Multiscale Mode Dynamics of a Tethered Membrane

Stochastic dynamics of a tethered membrane with a bond-fluctuating coarse-grained Monte Carlo simulation shows, in addition to diffusion, nondiffusive behavior sensitive to the type of membrane, its size, and quality of the solvent. Motion of the membrane’s center node is described by the variation of the mean-square displacement (R2n) with time step (t), i.e., R2n∝t2ν with the exponent ν≃1/8−1∕6 in the short time followed by subdiffusive power laws (i.e., ν∼1∕5, 1∕10) in the intermediate time regimes before reaching diffusion ν=1. The crossover between in-plane wrinkle modes is identified from the segmental (node) motion of the membrane

Globular Structure of a Human Immunodeficiency Virus-1 Protease (1DIFA dimer) in an Effective Solvent Medium by a Monte Carlo Simulation

A coarse-grained model is used to study the structure and dynamics of a human immunodeficiency virus-1 protease (1DIFA dimer) consisting of 198 residues in an effective solvent medium on a cubic lattice by Monte Carlo simulations for a range of interaction strengths. Energy and mobility profiles of residues are found to depend on the interaction strength and exhibit remarkable segmental symmetries in two monomers. Lowest energy residues such as Arg(41) and Arg(140) (most electrostatic and polar) are not the least mobile; despite the higher energy, the hydrophobic residues (Ile, Leu, and Val) are least mobile and form the core by pinning down the local segments for the globular structure. Variations in the gyration radius (R(g)) and energy (E(c)) of the protein show nonmonotonic dependence on the interaction strength with the smallest R(g) around the largest value of E(c). Pinning of the conformations by the hydrophobic residues at high interaction strength seems to provide seed for the protein chain to collapse

Random Coil to Globular Thermal Response of a Protein (H3.1) with Three Knowledge-Based Coarse-Grained Potentials

The effect of temperature on the conformation of a histone (H3.1) is studied by a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV). Despite unique energy and mobility profiles of its residues, the histone H3.1 undergoes a systematic (possibly continuous) structural transition from a random coil to a globular conformation on reducing the temperature. The range over which such a systematic response in variation of the radius of gyration (Rg) with the temperature (T) occurs, however, depends on the potential, i.e. ΔTMJ ≈ 0.013–0.020, ΔTBT ≈ 0.018–0.026, and ΔTBFKV ≈ 0.006–0.013 (in reduced unit). Unlike MJ and BT potentials, results from the BFKV potential show an anomaly where the magnitude of Rg decreases on raising the temperature in a range ΔTA ≈ 0.015–0.018 before reaching its steady-state random coil configuration. Scaling of the structure factor, S(q) ∝ q−1/ν, with the wave vector, q = 2π/λ, and the wavelength, λ, reveals a systematic change in the effective dimension (De∼1/ν) of the histone with all potentials (MJ, BT, BFKV): De∼3 in the globular structure with De∼2 for the random coil. Reproducibility of the general yet unique (monotonic) structural transition of the protein H3.1 with the temperature (in contrast to non-monotonic structural response of a similar but different protein H2AX) with three interaction sets shows that the knowledge-based contact potential is viable tool to investigate structural response of proteins. Caution should be exercise with the quantitative comparisons due to differences in transition regimes with these interactions

Conformational Response to Solvent Interaction and Temperature of a Protein (Histone h3.1) by a Multi-Grained Monte Carlo Simulation

Interaction with the solvent plays a critical role in modulating the structure and dynamics of a protein. Because of the heterogeneity of the interaction strength, it is difficult to identify multi-scale structural response. Using a coarse-grained Monte Carlo approach, we study the structure and dynamics of a protein (H3.1) in effective solvent media. The structural response is examined as a function of the solvent-residue interaction strength (based on hydropathy index) in a range of temperatures (spanning low to high) involving a knowledge-based (Miyazawa-Jernigan(MJ)) residue-residue interaction. The protein relaxes rapidly from an initial random configuration into a quasi-static structure at low temperatures while it continues to diffuse at high temperatures with fluctuating conformation. The radius of gyration (Rg) of the protein responds non-monotonically to solvent interaction, i.e., on increasing the residue-solvent interaction strength (fs), the increase in Rg (fs≤fsc) is followed by decay (fs≥fsc) with a maximum at a characteristic value (fsc) of the interaction. Raising the temperature leads to wider spread of the distribution of the radius of gyration with higher magnitude of fsc. The effect of solvent on the multi-scale (λ: residue to Rg) structures of the protein is examined by analyzing the structure factor (S(q),|q| = 2π/λ is the wave vector of wavelength, λ) in detail. Random-coil to globular transition with temperature of unsolvated protein (H3.1) is dramatically altered by the solvent at low temperature while a systematic change in structure and scale is observed on increasing the temperature. The interaction energy profile of the residues is not sufficient to predict its mobility in the solvent. Fine-grain representation of protein with two-node and three-node residue enhances the structural resolution; results of the fine-grained simulations are consistent with the finding described above of the coarse-grained description with one-node residue

Self-assembly dynamics for the transition of a globular aggregate to a fibril network of lysozyme proteins via a coarse-grained Monte Carlo simulation

The self-organizing dynamics of lysozymes (an amyloid protein with 148 residues) with different numbers of protein chains, Nc = 1,5,10, and 15 (concentration 0.004 – 0.063) is studied by a coarse-grained Monte Carlo simulation with knowledge-based residue-residue interactions. The dynamics of an isolated lysozyme (Nc = 1) is ultra-slow (quasi-static) at low temperatures and becomes diffusive asymptotically on raising the temperature. In contrast, the presence of interacting proteins leads to concentration induced protein diffusion at low temperatures and concentration-tempering sub-diffusion at high temperatures. Variation of the radius of gyration of the protein with temperature shows a systematic transition from a globular structure (at low T) to a random coil (high T) conformation when the proteins are isolated. The crossover from globular to random coil becomes sharper upon increasing the protein concentration (i.e. with Nc = 5,10), with larger Rg at higher temperatures and concentration; Rg becomes smaller on adding more protein chains (e.g. Nc = 15) a non-monotonic response to protein concentration. Analysis of the structure factor (S(q)) provides an estimate of the effective dimension (D ≥ 3, globular conformation at low temperature, and D ∼ 1.7, random coil, at high temperatures) of the isolated protein. With many interacting proteins, the morphology of the self-assembly varies with scale, i.e. at the low temperature (T = 0.015), D ∼ 2.9 on the scale comparable to the radius of gyration of the protein, and D ∼ 2.3 at the large scale over the entire sample. The global network of fibrils appears at high temperature (T = 0.021) with D ∼ 1.7 (i.e. a random coil morphology at large scale) involving tenuous distribution of micro-globules (at small scales)

Water vapor diffusion in Mars subsurface environments

The diffusion coefficient of water vapor in unconsolidated porous media is measured for various soil simulants at Mars-like pressures and subzero temperatures. An experimental chamber which simultaneously reproduces a low-pressure, low-temperature, and low-humidity environment is used to monitor water flux from an ice source through a porous diffusion barrier. Experiments are performed on four types of simulants: 40–70 µm glass beads, sintered glass filter disks, 1–3 µm dust (both loose and packed), and JSC Mars–1. A theoretical framework is presented that applies to environments that are not necessarily isothermal or isobaric. For most of our samples, we find diffusion coefficients in the range of 2.8 to 5.4 cm^2 s^-1 at 600 Pascal and 260 K. This range becomes 1.9–4.7 cm^2 s^-1 when extrapolated to a Mars-like temperature of 200 K. Our preferred value for JSC Mars–1 at 600 Pa and 200 K is 3.7 ± 0.5 cm^2 s^-1. The tortuosities of the glass beads is about 1.8. Packed dust displays a lower mean diffusion coefficient of 0.38 ± 0.26 cm^2 s^-1, which can be attributed to transition to the Knudsen regime where molecular collisions with the pore walls dominate. Values for the diffusion coefficient and the variation of the diffusion coefficient with pressure are well matched by existing models. The survival of shallow subsurface ice on Mars and the providence of diffusion barriers are considered in light of these measurements

Perbandingan Kualitas Layanan Berdasarkan Kategori Restoran : Studi Kasus Di Badung Bali

In service industry, service quality is used as one factor in competition. Culinaryindustry, such as restaurant, bar, cafe, or eatery booth are one dynamic sector intourism world. As a tourist destination either domestic or International, Bali createsa competitive business environment either local or International as well.American restaurant in average shows a higher score in service quality comparewith others. But Indonesian restaurant gives a higher scores in empathy dimension inservice quality. Customer is expecting a good services, especially in culinary industryin sustaining their businesses. The company should look carefully into aspects ofservice quality, hence they can be a winner in the competitive industry

Analysis of Fluorinated Polyimides Flown on the Materials International Space Station Experiment

This Technical Memorandum documents the results from the Materials on International Space Station Experiment (MISSE) series involving fluorinated polyimide films analyzed at NASA Marshall Space Flight Center. These films may be used in thermal control, sunshield, solar sail, solar concentrator, and other lightweight polymer film applications. Results include postflight structural integrity, visual observations, determination of atomic oxygen erosion yield, and optical property changes as compared to preflight values

Preferential Binding Effects On Protein Structure and Dynamics Revealed by Coarse-Grained Monte Carlo Simulation

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ∼ 1.3), random-coil (D ∼ 1.75), and globular (D ∼ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale