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

Site-selective quantum correlations revealed by magnetic anisotropy in the tetramer system SeCuO3

We present the investigation of a monoclinic compound SeCuO3 using x-ray powder diffraction, magnetization, torque and electron-spin-resonance (ESR). Structurally based analysis suggests that SeCuO3 can be considered as a 3D network of tetramers. The values of intra-tetramer exchange interactions are extracted from the temperature dependence of the susceptibility and amount to ~200 K. The inter-tetramer coupling leads to the development of long-range antiferromagnetic order at TN = 8 K. An unusual temperature dependence of the effective g-tensors is observed, accompanied with a rotation of macroscopic magnetic axes. We explain this unique observation as due to site-selective quantum correlations

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

Search for new phenomena in dijet events using 37 fb−1 of pp collision data collected at √s=13 TeV with the ATLAS detector

Dijet events are studied in the proton-proton collision data set recorded at s=13 TeV with the ATLAS detector at the Large Hadron Collider in 2015 and 2016, corresponding to integrated luminosities of 3.5 fb-1 and 33.5 fb-1 respectively. Invariant mass and angular distributions are compared to background predictions and no significant deviation is observed. For resonance searches, a new method for fitting the background component of the invariant mass distribution is employed. The data set is then used to set upper limits at a 95% confidence level on a range of new physics scenarios. Excited quarks with masses below 6.0 TeV are excluded, and limits are set on quantum black holes, heavy W′ bosons, W∗ bosons, and a range of masses and couplings in a Z′ dark matter mediator model. Model-independent limits on signals with a Gaussian shape are also set, using a new approach allowing factorization of physics and detector effects. From the angular distributions, a scale of new physics in contact interaction models is excluded for scenarios with either constructive or destructive interference. These results represent a substantial improvement over those obtained previously with lower integrated luminosity

Search for supersymmetry in final states with missing transverse momentum and multiple b-jets in proton-proton collisions at √s=13 TeV with the ATLAS detector

A search for supersymmetry involving the pair production of gluinos decaying via third-generation squarks into the lightest neutralino χ˜10 $$\left({\tilde{\chi}}_1^0\right)$$ is reported. It uses LHC proton-proton collision data at a centre-of-mass energy s=13 $$\sqrt{s}=13$$ TeV with an integrated luminosity of 36.1 fb−1 collected with the ATLAS detector in 2015 and 2016. The search is performed in events containing large missing transverse momentum and several energetic jets, at least three of which must be identified as originating from b-quarks. To increase the sensitivity, the sample is divided into subsamples based on the presence or absence of electrons or muons. No excess is found above the predicted background. For χ˜10 $${\tilde{\chi}}_1^0$$ masses below approximately 300 GeV, gluino masses of less than 1.97 (1.92) TeV are excluded at 95% confidence level in simplified models involving the pair production of gluinos that decay via top (bottom) squarks. An interpretation of the limits in terms of the branching ratios of the gluinos into third-generation squarks is also provided. These results improve upon the exclusion limits obtained with the 3.2 fb−1 of data collected in 2015

Electronic Excitations in Copper Oxides: Time-Dependent Density Functional Theory Calculations with a Self-Consistent Hybrid Kernel

A theoretical study of the electronic structure and optical response of three copper oxides (Cu2O, Cu4O3, and CuO) in the crystalline state is performed using an all-electron perturbative method based on time-dependent density functional theory. We use hybrid density functional theory to account reliably for the direct and indirect semiconducting nature of these materials, as well as for their magnetic ground state. We consider both global and range-separated standard functionals with empirical Hartree–Fock exchange fractions (B3LYP and HSE06) and functionals in which the fraction of Hartree–Fock exchange is determined from a self-consistent procedure, which requires the calculation of the static dielectric constant in the linear-response approximation. Hybrid exchange is found to be essential to reproduce the experimentally observed optical response of the three oxides. The excited-state calculations yield excellent agreement with experiment for the first optically allowed electronic transitions (with excitonic character) of Cu2O. For Cu4O3, an exciton with a small binding energy can be associated with experimentally observed optical features. In CuO, only one dipole allowed transition is found to contribute to the low-energy region of the optical spectrum

Metabolic Responses of Pseudomonas aeruginosa san ai to Nanoceria

Among numerous available nanomaterials, nanoceria (NC) has a particular importance based on its redox properties which are considered as a cause of antibacterial activity [1]. Pseudomonas aeruginosa is Gram-negative bacteria, well known for its ability to grow in diverse environments due to great potential for adaptation and its metabolic diversity. Its ability to overcome the challenges lies on bacterial cell-cell communication mechanism, known as quorum sensing (QS) system, which regulates expression of numerous genes [2]. To reveal effects of NC on metabolism of environmental isolate of polyextremophile P. aeruginosa san ai, production of exopolysaccharide, pigment – pyocyanin, siderophores – pyoverdine and pyochelin, as well accompanied changes related to QS, biofilm formation, and redox homeostasis were investigated. The minimal inhibitory concentration of NC against P. aeruginosa san ai is 8 mg/mL, which classifies it in a group of highly resistant Pseudomonas. P. aeruginosa san ai exhibited an important formation of biofilm, with OD590 readings of 0.21 for culture grown in LB and in range from 0.26 to 0.57 for culture from LB amended with increasing concentrations of NC (from 0.5 to 5 mg/mL). Accordingly, P. aeruginosa san ai can be classified as moderately adherent strain. Changes in alginate formation with increasement of 37% in the presence of NC, which have been detected, imply its engagement in the cell protection. An improved biofilm formation and production of alginate in the culture exposed to nanoceria clearly indicates their role in the first line of defence, according to previous data [3]. The up-regulation of both siderophores pyoverdine and pyocheline, was detected in cultures amended with NC, suggesting strong effect of NC on the iron homeostasis. The siderophore biosynthesis and transport require tight regulation, particularly in case of exposure to the toxic threat of ROS generated. Free radical species can trigger Fenton reaction further compromising the maintenance of intracellular iron levels. An improved production of pyoverdine- highly iron-specific siderophore, obtained in this study clearly documents how promptly and efficiently the bacteria reacts to overcome exhaustion of iron. Production of pyocyanin is almost 3 times higher in nanoceria amended culture than in control, clearly suggesting redox homeostasis disturbance caused by NC. Although NADH/NAD redox couple plays a major role in central metabolism of P. aeruginosa, another characteristic feature of P. aeruginosa is the ability to produce redox-active pyocyanin, which can react with NADH suggesting that electron transfer to pyocyanin may represent an adaptation that allows bacteria to modulate their intracellular redox state

The impact of Mediterranean oscillations on periodicity and trend of temperature in the valley of the Nisava river - a fourier and wavelet approach

Periodicity of temperature on three stations in the Nisava River valley in period 1949-2014, has been analyzed by means of Fourier and wavelet transforms. Combined periodogram based on fast Fourier transform shows considerable similarity among individual series and identffies significant periods on 2.2, 2.7, 3.3, 5, 6-7, and 8.2 years in all datasets. Wavelet coherence analysis connects strongest 6-7 years spectral component to Mediterranean oscillation, starting in 1980s. Combined periodogram of Mediterranean oscillation index reveals 6-7 years spectral component as a dominant mode in period 1949-2014. Wavelet power spectra and partial combined periodograms show absence of 6-7 years component before 1975, after which this component becomes dominant in the spectrum. Consistency between alternation in temperature trend in the Nisava River valley and change in periodicity of Mediterranean oscillation was found