@article{KozhalakovaZhubanovaMansurovetal.2010, author = {Kozhalakova, A. A. and Zhubanova, Azhar A. and Mansurov, Z. A. and Digel, Ilya and Tazhibayeva, S. M. and Artmann, Gerhard and Temiz Artmann, Ayseg{\"u}l}, title = {Adsorption of bacterial lipopolysaccharides on carbonized rice shell}, series = {Science of Central Asia (2010)}, journal = {Science of Central Asia (2010)}, pages = {50 -- 54}, year = {2010}, language = {en} } @article{StadlerDigelEmbsetal.2009, author = {Stadler, Andreas M. and Digel, Ilya and Embs, Jan P. and Unruh, Tobias and Tehei, M. and Zaccai, G. and B{\"u}ldt, G. and Artmann, Gerhard}, title = {From powder to solution : Hydration dependence of human hemoglobin dynamics correlated to body temperature}, series = {Biophysical Journal. 96 (2009), H. 12}, journal = {Biophysical Journal. 96 (2009), H. 12}, publisher = {Cell Press}, address = {Cambridge, Mass.}, isbn = {0006-3495}, pages = {5073 -- 5081}, year = {2009}, language = {en} } @article{KurzLinderTrzewiketal.2010, author = {Kurz, R. and Linder, Peter and Trzewik, J{\"u}rgen and R{\"u}ffer, M. and Artmann, Gerhard and Digel, Ilya and Rothermel, A. and Robitzki, A. and Temiz Artmann, Ayseg{\"u}l}, title = {Contractile tension and beating rates of self-exciting monolayers and 3D-tissue constructs of neonatal rat cardiomyocytes}, series = {Medical and Biological Engineering and Computing}, volume = {48}, journal = {Medical and Biological Engineering and Computing}, number = {1}, publisher = {Springer Nature}, address = {Cham}, issn = {1741-0444}, doi = {10.1007/s11517-009-0552-y}, pages = {59 -- 65}, year = {2010}, abstract = {The CellDrum technology (The term 'CellDrum technology' includes a couple of slightly different technological setups for measuring lateral mechanical tension in various types of cell monolayers or 3D-tissue constructs) was designed to quantify the contraction rate and mechanical tension of self-exciting cardiac myocytes. Cells were grown either within flexible, circular collagen gels or as monolayer on top of respective 1-mum thin silicone membranes. Membrane and cells were bulged outwards by air pressure. This biaxial strain distribution is rather similar the beating, blood-filled heart. The setup allowed presetting the mechanical residual stress level externally by adjusting the centre deflection, thus, mimicking hypertension in vitro. Tension was measured as oscillating differential pressure change between chamber and environment. A 0.5-mm thick collagen-cardiac myocyte tissue construct induced after 2 days of culturing (initial cell density 2 x 10(4) cells/ml), a mechanical tension of 1.62 +/- 0.17 microN/mm(2). Mechanical load is an important growth regulator in the developing heart, and the orientation and alignment of cardiomyocytes is stress sensitive. Therefore, it was necessary to develop the CellDrum technology with its biaxial stress-strain distribution and defined mechanical boundary conditions. Cells were exposed to strain in two directions, radially and circumferentially, which is similar to biaxial loading in real heart tissues. Thus, from a biomechanical point of view, the system is preferable to previous setups based on uniaxial stretching.}, language = {en} } @article{Digel2008, author = {Digel, Ilya}, title = {Controlling microbial adhesion : a surface engineering approach}, series = {Bioengineering in Cell and Tissue Research / Artmann, Gerhard M. ; Chien, Shu (Eds.)}, journal = {Bioengineering in Cell and Tissue Research / Artmann, Gerhard M. ; Chien, Shu (Eds.)}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {978-3-540-75408-4}, pages = {601 -- 625}, year = {2008}, language = {en} } @article{BassamHeschelerTemizArtmannetal.2012, author = {Bassam, Rasha and Hescheler, J{\"u}rgen and Temiz Artmann, Ayseg{\"u}l and Artmann, Gerhard and Digel, Ilya}, title = {Effects of spermine NONOate and ATP on the thermal stability of hemoglobin}, series = {BMC Biophysics}, volume = {5}, journal = {BMC Biophysics}, publisher = {BioMed Central}, address = {London}, issn = {2046-1682}, doi = {10.1186/2046-1682-5-16}, pages = {Art. 16}, year = {2012}, abstract = {Background Minor changes in protein structure induced by small organic and inorganic molecules can result in significant metabolic effects. The effects can be even more profound if the molecular players are chemically active and present in the cell in considerable amounts. The aim of our study was to investigate effects of a nitric oxide donor (spermine NONOate), ATP and sodium/potassium environment on the dynamics of thermal unfolding of human hemoglobin (Hb). The effect of these molecules was examined by means of circular dichroism spectrometry (CD) in the temperature range between 25°C and 70°C. The alpha-helical content of buffered hemoglobin samples (0.1 mg/ml) was estimated via ellipticity change measurements at a heating rate of 1°C/min. Results Major results were: 1) spermine NONOate persistently decreased the hemoglobin unfolding temperature T u irrespectively of the Na + /K + environment, 2) ATP instead increased the unfolding temperature by 3°C in both sodium-based and potassium-based buffers and 3) mutual effects of ATP and NO were strongly influenced by particular buffer ionic compositions. Moreover, the presence of potassium facilitated a partial unfolding of alpha-helical structures even at room temperature. Conclusion The obtained data might shed more light on molecular mechanisms and biophysics involved in the regulation of protein activity by small solutes in the cell.}, language = {en} } @article{DigelTemizArtmann2011, author = {Digel, Ilya and Temiz Artmann, Ayseg{\"u}l}, title = {The emperor's new body : seeking for a blueprint of limb regeneration in humans}, series = {Stem cell engineering : principles and applications / Gerhard M. Artmann ... eds.}, journal = {Stem cell engineering : principles and applications / Gerhard M. Artmann ... eds.}, publisher = {Springer}, address = {Berlin [u.a.]}, isbn = {978-3-642-11864-7}, pages = {3 -- 37}, year = {2011}, language = {en} } @article{Digel2011, author = {Digel, Ilya}, title = {Primary thermosensory events in cells}, series = {Transient receptor potential channels / Md. Shahidul Islam, ed.}, journal = {Transient receptor potential channels / Md. Shahidul Islam, ed.}, publisher = {Springer}, address = {Dordrecht [u.a.]}, isbn = {978-94-007-0264-6}, pages = {451 -- 468}, year = {2011}, language = {en} } @article{GutheilBergGrotendorst2012, author = {Gutheil, Inge and Berg, Tommy and Grotendorst, Johannes}, title = {Performance Analysis of Parallel Eigensolvers of two Libraries on BlueGene/P}, series = {Journal of Mathematics and Systems Science}, volume = {2}, journal = {Journal of Mathematics and Systems Science}, number = {4}, publisher = {David Publishing}, address = {Libertyville}, issn = {2159-5291}, doi = {10.17265/2159-5291/2012.04.003}, pages = {231 -- 236}, year = {2012}, abstract = {Many applications in computational science and engineering require the computation of eigenvalues and vectors of dense symmetric or Hermitian matrices. For example, in DFT (density functional theory) calculations on modern supercomputers 10\% to 30\% of the eigenvalues and eigenvectors of huge dense matrices have to be calculated. Therefore, performance and parallel scaling of the used eigensolvers is of upmost interest. In this article different routines of the linear algebra packages ScaLAPACK and Elemental for parallel solution of the symmetric eigenvalue problem are compared concerning their performance on the BlueGene/P supercomputer. Parameters for performance optimization are adjusted for the different data distribution methods used in the two libraries. It is found that for all test cases the new library Elemental which uses a two-dimensional element by element distribution of the matrices to the processors shows better performance than the old ScaLAPACK library which uses a block-cyclic distribution.}, language = {en} } @article{Grotendorst2012, author = {Grotendorst, Johannes}, title = {Supercomputer programmieren - ein besonderes Studienangebot in J{\"u}lich}, series = {Junge Wissenschaft. 27 (2012), H. 94}, journal = {Junge Wissenschaft. 27 (2012), H. 94}, publisher = {-}, isbn = {0179-8529}, pages = {12 -- 14}, year = {2012}, language = {de} } @article{Grotendorst2012, author = {Grotendorst, Johannes}, title = {IAS Winter School: Hierarchical Methods for Dynamics in Complex Molecular Systems}, series = {Innovatives Supercomputing in Deutschland : inSiDE. 10 (2012), H. 1}, journal = {Innovatives Supercomputing in Deutschland : inSiDE. 10 (2012), H. 1}, publisher = {-}, pages = {104}, year = {2012}, language = {en} }