2013 NCTS November Workshop on Critical Phenomena and Complex Systems

==================== Dr. Ing-Shouh Hwang (Institute of Physics, Academia Sinica; E-mail: [email protected]) Talk Title: Imaging of Soft Matters in Water with Atomic Force Microscopy Abstract: Operation of atomic force microscopy (AFM) in aqueous environment is of great importance. Only this environment allows us to image and probe biological samples in their physiological conditions, to observe native biological processes, and to study many fundamental issues in water-solid interfaces. AFM has been proved to achieve very high spatial resolution on surfaces in vacuum as well as in air. However, operation in aqueous solutions is still very challenging because the force sensitivity of AFM in water is usually much reduced compared with the environment in air or in vacuum. If AFM can be operated with high force sensitivity in the aqueous environment, many puzzles in life science, electrochemistry, and liquid-solid interfaces may be unraveled. In recent year, several techniques have been found to improve the force sensitivity in water. They allow high-resolution imaging of soft materials with little deformation. In this talk, these advanced techniques will be introduced and examples will be shown. ----------------------------------------------------Dr. Peter Kopčanský (Institute of Experimental Physics, Slovak Academy of Sciences, Slovakia; E-mail: [email protected]) Talk Title: Magnetic response of liquid crystals (LC) including bioLC doped by magnetic nanoparticles Abstract: Liquid crystals (LC) are very sensitive to application of an external electric field due to the large value of dielectric anisotropy while are practically insensitive to application of magnetic field. Material with high sensitivity to magnetic field could be very useful for many applications. Thermovision camera based on liquid crystals maps temperature field distribution for example. Similar equipment for mapping magnetic field distribution could be developed on the base of LC with high sensitivity to magnetic field. The way how to improve sensitivity of currently used LC to magnetic field is to dope them with magnetic nanoparticles. The solution is the production of so called ferronematics, ferrocholesterics, ferrosmectics etc. i.e. stable colloidal suspension of LC with small volume concentrations of magnetic nanoparticles. In the lecture will be presented properties of magnetic nanoparticles, magnetic fluids as well as their mixtures with LC, theory of ferronematics (Brochard de Gennes as well as Burylov Raikher) [1, 2]. In the presentation will be illustrated many examples of the influence of magnetic field as well combination of magnetic and electric field on the structural transitions let say Freedericksz transition in ferromematics wirh various LC i.e. calamitic liquid crystals [3], banana like, lyothropic as well as biological LC, dependencies on concentration, on shape of magnetic particles etc. The low magnetic field response in studied samples will be presented too [4]. This is important for the construction of magnetovision camera as described above. The effect of magnetic particles and magnetic field on the phase transition as nematic-isotropic transition will be presented also.Results will be discussed in frame of Burylov Raikher theory as well as in frame of mean field theory. Acknowledgements: This work was supported by the Slovak Academy of Sciences, in the framework of CEX-NANOFLUID, projects VEGA 0045, the Slovak Research and Development Agency under the contract No. APVV-0171-10, Ministry of Education Agency for Structural Funds of EU in frame of project 26220120021, 26220120033 and 26110230061, and M-era.Net-MACOSYS. References: [1] F. Brochard, P.G. de Gennes, J.Phys. (Paris), 31 (1970) 691-708 [2] S.V. Burylov, Y.L. Raikher, J.Phys. Lett. A 149, 279 (1990) [3] P. Kopcansky, N. Tomasovicova, M. Koneracka, V. Zavisova, M. Timko, A. Dzarova, A. Sprincova, N. Eber, K. Fodor-Csorba, T. Toth-Katona, A. Vajda, J. Jadzyn, Phys Rev E 78 (2008) 011702/1-5 [4] N.Tomasovicova, M.Timko, Z.Mitroova, M.Koneracka, M.Rajnak, N.Eber, T.Toth-Katona, X.Chaud, J.Jadzyn, P.Kopcansky, Phys. Rev. E 87 (2013) 014501 ----------------------------------------------------Dr. Shura Hayryan (Institute of Physics, Academia Sinica; E-mail: [email protected]) Talk Title: Improving the parameters of the Poisson-Boltzmann equation for complex biomolecular systems Abstract: Here we propose an improved parameterization of the Poisson-Boltzmann equation for calculating the electrostatic potential of the solvated biological macromolecules. Using our earlier proposed cavity triangulation algorithm, we identify exactly the internal grid points of the macromolecule and assign the value of electrostatic constant to this points correctly. We applied our method to calculate the electrostatic energy of several proteins in water environment and compared the results with published data. The analysis of the results show that our method assigns the value of parameters more realistically. ----------------------------------------------------Dr. Tibor Kozar (Institute of Experimental Physics, Slovak Academy of Sciences, Slovakia; E-mail: [email protected]) Talk Title: From “bio” to “nano” – Computational Models and Strategies Abstract: Although the bulk size of certain nanoparticles can be compared to the size of some proteins, the size of such system can significantly increase when nanoparticles are interacting with certain prorteins. Computer-aided nanoparticle design, modeling, and engineering demonstrate several characteristics comparable to biomacromolecular modeling. The structural features of these supramolecular systems, like electrostatic and magnetic properties, together with environmental effects (solvent, packing interactions, etc.) can be evaluated using similar modeling tools. Standard as well as coarse-grained molecular dynamics and other computational methods are considered suitable for computer-aided modeling of large biomolecular or nanoparticle systems. Significant methodological improvement (mainly GPGPU computing), implemented during last few years, facilitated computer demands originating from huge number of atoms involved in computations of these complex molecular systems [1]. In addition to using GPGPU programs for bioand nanoparticle modeling we were also interested in high-throughput virtual screening related to several protein targets. We made significant performance throughput by calculating several hundreds of thousand of docking poses per day using all available high-performane/high-throughput computational resources. Examples of computer-aided modeling experiments will be presentated, concentrating on the speed benefits, given mainly by the state-of-the-art GPGPU technologies. Acknowledgements: This work was supported by Slovak grant agencies: APVV (projects APVV-0171-10, APVV-0282-11, APVV-0526-11) and VEGA (project 2/0073/10). The support for SAS Slovakia/NSC Taiwan joint research project is acknowledged as well. Supports from EU projects 26220120021, 2622012033, 2611230061 and 26210120002 are gratefully acknowledged as well. References: [1] T. Kozar, GPU Computing in Biomolecular Modeling and Nanodesign, in: G. Adam, J. Busa, M. Hnatic (Eds.) Lecture Notes in Computer Science: Mathematical Modeling and Computational Sciences, Springer Verlag, Heidelberg, Dordrecht, 2012, pp. 276-283. ----------------------------------------------------Dr. Zuzana Gažová (Institute of Experimental Physics, Slovak Academy of Sciences, Slovakia; E-mail: [email protected]) Talk Title: Self-assembly amyloid systems of proteins Abstract: Interest in the phenomenon of amyloid formation by polypeptides has developed rapidly in recent years because of links between amyloid formation and a range of disorders, including Alzheimer’s disease and type II diabetes. Accordingly, there is a considerable world-wide interest to identify entities that can influence the aggregation processes in order to speed-up the drug development process for the above mentioned diseases. The precise mechanism of toxicity of amyloid aggregates is not fully elucidated; however, there are evidences that prevention or reversion of the amyloid aggregation is beneficial. Recently, the increasing attention is focused on searching for agents able to intervene against amyloid aggregates. The promising group of aggregation inhibitors is small molecules. We screened a group of about hundred compounds for their ability to interfere with amyloidal aggregation of poly/peptides. We found several derivatives of acridine, phytoalexin and polyphenols with significant inhibiting abilities. Our results indicate important relationship between compound structure and anti-amyloidal activity. Tripeptides containing amino acids with aromatic rings were shown as the most potent inhibitors revealed by the virtual screening. The special attention was devoted to nanoparticles as novel agents able to affect amyloidal aggregation of poly/peptides. Acknowledgement. This work was supported by the projects: VEGA 0181, APVV SK-RO-0016-12, APVV-0171-10 and ESF 26110230061. ----------------------------------------------------Prof. Hisashi Okumura (Research Center for Computational Science, Institute for Molecular Science & Department of Structural Molecular Science, The Graduate University for Advanced Studies, Japan; E-mail: [email protected]) Talk Title: Molecular Dynamics Simulations for Amyloid Disruption by Supersonic Wave Abstract: Amyloids are insoluble and misfolded fibrous protein aggregates and associated with more than 20 serious human diseases. Recently, there are some experimental reports that cavitation disrupts amyloid fibrils. However, it is still unknown how the cavitation or bubble in water disrupts the amyloid fibrils at atomic level. In order to answer this problem, we performed non-equilibrium molecular dynamics simulations of an amyloid- (A) oligomer in explicit water, which constitutes an amyloid fibril. Amyloid- fibrils are known to be associated with the Alzheimer’s disease. It was reported experimentally that the structure of A42, consisting of 42 amino acids, has two intermolecular -sheet regions in the amyloid fibrils. These two -sheets are constructed by the residues 18-26 (1) and the residues 31-42 (2). We used twelve A peptide molecules, 10169 water molecules, and twelve sodium ions as counter ions. The simulation was started from the experimentally-known amyloid oligomer structure in the amyloid fibril. To express supersonic wave, sinusoidal pressure was applied between -100 MPa and 300 MPa. Snapshots of this simulation are illustrated in Fig. 1. When the pressure was decreased to a negative value of -100 MPa from a room pressure, a bubble formation was observed around the C-terminal region, 2, in which all the amino acid residues were hydrophobic. Even after the bubble size increased, the secondary structures of the oligomer were maintained. When the pressure was increased to a positive value, the bubble shrank and collapsed, and the oligomer was disrupted. At this time, most water molecules attacked the hydrophilic residues in 1. Figure 1. Snapshots of the non-equilibrium molecular dynamics simulation of the amyloid- oligomer in explicit water. The amyloid- oligomer was disrupted when the bubble collapsed.