Swapping Mechanism Research Articles

MARS: Mobile Application Relaunching Speed-Up through Flash-Aware Page Swapping

The approach for fast application relaunching on the current Android system is to cache background applications in memory. This mechanism is limited by the available memory size. In addition, the application state may not be easily recovered. We propose a prototype system, MARS, to enable page swapping and cache more applications. MARS can speed up the application relaunching and restore the application state. As a new page swapping design for optimizing application relaunching, MARS isolates Android runtime Garbage Collection (GC) from page swapping for compatibility and employs several flash-aware techniques for swap-in speedup. Two main components of MARS are page slot allocation and read/write control. Page slot allocation reorganizes page slots in swap area to produce sequential reads and improve the performance of swap-in. Read/Write control addresses the read/write interference issue by reducing concurrent and extra internal writes. Compared to the conventional Linux page swapping, these two components can scale up the read bandwidth up to about 3.8 times. Application tests on a Google Nexus 4 phone show that MARS reduces the launching time of applications by 50 - 80 percent. The modified page swapping mechanism can outperform the conventional Linux page swapping up to four times.

Structural Studies of the Oligomerization Process of Human Cystatin C Variants

Human cystatin C (HCC), an inhibitor of cysteine proteases, is also involved in amyloidogenic processes within the human body. In the crystal structure, as in solution, wild-type (WT) cystatin C dimerizes via a domain swapping mechanism [1,2]. The same process has also been shown to be important for protein oligomerization [2]. Aggregation of HCC results in a heterogeneous mixture of species, both oligomeric and fibrillar, with varying shapes, sizes and molecular weights.The goal of our study was to characterize the assembly process of potentially neurotoxic oligomers of WT and variant HCC in solution. The oligomerization processes of several point mutation variants of HCC (V57N, V57P, V57D, V57G and L68V), with specific dimerization propensities [3], were compared to the WT protein. Prepared oligomers were purified by size-exclusion chromatography and using TEM and AFM studies, we observed characteristic donut-like structures along with fibrils and we determined the size distribution of cystatin C oligomers obtained from the WT and variant forms. Independently, the oligomerization process was analyzed by fluorescence spectroscopy and visualized by native electrophoresis. Additionally, induced secondary structure changes were characterised by circular dichroism (CD) and infrared (FTIR) spectroscopies. Finally, the structural studies were supplemented with the modelling of the larger HCC oligomers using molecular dynamics simulations, allowing the identification of the most stable oligomeric forms of HCC to be determined.This research project was financed by the National Science Centre (Poland), decision no. 2012/06/M/ST4/00036.[1] Janowski R, Kozak M, Jankowska E et al. (2001). Nature Struct. Mol. Biol. 8, 316.[2] Wahlbom M, Wang X, Lindstrom V, et al. (2007). J. Biol. Chem. 282, 18318.[3] Szymanska A, Jankowska E, Orlikowska M, et al. (2012) Front. Mol. Neurosci., 5, 82

Monte-Carlo Simulation of the Ionic Transport of Electrolyte Solutions at High Concentrations Based on the Pseudo-Lattice Model

The theoretical understanding of the ionic transport in electrolyte solutions is not yet well-established at high concentrations, such as at C/mol · L− 1 > 1. In our present study, two transport phenomena—self-diffusion and ionic conduction—of the electrolyte solution at high concentrations (roughly 0.05 ⩽ C/mol · L− 1 ⩽ 3) are computationally simulated by a kinetic Monte-Carlo scheme. A “swap mechanism” in the three-dimensional pseudo-lattice is proposed to model the movement of ions and solvent, in which only the nearest-neighbor interaction is considered. The energy difference between the before- and after-swap states, based on which the stochastic Monte-Carlo process occurs, is found to be expressed in only two energetic terms; the coulombic repulsion between ions with the identical sign, , and the heat of dissolution of the ionic crystal, . The self-diffusion coefficients of both ions and solvent decrease with the increase in the ionic concentration, which qualitatively agree with the experimental observation. The asymmetric bell-shape of the specific conductivity, σ, principally originates from the coulombic repulsion. The ionic concentration at which the maximum σ occurs well coincides with that of the experimentally observed results. The -dependency reveals that, ceteris paribus, σ marks the highest at around , out of the range of which σ is attenuated by either the ion-ion or ion-solvent interaction. Finally, the limitations in the model are addressed.

Acinetobactin Isomerization Enables Adaptive Iron Acquisition in Acinetobacter baumannii through pH-Triggered Siderophore Swapping.

Pathogenic strains of Acinetobacter baumannii excrete multiple siderophores that enhance iron scavenging from host sources. The oxazoline siderophore pre-acinetobactin undergoes an unusual non-enzymatic isomerization, producing the isoxazolidinone acinetobactin. In this study, we explored the kinetics, mechanism, and biological consequence of this siderophore swapping. Pre-acinetobactin is excreted to the extracellular space where the isomerization to acinetobactin occurs with a pH-rate profile consistent with 5-exo-tet cyclization at C5' with clean stereochemical inversion. Pre-acinetobactin persists at pH <6, and acinetobactin is rapidly formed at pH >7, matching each siderophore's pH preference for iron(III) chelation and A. baumannii growth promotion. Acinetobactin isomerization provides two siderophores for the price of one, enabling A. baumannii to sequester iron over a broad pH range likely to be encountered during the course of an infection.

Engineered Domain Swapping as an On/Off Switch for Protein Function

Domain swapping occurs when identical proteins exchange segments in reciprocal fashion. Natural swapping mechanisms remain poorly understood, and engineered swapping has the potential for creating self-assembling biomaterials that encode for emergent functions. We demonstrate that induced swapping can be used to regulate the function of a target protein. Swapping is triggered by inserting a "lever" protein (ubiquitin) into one of four loops of the ribose binding protein (RBP) target. The lever splits the target, forcing RBP to refold in trans to generate swapped oligomers. Identical RBP-ubiquitin fusions form homo-swapped complexes with the ubiquitin domain acting as the hinge. Surprisingly, some pairs of non-identical fusions swap more efficiently with each other than they do with themselves. Nuclear magnetic resonance experiments reveal that the hinge of these hetero-swapped complexes maps to a region of RBP distant from both ubiquitins. This design is expected to be applicable to other proteins to convert them into functional switches.

Robust, tunable genetic memory from protein sequestration combined with positive feedback.

Natural regulatory networks contain many interacting components that allow for fine-tuning of switching and memory properties. Building simple bistable switches, synthetic biologists have learned the design principles of complex natural regulatory networks. However, most switches constructed so far are so simple (e.g. comprising two regulators) that they are functional only within a limited parameter range. Here, we report the construction of robust, tunable bistable switches in Escherichia coli using three heterologous protein regulators (ExsADC) that are sequestered into an inactive complex through a partner swapping mechanism. On the basis of mathematical modeling, we accurately predict and experimentally verify that the hysteretic region can be fine-tuned by controlling the interactions of the ExsADC regulatory cascade using the third member ExsC as a tuning knob. Additionally, we confirm that a dual-positive feedback switch can markedly increase the hysteretic region, compared to its single-positive feedback counterpart. The dual-positive feedback switch displays bistability over a 106-fold range of inducer concentrations, to our knowledge, the largest range reported so far. This work demonstrates the successful interlocking of sequestration-based ultrasensitivity and positive feedback, a design principle that can be applied to the construction of robust, tunable, and predictable genetic programs to achieve increasingly sophisticated biological behaviors.

Efficient network mobility support scheme for proxy mobile IPv6

The recent rapid proliferation of mobile devices has significantly increased the importance of network mobility (NEMO) technology for Internet access, which enables all the nodes within a mobile network to provide session continuity when the mobile network moves. This paper proposes an efficient network mobility support scheme with direct home network prefix (HNP) assignment to reduce the location update cost and packet tunneling cost. In the proposed scheme, the moving mobile access gateway (mMAG), instead of the local mobility anchor (LMA), assigns a mobile node (MN)’s HNP using a sub-prefix of its own HNP when an MN is attached to the mMAG. An IP address swapping mechanism is used to deliver the packets destined for MNs moved to the mMAG without an additional tunnel header. In the proposed scheme, the mMAG also performs a location update on behalf of the MNs. Therefore, the proposed scheme can reduce both the location update cost and the packet tunneling cost. Numerical analysis and simulation results show that the proposed scheme outperforms the existing schemes in terms of the total cost, throughput, and signaling overhead.

Analysis of Silicon Based Surface Plasmon Resonance Sensors with Different Amino Acids

A semiconductor prism coupler based nano-plasmonic sensor consisting of a high refractive index (RI) silicon prism, a gold (Au) metal film and different amino acids was used as a dielectric sample for sensing in the in the Attenuated Total Internal Reflection (ATIR) mode. An additional silicon nano-layer has been used for increasing stability and sensitivity of the surface plasmon resonance-sensor which causes enhancement of the evanescent field near the metal-analyte interface compared to the traditional three layer structure. Positional swap of the silicon nano-layer from above the metal surface to below the metal surface causes further enhances of the evanescent field near the metal-analyte interface. Performance of the nano-plasmonic sensors depending upon the high refractive index silicon prism, additional silicon nano-layer and swapping mechanism is discussed with the help of sensing performance for different amino acids with corresponding image response for the proposed nano-plasmonic sensor in a MATLAB environment.

Energetic Calculations to Decipher pH-Dependent Oligomerization and Domain Swapping of Proteins.

Domain swapping mechanism is a specialised mode of oligomerization of proteins in which part of a protein is exchanged in a non-covalent manner between constituent subunits. This mechanism is highly affected by several physiological conditions. Here, we present a detailed analysis ofthe effect of pH on different regions of the domain swapped oligomer by considering examples which are known to be sensitive to pH in transiting from monomeric to domain-swapped dimeric form. The energetic calculations were performed using a specialized method which considers changes in pH and subsequent changes in the interactions between subunits. This analysis provides definitive hints about the pH-dependence switch from monomer to domain-swapped oligomer and the steps that may be involved in the swapping mechanism.

New Insights into the Molecular Mechanism of E-Cadherin-Mediated Cell Adhesion by Free Energy Calculations.

Three-dimensional domain swapping is an important mode of protein association leading to the formation of stable dimers. Monomers associating via this mechanism mutually exchange a domain to form a homodimer. Classical cadherins, an increasingly important target for anticancer therapy, use domain swapping to mediate cell adhesion. However, despite its importance, the molecular mechanism of domain swapping is still debated. Here, we study the conformational changes that lead to activation and dimerization via domain swapping of E-cadherin. Using state-of-the-art enhanced sampling atomistic simulations, we reconstruct its conformational free energy landscape, obtaining the free energy profile connecting the inactive and active form. Our simulations predict that the E-cadherin monomer populates the open and closed forms almost equally, which is in agreement with the proposed "selected fit" mechanism in which monomers in an active conformational state bind to form a homodimer, analogous to the conformational selection mechanism often observed in ligand-target binding. Moreover, we find that the open state population is increased in the presence of calcium ions at the extracellular boundary, suggesting their possible role as allosteric activators of the conformational change.

Double dividend hypothesis: Can it be validated by carbon taxation swap with payroll taxes?

This paper is concerned with the proficiency assessment of the environmental tax reform to tackle the pollution and simultaneously decrease the tax burden of pre-existent labor taxation. In comparison with mainstream literature, we focus exclusively on the reduction of the tax distortions that affect labor demand, using the revenues generated by environmental levies. Our starting point is the double dividend hypothesis with respect to the environmental taxation. The main objective of this paper is to validate the second dividend hypothesis, hence testing the carbon taxation ability to reduce harmful effects of taxes on inputs such as labor. Following the trajectory of the double dividend hypothesis, the paper examines the potential of carbon taxation enactment accompanied by the payroll tax cuts in order to lower the efficiency costs of these pre-existent distortionary taxes. The feasibility of tax swap mechanism between environmental and payroll taxation is verified through estimating and comparing their efficiency costs. The results obtained from empirical analysis confirm that there is a high potential of swapping these taxes and implementing offsetting measures, where the efficiency costs of payroll taxation are considerably larger than of environmental taxation. Hence, we conclude that there is “enough room” for this tax swap mechanism to take place which would have a two-folded outcome – environment protection improvement and decreasing the efficiency costs of the fiscal system. Given the fact that the efficiency costs of environmental taxes are considerably lower (both in absolute and percentage values), than payroll taxation in the EU, it is possible to apply payroll tax cuts and consequently increase the ratio of environmental taxation. DOI: http://dx.doi.org/10.5755/j01.ee.26.1.8399

(-)-epigallocatechin-3-gallate inhibits fibrillogenesis of chicken cystatin.

Previous studies have reported that (-)-epigallocatechin-3-gallate (EGCG), the most abundant flavonoid in green tea, can bind to unfolded native polypeptides and prevent conversion to amyloid fibrils. To elucidate whether this antifibril activity is specific to disease-related target proteins or is more generic, we investigated the ability of EGCG to inhibit amyloid fibril formation of amyloidogenic mutant chicken cystatin I66Q, a generic amyloid-forming model protein that undergoes fibril formation through a domain swapping mechanism. We demonstrated that EGCG was a potent inhibitor of amyloidogenic cystatin I66Q amyloid fibril formation in vitro. Computational analysis suggested that EGCG prevented amyloidogenic cystatin fibril formation by stabilizing the molecule in its native-like state as opposed to redirecting aggregation toward disordered and amorphous aggregates. Therefore, although EGCG appears to be a generic inhibitor of amyloid-fibril formation, the mechanism by which it achieves such inhibition may be specific to the target fibril-forming polypeptide.

Compressed and shared swap to extend available memory in virtualized consumer electronics

Virtualization has recently been applied to consumer electronic (CE) devices such as smart TVs and smartphones. In these virtualized CE devices, memory is a valuable resource, because the virtual machines (VMs) on the devices must share the same physical memory. However, physical memory is usually partitioned and allocated to each VM. This partitioning technique may result in memory shortages, which can seriously degrade application performance. This paper proposes a new swap mechanism for virtualized CE devices with flash memory. This proposed mechanism reduces memory consumption by compressing and sharing unused pages. This swap mechanism stores the unused page in memory of another VM, to increase the available memory of the original VM. The proposed swap mechanism is implemented on the Xen hypervisor and Linux. The mechanism improves the application performance by up to 38% by significantly reducing the number of swap-out requests. The swap-out requests are reduced by up to 88% compared to previous swap mechanisms. Moreover, the mechanism reduces memory consumption of the swap area by up to 79%.

Enhancement of Selection, Bubble and Insertion Sorting Algorithm

In everyday life there is a large amount of data to arrange because sorting removes any ambiguities and make the data analysis and data processing very easy, efficient and provides with cost less effort. In this study a set of improved sorting algorithms are proposed which gives better performance and design idea. In this study five new sorting algorithms (Bi-directional Selection Sort, Bi-directional bubble sort, MIDBiDirectional Selection Sort, MIDBidirectional bubble sort and linear insertion sort are presented. Bi-directional Selection Sort and MIDBiDirectional Selection Sort are the enhancement on basic selection sort while Bidirectional bubble sort and MIDBidirectional bubble sort are the enhancement on basic bubble sort by changing the selection and swapping mechanism of data for sorting. Enhanced sorting algorithms reduced the iteration by half and quarter times respectively. Asymptotically complexities of these algorithms are reduced to O (n 2 /2) and O (n 2 /4) from O (n 2 ). Linear insertion sort is the enhancement of insertion sort by changing the design of algorithm (convert two loops to one loop). So asymptotically this algorithm is converted to linear time complexity from quadratic complexity. These sorting algorithms are described using C. The proposed algorithms are analyzed using asymptotic analysis and also using machine-running time and compared with their basic sorting algorithms. In this study we also discuss how the performance and complexity can be improved by optimizing the code and design.

Fast and rewritable colloidal assembly via field synchronized particle swapping

We report a technique to realize reconfigurable colloidal crystals by using the controlled motion of particle defects above an externally modulated magnetic substrate. The transport of particles is induced by applying a uniform rotating magnetic field to a ferrite garnet film characterized by a periodic lattice of magnetic bubbles. For filling factor larger than one colloid per bubble domain, the particle current arises from propagating defects where particles synchronously exchange their position when passing from one occupied domain to the next. The amplitude of an applied alternating magnetic field can be used to displace the excess particles via a swapping mechanism, or to mobilize the entire colloidal system at a predefined speed.

Swap Mechanism for Medical Clustering Problems

Swap Mechanism for Medical Clustering Problems

Aggregation of Oxidation-Mimicking Mutants of Gamma-D Crystallin Supports a Domain Swapping Model

Crystallization, amyloidogenesis, and native-state polymerization of proteins have been studied extensively, but far less is known about protein aggregation from folding intermediates. Cataract is a protein misfolding disorder resulting from formation of light-scattering aggregates of proteins from the crystallin family, which account for 90% of all protein in the human eye lens. A major model of cataract development is the aggregation of γ-crystallins induced by accumulation of oxidative damage. Oxidative damage can convert hydrophobic core residues to hydrophilic ones, such as tryptophan to kynurenine. Conversely, a number of hydrophilic core substitutions in the γD-crystallin gene cause hereditary early-onset cataract. We investigated the aggregation of hydrophilic core mutants of γD-crystallin mimicking effects of oxidative damage. We present evidence that such mutations lead to structured, non-covalent, non-amyloid aggregation of the protein, which proceeds under physiological conditions in vitro with little or no loss of secondary structure. The aggregates are reversible by changes in pH, but not in temperature. Moreover, a wild-type/mutant mixture can yield dramatic enhancement in light scattering without aggregation of the wild-type protein itself. We conclude that such aggregation proceeds from a folding intermediate or slightly altered conformation accessible under physiological conditions. Domain swapping mechanisms can account for this aggregation behavior.

F-PMIPv6 네트워크에서 지능적인 계층적 이동성 지원 기법

In this paper, we propose a new mobility management scheme, called i-FP(intelligent Fast PMIPv6). Our proposed i-FP scheme is addressed for solving the existing local mobility management problems from legacy frameworks. To move MN(Mobile Node) to other networks in one domain, i-FP employs three network entities which are extended from PMIPv6(Proxy Mobile IPv6), LMA(Local Mobility Anchor), MAG(Mobile Access Gateway) and MN. In i-FP, the three network entities can reduce the handover delay time of MNs. Also, i-FP uses an IP header swapping mechanism to avoid the traffic overhead and improve the throughput of network. To evaluate the performance of i-FP, we analyze our i-FP, HMIPv6(Hierarchical Mobile IPv6) and PMIPv6 which are legacy protocols of local mobility management in terms of various parameters. Finally, our i-FP scheme shows good performance(reduction of routing hops 10.2%, signaling costs 58.5% and handover delay 16.3%) than other network schemes for the total cost.

The Model of Amyloid Aggregation of Escherichia coli RNA Polymerase σ 70 Subunit Based on AFM Data and In Vitro Assays

To propose a model for recently described amyloid aggregation of E.coli RNA polymerase σ(70) subunit, we have investigated the role of its N-terminal region. For this purpose, three mutant variants of protein with deletions Δ1-73, Δ1-100 and Δ74-100 were constructed and studied in a series of in vitro assays and using atomic force microscopy (AFM). Specifically, all RNA polymerase holoenzymes, reconstituted with the use of mutant σ subunits, have shown reduced affinity for promoter-containing DNA and reduced activity in run-off transcription experiments (compared to that of WT species), thus substantiating the modern concept on the modulatory role of N-terminus in formation of open complex and transcription initiation. The ability of mutant proteins to form amyloid-like structures has been investigated using AFM, which revealed the increased propensity of mutant proteins to form rodlike aggregates with the effect being more pronounced for the mutant with the deletion Δ1-73 (10 fold increase). σ(70) subunit aggregation ability has shown complex dependence on the ionic surrounding, which we explain by Debye screening effect and the change of the internal state of the protein. Basing on the obtained data, we propose the model of amyloid fibril formation by σ(70) subunit, implying the involvement of N-terminal region according to the domain swapping mechanism.

Aggregation of Trp>Glu Mutants of the Human Gamma-D Crystallin: A Model for Hereditary or UV-Induced Cataract

Cataract is a protein misfolding disorder resulting from formation of light-scattering aggregates of proteins from the crystallin family. These long-lived proteins account for 90% of all protein in the human eye lens. The γD crystallin consists of two symmetrical domains, each of which has a duplicated Greek key fold. Maintaining this topologically complex native fold of the γD crystallin is essential for lens transparency. A number of point mutants in the γD crystallin gene cause early-onset cataract. UV-B exposure accelerates cataract onset, and UV irradiation of purified wild-type γD results in aggregation in vitro. A distinctive feature of the Greek key fold is the presence of highly conserved buried tryptophans. Replacements of tryptophan by charged glutamate groups may represent a model of UV-induced photodamage -- introduction of a charged group into the hydrophobic core generating “denaturation from within.” We show that such Trp>Glu mutants can display vastly increased aggregation propensity under physiological conditions in vitro. Furthermore, a striking property of these mutants is their ability to drive the wild-type protein into the aggregated state. Domain swapping mechanisms can account for this aggregation behavior.