its zero-stress geometry defined based on the actual CCA in vivo configuration. The approximation to the CCA residual stress state is then obtained by exposing the auxiliary CCA model to a volumetric deformation, enforced via adequate thermal dilatations. The approach is validated on a circular arterial model and by predicting the CCA cut-open zero-stress state.

Published
2017

7. Modeliranje mehaničkog odziva dvoslojne stijenke arterije uporabom termo-mehaničke analogije

Author

Janez Urevc, Vojko Flis, Milan Brumen, Boris Štok, Janez Urevc, Vojko Flis, Milan Brumen, and Boris Štok

Abstract

Ovaj rad obrađuje problem predviđanja mehaničkog odziva dijela zajedničke arterije glave (ZAG). Zaostala naprezanja u arteriji uzeta su u obzir uporabom termo-mehaničke analogije (TMA), koja se primjenjuje u ovom radu za potrebe modeliranja mehaničkog odziva dvoslojne strukture stijenke arterije. Obično se modeliranju zaostalih naprezanja u arteriji pristupi s uzdužno otvorenim modelom arterije, tzv. cut-open section, koji u slučaju bolesnikove arterije nije poznat. S TMA pristupom, umjesto uporabe uzdužno prerezane stijenke arterije, koja doduše osigurava početno stanje bez zaostalih naprezanja, u termo-mehaničkom modelu zajedničke arterije glave također je postignuto početno stanje bez zaostalih naprezanja ali na modelu stvarne, in vivo arterije. Tim pristupom, zaostalo naprezanje u ZAG aproksimirano je podvrgavanjem ZAG modela obujamskom deformacijom, t.j. primjenom odgovarajućih termičkih dilatacija. Takav pristup potvrđen je na modelu arterije kružnog presjeka i postizanjem stanja bez naprezanja u slučaju uzdužnog rezanja stijenke., This work deals with the prediction of the mechanical response of a section of a human common carotid artery (CCA). The arterial residual stress state is accounted for using the thermomechanical analogy (TMA) approach, which is applied in this work to model the mechanical response of a two-layered arterial structure. The starting point to model the arterial residual stress state is normally the cut-open section, which is in the case of patient-specific artery not known. With TMA approach, however, instead of using the arterial zero-stress cut-open configuration to predict the arterial residual stress state, a thermomechanical model of the CCA is considered with its zero-stress geometry defined based on the actual CCA in vivo configuration. The approximation to the CCA residual stress state is then obtained by exposing the auxiliary CCA model to a volumetric deformation, enforced via adequate thermal dilatations. The approach is validated on a circular arterial model and by predicting the CCA cut-open zero-stress state.

Published
2017

8. Polyelectrolyte microcapsules and coated CaCO3 particles as fluorescence activated sensors in flowmetry

Author

Uta Riebentanz, Edwin Donath, David Haložan, and Milan Brumen

Subjects
Micrometre, chemistry.chemical_compound, Colloid and Surface Chemistry, Materials science, chemistry, Biochemistry, Chemical engineering, Microparticle, Fluorescence, Polyelectrolyte, Acrylic acid
Abstract

Polyelectrolyte multilayer film capsules with different micrometer sizes were assembled for pH and salt sensing devices. Encapsulation of labelled poly(acrylic acid) (PAA AF ) in CaCO 3 particles increases their potential usage in the biological environment. Microcapsules were analyzed with flowcytometry to obtain individual response of a spherical-like microsensor that behaves as Donnan system. The linear pH response of microparticles and microcapsules is quite broad and is useful in physiological range. The salt response is up to 0.1 M and was also predicted with simple mathematical model.

Published
2009
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9. Morphology of solidified polysulfone structures obtained by wet phase separation

Author

Vladimir Kaiser, Chrtomir Stropnik, Milan Brumen, and Vojko Musil

Subjects
chemistry.chemical_classification, Spinodal, Chromatography, Ternary numeral system, Polymers and Plastics, Chemistry, Organic Chemistry, Nucleation, General Physics and Astronomy, Concentration effect, Polymer, chemistry.chemical_compound, Chemical engineering, Phase (matter), Materials Chemistry, Polysulfone, Phase diagram
Abstract

Evidence is presented that all three theoretically predicted modes of phase separation take place in the ternary system polysulfone(PSf)/ N , N -dimethyl acetamide(DMA)/water during the process of wet phase separation (WPS). The elementary process of solidification is reconsidered with regard to the (non-) equilibrium phase separation. Cast solutions with more than 15 wt% of PSf undergo nucleation and growth of the polymer lean phase with formation of separation membranes characterised by a cellular structure. When cast solutions with about 5–7 wt% of PSf undergo WPS, somewhere inside the ternary system conditions are established so that alongside other solidified PSf structures the bicontinuous spinodal structures superimposed by bead-like structures are also formed. Variety of lacy PSf structures with less/more polymer beads is the manifestation of the primary phase separation by the spinodal mode superimposed by the secondary phase separation taking place by heterogeneous nucleation and growth of the polymer rich phase mode. Latex formation during the WPS will also be explained. Skin formation on the cast solution – coagulation bath interface by direct accumulation of polymer is established regardless of the PSf content in the cast solution.

Published
2007
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10. Applying thermomechanical analogy to predict the arterial residual stress state

Author

Janez Urevc, Milan Brumen, Boris Štok, and Vojko Flis

Subjects
Materials science, Field (physics), Thermodynamic equilibrium, business.industry, Mechanical Engineering, Numerical analysis, Bending, Structural engineering, Residual, Finite element method, Mechanics of Materials, Residual stress, Hyperelastic material, business
Abstract

The prediction of the arterial zero-stress state is as of yet an unresolved problem in the field of modelling the mechanical response of patientspecific arteries. This is because the configuration associated with arterial zero-stress state is impossible to obtain experimentally. However, the zero-stress configuration (or, equivalently, the residual stresses related to this configuration) represents the crucial data of any numerical analysis. In this study, the mechanical response of a pre-stressed, pressurised, hyperelastic tube (representing the artery) is determined without knowing the initial zero-stress configuration of the artery. Instead, to predict the arterial residual (bending and stretching) stresses, a corresponding thermomechanical analogy is used. As shown in the paper, the arterial residual stress state can equally be obtained by thermally loading a properly defined closed tube. Thus, based on the loaded state of the corresponding thermomechanical model, the arterial residual stress sate is constructed, from where the arterial loaded state can be obtained. The initial configuration of the thermomechanical model is defined on the basis of the arterial loaded configuration. The methodology is validated by predicting the zero-stress state of the artery. The predicted equilibrium state of the artery, when cut longitudinally and transversally, has the form of an opened-up tube with a relatively low stress state in comparison to the arterial residual stresses. The results thus demonstrate that arterial residual stresses that are predicted with the corresponding thermomechanical model exhibited the bending distribution, which proves the methodology to be adequate. Določitev breznapetostnega stanja arterij predstavlja še vedno nerazrešen problem na področju numeričnega modeliranja mehanskega odziva realnih arterij. Breznapetostno stanje arterije, ki ima v splošnem obliko krožnega sektorja, je namreč eksperimentalno nemogoče določiti. Oblika breznapetostnega stanja (oziroma temu pripadajoče zaostalo napetostno stanje) pa je pomembno zato, ker predstavlja začetno stanje in tako ključen podatek sleherne numerične analize. Arterije se za karakterizacijo njihovega mehanskega odziva običajno obravnava kot idealno krožne cevi, to pomeni idealno krožne in ravne. Takšna poenostavitev omogoča določitev zaostalih napetosti arterije brez poznavanja njihovega breznapetostnega stanja. Prisotnost zaostalih napetosti je posledica homogenizacije odziva arterij in vivo. Napetostno stanje arterije in vivo bi bilo namreč izrazito nehomogeno z velikim transmuralnim gradientom brez upoštevanja zaostalih napetosti. Zaradi njihove porazdelitve skozi debelino žilne stene se jih običajno asociira z upogibnimi napetostmi. Na notranji površini kolobarja so zaostale napetosti tlačne, medtem ko so na zunanji površini natezne.

Published
2015

11. Theoretical model of the interactions between Ca2+, calmodulin and myosin light chain kinase

Author

Stefan Schuster, Aleš Fajmut, and Milan Brumen

Subjects
Myosin Light Chains, Myosin light-chain kinase, Calmodulin, Cations, Divalent, Biophysics, Kinetic scheme, macromolecular substances, Biochemistry, Mathematical model, Structural Biology, Ca2+/calmodulin-dependent protein kinase, Genetics, Phosphorylation, Myosin light chain kinase, Myosin-Light-Chain Kinase, Molecular Biology, biology, Chemistry, Cell Biology, Smooth muscle contraction, Models, Theoretical, biology.protein, Calcium, Ca2 calmodulin
Abstract

Active Ca2+/calmodulin (CaM)-dependent myosin light chain kinase (MLCK) plays an important role in the process of MLC phosphorylation and consecutive smooth muscle contraction. Here, we propose a mathematical model of a detailed kinetic scheme describing interactions among Ca2+, CaM and MLCK and taking into account eight different aggregates. The main model result is the prediction of the Ca2+ dependent active form of MLCK, which is in the model taken as proportional to the concentration of Ca4CaM · MLCK complex. Wegscheider’s condition is additionally applied as a constraint enabling the prediction of some parameter values that have not yet been obtained by experiments.

Published
2005
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12. Hollow Polyelectrolyte Shells: Exclusion of Polymers and Donnan Equilibrium

Author

Gleb B. Sukhorukov, Edwin Donath, Milan Brumen, and Helmuth Möhwald

Subjects
chemistry.chemical_classification, Chemistry, Capsule, Polymer, Polyelectrolyte, Surfaces, Coatings and Films, Ion, Core (optical fiber), Polyelectrolyte adsorption, Chemical engineering, Polymer chemistry, Materials Chemistry, Semipermeable membrane, Physical and Theoretical Chemistry, Dissolution
Abstract

Hollow polyelectrolyte capsules were fabricated by means of stepwise adsorption of polyelectrolytes followed by dissolution of the templating core. The capsule wall thickness was approximately 20 nm. The diameter of the capsules is given by the size of the templates (3.3 μm). These capsules exclude poly(styrenesulfonate) (PSS) from a molecular weight of 4200 upward but are permeable for small ions and 6-carboxyfluorescein (6-CF). By means of adding PSS in acidic form to the bulk solution, a Donnan equilibrium between the bulk and internal solution encapsulated within the capsules was created. The pH in the capsule interior is more basic. This difference in pH is larger than a unit for capsules of 3.3 μm in diameter. Addition of NaCl decreases this pH difference. A theoretical model is developed that describes the observed pH difference. The essential assumptions of the model are the selective permeability of the capsule wall, charging of the capsule together with its interior according to its capacitance,...

Published
1999
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13. Contributory presentations/posters

Author

N. Manoj, V. R. Srinivas, A. Surolia, M. Vijayan, K. Suguna, R. Ravishankar, R. Schwarzenbacher, K. Zeth, null Diederichs, G. M. Kostner, A. Gries, P. Laggner, R. Prassl, null Madhusudan, Pearl Akamine, Nguyen-huu Xuong, Susan S. Taylor, M. Bidva Sagar, K. Saikrishnan, S. Roy, K. Purnapatre, P. Handa, U. Varshney, B. K. Biswal, N. Sukumar, J. K. Mohana Rao, A. Johnson, Vasantha Pattabhi, S. Sri Krishna, Mira Sastri, H. S. Savithri, M. R. N. Murthy, Bindu Pillai, null Kannan, M. V. Hosur, Mukesh Kumar, Swati Patwardhan, K. K. Kannan, B. Padmanabhaa, S. Sasaki-Sugio, M. Nukaga, T. Matsuzaki, S. Karthikevan, S. Sharma, A. K. Sharma, M. Paramasivam, P. Kumar, J. A. Khan, S. Yadav, A. Srinivasan, T. P. Singh, S. Gourinath, Neelima Alam, A. Srintvasan, Vikas Chandra, Punit Kaur, Ch. Betzel, S. Ghosh, A. K. Bera, S. Bhattacharya, S. Chakraborty, A. K. Pal, B. P. Mukhopadhyay, I. Dey, U. Haldar, Asok Baneriee, Jozef Sevcik, Adriana Solovicova, K. Sekar, M. Sundaralingam, N. Genov, Dong-cai Liang, Tao Jiang, Ji-ping Zhang, Wen-rui Chang, Wolfgang Jahnke, Marcel Blommers, S. C. Panchal, R. V. Hosur, Bindu Pillay, Puniti Mathur, S. Srivatsun, Ratan Mani Joshi, N. R. Jaganathan, V. S. Chauhan, H. S. Atreya, S. C. Sahu, K. V. R. Chary, Girjesh Govil, Elisabeth Adjadj, Éric Quinjou, Nadia Izadi-Pruneyre, Yves Blouquit, Joël Mispelter, Bernadette Heyd, Guilhem Lerat, Philippe Milnard, Michel Desmadreil, Y. Lin, B. D. Nageswara Rao, Vidva Raghunathan, Mei H. Chau, Prashant Pesais, Sudha Srivastava, Evans Coutinho, Anil Saran, Leizl F. Sapico, Jayson Gesme, Herbert Lijima, Raymond Paxton, Thamarapu Srikrishnan, C. R. Grace, G. Nagenagowda, A. M. Lynn, Sudha M. Cowsik, Sarata C. Sahu, S. Chauhan, A. Bhattacharya, G. Govil, Anil Kumar, Maurizio Pellecchia, Erik R. P. Zuiderweg, Keiichi Kawano, Tomoyasu Aizawa, Naoki Fujitani, Yoichi Hayakawa, Atsushi Ohnishi, Tadayasu Ohkubo, Yasuhiro Kumaki, Kunio Hikichi, Katsutoshi Nitta, V. Rani Parvathy, R. M. Kini, Takumi Koshiba, Yoshihiro Kobashigawa, Min Yao, Makoto Demura, Astushi Nakagawa, Isao Tanaka, Kunihiro Kuwajima, Jens Linge, Seán O. Donoghue, Michael Nilges, G. Chakshusmathi, Girish S. Ratnaparkhi, P. K. Madhu, R. Varadarajan, C. Tetreau, M. Tourbez, D. Lavalette, M. Manno, P. L. San Biagio, V. Martorana, A. Emanuele, S. M. Vaiana, D. Bulone, M. B. Palma-Vittorelli, M. U. Palma, V. D. Trivedi, S. F. Cheng, W. J. Chien, S. H. Yang, S. Francis, D. K. Chang, Renn Batra, Michael A. Geeves, Dietmar J. Manstein, Joanna Trvlska, Pawel Grochowski, Maciej Geller, K. Ginalski, P. Grochowski, B. Lesyng, P. Lavalette, Y. Blouquit, D. Roccatano, A. Amadei, A. Di Nola, H. J. C. Berendsen, Bosco Ho, P. M. G. Curmi, H. Berry, D. Lairez, E. Pauthe, J. Pelta, V. Kothekar, Shakti Sahi, M. Srinivasan, Anil K. Singh, Kartha S. Madhusudnan, Fateh S. Nandel, Harpreet Kaur, Balwinder Singh, D. V. S. Jain, K. Anton Feenstra, Herman J. C. Berendsen, F. Tama, Y. -H. Sanejouand, N. Go, Deepak Sharma, Sunita Sharma, Santosh Pasha, Samir K. Brahmachari, R. Viiavaraghavan, Jyoti Makker, Sharmisllia Dey, S. Kumar, G. S. Lakshmikanth, G. Krishnamoorthy, V. M. Mazhul, E. M. Zaitseva, Borys Kierdaszuk, J. Widengren, B. Terry, Ü. Mets, R. Rigler, R. Swaminathan, S. Thamotharan, N. Yathindra, Y. Shibata, H. Chosrowjan, N. Mataga, I. Morisima, Tania Chakraharty, Ming Xiao, Roger Cooke, Paul Selvin, C. Branca, A. Faraone, S. Magazù, G. Maisano, P. Migliardo, V. Villari, Digambar V. Behere, M. Sharique Zahida Waheed Deva, M. Brunori, F. Cutruzzolà, Q. H. Gibson, C. Savino, C. Travaglini-Allocatelli, B. Vallone, Swati Prasad, Shyamalava Mazumdar, Samaresh Mitra, P. Soto, R. Fayad, I. E. Sukovataya, N. A. Tyulkova, Sh. V. Mamedov, B. Aktas, M. Canturk, B. Aksakal, R. Yilgin, K. I. Bogutska, N. S. Miroshnichenko, S. Chacko, M. DiSanto, J. A. Hypolite, Y-M. Zheng, A. J. Wein, M. Wojciechowski, T. Grycuk, J. Antosiewicz, Marc A. Ceruso, Alfredo Di Nola, Subhasis Bandvopadhvay, Bishnu P. Chatterjee, Devapriva Choudhury, Andrew Thompson, Vivian Stojanoff, Jerome Pinkner, Scott Hultgren, Stefan Khight, Delphine Flatters, Julia Goodfellow, Fumi Takazawatt, Minoru Kanehisa, Masaki Sasai, Hironori Nakamura, Wang Bao Han, Yuan Zheng, Wang Zhi Xin, Pan xin Min, Vlnod Bhakuni, Sangeeta Kulkarni, Atta Ahmad, Koodathingal Prakash, Shashi Prajapati, Alexey Surin, Tomoharu Matsumoto, Li Yang, Yuki Nakagawa, Kazumoto Kimura, Yoshiyuki Amemiya, Gennady V. Semisotnov, Hiroshi Kihara, Saad Tayyab, Salman Muzammil, Yogesh Kumar, Vinod Bhakuni, Monica Sundd, Suman Kundu, M. V. Jagannadham, Medicherla V. Jagannadham, Bina Chandani, Ruby Dhar, Lalankumar Sinha, Deepti Warrier, Sonam Mehrotra, Purnima Khandelwal, Subhendu Seth, Y. U. Sasidhar, C. Ratna Prabha, Arun Gidwani, K. P. Madhusudan, Akira R. Kinjo, Ken Nishikawa, Suvobrata Chakravarty, Raghavan Varadarajan, K. Noyelle, P. Haezebrouck, M. Joniau, H. Van Dael, Sheffali Dash, Indra Brata Jha, Rajiv Bhat, Prasanna Mohanty, A. K. Bandyopadhyay, H. M. Sonawat, Ch. Mohan Rao, Siddhartha Datta, K. Rajaraman, B. Raman, T. Ramakrishna, A. Pande, J. Pande, S. Betts, N. Asherie, O. Ogun, J. King, G. Benedek, I. V. Sokolova, G. S. Kalacheva, Masashi Sonoyama, Yasunori Yokoyama, Kunihiro Taira, Shigeki Mitaku, Chicko Nakazawal, Takanori Sasakil, Yuri Mukai, Naoki Kamo, Seema Dalal, Lynne Regan, Shigeki Mituku, Mihir Roychoudhury, Devesh Kumar, Dénes Lőrinczv, Franciska Könczöl, László Farkas, Joseph Belagyi, Christoph Schick, Christy A. Thomson, Vettai S. Ananthanarayanan, E. G. Alirzayeva, S. N. Baba-Zade, M. Michael Gromiha, M. Oobatake, H. Kono, J. An, H. Uedaira, A. Sarai, Kazufumi Takano, Yuriko Yamagata, Katsuhide Yutani, Gouri S. Jas, Victor Muñoz, James Hofrichter, William A. Eaton, Jonathan Penoyar, Philip T. Lo Verde, J. Kardos, Á. Bódi, I. Venekei, P. Závodszky, L. Gráf, András Szilágyi, Péter Závodszky, R. D. Allan, J. Walshaw, D. 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Macpherson, D. O’Hare, C. P. Winlove, P. R. Unwin, R. Phillip, S. Banerjee, G. Ravindra Kumar, K. Nagayaka, R. Danev, S. Sugitani, K. Murata, Michael Gősch, H. Blom, P. Thyberg, Z. Földes-Papp, G. Björk, J. Holm, T. Heino, Masashi Yokochi, Fuyuhiko Inagaki, Masami Kusunoki, E. K. Matthews, J. Pines, Yu. P. Chukova, Vitaly K. Koltover, Geetanjali Bansal, Uma Singh, M. P. Bansal, Kotoko Nakata, Tastuya Nakano, Tsuguchika Kaminuma, B. P. S. Kang, U. Singh, Bonn Kirn, Neja Potocnik, Vito Stare, Latal Shukla, V. Natarajan, T. P. A. Devasagayam, M. D. Sastry, P. C. Kesavan, R. Sayfutdinov, V. V. Adamovich, D. Yu. Rogozin, A. G. Degermendzhy, C. L. Khetrapal, G. A. Nagana Gowda, Kedar Nath Ghimire, Ishida Masaru, H. Fujita, S. Ishiwata, Y. Kishimoto, S. Kawahara, M. Suzuki, H. Mori, M. Mishina, Y. Kirino, H. Ohshima, A. S. Dukhin, V. N. Shilov, P. J. Goetz, and R. K. Mishra

Subjects
0303 health sciences, biology, General Medicine, 010402 general chemistry, 01 natural sciences, Horseradish peroxidase, General Biochemistry, Genetics and Molecular Biology, 0104 chemical sciences, 03 medical and health sciences, Biochemistry, Manganese porphyrin, biology.protein, Enzyme reconstitution, General Agricultural and Biological Sciences, 030304 developmental biology
Published
1999
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14. Mathematical modelling of ca(2+) oscillations in airway smooth muscle cells

Author

Milan Brumen, Etienne Roux, Aleš Fajmut, and Andrej Dobovišek

Subjects
Oscillation, Endoplasmic reticulum, Cell, Biophysics, Cell Biology, Anatomy, Biology, Atomic and Molecular Physics, and Optics, Hedgehog signaling pathway, Article, Cytosol, Membrane, medicine.anatomical_structure, medicine, Molecular Biology, Acetylcholine, Intracellular, medicine.drug
Abstract

The action of different agonists such as acetylcholine on the membrane of airway smooth muscle cells may induce cytosolic Ca(2+) oscillations which can be a part of the Ca(2+) signalling pathway, eventually leading to cell contraction. The aim of the present study is to present a mathematical model of the possible effect of the initial Ca(2+) distribution within the cell on the form and frequency of induced Ca(2+) oscillations. It takes into account intracellular Ca(2+) stores such as sarcoplasmic reticulum and cytosolic proteins as well as Ca(2+) exchange across the plasma membrane. We are able to demonstrate a closer agreement of model predictions with observed Ca(2+) traces for a significantly wider range of parameter values, as was previously reported. We show also that the total cellular Ca(2+) content is an important system parameter especially because of the content in sarcoplasmic reticulum. At a total Ca(2+) increase of about 20%, the oscillation frequency increases by 25%; also, damped oscillations become sustained. Cases are indicated in which such a situation could occur.

Published
2013

15. The wet phase separation: the effect of cast solution thickness on the appearance of macrovoids in the membrane forming ternary cellulose acetate/acetone/water system

Author

Milan Brumen, Vojko Musil, Nusa Vogrin, and Črtomir Stropnik

Subjects
chemistry.chemical_classification, Filtration and Separation, Polymer, Biochemistry, Cellulose acetate, chemistry.chemical_compound, Membrane, chemistry, Chemical engineering, Polymer chemistry, Acetone, Coagulation (water treatment), General Materials Science, Physical and Theoretical Chemistry, Ternary operation
Abstract

We report on novel observations on the appearance of macrovoids in the ternary cellulose acetate (CA)/acetone (ACE)/water membrane forming system. The membranes are prepared by the wet phase separation whereby the cast solution is composed of ACE and polymer, and the coagulation bath is pure water only. It is found that the macrovoid formation in a 12.5 wt.% cast solution strongly depends on the cast solution thickness: macrovoids appear at the thickness of 500 μm but not at 150 and 300 μm.

Published
2002
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16. Enzyme kinetics and the maximum entropy production principle

Author

Domagoj Kuić, Andrej Dobovišek, Milan Brumen, Zeljana Bonacic-Losic, Pasko Zupanovic, and Davor Juretić

Subjects
Entropy, Biophysics, Thermodynamics, 01 natural sciences, Biochemistry, Michaelis–Menten kinetics, beta-Lactamases, 03 medical and health sciences, Reaction rate constant, 0103 physical sciences, Enzyme kinetics, 010306 general physics, 030304 developmental biology, 0303 health sciences, Chemistry, Entropy production, Quantitative Biology::Molecular Networks, Organic Chemistry, State (functional analysis), Maximization, Kinetics, evolution, enzyme, β lactamase, maximum entropy production principle, Forward rate, Biocatalysis, Constant (mathematics), Algorithms
Abstract

A general proof is derived that entropy production can be maximized with respect to rate constants in any enzymatic transition. This result is used to test the assumption that biological evolution of enzyme is accompanied with an increase of entropy production in its internal transitions and that such increase can serve to quantify the progress of enzyme evolution. The state of maximum entropy production would correspond to fully evolved enzyme. As an example the internal transition ES ↔ EP in a generalized reversible Michaelis–Menten three state scheme is analyzed. A good agreement is found among experimentally determined values of the forward rate constant in internal transitions ES → EP for three types of β-Lactamase enzymes and their optimal values predicted by the maximum entropy production principle, which agrees with earlier observations that β-Lactamase enzymes are nearly fully evolved. The optimization of rate constants as the consequence of basic physical principle, which is the subject of this paper, is a completely different concept from a) net metabolic flux maximization or b) entropy production minimization (in the static head state), both also proposed to be tightly connected to biological evolution.

Published
2010

17. Contribution of Rho kinase to the early phase of the calcium-contraction coupling in airway smooth muscle

Author

Prisca, Mbikou, Ales, Fajmut, Milan, Brumen, and Etienne, Roux

Subjects
Male, rho-Associated Kinases, Isometric Contraction, Animals, Bronchi, Calcium, Muscle, Smooth, Calcium Signaling, Rats, Wistar, Rats
Abstract

We investigated theoretically and experimentally the role of Rho kinase (RhoK) in Ca(2+)-contraction coupling in rat airways. Isometric contraction was measured on tracheal, extrapulmonary and intrapulmonary bronchial rings. Intracellular [Ca(2+)] was recorded in freshly isolated tracheal myocytes. Stimulation by carbachol (0.3 and 10 μm) and 50 mm external KCl induced a short-time, Hill-shaped contraction obtained within 90 s, followed by a sustained or an additional delayed contraction. Responses of [Ca(2+)](i) to acetylcholine consisted in a fast peak followed by a plateau and, in 42% of the cells, superimposed Ca(2+) oscillations. The RhoK inhibitor Y27632 (10 μm) did not alter the [Ca(2+)](i) response. Whatever the agonist, Y27632 did not modify the basal tension but decreased the amplitude of the short-duration response, without altering the additional delayed contraction. The Myosin Light Chain Phosphatase (MLCP) inhibitor calyculin A increased the basal tension and abolished the effect of RhoK. KN93 (Ca(2+)-calmodulin-dependent protein kinase II inhibitor) and DIDS (inhibitor of Ca(2+)-activated Cl(-) channels) had no influence on the RhoK effect. We built a theoretical model of Ca(2+)-dependent active/inactive RhoK ratio and subsequent RhoK-dependent MLCP inactivation, which was further coupled with a four-state model of the contractile apparatus and Ca(2+)-dependent MLCK activation. The model explains the time course of the short-duration contraction and the role of RhoK by Ca(2+)-dependent activation of MLCK and RhoK, which inactivates MLCP. Oscillatory and non-oscillatory [Ca(2+)](i) responses result in a non-oscillatory contraction, the amplitude of which is encoded by the plateau value and oscillation frequency. In conclusion, Ca(2+)-dependent but CaMK II-independent RhoK activation contributes to the early phase of the contractile response via MLCP inhibition.

Published
2010

18. Bacterial chemotaxis and entropy production

Author

Milan Brumen, Marko Jagodič, Davor Juretić, and Paško Županović

Subjects
bacterial chemotaxis, entropy production, Bacteria, Entropy production, Capillary action, Chemotaxis, Entropy, Acceleration, Energy metabolism, chemistry.chemical_element, Thermodynamics, Articles, Biology, biology.organism_classification, Models, Biological, Oxygen, General Biochemistry, Genetics and Molecular Biology, Quantitative Biology::Cell Behavior, Quantitative Biology::Subcellular Processes, Biochemistry, chemistry, Maximum entropy production, Energy Metabolism, General Agricultural and Biological Sciences
Abstract

Entropy production is calculated for bacterial chemotaxis in the case of a migrating band of bacteria in a capillary tube. It is found that the speed of the migrating band is a decreasing function of the starting concentration of the metabolizable attractant. The experimentally found dependence of speed on the starting concentration of galactose, glucose and oxygen is fitted with power-law functions. It is found that the corresponding exponents lie within the theoretically predicted interval. The effect of the reproduction of bacteria on band speed is considered, too. The acceleration of the band is predicted due to the reproduction rate of bacteria. The relationship between chemotaxis, the maximum entropy production principle and the formation of self-organizing structure is discussed.

Published
2010

19. Lipid layers on polyelectrolyte multilayer supports

Author

Martin Fischlechner, Luis Cuellar, Irina Estrela-Lopis, Markus Zaulig, Milan Brumen, Sergio Moya, Edwin Donath, Stefan Meyer, Paul Messner, Joseba Irigoyen, and Paula Pescador

Subjects
chemistry.chemical_classification, Bilayer, Vesicle, Fluorescence recovery after photobleaching, General Chemistry, Phosphatidylserine, Polymer, Condensed Matter Physics, Polyelectrolyte, chemistry.chemical_compound, Adsorption, chemistry, Chemical engineering, Phosphatidylcholine, Organic chemistry, lipids (amino acids, peptides, and proteins)
Abstract

The mechanism of formation of supported lipid layers from phosphatidylcholine and phosphatidylserine vesicles in solution on polyelectrolyte multilayers was studied by a variety of experimental techniques. The interaction of zwitterionic and acidic lipid vesicles, as well as their mixtures, with polyelectrolyte supports was followed in real time by micro-gravimetry. The fabricated lipid–polyelectrolyte composite structures on top of multilayer coated colloidal particles were characterized by flow cytometry and imaging techniques. Lipid diffusion over the macroscopic scale was quantified by fluorescence recovery after photobleaching, and the diffusion was related to layer connectivity. The phospholipid–polyelectrolyte binding mechanism was investigated by infrared spectroscopy. A strong interaction of polyelectrolyte primary amino groups with phosphate and carboxyl groups of the phospholipids, leading to dehydration, was observed. Long-range electrostatic attraction was proven to be essential for vesicle spreading and rupture. Fusion of lipid patches into a homogeneous bilayer required lateral mobility of the lipids on the polyelectrolyte support. The binding of amino groups to the phosphate group of the zwitterionic lipids was too weak to induce vesicle spreading, but sufficient for strong adsorption. Only the mixture of phosphatidylcholine and phosphatidylserine resulted in the spontaneous formation of bilayers on polyelectrolyte multilayers. The adsorption of phospholipids onto multilayers displaying quarternary ammonium polymers produced a novel 3D lipid polyelectrolyte structure on colloidal particles.

Published
2008
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