Strong Dynamical Heterogeneity and Universal Scaling in Driven Granular Fluids

Large-scale simulations of two-dimensional bidisperse granular fluids allow us to determine spatial correlations of slow particles via the four-point structure factor S-4 (q, t). Both cases, elastic (epsilon = 1) and inelastic (epsilon < 1) collisions, are studied. As the fluid approaches structural arrest, i.e., for packing fractions in the range 0.6 <= phi <= 0.805, scaling is shown to hold: S-4 (q, t)/chi(4)(t) = s(q xi(t)). Both the dynamic susceptibility chi(4)(tau(alpha)) and the dynamic correlation length xi(tau(alpha)) evaluated at the alpha relaxation time tau(alpha) can be fitted to a power law divergence at a critical packing fraction. The measured xi(tau(alpha)) widely exceeds the largest one previously observed for three-dimensional (3d) hard sphere fluids. The number of particles in a slow cluster and the correlation length are related by a robust power law, chi(4)(tau(alpha)) approximate to xi(d-p) (tau(alpha)), with an exponent d - p approximate to 1.6. This scaling is remarkably independent of epsilon, even though the strength of the dynamical heterogeneity at constant volume fraction depends strongly on epsilon.

Supporting Task-oriented Navigation in IDEs with Configurable HeatMaps

Mainstream IDEs generally rely on the static structure of a software project to support browsing and navigation. We propose HeatMaps, a simple but highly configurable technique to enrich the way an IDE displays the static structure of a software system with additional kinds of information. A heatmap highlights software artifacts according to various metric values, such as bright red or pale blue, to indicate their potential degree of interest. We present a prototype system that implements heatmaps, and we describe an initial study that assesses the degree to which different heatmaps effectively guide developers in navigating software.

Querying Runtime Information in the IDE

Code queries focus mainly on the static structure of a system. To comprehend the dynamic behavior of a system however, a software engineer needs to be able to reason about the dynamics of this system, for instance by querying a database of dynamic information. Such a querying mechanism should be directly available in the IDE where the developers implements, navigates and reasons about the software system. We propose (i) concepts to gather dynamic information, (ii) the means to query this information, and (iii) tools and techniques to integrate querying of dynamic information in the IDE, including the presentation of results generated by queries.

Monte Carlo simulation on a system of hard cylinders at a very high packing fraction

Using the Monte Carlo method the behavior of a system of true hard cylinders has been studied. Values of the length-to-breadth ratio L/D and packing fraction η have been chosen similar to those of real nematic liquid crystals. Results include radial distribution function g(r), structure factor S(k), and orientational order parameter M. These results lead to the conclusion that the hard cylinder model may be a useful reference for real mesomorphic phases.

Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions

Recombination of genes is essential to the evolution of genetic diversity, the segregation of chromosomes during cell division, and certain DNA repair processes. The Holliday junction, a four-arm, four-strand branched DNA crossover structure, is formed as a transient intermediate during genetic recombination and repair processes in the cell. The recognition and subsequent resolution of Holliday junctions into parental or recombined products appear to be critically dependent on their three-dimensional structure. Complementary NMR and time-resolved fluorescence resonance energy transfer experiments on immobilized four-arm DNA junctions reported here indicate that the Holliday junction cannot be viewed as a static structure but rather as an equilibrium mixture of two conformational isomers. Furthermore, the distribution between the two possible crossover isomers was found to depend on the sequence in a manner that was not anticipated on the basis of previous low-resolution experiments.

Muramic lactam in peptidoglycan of Bacillus subtilis spores is required for spore outgrowth but not for spore dehydration or heat resistance

Bacterial endospores derive much of their longevity and resistance properties from the relative dehydration of their protoplasts. The spore cortex, a peptidoglycan structure surrounding the protoplasm, maintains, and is postulated to have a role in attaining, protoplast dehydration. A structural modification unique to the spore cortex is the removal of all or part of the peptide side chains from the majority of the muramic acid residues and the conversion of 50% of the muramic acid to muramic lactam. A mutation in the cwlD gene of Bacillus subtilis, predicted to encode a muramoyl-l-alanine amidase, results in the production of spores containing no muramic lactam. These spores have normally dehydrated protoplasts but are unable to complete the germination/outgrowth process to produce viable cells. Addition of germinants resulted in the triggering of germination with loss of spore refractility and the release of dipicolinic acid but no degradation of cortex peptidoglycan. Germination in the presence of lysozyme allowed the cwlD spores to produce viable cells and showed that they have normal heat resistance properties. These results (i) suggest that a mechanical activity of the cortex peptidoglycan is not required for the generation of protoplast dehydration but rather that it simply serves as a static structure to maintain dehydration, (ii) demonstrate that degradation of cortex peptidoglycan is not required for spore solute release or partial spore core rehydration during germination, (iii) indicate that muramic lactam is a major specificity determinant of germination lytic enzymes, and (iv) suggest the mechanism by which the spore cortex is degraded during germination while the germ cell wall is left intact.

Neutron-mapping polymer flow: Scattering, flow visualization, and molecular theory

Flows of complex fluids need to be understood at both macroscopic and molecular scales, because it is the macroscopic response that controls the fluid behavior, but the molecular scale that ultimately gives rise to rheological and solid-state properties. Here the flow field of an entangled polymer melt through an extended contraction, typical of many polymer processes, is imaged optically and by small-angle neutron scattering. The dual-probe technique samples both the macroscopic stress field in the flow and the microscopic configuration of the polymer molecules at selected points. The results are compared with a recent tube model molecular theory of entangled melt flow that is able to calculate both the stress and the single-chain structure factor from first principles. The combined action of the three fundamental entangled processes of reptation, contour length fluctuation, and convective constraint release is essential to account quantitatively for the rich rheological behavior. The multiscale approach unearths a new feature: Orientation at the length scale of the entire chain decays considerably more slowly than at the smaller entanglement length.

Protein-protein interactions in ovalbumin solutions studied by small angle scattering: effect of ionic strength, and the chemical nature of cations

The influence of ionic strength and of the chemical nature of cations on the protein-protein interactions in ovalbumin solution was studied using small-angle X-ray and neutron scattering (SAXS/SANS). The globular protein ovalbumin is found in dimeric form in solutions as suggested by SANS/SAXS experiments. Due to the negative charge of the proteins at neutral pH, the protein-protein interactions without any salt addition are dominated by electrostatic repulsion. A structure factor related to screened Coulombic interactions together with an ellipsoid form factor was used to fit the scattering intensity. A monovalent salt (NaCl) and a trivalent salt (YCl3) were used to study the effect of the chemical nature of cations on the interaction in protein solutions. Upon addition of NaCl, with ionic strength below that of physiological conditions (150 mM), the effective interactions are still dominated by the surface charge of the proteins and the scattering data can be understood using the same model. When yttrium chloride was used, a reentrant condensation behavior, i.e., aggregation and subsequent redissolution of proteins with increasing salt concentration, was observed. SAXS measurements reveal a transition from effective repulsion to attraction with increasing salt concentration. The solutions in the reentrant regime become unstable after long times (several days). The results are discussed and compared with those from bovine serum albumin (BSA) in solutions.

Protein interactions studied by SAXS:effect of ionic strength and protein concentration for BSA in aqueous solutions

We have studied a series of samples of bovine serum albumin (BSA) solutions with protein concentration, c, ranging from 2 to 500 mg/mL and ionic strength, I, from 0 to 2 M by small-angle X-ray scattering (SAXS). The scattering intensity distribution was compared to simulations using an oblate ellipsoid form factor with radii of 17 x 42 x 42 A, combined with either a screened Coulomb, repulsive structure factor, S-SC(q), or an attractive square-well structure factor, S-SW(q). At pH = 7, BSA is negatively charged. At low ionic strength, I <0.3 M, the total interaction exhibits a decrease of the repulsive interaction when compared to the salt-free solution, as the net surface charge is screened, and the data can be fitted by assuming an ellipsoid form factor and screened Coulomb interaction. At moderate ionic strength (0.3-0.5 M), the interaction is rather weak, and a hard-sphere structure factor has been used to simulate the data with a higher volume fraction. Upon further increase of the ionic strength (I >= 1.0 M), the overall interaction potential was dominated by an additional attractive potential, and the data could be successfully fitted by an ellipsoid form factor and a square-well potential model. The fit parameters, well depth and well width, indicate that the attractive potential caused by a high salt concentration is weak and long-ranged. Although the long-range, attractive potential dominated the protein interaction, no gelation or precipitation was observed in any of the samples. This is explained by the increase of a short-range, repulsive interaction between protein molecules by forming a hydration layer with increasing salt concentration. The competition between long-range, attractive and short-range, repulsive interactions accounted for the stability of concentrated BSA solution at high ionic strength.

Ütemvakság

A gazdaság növekedés felgyorsulása hosszú távon először szükségszerűen csak egy rövid helyreállítási perióduson keresztül valósulhat meg, amelynek során a növekedés ütemét a válságok miatt elmaradt vagy más okból elmulasztott növekedés pótlása gyorsítja fel. Ez azonban messze nem jelenti a hosszú távú növekedési ütem felgyorsulását. A jelenséget először Jánossy Ferenc írta le, akinek megállapításai ma is érvényesek: egy jelentős visszaesés, majd stagnálás után a növekedési ütem 2005 után visszaállt az 1980 óta kialakult 1,5 százalékos hosszú távú ütemre. A Jánossy-féle szakmastruktúra-tényező nem más, mint a tudástőke: a munkaképes lakosság személyes tudása, jártassága és motivációja. Ezek az összetevők egy újrafogalmazott termelési függvény emberi elemei számos új és már korábban is ismert tényező mellett. Az emberi erőforrások nyilvántartása nem kompetenciaalapú, és emiatt a hosszú távú növekedési ütem alacsony szintjét sem tudjuk megmagyarázni. A növekedési ütem ingadozásai mögött elsősorban gazdaságpolitikai hibákat, érdemeket keresünk, holott az emberi beruházások elégtelen szintje jelenti a problémát, amely a múlt örökségnek és a jelen terheinek súlya alatt nem oldódik meg automatikusan. A magyar gazdaság egy újabb helyreállítási periódus előtt áll, s a gazdasági átalakítás alapvető feladata a foglalkoztatható lakosság aktivizálása, enélkül minden növekedési gyorsulás csak átmeneti helyreállítási periódus marad. JEL kód: B23, C22, E01, O11. /===/ Acceleration of economic growth in the long term can primarily be achieved only through a short period of consolidation, in which the growth rate of growth by recession or made up for by growth potential neglected for other reasons. But this is far from equivalent to an acceleration of the long-term growth rate. The phenomenon was described first by Ferenc Jánossy, whose conclusions remain valid to this day: after a substantial slump and a period of stagnation, the growth rate recovered after 2005 the long-term rate of 1.5 per cent that had set in after 1980. Jánossy's trade structure factor amounts to capital in knowledge: the personal know-how, expertise and motivation of the able-bodied population. These factors are the human constituents of a newly formulated production function, along with numerous new and previously known factors. The registration of human resources is competence- based and so it cannot explain the low level of the long-term growth rate either. People tend primarily to see failures and achievements of economic policy behind the failures and achievements of economic policy, when the real problem is inadequate human investment, which will not resolve itself automatically under the weight of the past and present burdens. The Hungarian economy is on the brink of a new period of recovery, and the basic task of economic transformation is to activate the employable population, without which any acceleration of growth will amount only to a temporary period of recovery.

An aspect-oriented approach to designing role-based access control services

Access control (AC) limits access to the resources of a system only to authorized entities. Given that information systems today are increasingly interconnected, AC is extremely important. The implementation of an AC service is a complicated task. Yet the requirements to an AC service vary a lot. Accordingly, the design of an AC service should be flexible and extensible in order to save development effort and time. Unfortunately, with conventional object-oriented techniques, when an extension has not been anticipated at the design time, the modification incurred by the extension is often invasive. Invasive changes destroy design modularity, further deteriorate design extensibility, and even worse, they reduce product reliability. ^ A concern is crosscutting if it spans multiple object-oriented classes. It was identified that invasive changes were due to the crosscutting nature of most unplanned extensions. To overcome this problem, an aspect-oriented design approach for AC services was proposed, as aspect-oriented techniques could effectively encapsulate crosscutting concerns. The proposed approach was applied to develop an AC framework that supported role-based access control model. In the framework, the core role-based access control mechanism is given in an object-oriented design, while each extension is captured as an aspect. The resulting framework is well-modularized, flexible, and most importantly, supports noninvasive adaptation. ^ In addition, a process to formalize the aspect-oriented design was described. The purpose is to provide high assurance for AC services. Object-Z was used to specify the static structure and Predicate/Transition net was used to model the dynamic behavior. Object-Z was extended to facilitate specification in an aspect-oriented style. The process of formal modeling helps designers to enhance their understanding of the design, hence to detect problems. Furthermore, the specification can be mathematically verified. This provides confidence that the design is correct. It was illustrated through an example that the model was ready for formal analysis. ^

The conformational landscape of RNA translational regulators and their potential as drug discovery targets

RNA is an underutilized target for drug discovery. Once thought to be a passive carrier of genetic information, RNA is now known to play a critical role in essentially all aspects of biology including signaling, gene regulation, catalysis, and retroviral infection. It is now well-established that RNA does not exist as a single static structure, but instead populates an ensemble of energetic minima along a free-energy landscape. Knowledge of this structural landscape has become an important goal for understanding its diverse biological functions. In this case, NMR spectroscopy has emerged as an important player in the characterization of RNA structural ensembles, with solution-state techniques accounting for almost half of deposited RNA structures in the PDB, yet the rate of RNA structure publication has been stagnant over the past decade. Several bottlenecks limit the pace of RNA structure determination by NMR: the high cost of isotopic labeling, tedious and ambiguous resonance assignment methods, and a limited database of RNA optimized pulse programs. We have addressed some of these challenges to NMR characterization of RNA structure with applications to various RNA-drug targets. These approaches will increasingly become integral to designing new therapeutics targeting RNA.

Growth Factor Stimulation Improves The Structure And Properties Of Scaffold-free Engineered Auricular Cartilage Constructs.

The reconstruction of the external ear to correct congenital deformities or repair following trauma remains a significant challenge in reconstructive surgery. Previously, we have developed a novel approach to create scaffold-free, tissue engineering elastic cartilage constructs directly from a small population of donor cells. Although the developed constructs appeared to adopt the structural appearance of native auricular cartilage, the constructs displayed limited expression and poor localization of elastin. In the present study, the effect of growth factor supplementation (insulin, IGF-1, or TGF-β1) was investigated to stimulate elastogenesis as well as to improve overall tissue formation. Using rabbit auricular chondrocytes, bioreactor-cultivated constructs supplemented with either insulin or IGF-1 displayed increased deposition of cartilaginous ECM, improved mechanical properties, and thicknesses comparable to native auricular cartilage after 4 weeks of growth. Similarly, growth factor supplementation resulted in increased expression and improved localization of elastin, primarily restricted within the cartilaginous region of the tissue construct. Additional studies were conducted to determine whether scaffold-free engineered auricular cartilage constructs could be developed in the 3D shape of the external ear. Isolated auricular chondrocytes were grown in rapid-prototyped tissue culture molds with additional insulin or IGF-1 supplementation during bioreactor cultivation. Using this approach, the developed tissue constructs were flexible and had a 3D shape in very good agreement to the culture mold (average error <400 µm). While scaffold-free, engineered auricular cartilage constructs can be created with both the appropriate tissue structure and 3D shape of the external ear, future studies will be aimed assessing potential changes in construct shape and properties after subcutaneous implantation.

Role of the 6-20 disulfide bridge in the structure and activity of epidermal growth factor

Two synthetic analogues of murine epidermal. growth factor, [Abu6, 20] mEGF4-48 (where Abu denotes amino-butyric acid) and [G1, M3, K21, H40] mEGF1-48, have been investigated by NMR spectroscopy. [Abu6, 20] mEGF4-48 was designed to determine the contribution of the 6-20 disulfide bridge to the structure and function of mEGF The overall structure of this analogue was similar to that of native mEGF, indicating that the loss of the 6-20 disulfide bridge did not affect the global fold of the molecule. Significant structural differences were observed near the N-terminus, however, with the direction of the polypeptide chain between residues four and nine being altered such that these residues were now located on the opposite face of the main beta-sheet from their position in native mEGF Thermal denaturation experiments also showed that the structure of [Abu6, 20] mEGF4-48 was less stable than that of mEGF. Removal of this disulfide bridge resulted in a significant loss of both mitogenic activity in Balb/c 3T3 cells and receptor binding on A431 cells compared with native mEGF and mEGF4-48, implying that the structural changes in [Abu6, 20] mEGF4-48, although limited to the N-terminus, were sufficient to interfere with receptor binding. The loss of binding affinity probably arose mainly from steric interactions of the dislocated N-terminal region with part of the receptor binding surface of EGF [G1, M3, K21, H40] mEGF1-48 was also synthesized in order to compare the synthetic polypeptide with the corresponding product of recombinant expression. Its mitogenic activity in Balb/c 3T3 cells was similar to that of native mEGF and analysis of its H-1 chemical shifts suggested that its structure was also very similar to native.