A growing string method for determining transition states: comparison to the nudged elastic band and string methods

Interpolation methods such as the nudged elastic band and string methods are widely used for calculating minimum energy pathways and transition states for chemical reactions. Both methods require an initial guess for the reaction pathway. A poorly chosen initial guess can cause slow convergence, convergence to an incorrect pathway, or even failed electronic structure force calculations along the guessed pathway. This paper presents a growing string method that can find minimum energy pathways and transition states without the requirement of an initial guess for the pathway. The growing string begins as two string fragments, one associated with the reactants and the other with the products. Each string fragment is grown separately until the fragments converge. Once the two fragments join, the full string moves toward the minimum energy pathway according to the algorithm for the string method. This paper compares the growing string method to the string method and to the nudged elastic band method using the alanine dipeptide rearrangement as an example. In this example, for which the linearly interpolated guess is far from the minimum energy pathway, the growing string method finds the saddle point with significantly fewer electronic structure force calculations than the string method or the nudged elastic band method.     

Molecular clips form isostructural dimeric aggregates from benzene to water

We report the synthesis and characterization of eight C-shaped methylene-bridged glycoluril dimers (1-8) bearing hydrogen-bonding amide groups on their aromatic rings. Compounds 1-6 undergo tight dimerization in CDCl3 solution (Ks > 9 x 10(5) M(-1)); binary mixtures of 1-7 form mixtures of homodimers and heterodimers in moderately selective dimerization processes (0.23 < or = Keq < or = 768; 0.253 < or = chiAB < 0.933). The high affinity formation of 1.1-6.6 is due to the commensurate nature of the geometrical constraints imposed by the pi-pi interactions and only two hydrogen bonds. The differential response of the strengths of the pi-pi interactions and H-bonds of 2.2 to changes in solvent polarity--from C6D6 to D2O--results in the formation of a solvent-independent isostructural aggregate that exhibits high affinity dimerization across the full range of solvents.     

Thickness of the hydration layer of a protein from molecular dynamics simulation

Water molecules around a protein exhibit slow dynamics with respect to that of pure bulk water. One important issue in protein hydration is the thickness of the hydration layer (i.e., the distance from the protein surface up to which the water dynamics is influenced by the protein). Estimation of thickness is crucial to understand better the properties of "biological water" and the role that it plays in guiding the protein's function. We have performed an atomistic molecular dynamics simulation of an aqueous solution of the protein villin headpiece subdomain or HP-36 to estimate the thickness of its hydration water. In particular, several dynamical properties of water around different segments (three alpha-helices) of the protein have been calculated by varying the thickness of the hydration layers. It is found that in general the influence of the helices on water properties extends beyond the first hydration layer. However, the heterogeneous nature of water among the first hydration layers of the three helices diminishes as the thickness is increased. It indicates that, for a small protein such as HP-36, the thickness of "biological water" is uniform for different segments of the protein.     

Self-assembled structures of hydroxyapatite in the biomimetic coating on a bioinert ceramic substrate

The tribological properties of alumina ceramic are excellent due in part to a high wettability because of the hydrophilic surface and fluid film lubrication that minimizes the adhesive wear. Such surfaces are further modified with bioactive glass/ceramic coating to promote direct bone apposition in orthopedic applications. The present communication reports the biomimetic coating of calcium hydroxyapatite (HAp) on dense (2-3% porosity) alumina (alpha-Al(2)O(3)) substrate (1cmx1cmx0.5cm), at 37 degrees C. After a total period of 6 days immersion in simulated body fluid (SBF), at 37 degrees C, linear self-assembled porous (pore size: approximately 0.2mum) structures (length: approximately 375.39mum and width: 5-6mum) of HAp were obtained. The phenomenon has been demonstrated by self-assembly and diffusion-limited aggregation (DLA) principles. Structural and compositional characterization of the coating was carried out using SEM with EDX facility, XRD and FT-IR data.     

Micellar shape transition under dilute salt-free conditions: promotion and self-fluorescence monitoring of stimuli-responsive viscoelasticity by 1- and 2-naphthols

Effect of 1 and 2-naphthols on the shape transition of cetyl trimethylammonium bromide (CTAB) and cetylpyridinium bromide (CPB) micelles are studied. Stimuli-responsive viscoelastic gels of long wormlike micelles are formed at low surfactant concentrations in the presence of neutral naphthols, where H-bonding plays a key role in micellar shape transition in the absence of any charge screening. Micelle-embedded naphthols also act as novel self-fluorescence probes for monitoring viscoelasticity of the system as a function of applied shear. 1H NMR study shows that the solubilization sites of naphthols in the micelle are located near the surface. While UV absorption and Fourier transform infrared studies confirm the presence of intermolecular H-bonds in micelle embedded naphthols, transmission electron micrographs of vacuum-dried samples at room temperature demonstrate the transition in shape from sphere to rodlike micelles.     

JR 400–NaAOT interaction: a detailed thermodynamic study of polymer–surfactant interaction bearing opposite charges

The present study entails interaction between the cationic polymer N,N-dimethylhydroxyethyl cellulose (JR 400) and the double-tailed anionic surfactant Na-bis-2-ethyhexylsulphosuccinate (NaAOT). This oppositely charged polymer and surfactant are expected to cause coacervation and precipitation; hence, we have observed formation of thick solution similar to diluted gel at [JR 400]?~?0.01 and 0.10 %?w/v in aqueous solution. Viscometry, conductometry, tensiometry, and microcalorimetry techniques are used to monitor the interaction process. The results are explained in the light of both intrachain and interchain linking by way of NaAOT reverse micelle formation. Adsorption of NaAOT monomers onto the charged side chains of the polymer shields interchain electrostatic repulsion, leading to the formation of hydrophobic microdomains and microscopic heterogeneity in the solution. The morphologies of the domains depend on the level of addition of NaAOT in the system. The different stages of physiochemical changes that arise in solution have been identified by the use of different techniques, and correlations of the results have been attempted in terms of pragmatic models.     

ICP-MS multielement determination in fly ash after microwave-assisted digestion of samples

A microwave assisted digestion procedure has been developed for dissolution of fly ash samples prior to the inductively coupled plasma-mass spectrometric determination of their elemental composition. The developed methodology was validated by carrying out the analysis of two high-silicate containing reference materials (CRM 134R sewage amended soil and NIES JR 1 rock) and by means of the comparison between results found by microwave-assisted digestion and ICP-MS of fly ash samples with those found by neutron activation analysis (NAA) for Sb, Cs, Cr, Co, Fe, U and Zn determination. The method developed can be recommended for routine multielement analysis of fly ash.     

A DNS Study of Closure Relations for Convection Flux Term in Transport Equation for Mean Reaction Rate in Turbulent Flow

The present work aims at modeling the entire convection flux \(\overline {\rho \mathbf {u}W}\) in the transport equation for a mean reaction rate \(\overline {\rho W}\) in a turbulent flow, which (equation) was recently put forward by the present authors. In order to model the flux, several simple closure relations are developed by introducing flow velocity conditioned to reaction zone and interpolating this velocity between two limit expressions suggested for the leading and trailing edges of the mean flame brush. Subsequently, the proposed simple closure relations for \(\overline {\rho \mathbf {u}W}\) are assessed by processing two sets of data obtained in earlier 3D Direct Numerical Simulation (DNS) studies of adiabatic, statistically planar, turbulent, premixed, single-step-chemistry flames characterized by unity Lewis number. One dataset consists of three cases characterized by different density ratios and is associated with the flamelet regime of premixed turbulent combustion. Another dataset consists of four cases characterized by different low Damköhler and large Karlovitz numbers. Accordingly, this dataset is associated with the thin reaction zone regime of premixed turbulent combustion. Under conditions of the former DNS, difference in the entire, \(\overline {\rho {u}W}\), and mean, \(\tilde {u}\overline {\rho W}\), convection fluxes is well pronounced, with the turbulent flux, \(\overline {\rho u^{\prime \prime }W^{\prime \prime }}\), showing countergradient behavior in a large part of the mean flame brush. Accordingly, the gradient diffusion closure of the turbulent flux is not valid under such conditions, but some proposed simple closure relations allow us to predict the entire flux \(\overline {\rho \mathbf {u}W}\) reasonably well. Under conditions of the latter DNS, the difference in the entire and mean convection fluxes is less pronounced, with the aforementioned simple closure relations still resulting in sufficiently good agreement with the DNS data.     

Aspirin-induced Bcl-2 translocation and its phosphorylation in the nucleus trigger apoptosis in breast cancer cells

Here, we report that B-cell lymphoma 2 (Bcl-2) is a novel target molecule of aspirin in breast cancer cells. Aspirin influenced the formation of a complex by Bcl-2 and FKBP38 and induced the nuclear translocation of Bcl-2 and its phosphorylation. These events inhibited cancer cell proliferation and subsequently enhanced MCF-7 breast cancer cell apoptosis. Bcl-2 knockdown using small interfering RNA (siRNA) delayed apoptotic cell death, which correlated with increased proliferation following aspirin exposure. In contrast, Bcl-2 overexpression enhanced the onset of aspirin-induced apoptosis, which was also associated with a significant increase in Bcl-2 phosphorylation in the nucleus. Therefore, this study may provide novel insight into the molecular mechanism of aspirin, particularly its anticancer effects in Bcl-2- and estrogen receptor-positive breast cancer cells.