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The aim of our research is to develop a theory, which can predict the behavior of confined fluids in nanoslit pores. The nanoslit pores studied in this work consist of two structureless and parallel walls in the xy plane located at z = 0 and z = H, in equilibrium with a bulk homogeneous fluid at the same temperature and at a given uniform bulk density. We have derived the following general equation for prediction of the normal pressure tensor P zz of confined inhomogeneous fluids in nanoslit pores:where $$ \vec{r}_{12} \equiv \vec{r}_{1} - \vec{r}_{2} $$ is the intermolecular position vector of molecule 2 with respect to molecule 1 and $$ r_{12z} = |\vec{r}_{12} |_{z} $$ is the projection of distance of molecule 1 from molecule 2 in the z-direction. This equation may be solved for any fluid possessing a defined intermolecular pair-potential energy function, $$ \varphi \left( {\vec{r}_{12} } \right) ,$$ confined in a nanoslit pore and with a given fluid molecules—wall interaction potential function ϕext. As an important example of its application we have solved this equation for the hard-sphere fluid confined between two parallel–structureless hard walls with different nanometer distances and at various uniform bulk densities. Our results indicate the oscillatory form of the normal pressure tensor versus distance from the wall at high densities. As the density of the nanoconfined fluid decreases, the height and depth of the normal pressure tensor oscillations are reduced. [ABSTRACT FROM AUTHOR]

Under extreme loading conditions most often the extent of material and structural fracture is pervasive in the sense that a multitude of cracks are nucleating, propagating in arbitrary directions, coalescing, and branching. Pervasive fracture is a highly nonlinear process involving complex material constitutive behavior, material softening, localization, surface generation, and ubiquitous contact. A pure Lagrangian computational method based on randomly close packed Voronoi tessellations is proposed as a rational and robust approach for simulating the pervasive fracture of materials and structures. Each Voronoi cell is formulated as a finite element using the Reproducing Kernel Method. Fracture surfaces are allowed to nucleate only at the intercell faces, and cohesive tractions are dynamically inserted. The randomly seeded Voronoi cells provide a regularized random network for representing fracture surfaces. Example problems are used to demonstrate the proposed numerical method. The primary numerical challenge for this class of problems is the demonstration of model objectivity and, in particular, the identification and demonstration of a measure of convergence for engineering quantities of interest. [ABSTRACT FROM AUTHOR]

We investigate the interactions of lattice phonons with Frenkel exciton, which has a small radius in a two- dimensional discrete molecular lattice, by the virtue of the quasi-discreteness approximation and the method of multiple- scale, and obtain that the self-trapping can also appear in the two-dimensional discrete molecular lattice with harmonic and nonlinear potential. The excitons' effect on the molecular lattice does not distort it but only causes it to localize which enables it to react again through phonon coupling to trap the energy and prevent its dispersion. [ABSTRACT FROM AUTHOR]

The article presents a study which prepared polyacrylamide (PAM) aqueous dispersions, with the use of poly(sodium acrylic acid) (PAANa) as stabilizer. The study performed acrylamide's dispersion polymerization in aqueous solution of ammonium sulfate (AS). Results suggest the stability of the PAM aqueous dispersions during long storage.

In a charged colloidal system, the influence on depletion interaction between two like-charged macro-ions is studied through Monte Carlo simulation in this paper. The numerical results show that this depletion force is affected by both the electrostatic interactions between charged spheres and charged plates and by the geometrical factor of the two charged plates, and they further indicate that the influence of geometrical confinement on the depletion interaction is larger than that of electrostatic potential. [ABSTRACT FROM AUTHOR]

The nature of the nucleosomal barrier that regulates access to the underlying DNA during many cellular processes is not fully understood. Here we present a detailed map of histone-DNA interactions along the DNA sequence to near base pair accuracy by mechanically unzipping single molecules of DNA, each containing a single nucleosome. This interaction map revealed a distinct ∼5-bp periodicity that was enveloped by three broad regions of strong interactions, with the strongest occurring at the dyad and the other two about ±40-bp from the dyad. Unzipping up to the dyad allowed recovery of a canonical nucleosome upon relaxation of the DNA, but unzipping beyond the dyad resulted in removal of the histone octamer from its initial DNA sequence. These findings have important implications for how RNA polymerase and other DNA-based enzymes may gain access to DNA associated with a nucleosome. [ABSTRACT FROM AUTHOR]

Stability of a vertically aligned microparticle pair in a stratified glow DC discharge is experimentally investigated. Using laser perturbations, it is shown that, for the same discharge parameters, a pair of microparticles can be suspended in two stable configurations: vertical and horizontal. The interparticle interaction and the electric field of the stratum in the region of particle levitation are quantitatively investigated for the first time. The decharging effect of the lower (downstream) particle by the ion flow wake is also observed for the first time in a glow discharge. The obtained experimental data made it possible to check the analytical criteria for the configurational stability of the system. [ABSTRACT FROM AUTHOR]

A procedure is presented for refinement of a homology model of E. coli tRNAVal, originally based on the X-ray structure of yeast tRNAPhe, using experimental residual dipolar coupling (RDC) and small angle X-ray scattering (SAXS) data. A spherical sampling algorithm is described for refinement against SAXS data that does not require a globbic approximation, which is particularly important for nucleic acids where such approximations are less appropriate. Substantially higher speed of the algorithm also makes its application favorable for proteins. In addition to the SAXS data, the structure refinement employed a sparse set of NMR data consisting of 24 imino N–HN RDCs measured with Pf1 phage alignment, and 20 imino N–HN RDCs obtained from magnetic field dependent alignment of tRNAVal. The refinement strategy aims to largely retain the local geometry of the 58% identical tRNAPhe by ensuring that the atomic coordinates for short, overlapping segments of the ribose-phosphate backbone and the conserved base pairs remain close to those of the starting model. Local coordinate restraints are enforced using the non-crystallographic symmetry (NCS) term in the XPLOR-NIH or CNS software package, while still permitting modest movements of adjacent segments. The RDCs mainly drive the relative orientation of the helical arms, whereas the SAXS restraints ensure an overall molecular shape compatible with experimental scattering data. The resulting structure exhibits good cross-validation statistics (jack-knifed Q free = 14% for the Pf1 RDCs, compared to 25% for the starting model) and exhibits a larger angle between the two helical arms than observed in the X-ray structure of tRNAPhe, in agreement with previous NMR-based tRNAVal models. [ABSTRACT FROM AUTHOR]

We utilize a multiphase model, CON-AIR (Condensed Phase to Air Transfer Model), to show that the photochemistry of nitrate (NO3- ) in and on ice and snow surfaces, specifically the quasi-liquid layer (QLL), can account for NOx volume fluxes, concentrations, and [NO]/[NO2] (γ=[NO]/[NO2]) measured just above the Arctic and coastal Antarctic snowpack. Maximum gas phase NOx volume fluxes, concentrations and γ simulated for spring and summer range from 5.0×104 to 6.4×105 molecules cm-3 s-1, 5.7×108 to 4.8×109 molecules cm-3, and ∼0.8 to 2.2, respectively, which are comparable to gas phase NOx volume fluxes, concentrations and γ measured in the field. The model incorporates the appropriate actinic solar spectrum, thereby properly weighting the different rates of photolysis of NO3- and NO2- . This is important since the immediate precursor for NO, for example, NO2- , absorbs at wavelengths longer than nitrate itself. Finally, one-dimensional model simulations indicate that both gas phase boundary layer NO and NO2 exhibit a negative concentration gradient as a function of height although [NO]/[NO2] are approximately constant. This gradient is primarily attributed to gas phase reactions of NOx with halogens oxides (i.e. as BrO and IO), HOx, and hydrocarbons, such as CH3O2. [ABSTRACT FROM AUTHOR]

The partition function and the one- and two-body distribution functions are evaluated for two hard spheres with different sizes constrained into a spherical pore. The equivalent problem for hard disks is addressed too. We establish a relation valid for any dimension between these partition functions, second virial coefficient for inhomogeneous systems in a spherical pore, and third virial coefficients for polydisperse hard spheres mixtures. Using the established relation we were able to evaluate the cluster integral b 2( V) related with the second virial coefficient for the Hard Disc system into a circular pore. Finally, we analyse the behaviour of the obtained expressions near the maximum density. [ABSTRACT FROM AUTHOR]

Residual dipolar couplings (RDCs) complement standard NOE distance and J-coupling torsion angle data to improve the local and global structure of biomolecules in solution. One powerful application of RDCs is for domain orientation studies, which are especially valuable for structural studies of nucleic acids, where the local structure of a double helix is readily modeled and the orientations of the helical domains can then be determined from RDC data. However, RDCs obtained from only one alignment media generally result in degenerate solutions for the orientation of multiple domains. In protein systems, different alignment media are typically used to eliminate this orientational degeneracy, where the combination of RDCs from two (or more) independent alignment tensors can be used to overcome this degeneracy. It is demonstrated here for native E. coli tRNAVal that many of the commonly used liquid crystalline alignment media result in very similar alignment tensors, which do not eliminate the 4-fold degeneracy for orienting the two helical domains in tRNA. The intrinsic magnetic susceptibility anisotropy (MSA) of the nucleobases in tRNAVal was also used to obtain RDCs for magnetic alignment at 800 and 900 MHz. While these RDCs yield a different alignment tensor, the specific orientation of this tensor combined with the high rhombicity for the tensors in the liquid crystalline media only eliminates two of the four degenerate orientations for tRNAVal. Simulations are used to show that, in optimal cases, the combination of RDCs obtained from liquid crystalline medium and MSA-induced alignment can be used to obtain a unique orientation for the two helical domains in tRNAVal. [ABSTRACT FROM AUTHOR]

Statistical characteristics of spontaneous activity (distribution of interspike intervals, hazard function, autocorrelation function, autocorrelation function for the process with mixed intervals, and interdependence between adjoining intervals) were analyzed for 123 neurons of the frog medullar dorsal nucleus (homolog of the mammalian cochlear nucleus). In the majority of cells, this activity was distinct from the Poisson process, and firing periodicity was noticed in some cases. In addition, deviations of the spontaneous activity from the renewal process were usually observed. Weak yet reliable positive interspike-interval correlation was typical of most neurons; however, a negative correlation between short adjoining intervals was recorded for some units. These data suggest the effects of memory in the activity of single neurons of the auditory system. [ABSTRACT FROM AUTHOR]

For base-paired nucleic acids, variations in 1 J NH and the imino 1H chemical shift are both dominated by hydrogen bond length. In the absence of molecular alignment, the 1 J NH coupling for the imino proton then can be approximated by 1 J NH = (1.21Hz/ppm)δH − 103.5 ± 0.6 Hz, where δH represents the chemical shift of the imino proton in ppm. This relation permits imino residual dipolar couplings (RDCs) resulting from magnetic susceptibility anisotropy (MSA) to be extracted from measurement of (1 J NH + RDC) splittings at a single magnetic field strength. Magnetic field-induced RDCs were measured for tRNAVal and the alignment tensor determined from magnetic-field alignment of tRNAVal agrees well with the tensor calculated by summation of the MSA tensors of the individual nucleobases. [ABSTRACT FROM AUTHOR]

Abstract  In this work, we study the temperature-induced development of “dynamically arrested” states in dense suspensions of “soft colloids” (multi-arm star polymers and/or block-copolymers micelles) by means of molecular dynamics (MD) simulations. Temperature increase in marginal solvents results in “soft sphere” swelling, dynamical arrest, and eventually crystallization. However, two distinct “dynamically arrested” states were found, one almost amorphous (“glassy”) and one with a considerable degree of crystallinity, yet lower than that of the fully equilibrated crystal. It is remarkable that even that latter state permitted self-diffusion in the timescale of the simulations, an effect that underlies the importance of the “ultra-soft” nature of inter-particle potential. The “number of connections” criterion for crystallinity proved to be very successful in identifying the ultimate thermodynamic trend from the very early stages of the α-relaxation. [ABSTRACT FROM AUTHOR]

A combination of single-molecule spectroscopy and analysis with simulations is used to provide detailed information about the structural and dynamic properties of a fluorescent polymer MEH-PPV (poly[2-methoxy-5-(2'-ethylhexyloxy)-1 ,4-phenylenevinylene]) immersed in a nematic and smectic solvent. In nematic solvents, single-polymer molecules are oriented strongly along the solvent director, much more so than the solvent molecules, confirming Onsager's old prediction. The diffusion anisotropy parallel and perpendicular to the solvent director, however, is less than two, which is similar to that of a spherical colloid in a nematic solvent. In smectic solvents, there is a second orientation of the dissolved polymer perpendicular to the solvent director, which we hypothesize is caused by the polymer occupying the interlayer volume. The research discussed here emphasizes the importance of organization in complex fluids and suggests that the interplay of order on different length scales could be exploited to fabricate novel nanostructured materials. [ABSTRACT FROM AUTHOR]

Using a variety of computational techniques, I investigate how the self-assembly of complex mixtures can be guided by surfaces or external stimuli to form spatially regular or temporally periodic patterns. Focusing on mixtures in confined geometries, I examine how thermodynamic and hydrodynamic effects can be exploited to create regular arrays of nanowires or monodisperse, particle-filled droplets. I also show that an applied light source and chemical reaction can he harnessed to create hierarchically ordered Patterns in ternary, phase-separating mixtures. Finally, I consider the combined effects of confining walls and a chemical reaction to demonstrate that a swollen polymer gel can be driven to form dynamically periodic structures. in addition to illustrating the effectiveness of external factors in directing the self-organization of multicomponent mixtures, the selected examples illustrate how coarse-grained models can be used to capture both the equilibrium phase behavior and the dynamics of these complex systems. [ABSTRACT FROM AUTHOR]

Density-functional theory (DFT) and its variations provide a fruitful approach to the computational modeling of the microscopic structures and phase behavior of soft-condensed matter. The methodology takes deep root in quantum mechanics but shares a mathematical similarity with a number of classical approaches in statistical mechanics. This review discusses different strategies commonly used to formulate the free-energy functional of complex fluids for either phenomena-oriented applications or as a generic description of the thermodynamic nonideality owing to various components of intermolecular forces. We emphasize the connections among different schemes of DFT approximations, their underlying assumptions, and inherent limitations. We also address extensions of equilibrium DFT to phenomenological theories for the dynamic properties of complex fluids and for the kinetics of phase transitions. In addition, we highlight the recent literature concerning applications of DFT to diverse static and time-dependent phenomena in complex fluids. [ABSTRACT FROM AUTHOR]

The importance of developing multi-disciplinary approaches to solving problems relating to anthropogenic pollution is now clearly appreciated by the scientific community, and this is especially evident in boreal ecosystems exposed to escalating threats of petroleum hydrocarbon (PHC) contamination through expanded natural resource extraction activities. This review aims to synthesize information regarding the fate and behaviour of PHCs in boreal forest soils in both ecological and sustainable management contexts. From this, we hope to evaluate potential management strategies, identify gaps in knowledge and guide future research. Our central premise is that mycorrhizal systems, the ubiquitous root symbiotic fungi and associated food-web communities, occupy the structural and functional interface between decomposition and primary production in northern forest ecosystems (i.e. underpin survival and productivity of the ecosystem as a whole), and, as such, are an appropriate focal point for such a synthesis. We provide pertinent basic information about mycorrhizas, followed by insights into the ecology of ecto- and ericoid mycorrhizal systems. Next, we review the fate and behaviour of PHCs in forest soils, with an emphasis on interactions with mycorrhizal fungi and associated bacteria. Finally, we summarize implications for ecosystem management. Although we have gained tremendous insights into understanding linkages between ecosystem functions and the various aspects of mycorrhizal diversity, very little is known regarding rhizosphere communities in PHC-contaminated soils. This makes it difficult to translate ecological knowledge into environmental management strategies. Further research is required to determine which fungal symbionts are likely to survive and compete in various ecosystems, whether certain fungal - plant associations gain in ecological importance following contamination events, and how PHC contamination may interfere with processes of nutrient acquisition and exchange and metabolic processes. Research is also needed to assess whether the metabolic capacity for intrinsic decomposition exists in these ecosystems, taking into account ecological variables such as presence of other organisms (and their involvement in syntrophic biodegradation), bioavailability and toxicity of mixtures of PHCs, and physical changes to the soil environment. [ABSTRACT FROM AUTHOR]

A two-dimensional hexagonal colloidal crystal of charged particles obeying the general nonlinear Poisson-Boltzmann equation is studied by the numerical method. Force constants and pressure in a system, as well as elastic constants of a crystal, are calculated on the basis of the solutions of the equation. Calculation procedures are described briefly and numerical data are reported. The effect of nonlinearity of charge distribution on the manifestation of many-body interactions and on the validity of the approximation of interaction of the nearest neighbors is considered. [ABSTRACT FROM AUTHOR]

Thermo-sensitive colloidal crystals are prepared simply by mixing colloidal silica spheres and large thermo-sensitive gel spheres. The thermo-reversible change in the lattice spacing of colloidal crystals of monodisperse silica spheres (CS82, 103 nm in diameter) depends on the size of the admixed temperature-sensitive gel spheres. For spheres with sizes less and greater than that of the silica spheres, the lattice spacing upon temperature increase above the lower critical solution temperature of poly( N-isopropyl acrylamide) decreases (cf. Okubo et al. Langmuir 18:6783, 2002) and increases, respectively. A mechanism, which is able to explain these experimental findings, is proposed. Moreover, crystal growth rates and the rigidities of the thermo-sensitive colloidal crystals are studied. [ABSTRACT FROM AUTHOR]

An electrical double layer of a spherical macroion with single-, double-, and triple-charged counterions in aqueous solution of 1: 1 background electrolyte at different concentrations are studied by the molecular dynamics method for models with discrete and continuous surface charge distribution. Radial profiles of ion partial densities and the electric potential distribution in the double layer are calculated. The degree of counterion binding with a macroion is determined. The effect of water permittivity on the structure of electrical double layer is studied. [ABSTRACT FROM AUTHOR]

We describe the simplification of 13C–13C correlation spectra obtained from a microcrystalline protein sample expressed on a growth medium of 10% fully 13C labeled glucose diluted in 90% natural abundance glucose as compared to a fully labeled sample. Such a labeling scheme facilitates the backbone and side-chain resonance assignment of Phe, Tyr, His, Asp, Asn, Ile, Lys and Pro and yields an unambiguous stereospecific assignment of the valine Cγ1, Cγ2 13C resonances and of Leucine Cδ2. [ABSTRACT FROM AUTHOR]

A three-dimensional continuum model of the generation of aggregates of spherical particles is developed that allows us to reproduce natural conditions of structure formation in real disperse systems with an arbitrary viscosity of a dispersion medium. The exchange between translational and rotational degrees of freedom for aggregates, subaggregates, and single particles at an arbitrary interparticle interaction potential, as well as at the preset functions of the distribution over particle sizes and thicknesses of the adsorption layer, is taken into account in the model. The interaction potential of the particles includes electrostatic (among them, screened), elastic, and van der Waals interactions and allows for the effect of external electric, magnetic, and gravitational fields. Structural and statistical characteristics of aggregates formed at different stages of particle coagulation are studied, and the quasi-ordering of single subaggregates in the elastic adsorption layer of particles is revealed. The model can be applied to the study of optical absorption by large aggregates of nanoparticles with natural structure and the kinetics of sol aggregation as functions of the properties of the adsorption layer of particles and the action of external physical factors. [ABSTRACT FROM AUTHOR]

We demonstrate – using the data base of all deposited DNA and RNA structures aligned in Pf1-medium and RDC refined – that for nucleic acids in a Pf1-medium the electrostatic alignment tensor can be predicted reliably and accurately via a simple and fast calculation based on the gyration tensor spanned out by the phosphodiester atoms. The rhombicity is well predicted over its full range from 0 to 0.66, while the alignment tensor orientation is predicted correctly for rhombicities up to ca. 0.4, for larger rhombicities it appears to deviate somewhat more than expected based on structural noise and measurement error. This simple analytical approach is based on the Debye–Huckel approximation for the electrostatic interaction potential, valid at distances sufficiently far away from a poly-ionic charged surface, a condition naturally enforced when the charge of alignment medium and solute are of equal sign, as for nucleic acids in a Pf1-phage medium. For the usual salt strengths and nucleic acid sizes, the Debye–Huckel screening length is smaller than the nucleic acid size, but large enough for the collective of Debye–Huckel spheres to encompass the whole molecule. The molecular alignment is then purely electrostatic, but it’s functional form is under these conditions similar to that for steric alignment. The proposed analytical expression allows for very fast calculation of the alignment tensor and hence RDCs from the conformation of the nucleic acid molecule. This information provides opportunities for improved structure determination of nucleic acids, including better assessment of dynamics in (multi-domain) nucleic acids and the possibility to incorporate alignment tensor prediction from shape directly into the structure calculation process. The procedures are incorporated into MATLAB scripts, which are available on request. [ABSTRACT FROM AUTHOR]

The estimation of conditional probability was used to demonstrate the effect of the postspike changes in neuron excitability on its response to the second burst in a pair with an interval between bursts ranging from 50 to 200 ms. The responses of the neurons of the inferior colliculus to pairs of low-intensity tone bursts were recorded extracellularly in anesthetized albino mice. The probability of the response to the second burst in a pair was estimated under two conditions: the presence and the absence of a spike in the response to the first burst. If the interval between burst was 50 ms, the probability of response was decreased in most neurons where there was a spike in the response to the first burst. The opposite trend was observed in a small proportion of neurons. If the interval was increased, it weakened the dependence of the response to the second burst on the character of the response to the first one. The suppression of inhibitory inputs by bicuculline emphasized the postspike refractoriness rather than canceled it. The possible mechanisms of the interdependence between the responses to two consecutive signals are discussed. [ABSTRACT FROM AUTHOR]

Understanding the microscopic structure and macroscopic properties of condensed matter from a molecular perspective is important for both traditional and modern chemical engineering. A cornerstone of such understanding is provided by statistical mechanics, which bridges the gap between molecular events and the structural and physiochemical properties of macro- and mesoscopic systems. With ever-increasing computer power, molecular simulations and ab initio quantum mechanics are promising to provide a nearly exact route to accomplishing the full potential of statistical mechanics. However, in light of their versatility for solving problems involving multiple length and timescales that are yet unreachable by direct simulations, phenomenological and semiempirical methods remain relevant for chemical engineering applications in the foreseeable future. Classical density functional theory offers a compromise: on the one hand, it is able to retain the theoretical rigor of statistical mechanics and, on the other hand, similar to a phenomenological method, it demands only modest computational cost for modeling the properties of uniform and inhomogeneous systems. Recent advances are summarized of classical density functional theory with emphasis on applications to quantitative modeling of the phase and interfacial behavior of condensed fluids and soft materials, including colloids, polymer solutions, nanocomposites, liquid crystals, and biological systems. Attention is also given to some potential applications of density functional theory to material fabrications and biomolecular engineering. [ABSTRACT FROM AUTHOR]

Recently we reported that the alignment tensor of a biological macromolecule, which was dissolved in a dilute suspension of highly negatively charged filamentous phage at close to neutral pH, can be predicted from the molecule’s 3D charge distribution and shape (Zweckstetter et al. 2004). Here it is demonstrated that this approach is also applicable to alignment of proteins in liquid crystalline phases formed by filamentous phage at low pH. Residual dipolar couplings (RDCs) predicted by our simple electrostatic model for the B1 domain of protein G in fd phage at pH 3 fit very well with the experimental values. The sign of charge–shape predicted one-bond 1H–15N dipolar couplings for the B1 domain of protein G (GB1) was inverted at pH 3 compared to neutral pH, in agreement with experimental observations. Our predictions indicate that this is a feature specific for GB1. In addition, it is shown that RDCs induced in the protein ubiquitin by the presence of a positively charged surfactant system comprising cetylpyridinium bromide/hexanol/sodium bromide can be predicted accurately by a simple electrostatic alignment model. This shows that steric and electrostatic interactions dominate weak alignment of biomolecules for a wide range of pH values both in filamentous phage and in surfactant liquid crystalline phases. [ABSTRACT FROM AUTHOR]

The solution structure of murine γS-crystallin (γS) has been determined by multidimensional triple resonance NMR spectroscopy, using restraints derived from two sets of dipolar couplings, recorded in different alignment media, and supplemented by a small number of NOE distance restraints. γS consists of two topologically similar domains, arranged with an approximate twofold symmetry, and each domain shows close structural homology to closely related (∼50% sequence identity) domains found in other members of the γ-crystallin family. Each domain consists of two four-strand 'Greek key' β-sheets. Although the domains are tightly anchored to one another by the hydrophobic surfaces of the two inner Greek key motifs, the N-arm, the interdomain linker and several turn regions show unexpected flexibility and disorder in solution. This may contribute entropic stabilization to the protein in solution, but may also indicate nucleation sites for unfolding or other structural transitions. The method used for solving the γS structure relies on the recently introduced molecular fragment replacement method, which capitalizes on the large database of protein structures previously solved by X-ray crystallography and NMR. [ABSTRACT FROM AUTHOR]

New 3D HCN quantitativeJ(QJ) pulse schemes are presented for the precise and accurate measurement of one-bond15N1/9-13C1',15N1/9-13C6/8, and15N1/9-13C2/4 residual dipolar couplings (RDCs) in weakly aligned nucleic acids. The methods employ1H-13C multiple quantum (MQ) coherence or TROSY-type pulse sequences for optimal resolution and sensitivity. RDCs are obtained from the intensity ratio of H1'-C1'-N1/9 (MQ-HCN-QJ) or H6/8-C6/8-N1/9 (TROSY-HCN-QJ) correlations in two interleaved 3D NMR spectra, with dephasing intervals of zero (reference spectrum) and ~1/(2JNC) (attenuated spectrum). The different types of15N-13C couplings can be obtained by using either the 3D MQ-HCN-QJ or TROSY-HCN-QJ pulse scheme, with the appropriate setting of the duration of the constant-time15N evolution period and the offset of two frequency-selective13C pulses. The methods are demonstrated for a uniformly13C,15N-enriched 24-nucleotide stem-loop RNA sequence, helix-35?, aligned in the magnetic field using phage Pf1. For measurements of RDCs systematic errors are found to be negligible, and experiments performed on a 1.5 mM helix-35? sample result in an estimated precision of ca. 0.07 Hz for1 DNC, indicating the utility of the measured RDCs in structure validation and refinement. Indeed, for a complete set of15N1/9-13C1',15N1/9-13C6/8, and15N1/9-13C2/4 dipolar couplings obtained for the stem nucleotides, the measured RDCs are in excellent agreement with those predicted for an NMR structure of helix-35?, refined using independently measured observables, including13C-1H,13C-13C and1H-1H dipolar couplings. [ABSTRACT FROM AUTHOR]

The B- to Z-DNA transition free energy as a function of the size and charge of added ions is investigated by Monte Carlo simulation for simple grooved B- and Z-DNA models. It is shown that the electrostatic contribution to the free energy depends almost linearly on the logarithm of the sail concentration for all the systems. The effect of increasing the size of the ions is to make the curves steeper, although its influence on the transition midpoint is more complex. Divalent cations markedly reduce both the slope and the transition midpoint with respect to monovalent ions. These conclusions are in agreement with the experimental findings. The effect of increasing the charge of the anions--not yet experimentally studied--is less pronounced. [ABSTRACT FROM AUTHOR]

NMR spectra of ubiquitin in the presence of bicelles at a concentration of 25% w/v have been recorded under sample spinning conditions for different angles of rotation. For an axis of rotation equal to the magic angle, the 1H/15N HSQC recorded without any 1H decoupling in the indirect dimension corresponds to the classical spectrum obtained on a protein in an isotropic solution and allows the measurement of scalar J-couplings 1JNH. For an angle of rotation smaller than the magic angle, the bicelles orient with their normal perpendicular to the spinning axis, whereas for an angle of rotation greater than the magic angle the bicelles orient with their normal along the spinning axis. This bicelle alignment creates anisotropic conditions that give rise to the observation of residual dipolar couplings in ubiquitin. The magnitude of these dipolar couplings depends directly on the angle that the rotor makes with the main magnetic field. By changing this angle in a controlled manner, residual dipolar couplings can be either scaled up or down thus offering the possibility to study simultaneously a wide range of dipolar couplings in the same sample. [ABSTRACT FROM AUTHOR]

NVT Monte Carlo simulations were used to assess the effective interaction between pairs of colloid particles dissolved in non-adsorbing polymer solutions. The polymers were represented as freely-jointed-hard-sphere chains composed of 10, 20, or 30 segments. The size of the interacting colloid particles was similar to or smaller than the radius of gyration of the polymers. Results show a short-range colloid-colloid depletion attraction. At low polymer concentration, this attraction slowly decays to zero at increasing separations. At higher polymer concentration, the depletion attraction is coupled to a mid-range repulsion, especially for solutions of short, stiff polymers. From the simulated forces, osmotic second virial coefficients were computed for colloids as a function of polymer concentration. The calculated osmotic second virial coefficients exhibit a non-monotonic dependence on polymer concentration, in qualitative agreement with experimental results. The simulated colloid-colloid potentials of mean force were used, within a perturbation theory, to calculate fluid-fluid and fluid-solid coexistence curves. The colloids are treated as a pseudo one-component system, and the polymers in solution are considered only through the effective pair potential between the dissolved colloids. When long flexible polymers are dissolved in solution, the phase diagram for small colloid particles shows a fluid-fluid coexistence curve at low colloid packing fraction, and a fluid-solid coexistence curve at higher packing fraction. As the size of the colloid particles increases, the molecular weight of the polymer decreases, or the polymer concentration in solution increases, the fluid-fluid coexistence curve becomes metastable with respect to the fluid-solid coexistence curve. [ABSTRACT FROM AUTHOR]

For the purpose of studying some physical properties in addition to the mechanism of the melting phenomena, five bismuth alloys Bi 55.5 Pb 44.5 , Bi 50 Pb 25 Sn 25 , Bi 50 Pb 25 Cd 25 , Bi 50 Pb 25 Sn 18.75 Cd 6.25 and Bi 50 Pb 25 Sn 6.25 Cd 18.75 of melting points in the range from 338.5 to 396.5 K were prepared and studied by different techniques. The near-surface materials have been characterized by microhardness together with the wetting characteristics on CuZn 30 substrates as a function of time. The mechanism of melting from the point of view of the order of reaction ( n ) was explored by applying two different techniques, namely, differential thermal analysis and the electrical resistivity as a function of temperature. [ABSTRACT FROM AUTHOR]

Residual dipolar couplings (RDC) between nuclear spins in partially aligned samples offer unique insights into biomacromolecular structure and dynamics. To fully benefit from the RDC data, accurate knowledge of the magnitude (Da) and rhombicity (R) of the molecular alignment tensor, A, is important. An extended histogram method (EHM) is presented which extracts these parameters more effectively from dipolar coupling data. The method exploits the correlated nature of RDCs for structural elements of planar geometry, such as the one-bond 13C′i-13Ciα, 13C′i-15Ni+1, and 15Ni+1-1HNi+1 couplings in peptide bonds of proteins, or suitably chosen combinations of 1DC1′H1′, 1DC2′H2′, 1DC1′C2′, 2DC2′H1′, 2DC1′H2′, and 3DH1′H2′ couplings in nucleic acids, to generate an arbitrarily large number of synthetic RDCs. These synthetic couplings result in substantially improved histograms and resulting values of Da and R, compared with histograms generated solely from the original sets of correlated RDCs, particularly when the number of planar fragments for which couplings are available is small. An alternative method, complementary to the EHM, is also described, which uses a systematic grid search procedure, based on least-squares fitting of sets of correlated RDCs to structural elements of known geometry, and provides an unambiguous lower limit for the degree of molecular alignment. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations have been carried out for the simple few-body systems of two hard-disk particles confined within a 2-dimensional rectangular box. Wall pressures, the collision frequencies, density profiles, two-particle probability distributions, and position autocorrelation functions were computed to examine the thermodynamic, structural and time-dependent properties of such systems. Excellent agreement was found between simulation results and theoretical predictions recently proposed by Munakata and Hu. Detailed dynamic effects are also discussed to describe configurational particle trajectories including fast/slow relaxation processes observed in the position autocorrelation functions. [ABSTRACT FROM AUTHOR]

Heat transfer properties of premelted ice in silica powders were studied in a temperature range slightly below 0°C. The thermal conductivity of the ice was found to be much smaller than that of bulk ice. A drop in the thermal conductivity is observed at the melting, similar to bulk behavior, but the magnitude of the drop is much smaller than that found in the bulk phase. The heat transfer rate versus temperature gradient of ice in silica powders was found to deviate slightly from a perfectly linear behavior. The deviation could be due to a disruption of homogeneity of the powder media, due to a thermomolecular pressure. Such an effect needs to be further confirmed by future experiments. [ABSTRACT FROM AUTHOR]

Colloidal single crystals of cationic polymer spheres (198?250 nm in diameter) in deionized aqueous dispersions were formed for the first time. The spheres used were poly(styrene- co-methacryloyloxyphenyldimethylsulfonium) cations. These cations are unstable in deionized suspensions with mixed beds of cation-exchange and anion-exchange resins. This was clarified by reflection spectroscopy, pH, conductance and ?-potential measurements for 250 days after suspension preparation. Colloidal crystals formed over a period of 24 h for the deionized suspensions at sphere concentrations higher than 0.09 in volume fraction. The nearest-neighbor intersphere distances coincide satisfactorily with the calculated values using the diameter and the concentration of the spheres. Alloy crystals formed from binary mixtures of the cationic polymer spheres and the anionic silica spheres when the ratio of the volume fraction of cationic spheres against the sum of the both cationic and anionic spheres was smaller than 0.3. [ABSTRACT FROM AUTHOR]

We present Monte Carlo results for the pair distribution function of three simple fluid models, with pairwise interactions, which have low triple point temperatures and mimic some aspects of Na and Hg liquid metals. The results are then used to get the direct correlation function, by numerical solution of the Ornstein-Zernike equation, and to characterize the decay modes of any density distribution towards the bulk fluid. The Fisher-Widom line is obtained from the crossing of the two lowest inverse decay lengths, associated to monotonic and to oscillatory decay modes. For the pair potential models with a soft repulsive core, the Fisher-Widom line appears well below the critical temperature and has positive slope of the temperature with respect to the density, contrary to previous results for the Lennard-Jones and square-well potentials which had located that line quite close to T[SUBc] and with negative slope. [ABSTRACT FROM AUTHOR]

Reports on the basic properties of the small-angle scattering (SAS) correlation functions which are represented for a tetrahedron of edge length a. Determination of the distance distribution density function and the chord length distribution density; Analytic expressions for large scattering vectors.

Examines the structural characteristics of polycarbosilane dendrimers with different molecular architecture in solutions by small-angle neutron and X-ray scattering. Sizing up of the same linear dimensions for the dendrimers both in benzene and chloroform; Solvent molecules penetration from the comparison of the partial and effective scattering volume for the dendrimers in solution.

The use of mechanically strained acrylamide/acrylate copolymers is reported as a new alignment medium for biomacromolecules. Compared to uncharged, strained polyacrylamide gels, the negative charges of the acrylamide/acrylate copolymer strongly alter the alignment tensor and lead to pronounced electroosmotic swelling. The swelling itself can be used to achieve anisotropic, mechanical strain. The method is demonstrated for the alignment of TipAS, a 17 kDa antibiotic resistance protein, as well as for human ubiquitin, where alignment tensors with an AZZ,NH of up to 60 Hz are achieved at a gel concentration of 2% (w/v). The alignment can be modulated by the variation of pH, ionic strength, and gel concentration. The high mechanical stability of the swollen gels makes it possible to obtain alignment at polymer concentrations of less than 1% (w/v). [ABSTRACT FROM AUTHOR]