Composition dependent multiple structural transformations of myoglobin in aqueous ethanol solution: A combined experimental and theoretical study

Experimental studies (circular dichroism and ultra-violet (UV) absorption spectra) and large scale atomistic molecular dynamics simulations (accompanied by order parameter analyses) are combined to establish a number of remarkable (and unforeseen) structural transformations of protein myoglobin in aqueous ethanol mixture at various ethanol concentrations. The following results are particularly striking. (1) Two well-defined structural regimes, one at x(EtOH) similar to 0.05 and the other at x(EtOH) similar to 0.25, characterized by formation of distinct partially folded conformations and separated by a unique partially unfolded intermediate state at x(EtOH) similar to 0.15, are identified. (2) Existence of non-monotonic composition dependence of (i) radius of gyration, (ii) long range contact order, (iii) residue specific solvent accessible surface area of tryptophan, and (iv) circular dichroism spectra and UV-absorption peaks are observed. Interestingly at x(EtOH) similar to 0.15, time averaged value of the contact order parameter of the protein reaches a minimum, implying that this conformational state can be identified as a molten globule state. Multiple structural transformations well known in water-ethanol binary mixture appear to have considerably stronger effects on conformation and dynamics of the protein. We compare the present results with studies in water-dimethyl sulfoxide mixture where also distinct structural transformations are observed along with variation of co-solvent composition. (C) 2015 AIP Publishing LLC.

Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers

A new class of dendrimers, the poly(propyl ether imine) (PETIM) dendrimer, has been shown to be a novel hyperbranched polymer having potential applications as a drug delivery vehicle. Structure and dynamics of the amine terminated PETIM dendrimer and their changes with respect to the dendrimer generation are poorly understood. Since most drugs are hydrophobic in nature, the extent of hydrophobicity of the dendrimer core is related to its drug encapsulation and retention efficacy. In this study, we carry out fully atomistic molecular dynamics (MD) simulations to characterize the structure of PETIM (G2-G6) dendrimers in salt solution as a function of dendrimer generation at different protonation levels. Structural properties such as radius of gyration (R-g), radial density distribution, aspect ratio, and asphericity are calculated. In order to assess the hydrophilicity of the dendrimer, we compute the number of bound water molecules in the interior of dendrirner as well as the number of dendrimer-water hydrogen bonds. We conclude that PETIM dendrimers have relatively greater hydrophobicity and flexibility when compared with their extensively investigated PAMAM counterparts. Hence PETIM dendrimers are expected to have stronger interactions with lipid membranes as well as improved drug encapsulation and retention properties when compared with PAMAM dendrimers. We compute the root-mean-square fluctuation of dendrimers as well as their entropy to quantify the flexibility of the dendrimer. Finally we note that structural and solvation properties computed using force field parameters derived based on the CHARMM general purpose force field were in good quantitative agreement with those obtained using the generalized Amber force field (GAFF).

Photometric metallicity map of the Large Magellanic Cloud

We have estimated a metallicity map of the Large Magellanic Cloud (LMC) using the Magellanic Cloud Photometric Survey (MCPS) and Optical Gravitational Lensing Experiment (OGLE III) photometric data. This is a first of its kind map of metallicity up to a radius of 4 degrees-5 degrees, derived using photometric data and calibrated using spectroscopic data of Red Giant Branch (RGB) stars. We identify the RGB in the V, (V - I) colour-magnitude diagrams of small subregions of varying sizes in both data sets. We use the slope of the RGB as an indicator of the average metallicity of a subregion, and calibrate the RGB slope to metallicity using spectroscopic data for field and cluster red giants in selected subregions. The average metallicity of the LMC is found to be Fe/H] = -0.37 dex (sigmaFe/H] = 0.12) from MCPS data, and Fe/H] = -0.39 dex (sigmaFe/H] = 0.10) from OGLE III data. The bar is found to be the most metal-rich region of the LMC. Both the data sets suggest a shallow radial metallicity gradient up to a radius of 4 kpc (-0.049 +/- 0.002 dex kpc(-1) to -0.066 +/- 0.006 dex kpc(-1)). Subregions in which the mean metallicity differs from the surrounding areas do not appear to correlate with previously known features; spectroscopic studies are required in order to assess their physical significance.

Nanomechanical Mapping, Hierarchical Polymer Dynamics, and Miscibility in the Presence of Chain-End Grafted Nanoparticles

To improve the spatial distribution of nano particles in a polymeric host and to enhance the interfacial interaction with the host, the use of chain-end grafted nanoparticle has gained popularity in the field of polymeric nanocomposites. Besides changing the material properties of the host, these grafted nanoparticles strongly alter the dynamics of the polymer chain at both local and cooperative length scales (relaxations) by manipulating the enthalpic and entropic interactions. It is difficult to map the distribution of these chain-end grafted nanoparticles in the blend by conventional techniques, and herein, we attempted to characterize it by unique technique(s) like peak force quantitative nanomechanical mapping (PFQNM) through AFM (atomic force microscopy) imaging and dielectric relaxation spectroscopy (DRS). Such techniques, besides shedding light on the spatial distribution of the nanoparticles, also give critical information on the changing elasticity at smaller length scales and hierarchical polymer chain dynamics in the vicinity of the nanoparticles. The effect of one-dimensional rodlike multiwall carbon nanotubes (MWNTs), with the characteristic dimension of the order of the radius of gyration of the polymeric chain, on the phase miscibility and chain dynamics in a classical LCST mixture of polystyrene/ poly(vinyl methyl ether) (PS/PVME) was examined in detail using the above techniques. In order to tune the localization of the nanotubes, different molecular weights of PS (13, 31, and 46 kDa), synthesized using RAFT (reversible addition fragmentation chain transfer) polymerization, was grafted onto MWNTs in situ. The thermodynamic miscibility in the blends was assessed by low-amplitude isochronal temperature sweeps, the spatial distribution of MWNTs in the blends was evaluated by PFQNM, and the hierarchical polymer chain dynamics was studied by DRS. It was observed that the miscibility, concentration fluctuation, and cooperative relaxations of the PS/PVME blends are strongly governed by the spatial distribution of MWNTs in the blends. These findings should help guide theories and simulations of hierarchical chain dynamics in LCST mixtures containing rodlike nanoparticles.

Nanomechanical Mapping, Hierarchical Polymer Dynamics, and Miscibility in the Presence of Chain-End Grafted Nanoparticles

To improve the spatial distribution of nano particles in a polymeric host and to enhance the interfacial interaction with the host, the use of chain-end grafted nanoparticle has gained popularity in the field of polymeric nanocomposites. Besides changing the material properties of the host, these grafted nanoparticles strongly alter the dynamics of the polymer chain at both local and cooperative length scales (relaxations) by manipulating the enthalpic and entropic interactions. It is difficult to map the distribution of these chain-end grafted nanoparticles in the blend by conventional techniques, and herein, we attempted to characterize it by unique technique(s) like peak force quantitative nanomechanical mapping (PFQNM) through AFM (atomic force microscopy) imaging and dielectric relaxation spectroscopy (DRS). Such techniques, besides shedding light on the spatial distribution of the nanoparticles, also give critical information on the changing elasticity at smaller length scales and hierarchical polymer chain dynamics in the vicinity of the nanoparticles. The effect of one-dimensional rodlike multiwall carbon nanotubes (MWNTs), with the characteristic dimension of the order of the radius of gyration of the polymeric chain, on the phase miscibility and chain dynamics in a classical LCST mixture of polystyrene/ poly(vinyl methyl ether) (PS/PVME) was examined in detail using the above techniques. In order to tune the localization of the nanotubes, different molecular weights of PS (13, 31, and 46 kDa), synthesized using RAFT (reversible addition fragmentation chain transfer) polymerization, was grafted onto MWNTs in situ. The thermodynamic miscibility in the blends was assessed by low-amplitude isochronal temperature sweeps, the spatial distribution of MWNTs in the blends was evaluated by PFQNM, and the hierarchical polymer chain dynamics was studied by DRS. It was observed that the miscibility, concentration fluctuation, and cooperative relaxations of the PS/PVME blends are strongly governed by the spatial distribution of MWNTs in the blends. These findings should help guide theories and simulations of hierarchical chain dynamics in LCST mixtures containing rodlike nanoparticles.

Folding of Protein L with Implications for Collapse in the Denatured State Ensemble

A fundamental question in protein folding is whether the coil to globule collapse transition occurs during the initial stages of folding (burst phase) or simultaneously with the protein folding transition. Single molecule fluorescence resonance energy transfer (FRET) and small-angle X-ray scattering (SAXS) experiments disagree on whether Protein L collapse transition occurs during the burst phase of folding. We study Protein L folding using a coarse-grained model and molecular dynamics simulations. The collapse transition in Protein L is found to be concomitant with the folding transition. In the burst phase of folding, we find that FRET experiments overestimate radius of gyration, R-g, of the protein due to the application of Gaussian polymer chain end-to-end distribution to extract R-g from the FRET efficiency. FRET experiments estimate approximate to 6 angstrom decrease in R-g when the actual decrease is approximate to 3 angstrom on guanidinium chloride denaturant dilution from 7.5 to 1 M, thereby suggesting pronounced compaction in the protein dimensions in the burst phase. The approximate to 3 angstrom decrease is close to the statistical uncertainties of the R-g data measured from SAXS experiments, which suggest no compaction, leading to a disagreement with the FRET experiments. The transition-state ensemble (TSE) structures in Protein L folding are globular and extensive in agreement with the Psi-analysis experiments. The results support the hypothesis that the TSE of single domain proteins depends on protein topology and is not stabilized by local interactions alone.

Influence of Indenter Tip Roundness on Hardness Behavior in Nanoindentation

In this paper. the effect of indenter tip roundness on hardness behavior for two typical elastic perfectly plastic materials is studied by means of finite element simulation. A rigid conical indenter of semi apex angle 70.3 degrees fitted smoothly with a spherical tip is employed. It is shown that as the indentation depth increases hardness first rises from zero, reaches a maximum and then decreases slowly approaching asymptotically the limiting value equal to that due to a conical indenter of ideally sharp tip. The range within which hardness varies appreciably is comparable to the radius of the indenter tip. The difference between the maximum value and the limiting value depends on the yield stress over the Young's modulus ratio. The smaller this ratio the greater the difference is. Numerical simulation also provides an opportunity for checking the accuracy and limitations of the widely used Oliver-Pharr method.

Electrical and field emission investigation of individual carbon nanotubes from plasma enhanced chemical vapour deposition

Plasma enhanced chemical vapour deposition (PECVD) is a controlled technique for the production of vertically aligned multiwall carbon nanotubes for field emission applications. In this paper, we investigate the electrical properties of individual carbon nanotubes which is important for designing field emission devices. PECVD nanotubes exhibit a room temperature resistance of 1-10 kΩ/μm length (resistivity 10-6 to 10-5 Ω m) and have a maximum current carrying capability of 0.2-2 mA (current density 107-108 A/cm2). The field emission characteristics show that the field enhancement of the structures is strongly related to the geometry (height/radius) of the structures and maximum emission currents of ∼ 10 μA were obtained. The failure of nanotubes under field emission is also discussed. © 2002 Elsevier Science B.V. All rights reserved.

Energy Dissipation In Fracture Of Bulk Metallic Glasses Via Inherent Competition Between Local Softening And Quasi-Cleavage

Compression, tension and high-velocity plate impact experiments were performed on a typical tough Zr41.2Ti13.8Cu10Ni12.5Be22.5 (Vit 1) bulk metallic glass (BMG) over a wide range of strain rates from similar to 10(-4) to 10(6) s(-1). Surprisingly, fine dimples and periodic corrugations on a nanoscale were also observed on dynamic mode I fracture surfaces of this tough Vit 1. Taking a broad overview of the fracture patterning of specimens, we proposed a criterion to assess whether the fracture of BMGs is essentially brittle or plastic. If the curvature radius of the crack tip is greater than the critical wavelength of meniscus instability [F. Spaepen, Acta Metall. 23 615 (1975); A.S. Argon and M. Salama, Mater. Sci. Eng. 23 219 (1976)], microscale vein patterns and nanoscale dimples appear on crack surfaces. However, in the opposite case, the local quasi-cleavage/separation through local atomic clusters with local softening in the background ahead of the crack tip dominates, producing nanoscale periodic corrugations. At the atomic cluster level, energy dissipation in fracture of BMGs is, therefore, determined by two competing elementary processes, viz. conventional shear transformation zones (STZs) and envisioned tension transformation zones (TTZs) ahead of the crack tip. Finally, the mechanism for the formation of nanoscale periodic corrugation is quantitatively discussed by applying the present energy dissipation mechanism.

Tuning The Geometrical Parameters Of Biomimetic Fibrillar Structures To Enhance Adhesion

Fibrillar structures are common features on the feet of many animals, such as geckos, spiders and flies. Theoretical analyses often use periodical array to simulate the assembly, and each fibril is assumed to be of equal load sharing (ELS). On the other hand, studies on a single fibril show that the adhesive interface is flaw insensitive when the size of the fibril is not larger than a critical one. In this paper, the Dugdale Barenblatt model has been used to study the conditions of ELS and how to enhance adhesion by tuning the geometrical parameters in fibrillar structures. Different configurations in an array of fibres are considered, such as line array, square and hexagonal patterns. It is found that in order to satisfy flaw-insensitivity and ELS conditions, the number of fibrils and the pull-off force of the fibrillar interface depend significantly on the fibre separation, the interface interacting energy, the effective range of cohesive interaction and the radius of fibrils. Proper tuning of the geometrical parameters will enhance the pull-off force of the fibrillar structures. This study may suggest possible methods to design strong adhesion devices for engineering applications.

The motion of a small bubble in waves

The motion of a single spherical small bubble due to buoyancy in the ideal fluid with waves is investigated theoretically and experimentally in this article. Assuming that the bubble has no effect on the wave field, equations of a bubble motion are obtained and solved. It is found that the nonlinear effect increases with the increase of the bubble radius and the rising time. The rising time and the motion orbit are given by calculations and experiments. When the radius of a bubble is smaller than 0.5mm and the distance from the free surface is greater than the wave height, the results of the present theory are in close agreement with measurements.

Diffusion dominated process for the crystal growth of a binary alloy

The pure diffusion process has been often used to study the crystal growth of a binary alloy in the microgravity environment. In the present paper, a geometric parameter, the ratio of the maximum deviation distance of curved solidification and melting interfaces from the plane to the radius of the crystal rod, was adopted as a small parameter, and the analytical solution was obtained based on the perturbation theory. The radial segregation of a diffusion dominated process was obtained for cases of arbitrary Peclet number in a region of finite extension with both a curved solidification interface and a curved melting interface. Two types of boundary conditions at the melting interface were analyzed. Some special cases such as infinite extension in the longitudinal direction and special range of Peclet number were reduced from the general solution and discussed in detail.

Notch sensitivity of circular rings subjected to impact loading

'Notch-sensitive regions' have been observed during a series of experimental investigations into the dynamic plastic behaviour and failure of thin-walled metallic radially notched circular rings with are-shaped supports subjected to concentrated impact loads. The experimental results show that the exterior notches at some regions have no effect on the deformation of the rings, but do have effect at the remaining regions. The notch-sensitive region is theoretically determined by using the equivalent structures technique; fairly good agreement has been reached between the simple theory and the experimental results. Both dimensional and theoretical analyses prove that whether a plastic hinge formed or not at the notched section does not depend on the mean radius of the ring and the input kinetic energy. It depends on the weak coefficient of the notched section and the angle of the support. Generally speaking, there are mainly three failure modes for a notched circular ring with are-shaped support under impact loading: Mode I, large inelastic deformation when the notch is outside the sensitive region, in this case the ring deforms as a normal one; Mode II, large inelastic deformation only at some part of the ring and tearing occurred at the notched sections; Mode III, large inelastic deformation and total rupture occurred at the notched sections. It is believed that the present study could assist the understanding of the dynamic behaviour and failure of other kinds of nonstraight components with macroscopic imperfections under impulsive loading.

Spatial and Temporal Variation of LURR and Its Implication for the Tendency of Earthquake Occurrence in Southern California

Based on the theory of LURR and its recent development, spatial and temporal variation of Y/Y-c (value of LURR/critical value of LURR) in the Southern California region during the period from 1980 through March, 2001 was studied. According to the previous study on the fault system and stress field in Southern California, we zoned the Southern California region into 11 parts in each of which the stress field is almost uniform. With the time window of one year, time moving step of three months, space window of a circle region with a radius of 100 km and space moving step of 0.25 degree in latitude and longitude direction, the evolution of Y/Y-c were snapshot. The scanning results show that obvious Y/Y-c anomalies occurred before 5/6 of strong earthquakes considered with a magnitude of 6.5 or greater. The critical regions of Y/Y-c are near the epicenters of the strong earthquakes and the Y/Y-c anomalies occur months to years prior to the earthquakes. The tendency of earthquake occurrence in the California region is briefly discussed on the basis of the examination of Y/Y-c.

Mechanics of adhesive contact on a power-law graded elastic half-space

We consider adhesive contact between a rigid sphere of radius R and a graded elastic half-space with Young's modulus varying with depth according to a power law E = E-0(z/c(0))(k) (0 < k < 1) while Poisson's ratio v remaining a constant. Closed-form analytical solutions are established for the critical force, the critical radius of contact area and the critical interfacial stress at pull-off. We highlight that the pull-off force has a simple solution of P-cr= -(k+3)pi R Delta gamma/2 where Delta gamma is the work of adhesion and make further discussions with respect to three interesting limits: the classical JKR solution when k = 0, the Gibson solid when k --> 1 and v = 0.5, and the strength limit in which the interfacial stress reaches the theoretical strength of adhesion at pull-off. (C) 2009 Elsevier Ltd. All rights reserved.