Network theory approach for data evaluation in the dynamic force spectroscopy of biomolecular interactions

Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output. Big efforts are devoted to develop methods for effective selection of the relevant experimental data, before taking the quantitative analysis of bond parameters. Here we present a methodology which is based on the application of graph theory. The force-distance curves corresponding to repeated pulling events are mapped onto their correlation network (mathematical graph). On these graphs the groups of similar curves appear as topological modules, which are identified using the spectral analysis of graphs. We demonstrate the approach by analyzing a large ensemble of the force-distance curves measured on: ssDNA-ssDNA, peptide-RNA (system from HIV1), and peptide-Au surface. Within our data sets the methodology systematically separates subgroups of curves which are related to different intermolecular interactions and to spatial arrangements in which the molecules are brought together and/or pulling speeds. This demonstrates the sensitivity of the method to the spatial degrees of freedom, suggesting potential applications in the case of large molecular complexes and situations with multiple binding sites

Thermodynamics of a model for RNA folding

We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base molecules with a flexible backbone and all possible pairing interactions equally allowed. The spatial pseudoknot structure of the model can be efficiently studied by introducing a $N \times N$ hermitian random matrix model at each chain site, and associating Feynman diagrams of these models to spatial configurations of the molecules. We obtain an exact expression for the topological expansion of the partition function of the system. We calculate exact and asymptotic expressions for the free energy, specific heat, entanglement and chemical potential and study their behavior as a function of temperature. Our results are consistent with the interpretation of $1/N$ as being a measure of the concentration of $\rm{Mg}^{++}$ in solution.Comment: 11 pages, 4 figure

Interfacial crack behavior in the stationary temperature field conditions

The brittle coatings, made of different materials, when subjected to elevated temperatures and in the heat exchange conditions, are susceptible to delamination. Those coatings, as well as thin films, can be used for various therm insulating deposits, e.g. in turbines of thermal power plants. Due to environmental temperature change, in layers made of materials having different thermal expansion coefficients, appear thermal stresses. In this paper driving forces causing delamination of one layer from the other are analyzed i.e. the interfacial fracture in the two-layered, bi-material sample. This analysis was limited to considering the sample behavior when exposed to the stationaiy temperature field. The energy release rate G, which is the driving force for this interfacial fracture, is changing with temperature and that variation is increasing with increase of the temperature difference between the environment and the sample. Analysis of this relation, between the G variation and temperature difference, can be used to predict the maximal temperature difference, which the two-layered sample can be subjected to, without appearance of delamination between layers

Interfacial crack behavior in the stationary temperature field conditions

The brittle coatings, made of different materials, when subjected to elevated temperatures and in the heat exchange conditions, are susceptible to delamination. Those coatings, as well as thin films, can be used for various therm insulating deposits, e.g. in turbines of thermal power plants. Due to environmental temperature change, in layers made of materials having different thermal expansion coefficients, appear thermal stresses. In this paper driving forces causing delamination of one layer from the other are analyzed i.e. the interfacial fracture in the two-layered, bi-material sample. This analysis was limited to considering the sample behavior when exposed to the stationaiy temperature field. The energy release rate G, which is the driving force for this interfacial fracture, is changing with temperature and that variation is increasing with increase of the temperature difference between the environment and the sample. Analysis of this relation, between the G variation and temperature difference, can be used to predict the maximal temperature difference, which the two-layered sample can be subjected to, without appearance of delamination between layers

Processing and properties of silver-metal oxide electrical contact materials

The presented study gives a brief overview of the experimental results of investigations of different production technologies of silver-metal oxide electrical contact materials in relation: processing method - properties. The two most common routes of production, i.e. internal oxidation/ingot metallurgy and powder metallurgy are demonstrated on the example of Ag-CdO and Ag-ZnO materials. For illustration of alternative processing routes that provide higher dispersion of metal-oxide particles in silver matrix more environmentally friendly Ag-SnO2 contact materials are used. Processing of electrical contact materials by mechanical mixing of starting powders in high energy ball mill is presented. The obtained experimental results of application of different methods of introduction of SnO2 nanoparticles in the silver matrix such as conventional powder metallurgy mixing and template method are given and discussed in terms of their influence on microstructure and physical properties (density, hardness and electrical conductivity) of the prepared Ag-SnO2 electrical contact materials

Dynamic Mechanical Properties of Aramid Fabrics Impregnated with Carbon Nanotube/Poly (Vinyl Butyral)/Ethanol Solution

In this study six samples of polyurethane/p-aramid multiaxial fabric forms (Colon fabrics) were coated with 10 wt.% poly (vinyl butyral) (PVB)/ethanol solution with the addition of multiwalled carbon nanotubes (MWCNT). The solution was impregnated on both sides of each of the fabrics. All composite samples consisted of four layers of the impregnated fabrics. The MWCNT/PVB content was 0, 0.1 and 1 wt.%. The three samples of the fabrics with different MWCNT/PVB content were coated with γ-aminopropyltriethoxysilane (AMEO silane)/ethanol solution due to the surface modification. The mechanical properties of the prepared composite samples were studied by dynamic mechanical analysis (DMA). The 60% increase in storage modulus was achieved by addition of MWCNT and impregnation of aramid fabrics with AMEO silane. The pristine multiwalled carbon nanotubes (MWCNT) were introduced in order to enhance additionally the mechanical properties of the materials for ballistic protection

Biocompatibility nanostructured biomaterials based on calcium aluminate

Introduction/Objective The aim of this paper was to verify the biocompatibility of the newly synthesized nanostructured material based on calcium aluminate after implantation into the subcutaneous tissue of rats. Methods The study included 18 rats aged 10–11 weeks, divided into two experimental groups (n = 9). In all animals, incision took place on the back and two pockets of 15 mm in depth were made, in which sterile polyethylene tubes with test materials [calcium aluminate cement (ALBO-CA), calcium silicate cement with the addition of hydroxyapatite (ALBO-CSHA), and mineral trioxide aggregate (MTA) for the control group) were implanted. Six rats of each group were sacrificed in three observational periods (seven, 15, 30 days). Pathohistological analysis included inflammation, bleeding, fibrous capsule, and tissue integrity around the implanted material. Results After seven days of treatment, ALBO-CA and ALBO-CSHA showed better tissue response compared to MTA, with a statistically significant difference in inflammation intensity (p = 0.2781). The difference in vascular congestion and thickness of the fibrous capsule after implantation of ALBO-CA material compared to MTA was also statistically significant (p = 0.5567). At the end of the 30-day evaluation period, an identical inflammatory response of connective tissue at the site of implanting ALBO-CA, ALBO-CSHA, and MTA (score of 0.7) was recorded. The formation of thick or moderately thick fibrous capsule was found to be the thickest in ALBO-CA (grade 3.7). There were no statistically significant differences between the parameters analyzed after 30 days. Conclusion Newly synthesized ALBO-CA showed a satisfactory tissue response and confirmed biocompatibility after implantation in subcutaneous tissue of rats. © 2018, Serbia Medical Society. All rights reserved

ENERGY EFFICIENCY AND USE OF RENEWABLE ENERGY SOURCES IN BUILDINGS CONSTRUCTION- PERSPECTIVE OF SUSTAINABLE DEVELOPMENT

In this paper are presented the overall energy needs of the buildings and measures to improve energy efficiency in buildings. It is shown the importance of sustainable construction as one of the important segments of environmental protection and sustainable development. It is also pointed out the importance of use of renewable energy sources in the construction of energy efficient buildings

In situ control of the helical and skyrmion phases in Cu2OSeO3 using high-pressure helium gas up to 5 kbar

We report a small-angle neutron scattering study of the helical and skyrmion lattice order in single crystal Cu2OSeO3 under quasihydrostatic helium gas pressures up to 5 kbar. By using helium gas as the pressure-transmitting medium (PTM) we ensure pressure application with improved hydrostaticity at cryogenic temperatures compared with previous reports where liquid PTMs were used. For 5-kbar He gas pressure we observe modest changes of the ambient pressure phase diagram; the critical temperature Tc changes by +2.8(2)%, while in the low-T limit the helical propagation vector |q| changes by −0.5(2)%, the lower critical field Hc1 changes by +2.5(1.0)%, and the upper critical field Hc2 remains unchanged within uncertainty. The skyrmion phase also changes little under pressure; its largest T extent varies from Tc − 2.5(5) K at ambient pressure to Tc − 3.0(5) K at 5 kbar, and its location in the phase diagram follows the pressure-driven shift of Tc. The weak pressure dependences of the critical magnetic fields and skyrmion phase contrast strongly with much stronger pressure-driven changes reported from previous quasihydrostatic pressure studies. Taking into account the present results and those of other uniaxial pressure data, we suggest that the results of previous quasihydrostatic pressure studies were influenced by inadvertent directional stress pressure components. Overall, our study represents a high-pressure study of the chiral magnetism in Cu2OSeO3 under the most hydrostatic high-pressure conditions to date and serves also as a salient reminder of the sensitivity of chiral magnets to deviations from hydrostaticity in quasihydrostatic high-pressure studies

Bloggers Behavior and Emergent Communities in Blog Space

Interactions between users in cyberspace may lead to phenomena different from those observed in common social networks. Here we analyse large data sets about users and Blogs which they write and comment, mapped onto a bipartite graph. In such enlarged Blog space we trace user activity over time, which results in robust temporal patterns of user--Blog behavior and the emergence of communities. With the spectral methods applied to the projection on weighted user network we detect clusters of users related to their common interests and habits. Our results suggest that different mechanisms may play the role in the case of very popular Blogs. Our analysis makes a suitable basis for theoretical modeling of the evolution of cyber communities and for practical study of the data, in particular for an efficient search of interesting Blog clusters and further retrieval of their contents by text analysis