Molecular Dynamics Simulation of Alkali Silicates Based on the Quantum Mechanical Potential Surfaces

Abstract

Two potential parameter sets for alkali silicates were derived on the basis of ab-initio MO calculations. One is a model containing completely ionic alkali (model I), and another is that derived from cluster calculations (model II). These sets were tested against the crystal, glass, and liquid of metasilicates. The model II can reproduce these structures well under constant pressure conditions, and is found to be better than model I as a whole.     

Predicting Liquid–Vapour Equilibria for Water Using an ab-initio Potential from Histogram Reweighting Monte Carlo Simulations

Abstract

The coexisting densities for an ab-initio model for water have been calculated using grand canonical Monte Carlo simulations with the histogram reweighting technique. Although good agreement with experimental data is found for the radial distribution function at room temperature, the predicted critical density and temperature are well below both the experimental value as well as predictions from semi-empirical potentials. Improvement in the repulsive part of the ab-initio potential is suggested as a way to obtain better agreement with experiment.     

Growth Analysis of Pulsed Laser Ablated Films

The spontaneous organization on a substrate of nanoparticles (NPs) nucleated in a laser-generated plasma results in self-assembling due to both direct specific interactions and to indirect ambient-mediated ones. A number of well-differentiated film morphologies are observed, from isolated NPs to percolated island structures. The distribution of the width of gaps between NPs, or islands formed upon NP coalescence in two representative percolated Au films, is lognormal, indicating that the growth process is random. A finer inspection of similar surface morphologies allows to correlate regularity in gap sizes and surface coverage to differences in film performance as substrates for surface-enhanced Raman spectroscopy.     

Physical and chemical perturbations induce the formation of protein aggregates with different structural features

The in vitro aggregation of the model GST–GFP fusion protein was induced by several effectors, including those mimicking variations occurring under cell stress conditions. In particular, we examined the effects of thermal treatments, redox state and pH variations, salt addition, and freezing and thawing cycles. The resulting aggregates displayed different morphologies as seen by electron microscopy, and different secondary and tertiary structures, as indicated by Fourier transform infrared spectroscopy and fluorescence. Therefore, proteins can be forced to undergo multiple aggregation pathways that lead to assemblies with different molecular structures and, possibly, specific physiological and pathological roles.In conclusion, great caution should be taken in inferring conclusions on protein aggregation and disaggregation in vivo from results obtained using aggregates produced under non-physiological perturbations.     

A Mechanistic Study of Au(III) Removal from Solution by Bacillus subtilis

Bacteria–Au interactions control the fate of Au in a variety of geologic systems. Although previous studies have determined that non-metabolizing Bacillus subtilis cells can remove Au(III) from solution via cell surface adsorption reactions, and that upon removal Au(III) is rapidly reduced to Au(I) and remains bound to the cell surface, the mechanism of Au(III) removal by B. subtilis is poorly understood. This study provides further constraints on the mechanisms responsible for Au(III) removal by B. subtilis by conducting batch Au(III) removal experiments as a function of pH and Au loading (Au:biomass ratio) using biomass with and without two different types of treatment: (1) a treatment to remove extracellular polymeric substances (EPS) from the biomass, and (2) a treatment to irreversibly block surface sulfhydryl sites from Au binding. The experimental results suggest that Au(III) removal can be attributed primarily to Au complexation with bacterial sulfhydryl sites, but that Au–amino binding is also important under some conditions. Our experiments also suggest that Au–sulfhydryl binding occurs predominantly on EPS molecules produced by B. subtilis, and that Au–amino binding is also important and is located within the bacterial cell envelope. These findings are the first to constrain the location of sulfhydryl-binding sites for B. subtilis biomass, and they are the first to demonstrate the important role played by bacterial EPS in the process of Au adsorption and reduction by bacteria.     

The Influence of Charge Calculation on Molecular Dynamics Simulation of Adenine in Water

Abstract

Molecular dynamics simulations of an aqueous solution of adenine have been performed using different methods of charge calculation to evaluate the influence of the values of the atomic charges on the dynamical results and to incorporate new information about the interaction between adenine and water. Four sets of partial charges where computed using ab-initio methods. In all cases the hydration properties of adenine were similar. These results support the view that the simulations by molecular dynamics, at least for the regime of infinite dilution, are not sensitive with respect to the different sets of partial charges used. A net hydrophobic behavior of the adenine molecule, on the water was observed.     

Fungal septins: one ring to rule it all?

Septins are a conserved family of GTP-binding proteins found in living organisms ranging from yeasts to mammals. They are able to polymerize and form hetero-oligomers that assemble into higher-order structures whose detailed molecular architecture has recently been described in different organisms. In Saccharomyces cerevisiae, septins exert numerous functions throughout the cell cycle, serving as scaffolds for many different proteins or as diffusion barriers at the bud neck. In other fungi, septins are required for the proper completion of diverse functions such as polarized growth or pathogenesis. Recent results from several fungi have revealed important differences in septin organization and regulation as compared with S. cerevisiae, especially during Candida albicans hyphal growth and in Ashbya gossypii. Here we focus on these recent findings, their relevance in the biology of these eukaryotes and in consequence the “renaissance” of the study of septin structures in cells showing a different kind of morphological behaviour.     

Additivity and non-additivity effects in the conformational changes of 1,2-ethanediol diformatein vacuo and in solution.Ab-initio and molecular mechanics descriptions

The performances of MM2 andab-initio SCF STO-3G calculations to describe conformational changes in (CH₂OCHO)₂ in vacuo and in solution are examined. We present and justify a simple procedure to add solvent effects to the MM2 conformational energies. The analysis is focused on the detection of non-additive effects in simultaneous conformational changes. We have found that the -CH₂-CH₂-group is generally effective in decoupling simultaneous conformational changes. The non-additive effects, actually present in specific classes of conformational changes, are reduced by a solvent contribution when full SCF calculations are employed, and emphasized when MM2 + solvent calculations are employed. A rationale of this finding is presented, and some suggestions are made for the correction of this artifact, due to the use of rigid charges.     

Identification of a complex genetic network underlying Saccharomyces cerevisiae colony morphology

When grown on solid substrates, different microorganisms often form colonies with very specific morphologies. Whereas the pioneers of microbiology often used colony morphology to discriminate between species and strains, the phenomenon has not received much attention recently. In this study, we use a genome‐wide assay in the model yeast Saccharomyces cerevisiae to identify all genes that affect colony morphology. We show that several major signalling cascades, including the MAPK, TORC, SNF1 and RIM101 pathways play a role, indicating that morphological changes are a reaction to changing environments. Other genes that affect colony morphology are involved in protein sorting and epigenetic regulation. Interestingly, the screen reveals only few genes that are likely to play a direct role in establishing colony morphology, with one notable example being FLO11, a gene encoding a cell‐surface adhesin that has already been implicated in colony morphology, biofilm formation, and invasive and pseudohyphal growth. Using a series of modified promoters for fine‐tuning FLO11 expression, we confirm the central role of Flo11 and show that differences in FLO11 expression result in distinct colony morphologies. Together, our results provide a first comprehensive look at the complex genetic network that underlies the diversity in the morphologies of yeast colonies.     

The triple helix ⇌ coil conversion of collagen-like polytripeptides in aqueous and nonaqueous solvents. Comparison of the thermodynamic parameters and the binding of water to (L-Pro-L-Pro-Gly)n and (L-Pro-L-Hyp-Gly)n

The collagen-like peptides (L -Pro-L -Pro-Gly)_n and (L -Pro-L -Hyp-Gly)_n with n = 5 and 10, were examined in terms of their triple helix ? coil transitions in aqueous and nonaqueous solvents. The peptides were soluble in 1,2-propanediol containing 3% acetic acid and they were found to form triple-helical structures in this solvent system. The water content of the solvent system and the amount of water bound to the peptides were assayed by equilibrating the solvent with molecular sieves and carrying out Karl Fischer titrations on the solvent phase. After the solvent was dehydrated, much less than one molecule of water per tripeptide unit was bound to the peptides. Since the peptides remained in a triple-helical conformation, the results indicated that water was not an essential component of the triple-helical structure. Comparison of peptides with the same chain length demonstrated that the presence of hydroxyproline increased the thermal stability of the triple helix even under anhydrous conditions. The results, therefore, did not support recent hypotheses that hydroxyproline stabilizes the triple helix of collagen and collagen-like peptides by a specific interaction with water molecules. Analysis of the thermal transition curves in several solvent systems showed that although the peptides containing hydroxyproline had t_m values which were 18.6° to 32.7°C higher, the effect of hydroxyproline on ΔG was only 0.1 to 0.3 kcal per tripeptide unit at 25°C. The results suggested, therefore, that the influence of hydroxyproline on helical stability may be explained by intrinsic effects such as dipole–dipole interactions or by changes in the solvation of the peptides by alcohol, acetic acid, and water. A direct calorimetric measurement of the transition enthalpy for (L -Pro-L -Pro-Gly)_n in 3% or 10% acetic acid gave a value of ?1.84 kcal per tripeptide unit for the coil-to-helix transition. From the value for enthalpy and from data on the effects of different chain lengths on the thermal transition, it was calculated that the apparent free energy for nucleation was +5 kcal/mol at 25°C (apparent nucleation parameter = 2 × 10^?4 M^?2). The value was dependent on solvent and on chemical modification of end groups.     

Helical Inversion of Gel Fibrils by Elongation of Perfluoroalkyl Chains as Studied by Vibrational Circular Dichroism

Vibrational circular dichroism (VCD) spectroscopy was applied to gelation by a chiral low‐molecular mass weight gelator, N,N’‐diperfluoroalkanoyl‐1,2‐trans‐diaminocyclohexane. Attention was focused on the winding effects of (–CF₂)_n chains on the gelating ability. For this purpose, a series of gelators were synthesized with perfluoroalkyl chains of different length (n = 6–8). When gelation was studied using acetonitrile as a solvent, the fibrils took different morphologies, depending on the chain length: twisted saddle‐like ribbon or helical ribbon from fibril (n = 6) and a helical ribbon from platelet (n = 8). The signs of VCD peaks assigned to the couplet of C=O stretching and to the C‐F stretching were also dependent on n, indicating that a gelator molecule changed conformation on elongating perfluoroalkyl chains. A model is proposed for the aggregation modes in fibrils. Chirality 28:361–364, 2016. © 2016 Wiley Periodicals, Inc.     

Crystal morphology study of N,N'-diacetylchitobiose by molecular dynamics simulation

Bisphenoidal shape of α-N,N′-diacetylchitobiose (α-(GlcNAc)₂) monohydrate crystals was obtained from aqueous solution. Crystal morphology was studied by computer simulation. Theoretical morphologies calculated by classic models (a BFDH model, a surface free-energy method, and an AE model) deviated significantly from that from the experimental crystal habit. Therefore, a solvent effect was considered by introducing an interface layer model based on molecular dynamics simulation in order to bridge this gap. The results of the simulation showed that the calculated habit is much closer to the experiment, meaning that the interface layer model describes the solvent effect very well. This model may also be applied for other oligosaccharide systems to study the relationship among crystal morphology, crystal structure, and solvation effects.     

Mutants of the bithorax complex and determinative states in the thorax of Drosophila melanogaster.

Homoeotic mutations of the bithorax complex cause segmental transformations. The genes in which these mutations occur are good candidates for genes that are involved in determination. The determination system in imaginal discs must have at least two functions. One is a cell heredity function that is responsible for maintaining the determined state during growth and development. A second is the expression of the determined state (e.g., different imaginal discs have different morphologies). The homoeotic mutations of the bithorax complex could be affecting either of these two functions. I have found that when posterior haltere disc cells, that are transformed by the mutation postbithorax so that they form wing cuticle in situ, regenerate anterior structures, these structures are anterior wing. This is the same result as that seen when wild-type posterior-wing disc cells regenerate anterior structures. On the other hand, when anterior haltere disc cells transformed by the mutation bithorax³, so that they produce wing cuticle in situ, regenerate, they produce posterior haltere structures. This is unlike wild-type anterior-wing disc cells, which regenerate posterior-wing structures. From these results, I conclude that bithorax³ affects the expression of the determined state and postbithorax affects the cell heredity of determination.     

A MEMS based amperometric detector for E. Coli bacteria using self-assembled monolayers

We developed a system for amperometric detection of Escherichia coli (E. coli) based on the integration of microelectromechanical systems (MEMS), self-assembled monolayers (SAMS), DNA hybridization, and enzyme amplification. Using MEMS technology, a detector array was fabricated which has multiple electrodes deposited on a Si wafer and was fully reusable. Using SAMs, a monolayer of the protein streptavidin was immobilized on the working electrode (Au) surface to capture rRNA from E. coli. Three different approaches can be used to immobilize streptavidin onto Au, direct adsorption of the protein on bare Au, binding the protein to a biotinylated thiol SAM on Au, and binding the protein to a biotinylated disulfide monolayer on Au. The biotinylated thiol approach yielded the best results. High specificity for E. coli was achieved using ssDNA–rRNA hybridization and high sensitivity was achieved using enzymatic amplification with peroxidase as the enzyme. The analysis protocol can be conducted with solution volumes on the order of a few microliters and completed in 40 min. The detection system was capable of detecting 1000 E. coli cells without polymerase chain reaction with high specificity for E. coli vs. the bacteria Bordetella bronchiseptica.     

The Roles of Mg over the Precipitation of Carbonate and Morphological Formation in the Presence of Arthrobacter sp. Strain MF-2

Microbial mineralization of carbonate is a research subject widely studied in the past decades. The magnesium ions (Mg²⁺), present in water systems, are a key determinant in biomineralization process of carbonate and they are widely found in calcium-based biominerals as an accessory component. However, the crystallization mechanism and morphological change of carbonate polymorphs in the presence of Mg²⁺ ions has not been clarified sufficiently. In this report, a series of culture experiments were performed for 50 days using the Arthrobacter sp. strain MF-2 in a M2 culture medium using Mg/Ca molar ratios (R) of 0, 1.5, 3, 6, 9, and 12 in solution. And the roles of Mg²⁺ ions on the crystal growth and morphological change of biogenic carbonate were investigated. Experimental results show: (1) MF-2 could induce aragonite, high-Mg calcite, and Ca-dolomite formation in M2 culture media with different R values. The increased stability of amorphous calcium carbonate suggests Mg²⁺ ions inhibit carbonate crystallization. (2) The mineral morphologies were varied (rod-shaped, dumbbell-shaped, cauliflower-like, spherical, etc.) in the medium with R = 1.5, but they became simple (spherical and lamellar) in high Mg²⁺ concentrations (Mg > 0.15 M, R > 3). (3) The increased ionic strength of Mg²⁺ ions in the environment has an influence on the polymorphs and morphologies of carbonate formed by controlling the metabolism of strain MF-2 and the activity of carbonic anhydrase.     

Modeling the interaction of a neutral polymer with small ions in solution. A theoretical study of ion binding to a neutral polymer

The interaction between NaCl and 1,2-dimethoxyethylene is used to model ion binding to a neutral polymer. The relative binding energies involving different ion-polymer structures were calculated using minimal basis STO-3G and split valence 3-21Gab-initio and CNDO/2 semi-empirical wavefunctions. The results obtained are consistent with an adsorption model in which the cation is primarily adsorbed on the oxygen sites. The counter ion is then bound by the charged polymer in a form consistent with an ion pair structure. These results are consistent with recent experimental studies on polyoxyethylene (POE). Additional calculations were performed to include specific interactions with the liquid environment. Electrostatic solvation effects, introduced through the self-consistent reaction field (SCRF) model, appear to be significant in the stabilization of a solvent-separated ion-pair structure. However, the global stabilization produced by both specific and electrostatic solvations predicts the preferential stabilization of an externally hydrated intimate ion pair.Dedicated to the memory of the late Professor Luis Sepulveda (1988).CMCA Contribution No 3.     

Cypsela micromorphology and anatomy in Cirsium sect. Epitrachys (Asteraceae,Carduoideae) and its taxonomic implications

Cirsium Miller, one of the largest genera of the Asteraceae (Carduoideae), contains more than 250 taxa. Turkey is one of its diversity centers and according to recent studies this genus is represented by 80 taxa. In the present study, cypsela morphologies, micromorphologies and anatomical structures of 17 C. sect. Epitrachys taxa distributed in Turkey are characterized in detail by using stereomicroscope, light microscope (LM) and scanning electron microscope (SEM). Cypselas are found to be obovate to narrowly oblong, or rarely oblanceolate. Based on SEM characters, six cypselas surface ornamentation types are identified, pericarp anatomical structures are described, as well as the structure of the testa. Crystal formations were observed in three taxa and secretory materials in the mesocarp were evaluated. Data obtained from this study are compared with previously published results and it is concluded that fruit micromorphological and anatomical characters are useful for the delimitation of taxa in Cirsium and may be useful for supraspecific classification.     

An intermittent mode of formation for the trace fossil Cruziana as a serial repetition of Rusophycus: the case of Cruziana tenella (Linnarsson )

Cruziana is one of the most recognizable trace fossils ascribed to arthropods. It ranges throughout the Phanerozoic and encompasses a diverse set of morphologies. The distinct features of Cruziana have incited fierce debate regarding its mode of formation. Here, we discuss critical aspects of trace fossil formation, namely epibenthic versus endobenthic origin and the ethology of the producer. Cruziana has largely been interpreted as a continuous ploughing trace fossil. It has been suggested, however, that at least some Cruziana could be structures resulting from the concatenation of Rusophycus‐type elements, although this claim remains unexplored. Cruziana tenella from the lower Cambrian of south‐central Sweden illustrates this intermittent mode of formation with a series of Rusophycus eutendorfensis leading into vertically undulating Cruziana that, at end stages of development, reflect a relatively equal depth distribution throughout the trace fossil and a great number of intergrading morphologies. In this study, a morphological evaluation of the intergrading morphologies of Cruziana tenella and Rusophycus eutendorfensis and a short morphometric analysis of the elements comprising Cruziana tenella suggests that at least in some cases Cruziana could be formed in intervals, as the serial overlap of distinct shallow Rusophycus could produce an apparently continuous cruzianaeform morphology. A comparison with possible evidence of intermittent formation on Cruziana semiplicata is made to illustrate the possibility of extending this mode of formation to larger Cruziana. An argument for the rise in the early Cambrian of a primitively intermittent mode of formation is made on the basis of energy efficiency.     

The contact separation force of the fruit burrs from five plant taxa dispersing by epizoochory

Abstract

Many plant diaspores dispersing by epizoochory bear special structures, such as burrs with hooks, which are responsible for the mechanical interlocking with animal fur or feathers. The number, dimensions and distribution of the interlocking structures on the diaspore can strongly vary depending on the plant species. In this study, to evaluate the interlocking ability of distantly related plants having different diaspore morphologies, the contact separation force (CSF) of single burrs was measured in Arctium lappa, Bidens tripartita, Desmodium sp., Uncinia uncinata and Xanthium strumarium. This force is required to separate the single burr from interlocking with the loop. Usually in the experiment, the burr was broken after separation. The CSFs differed significantly, ranging from 7.07 to 820.94?mN, among the five taxa studied. Six morphometrical variables were measured from each burr and the correlations between the CSFs and these morphometrical variables were analyzed. We have shown that (1) the burr length, (2) the diameter of the distal part and (3) the hook span had significant influences on the CSF. The comparison between the CSF and the fruit weight indicated that single burrs of all taxa studied could bear at least 100-fold weight of the diaspore.     

A solvent effect on the side-chain conformation of phenylalanine derivatives and phenylalanine residuces in dipeptides

Three phenylalanine derivatives, Ac-Phe-NHMe, H-Phe-NHMe, and Ac-Phe-OH, were selected as models of Phe residues situated at the internal, the N-terminal, and the C-terminal positions of peptide chains, respctively. The side-chain conformations of the three compounds were analyzed from the vicnal coupling constants ³J_αβR and ³J_αβS, of their ¹H- nmr spectra measured in various organic sovlent. The two β-protons were unambiguously assined by use of sterospecifically β-monodeuterated phenylalanines. The pro-S β-proton was always situated at lower field than the pro-R one when they were observed separately. The results of a solvent effect on the conformation of the tree compounds demonstrated that the rotamer populations are remarkable sensitive of the three compounds demonstrated that the rotamer populations are remarkably sensitive to solvent polarity and that the tendencies of the solvent effects are quite different from each other. Ac-Phe-OH Showed a trend similar to that of Ac-Phe-OEt reported by early workers. The rotamer populations of other derivatives (Ac-Phe-NMe₂, Ac-Phe-NH₂, Ac-Phe-OBu^t, and Ac-Phe-OBzl) and of Phe residues in some N-acetyl dipeptde esters (Ac-Phe-Gly-OMe, Ac-Phe-Val-OMe, and Ac-Gly-Phe-OMe) were also examined in several sovent, and it was found that substituents of the Phe carboxyl group—amides or esters—determine the tendency of the solvent effect. These results are interesting in the side-chain conformations of Phe residues in peptides and proteins in an environment of low polarity can be disscussed on this experimental basis. Factors responsible for the solvent effect are discussed from (1) a structural comparison of the compunds with various carboxylic substituents, (2) an expriment with cyclohexylalanine derivatives, and (3) the measurement in mixed solvents wiht similar polarity.