Energy Restraint Research Articles

Efficient routing in multicast mesh by using forwarding nodes and weighted cost function

Multicast Mesh based Mobile Ad-hoc NETworks (MANETs) provide efficient data transmission in energy restraint areas without a fixed infrastructure. In this paper, the authors present an improved version of protocol SLIMMER developed by them earlier, and name it SLIMMER-SN. Most mesh-based protocols suffer from redundancy; however, the proposed protocol controls redundancy through the concept of forwarding nodes. The proposed protocol uses remaining energy of a node to decide its energy efficiency. For measuring stability, a new metric called Stability of Node (SN) has been introduced which depends on transmission range, node density and node velocity. For data transfer, a weighted cost function selects the most energy efficient nodes / most stable nodes or a weighted combination of both. This makes the node selection criteria more dynamic. The protocol works in two steps: (1) calculating SN and (2) using SN value in the weighted cost function for selection of nodes. The study compared the proposed protocol, with other mesh-based protocols PUMA and SLIMMER, based on packet delivery ratio (PDR), throughput, end-to-end delay and average energy consumption under different simulation conditions. Results clearly demonstrate that SLIMMER-SN outperformed both PUMA and SLIMMER.

Incorporating an iterative energy restraint for the Surface Energy Balance System (SEBS)

The Surface Energy Balance System (SEBS) has proven itself as an effective remotely sensed estimator of actual evapotranspiration (ETa). However, it has several vulnerabilities associated with the partitioning of the available energy (AE) at the land surface. We introduce a two stage energy restraint process into the SEBS algorithm (SEBS-ER) to overcome these vulnerabilities. The first offsets the remotely sensed surface temperature to ensure the surface to air temperature difference reflects AE, while the second stage uses a domain based image search process to identify and adjust the proportions of sensible (H) and latent (λE) heat flux with respect to AE. We effectively implemented SEBS-ER over 61 acquisitions over two Landsat tiles (path 90 row 84 and path 91 row 85) in south-eastern Australia that feature heterogeneous land covers. Across the two areas we showed that the SEBS-ER algorithm has: greater resilience to perturbed errors in surface energy balance algorithm inputs; significantly improved accuracy (p<0.05) at two eddy covariance flux towers in heavily forested (RMSE 62.3Wm−2, R2 0.879) and sub-alpine grassland (RMSE 33.2Wm−2, R2 0.939) land covers; and greater temporal stability across 52 daily actual evapotranspiration (ETa) estimates compared to a temporally stable and independent ETa dataset. The energy restraint within SEBS-ER has reduced exposure to the complex errors and uncertainties within remotely sensed, meteorological, and land type SEBS inputs, providing more reliable and accurate spatially distributed ETa products.

Coarse-Grained Molecular Modeling of the Solution Structure Ensemble of Dengue Virus Nonstructural Protein 5 with Small-Angle X-ray Scattering Intensity.

An ensemble-modeling scheme incorporating coarse-grained simulations with experimental small-angle X-ray scattering (SAXS) data is applied to dengue virus 2 (DENV2) nonstructural protein 5 (NS5). NS5 serves a key role in viral replication through its two domains that are connected by a 10-residue polypeptide segment. A set of representative structures is generated from a simulated structure pool using SAXS data fitting by the non-negativity least squares (NNLS) or standard ensemble optimization method (EOM) based on a genetic algorithm (GA). It is found that a proper low-energy threshold of the structure pool is necessary to produce a conformational ensemble of two representative structures by both NNLS and GA that agrees well with the experimental SAXS profile. The stability of the constructed ensemble is validated also by molecular dynamics simulations with an all-atom force field. The constructed ensemble successfully revealed the domain-domain orientation and domain-contacting interface of DENV2 NS5. Using experimental data fitting and additional investigations with synthesized data, it is found that energy restraint on the conformational pool is necessary to avoid overinterpretation of experimental data by spurious conformational representations.

Structural Refinement from Restrained-Ensemble Simulations Based on EPR/DEER Data: Application to T4 Lysozyme

DEER (double electron-electron resonance) is a powerful pulsed ESR (electron spin resonance) technique allowing the determination of distance histograms between pairs of nitroxide spin-labels linked to a protein in a native-like solution environment. However, exploiting the huge amount of information provided by ESR/DEER histograms to refine structural models is extremely challenging. In this study, a restrained ensemble (RE) molecular dynamics (MD) simulation methodology is developed to address this issue. In RE simulation, the spin-spin distance distribution histograms calculated from a multiple-copy MD simulation are enforced, via a global ensemble-based energy restraint, to match those obtained from ESR/DEER experiments. The RE simulation is applied to 51 ESR/DEER distance histogram data from spin-labels inserted at 37 different positions in T4 lysozyme (T4L). The rotamer population distribution along the five dihedral angles connecting the nitroxide ring to the protein backbone is determined and shown to be consistent with available information from X-ray crystallography. For the purpose of structural refinement, the concept of a simplified nitroxide dummy spin-label is designed and parametrized on the basis of these all-atom RE simulations with explicit solvent. It is demonstrated that RE simulations with the dummy nitroxide spin-labels imposing the ESR/DEER experimental distance distribution data are able to systematically correct and refine a series of distorted T4L structures, while simple harmonic distance restraints are unsuccessful. This computationally efficient approach allows experimental restraints from DEER experiments to be incorporated into RE simulations for efficient structural refinement.

Rotamer Library of Spin Labeled Cysteines Attached to T4 Lysozyme Deduced from Molecular Dynamics Simulations Constrained by Double Electron-Electron Resonance (Deer) Experiments

DEER (Double Electron Electron Resonance) is a powerful pulsed EPR technique allowing the determination of spin-spin distance histograms between side-directed nitroxide label sites on a protein in their native environment. In this study, a novel molecular dynamics simulation method, the restrained ensemble (RE) method, has been used for the refinement of spin labels inserted in T4 Lysozyme (T4L) structures. In the RE method, the spin-spin distance distribution histograms calculated from a multiple-copy molecular dynamics simulations are forced, via a special ensemble-based energy restraint, to match those extracted from 51 EPR/DEER experimental spin-spin pairs. To examine the effect of the restraint on the rotameric state of the spin label at the 37 different sites in T4L, conventional long molecular dynamics (MD) and locally enhanced sampling (LES) simulations were also performed. As expected, the distance histograms obtained from the RE simulations are very similar to those obtained from experiment; however, the distance histograms from conventional long MD and LES simulations deviate from experiment. From the analysis of these simulations, a general trend is found in rotamer population distribution along five dihedral angles connecting the nitroxide ring to the protein backbone. Overall, the rotamer population obtained from the RE simulation agrees with those obtained from x-ray structure. From the analysis of the dynamics of nitroxide atoms in spin label side chains, a force field for a pseudo nitroxide dummy atom has been parameterized. This pseudo nitroxide was used in an RE simulation coupled with the EPR/DEER experimental distance distribution data to refine distorted structures of T4L. Thus, experimental restraints from DEER experiments in conjunction with RE simulations can be used to refine structural propertied of biological systems.

Mode of Membrane Interaction and Fusogenic Properties of a de Novo Transmembrane Model Peptide Depend on the Length of the Hydrophobic Core

Model peptides composed of alanine and leucine residues are often used to mimic single helical transmembrane domains. Many studies have been carried out to determine how they interact with membranes. However, few studies have investigated their lipid-destabilizing effect. We designed three peptides designated KALRs containing a hydrophobic stretch of 14, 18, or 22 alanines/leucines surrounded by charged amino acids. Molecular modeling simulations in an implicit membrane model as well as attenuated total reflection-Fourier transform infrared analyses show that KALR is a good model of a transmembrane helix. However, tryptophan fluorescence and attenuated total reflection-Fourier transform infrared spectroscopy indicate that the extent of binding and insertion into lipids increases with the length of the peptide hydrophobic core. Although binding can be directly correlated to peptide hydrophobicity, we show that insertion of peptides into a membrane is determined by the length of the peptide hydrophobic core. Functional studies were performed by measuring the ability of peptides to induce lipid mixing and leakage of liposomes. The data reveal that whereas KALR14 does not destabilize liposomal membranes, KALR18 and KALR22 induce 40 and 50% of lipid-mixing, and 65 and 80% of leakage, respectively. These results indicate that a transmembrane model peptide can induce liposome fusion in vitro if it is long enough. The reasons for the link between length and fusogenicity are discussed in relation to studies of transmembrane domains of viral fusion proteins. We propose that fusogenicity depends not only on peptide insertion but also on the ability of peptides to destabilize the two leaflets of the liposome membrane.

Refined X-ray crystal structures of the reactive site modified ovomucoid inhibitor third domains from silver pheasant (OMSVP3 ∗) and from Japanese quail (OMJPQ3 ∗)

Tetragonal and triclinic crystals of two ovomucoid inhibitor third domains from silver pheasant and Japanese quail, modified at their reactive site bonds Met18Glu19 (OMSVP3 ∗) and Lys18Asp19 (OMJPQ3 ∗), respectively, were obtained. Their molecular and crystal structures were solved using X-ray data to 2.5 Å and 1.55 Å by means of Patterson search methods using truncated models of the intact (virgin) inhibitors as search models. Both structures were crystallographically refined to R-values of 0.185 and 0.192, respectively, applying an energy restraint reciprocal space refinement procedure. Both modified inhibitors show large deviations from the intact derivatives only in the proteinase binding loops (Pro14 to Arg21) and in the amino-terminal segments (Leul to Val6). In the modified inhibitors the residues immediately adjacent to the cleavage site (in particular P2, P1, P1′) are mobile and able to adapt to varying crystal environments. The charged end-groups i.e. Met18 COO − and Glu19 NH 3 + in OMSVP3 ∗, and Lys18 COO − and Aspl9 NH 3 + in OMJPQ3 ∗, do not form ion pairs with one another. The hydrogen bond connecting the side-chains of Thr17 and Glu19 (i.e. residues on either side of the scissile peptide bond) in OMSVP3 is broken in the modified form, and the hydrogen-bond interactions observed in the intact molecules between the Asn33 side-chain and the carbonyl groups of loop residues P2 and P1′ are absent or weak in the modified inhibitors. The reactive site cleavage, however, has little effect on specific interactions within the protein scaffold such as the side-chain hydrogen bond between Asp27 and Tyr31 or the side-chain stacking of Tyr20 and Pro22. The conformational differences in the amino-terminal segment Leul to Val6 are explained by their ability to move freely, either to associate with segments of symmetry-related molecules under formation of a four-stranded β-barrel (OMSVP3 ∗ and OMJPQ3) or to bind to surrounding molecules. Together with the results given in the accompanying paper, these findings probably explain why K hyd of small protein inhibitors of serine proteinases is generally found to be so small.

The growth of inert gas bubbles within grains and at grain boundaries—a comparison of mechanisms

Abstract A brief survey is presented of mechanisms by which irradiation induced gas bubbles may grow and it concentrates on those processes, not directly dependent on continuing irradiation, which can cause rapid growth, including the situations where the gas pressure may exceed, be equal to, or be less than the surface energy restraint. The importance of bubble coalescence is emphasized. This occurs only to a very small extent by purely random motion but is much more strongly dependent on the response of bubbles to driving forces whereby their movement can be greatly increased. Bubbles situated on grain boundaries are subjected to a greater variety of driving forces than those within grains and those caused by grain boundary movement or directly by the action of stress are especially important. The sensitivity to stress system as well as magnitude is a particular feature and this relates to the anisotropy of overall shape changes, to gas release and to fracture.