Reversibility and hysteresis of the sharp yielding transition of a colloidal glass under oscillatory shear.

The mechanical response of glasses remains challenging to understand. Recent results indicate that the oscillatory rheology of soft glasses is accompanied by a sharp non-equilibrium transition in the microscopic dynamics. Here, we use simultaneous x-ray scattering and rheology to investigate the reversibility and hysteresis of the sharp symmetry change from anisotropic solid to isotropic liquid dynamics observed in the oscillatory shear of colloidal glasses (D. Denisov, M.T. Dang, B. Struth, A. Zaccone, P. Schall, Sci. Rep. 5 14359 (2015)). We use strain sweeps with increasing and decreasing strain amplitude to show that, in analogy with equilibrium transitions, this sharp symmetry change is reversible and exhibits systematic frequency-dependent hysteresis. Using the non-affine response formalism of amorphous solids, we show that these hysteresis effects arise from frequency-dependent non-affine structural cage rearrangements at large strain. These results consolidate the first-order-like nature of the oscillatory shear transition and quantify related hysteresis effects both via measurements and theoretical modelling.

[Landmark of the internal carotid artery stenting, anterior interventricular branch of the left coronary artery and vertebral artery in a patient with multifocal atherosclerosis].

Presented herein is a clinical case report concerning a 59-year-old male patient suffering from multifocal atherosclerosis after endured repeat acute ischaemic attacks in various arterial basins of the brain. Analysing his case history revealed functional class II-IV angina of effort. Ultrasonographic and angiographic findings showed a haemodynamically significant plaque in the ostium of the left internal carotid artery, hypoplasia of the right vertebral artery, a haemodynamically meaningful narrowing of the left vertebral artery, subtotal stenosis of the anterior interventricular branch and pronounced alterations in the right vertebral artery. The first stage of surgery consisted in stenting of the left internal carotid artery and anterior interventricular branch, followed by the second stage consisting in the stenting of the left vertebral artery with an angiographically good outcome. The check-up CT of the brain and 24-hour ECG monitoring showed no negative dynamics. In July 2005, the patient was subjected to craniocerebral microarterial shunting on the right. No relapses of AIAs have so far been observed.

[Autoimmune response in HIV-infected patients is directed against CD4 domain 4].

Phage display epitope library technology and a novel computer algorithm have been used for the localization of CD4 epitopes specific for monoclonal antibody (mAb) T6 and autoimmune antibodies found in an HIV infected patient. Both predicted epitope clusters have been shown to overlap and to be localized within the domain 4 of CD4. They included Cys303, Glu304, Glu330, and Lys331 amino acids. Few amino acids predicted by the algorithm as the epitope residues and two residues that did not relate to the epitope were sequentially substituted for Ala. Further analysis of the mutated forms of sCD4 expressed in 293T cells transfected with the corresponding DNAs, supported the predicted localization of the mAb T6 epitope. The results demonstrate that the autoimmune response in HIV-infected patients is directed against domain D4 of sCD4.

[Epitope mapping of antigenic determinants of hepatitis C virus proteins by phage display].

Study of individual hepatitis C (HCV) proteins could help to find a molecular structure and conformation, localization of antigenic and immunogenic determinants, to reveal of protective epitopes. It is necessary for practical medicine - development of diagnostic test-systems, vaccines and therapeutics. Linear and conformation dependent epitopes of HCV proteins was localized in this work and immunogenic properties of phage displayed peptides screened on monoclonal antibodies to HCV proteins have been investigated. Eleven epitopes of four HCV proteins have been studied. Three epitopes was found as linear, two epitopes were dependent on secondary structure of proteins and one epitope was dependent on tertiary structure of NS3 protein. Aminoacid sequences of other determinants have been determined and the distinct localization of these determinants will be continued after discovering of tertiary structure of HCV proteins. It was shown, that phage mimotope 3f4 is immunogenic and could induce specific hu- moral immune response to NS5A HCV protein. The data obtained could be useful for improving of HCV diagnostic test-systems, studying of amino acid substitutions and its influence on antigenic properties of the HCV proteins. The results could help to study an immune response in patients infected with different genotypes of HCV. Phage displayed peptides mimicking the antigenic epitopes of HCV proteins could be applied to development of HCV vaccine.

Universality of slip avalanches in flowing granular matter.

The search for scale-bridging relations in the deformation of amorphous materials presents a current challenge with tremendous applications in material science, engineering and geology. While generic features in the flow and microscopic dynamics support the idea of a universal scaling theory of deformation, direct microscopic evidence remains poor. Here, we provide the first measurement of internal scaling relations in the deformation of granular matter. By combining macroscopic force fluctuation measurements with internal strain imaging, we demonstrate the existence of robust scaling relations from particle-scale to macroscopic flow. We identify consistent power-law relations truncated by systematic pressure-dependent cutoff, in agreement with recent mean-field theory of slip avalanches in elasto-plastic materials, revealing the existence of a mechanical critical point. These results experimentally establish scale-bridging relations in the flow of matter, paving the way to a new universal theory of deformation.

Expansion of epitope cross-reactivity by anti-idiotype modulation of the primary humoral response.

The primary humoral response produces antigen-specific antibodies so to clear the initial infection, and generates a population of corresponding memory cells to prevent infection by future encounters with the same pathogen. The continuous genetic modification of a pathogen's exterior, however, is one mechanism used to evade the immune defenses of its host. Here we describe a novel means, involving anti-idiotypic antibodies, by which the host can counteract such pathogen genetic alterations by modulation of its primary humoral response. An autoimmune response against primary antibodies, Ab1's, creates anti-idiotypic antibodies (Ab2's), some of which (designated Ab2alpha) are able to bind the Ab1/antigen complex. We have discovered that binding of Ab2alpha to its corresponding Ab1 can expand Ab1's ability to bind variations of its antigen. This expanded epitope cross-reactivity is shown not only to increase the binding activity of Ab1 but also its ability to neutralize a variant infectious virus. MAb M77 is an Ab1, which is highly strain-specific for the HIV-1 envelope protein gp120(IIIB). This Ab1 can be rendered cross-reactive and neutralizing for an otherwise resistant HIV strain by its interaction with a unique anti-idiotypic Ab2alpha (GV12). Furthermore, molecular characterization of this expanded cross-reactivity was accomplished using combinatorial phage display peptide libraries.

Totally asymmetric simple exclusion process simulations of molecular motor transport on random networks with asymmetric exit rates.

Using the totally asymmetric simple-exclusion-process and mean-field transport theory, we investigate the transport in closed random networks with simple crossing topology-two incoming, two outgoing segments, as a model for molecular motor motion along biopolymer networks. Inspired by in vitro observation of molecular motor motion, we model the motor behavior at the intersections by introducing different exit rates for the two outgoing segments. Our simulations of this simple network reveal surprisingly rich behavior of the transport current with respect to the global density and exit rate ratio. For asymmetric exit rates, we find a broad current plateau at intermediate motor densities resulting from the competition of two subnetwork populations. This current plateau leads to stabilization of transport properties within such networks.

Super-radiant mode in InAs-monolayer-based Bragg structures.

We report direct experimental evidence of the collective super-radiant mode in Bragg structure containing 60 InAs monolayer-based quantum wells (QWs) periodically arranged in GaAs matrix. Time-resolved photoluminescence measurements reveal an appearance of the additional super-radiant mode, originated from coherent collective interaction of QWs. This mode demonstrates a super-linear dependence of the intensity and radiative decay rate on the excitation power. The super-radiant mode is not manifested in the case if only a small number of QWs is excited.

Hierarchical structure of donor splice site sequence multitude.

An analysis of donor splice site sequence (dsss) multitude was carried out. A special method was developed to study the multitude properties. The multitude of dsss was arranged as a hierarchical tree where the "root" consists of a small group of "ancestors", VAGgtVAG (gt stands in the beginning of intron, V=C,A,G). Every ancestor has its own clan of "descendants" which represent point mutants of it. The latter are split into "progenies". The first progeny looks like point mutants of the ancestors, the second as one-point mutants of sequences of the first progeny, and so forth. This picture looks like a hierarchical phylogenetic tree. The most striking property of the multitude is the successive monotonic decrease in occurrences of the sequences from one progeny to another. It is shown that such results may be modeled by a virtual mutational process.

Protective nucleosome centering at splice sites as suggested by sequence-directed mapping of the nucleosomes.

The characteristic AA(TT) sequence pattern of the nucleosome DNA derived earlier is used for prediction of nucleosome positions around splice junctions of eukaryotic genes. Two large datasets (2000 sequences each) were collected consisting of DNA segments with the exon/intron and intron/exon splice junctions, from various eukaryotic species. Positions of predicted nucleosomes near the junction sites were calculated. Those junctions which are found to belong to the nucleosomes, are located preferentially within a few base pairs from the midpoint of the nucleosome DNA. That is, obligatory GT- and AG-ends of the introns are more frequently located near the nucleosome dyad axis, within the best protected middle 10-15 base pairs of the nucleosome DNA. In addition, a tendency is observed for the strongest nucleosomes to form more often in the introns, in accordance with the hypothesis on the chromatin-organizing role of introns.

Visualizing the strain evolution during the indentation of colloidal glasses.

We use an analog of nanoindentation on a colloidal glass to elucidate the incipient plastic deformation of glasses. By tracking the motion of the individual particles in three dimensions, we visualize the strain field and glass structure during the emerging deformation. At the onset of flow, we observe a power-law distribution of strain indicating strongly correlated deformation, and reflecting a critical state of the glass. At later stages, the strain acquires a Gaussian distribution, indicating that plastic events become uncorrelated. Investigation of the glass structure using both static and dynamic measures shows a weak correlation between the structure and the emerging strain distribution. These results indicate that the onset of plasticity is governed by strong power-law correlations of strain, weakly biased by the heterogeneous glass structure.

Probing incipient plasticity by indenting colloidal glasses.

Glasses are lucrative engineering materials owing to their superior mechanical properties such as high strength and large elastic strain. A central question concerns incipient plasticity - the onset of permanent deformation - that is central to their relaxation, aging, yield and fracture. Here, we use an analogue of nano-indentation performed on a colloidal glass to obtain direct images of the incipient plasticity, allowing us to elucidate the onset of permanent deformation. We visualize the microscopic strain by following distorted nearest neighbor configurations, and observe a surprising hierarchical structure of deformation: at the onset of irreversible deformation, the strain acquires a robust fractal structure, and we measure its fractal dimension. These results give direct evidence that the onset of permanent deformation has the hallmarks of a critical point, in agreement with recent theoretical works.

Resolving structural modifications of colloidal glasses by combining x-ray scattering and rheology.

Glasses have liquid-like structure, but exhibit solid-like properties. A central question concerns the relation between the structure and mechanical properties of glasses, but structural changes remain difficult to resolve. We use a novel combination of rheology and x-ray scattering to resolve structural changes in colloidal glasses and link them directly to their mechanical behavior. By combining stress and structure factor measurements, we resolve shear induced changes in the nearest neighbor configuration as a function of applied stress, allowing us to elucidate the structural origin of the genuine shear banding transition of glasses.

Relation between self-organized criticality and grain aspect ratio in granular piles.

We investigate experimentally whether self-organized criticality (SOC) occurs in granular piles composed of different grains, namely, rice, lentils, quinoa, and mung beans. These four grains were selected to have different aspect ratios, from oblong to oblate. As a function of aspect ratio, we determined the growth (ß) and roughness (α) exponents, the avalanche fractal dimension (D), the avalanche size distribution exponent (τ), the critical angle (γ), and its fluctuation. At superficial inspection, three types of grains seem to have power-law-distributed avalanches with a well-defined τ. However, only rice is truly SOC if we take three criteria into account: a power-law-shaped avalanche size distribution, finite size scaling, and a universal scaling relation relating characteristic exponents. We study SOC as a spatiotemporal fractal; in particular, we study the spatial structure of criticality from local observation of the slope angle. From the fluctuation of the slope angle we conclude that greater fluctuation (and thus bigger avalanches) happen in piles consisting of grains with larger aspect ratio.

Simulation of a Casimir-like effect in a granular pile with avalanches.

Using a modified Bak-Tang-Wiesenfeld model for sand piles, we simulate a Casimir-like effect in a granular pile with avalanches. Results obtained in the simulation are in good agreement with results previously acquired experimentally: two parallel walls are attracted to each other at small separation distances, with a force decreasing with increasing distance. In the simulation only, at medium distances a weak repulsion exists. Additionally, with the aim of avalanche prevention, the possibility of suppressing self-organized criticality with an array of walls placed on the slope of the pile is investigated, but the prevention effect is found to be negligible.

Casimir-like effect on a granular pile.

We investigate experimentally a Casimir-like effect in a three-dimensional pile of rice, which has a power-law avalanche size distribution. We observe the change in distance between two Plexiglas sheets placed on the pile parallel to each other and parallel to the mean avalanche flow direction, while rice grains are continuously and uniformly falling on top of the pile. The resulting avalanches are fluctuations, confinement of which is found to drive the two plates together. During 25-h experimental runs, for initial intersheet distances ranging from 20.0 to 90.0 mm we observe changes in the range from 6.0 mm to less than 1.0 mm. A similar distance dependence is obtained from a simple analytical model.