Computer-aided Topological Analysis of the Faujasite Lattice II: Monte Carlo Solution for Zeolite-Y

Abstract

In this paper we extend to the case of Zeolite-Y the topological analysis of the Aluminum distributions of the Faujasite lattice proposed in a previous paper. Here the exact counting of all the inequivalent configurations is complicated by the huge number of possible structures, but the physically relevant distributions can be found by using a Monte Carlo method which turns out to be very efficient. We compare, whenever possible, the Monte Carlo results with the exact countings, and in all these cases we find a perfect agreement. Thus the approach seems to be applicable to the study of every class of Zeolites. In the first two sections the method is introduced, and in the third one the relevant results for the Zeolite-Y are presented and discussed.     

IFS-Simulation of Transport Phenomena on Complex Fractal Media

Abstract

We present in this work an off-lattice method of simulating transport phenomena on fractal structures based on the properties of Iterated Function Systems. The main advantages of this method, compared to classical lattice simulations are the facility of simulating transport processes on a great variety of fractal structures, the possibility of an accurate control of the lengthscale-approximation and the capability of simulating easily complex field-effects on the motion of diffusive particles. Some computer simulation data on fractal structures obtained with this method are presented.     

Comparison of computational modelling techniques for braided stent analysis

Abstract

Braided stents are associated with a number of complications in vivo. Accurate computational modelling of these devices is essential for the design and development of the next generation of these stents. In this study, two commonly utilised methods of computationally modelling filament interaction in braided stents are investigated: the join method and the weave method. Three different braided stent designs are experimentally tested and computationally modelled in both radial and v-block configurations. The results of the study indicate that while both methods are capable of capturing braided stent performance to some degree, the weave method is much more robust.     

Integrating life cycle assessment (LCA) and life cycle costing (LCC) in the early phases of aircraft structural design: an elevator case study

Purpose

The main objective of this paper is to develop a model that will combine economic and environmental assessment tools to support the composite material selection of aircraft structures in the early phases of design and application of the tool for an aircraft elevator.

Methods

An integrated life cycle cost (LCC) and life cycle assessment (LCA) methodology was used as part of the sustainable design approach for the laminate stacking sequence design. The model considered is the aircraft structure made of carbon fiber reinforce plastic prepreg and processed via hand layup-autoclave process which is the preferred method for the aircraft industry. The model was applied to a cargo aircraft elevator case study by comparing six different laminate configurations and two different carbon fiber prepreg materials across aircraft’s entire life cycle.

Results and discussion

The results show, in line with other studies using different methodologies (e.g., life cycle engineering, or LCE), that the combination of LCA with LCC is a worthwhile approach for comparing the different laminate configurations in terms of cost and environmental impact to support composite laminate stacking design by providing the best trade-off between cost and environment. Elevator LCC reduces 19% by changing the material type and applying different ply orientations. Elevator LCA score reduces 53% by selecting the optimum instead of best technical solution that minimizes the displacement. Improving the structural performance does not always lead to an increase in the cost.

     

Quantized Water Clusters Around Apolar Molecules

Abstract

In order to understand the mechanism of gas hydrate kinetics and to explore the existance of other new cavities in the hydrate structure, we have used Molecular Dynamics (MD) simulation to study a system comprising two Lennard-Jones particles and 214 water molecules. Equilibrium structure and properties of twelve cases have been investigated. Our findings were as follows: ? Apolar molecules promote spherical liquid water clusters in a hydrate-like labile cavity.

? The size of the cavity and the coordination number is dependent upon the size of the apolar molecule.

? The coordination number of water molecules is quantized in jumps of four.

? Similarities are observed between the labile cavities and cavities in solid hydrates and in other chemical structures such as Buckminsterfullerene.

? Such a simulation procedure suggests the possibility of other clusters which may exist in yet-to-be-found hydrates. A separate question involves whether such suggested cavities can be combined with other cavities into a space-filling crystal.

     

New phenylspirodrimane metabolites MBJ-0030, MBJ-0031, and MBJ-0032 isolated from the soil fungal strain Stachybotrys sp. f23793

ABSTRACT

Chemical screening of culture medium from the soil fungus Stachybotrys sp. resulted in the isolation of the three new phenylspirodrimanes MBJ-0030 (1), MBJ-0031 (2) and MBJ-0032 (3). Their structures were determined by detailed analysis of spectroscopic data. The absolute configurations of 1–3 were determined by modified Mosher’s and Marfey’s methods. In addition, cytotoxic and antimicrobial evaluations of the compounds were conducted.     

Interatomic Potentials in Conducting Polymer Systems

Abstract

Although the crystal structures of some ion-doped lattices of polyacetylene and polyparaphenylene have been investigated by diffraction methods there remain ambiguities both in the overall structures and in the precise locations of the dopant ions. We have used bonding and non-bonding interatomic potentials developed from empirical and quantum chemical data in a CASCADE atomistic lattice simulation method which permits full optimization of the lattic geometry. These calculations lead to stable structures which are consistent with diffraction data, and suggest the tendency of these lattices towards polymorphism.     

TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data

Background

Time series single-cell RNA sequencing (scRNA-seq) data are emerging. However, the analysis of time series scRNA-seq data could be compromised by 1) distortion created by assorted sources of data collection and generation across time samples and 2) inheritance of cell-to-cell variations by stochastic dynamic patterns of gene expression. This calls for the development of an algorithm able to visualize time series scRNA-seq data in order to reveal latent structures and uncover dynamic transition processes.

Results

In this study, we propose an algorithm, termed time series elastic embedding (TSEE), by incorporating experimental temporal information into the elastic embedding (EE) method, in order to visualize time series scRNA-seq data. TSEE extends the EE algorithm by penalizing the proximal placement of latent points that correspond to data points otherwise separated by experimental time intervals. TSEE is herein used to visualize time series scRNA-seq datasets of embryonic developmental processed in human and zebrafish. We demonstrate that TSEE outperforms existing methods (e.g. PCA, tSNE and EE) in preserving local and global structures as well as enhancing the temporal resolution of samples. Meanwhile, TSEE reveals the dynamic oscillation patterns of gene expression waves during zebrafish embryogenesis.

Conclusions

TSEE can efficiently visualize time series scRNA-seq data by diluting the distortions of assorted sources of data variation across time stages and achieve the temporal resolution enhancement by preserving temporal order and structure. TSEE uncovers the subtle dynamic structures of gene expression patterns, facilitating further downstream dynamic modeling and analysis of gene expression processes. The computational framework of TSEE is generalizable by allowing the incorporation of other sources of information.

     

Biological Properties of Antisense Oligonucleotides Conjugated to Different High-Molecular Mass Poly(Ethylen Glycols)

Abstract

The effect of the different structures of high-molecular weight poly(ethylen glycol) chains on the biological properties of the conjugated antisense oligonucleotide has been investigated and compared.     

Molecular Dynamics Simulations of NaCl-type Solid Solution Crystals: The First Application of Molecular Dynamics to Solid Solutions

Abstract

Solid solution crystals appear widely in the fields of earth sciences and inorganic material sciences. The physical properties of solid solutions may vary continuously with chemical composition. Sometimes, linear relationships of the properties with composition are assumed. However, this approximation is not always applicable (e.g., [1], [2], [3]). In order to elucidate the properties of solid solutions, studies on the relation between the macroscopic properties and the atomic configurations (microscopic property) in the crystal are desirable. One of the most effective approaches to the subject is molecular dynamics (MD). However, as far as the authors are aware there have been no molecular dynamics studies on solid solution crystals.     

Conformational Changes in DNA and Soft Modes

Abstract

In this paper we explore the applicability of the soft mode approach to study the conformational transitions of DNA. It is believed that the A-B conformation change is a first order transition. Soft mode theories only apply to the initial stages of a first order transition. However the mode softening in such a case can be the initiating factor which ultimately leads to the transition. The first order transition is, then, a breakdown of what otherwise would have been a true second order transition. The mode softening is causally connected to onset of the transition. We use the eigenvectors obtained from lattice dynamics calculations to identify the softmode. We use the eigenvector projections to form a force constimi matrix that is required to drive a mode soft. We explore the methods by which this force constant matrix can be formed. We suggest that the breaking of specific “water bridges” between phosphate groups in the two single strands can drive the conformation change.     

Joint position reproduction and joint position discrimination at the ankle are not related

Abstract

Purpose: Limited data in current literature can be found on the relation between the two commonly-used active proprioception assessment methods –active joint position reproduction (JPR) and active movement extent discrimination assessment (AMEDA). The current study compared the two active methods, JPR and AMEDA, to investigate their interrelationship over two studies that differed in task difficulty, using active ankle inversion movements made in weight-bearing to maximise ecological validity.

Methods: 50 participants volunteered in this research, 20 of whom on a harder protocol and the other 30 on an easier protocol, were tested by both methods, JPR and AMEDA. Proprioceptive acuity was represented by absolute error (AE) and variable error (VE) for JPR and by AE and the area under the curve (AUC) for AMEDA.

Results: Proprioceptive acuity scores are found to be significantly correlated within test methods but not between methods for either hard or easy tasks, where JPR AE and VE scores were not correlated with either AMEDA AE or AUC. Further, proprioceptive acuity scores were significantly higher on the easy task when tested with the AMEDA method, but not with JPR method.

Conclusion: Scores obtained from the two active movement proprioception tests, movement extent discrimination and joint position reproduction, were not significantly correlated. Taken together with previous findings, these results show that for proprioception, scores from the three classical psychophysical methods for measuring sensitivity (adjustment, limits and constant stimuli) are not correlated with each other. This suggests that each proprioception measurement system assesses a different aspect of proprioception.     

STERILIZATION OF SUSPENDED SEDIMENTS BY GAMMA RADIATION

SUMMARY

Gamma radiation as an alternative sterilization technique for silt and clay suspensions is evaluated. It is compared to autoclaving in regard to sterility and changes in physical and chemical properties of the suspensions. A minimum radiation dose rate of 5 kGy s^?1 led to sterilization and no changes in lattice structure or precipitation of the suspensoids were observed. The adsorbed ionic composition of the silt and clay particles was, however, altered and should be rectified before radiated suspensoids are used. Autoclaving resulted in sterility, but irreversible precipitation of the suspensoids made it less applicable where the colloidal properties of the clay and silt are to be maintained.     

Structure-Property Relationships in Liquid Crystals: Can Modelling do Better than Empiricism?

Abstract

This paper reviews the relationships observed experimentally between the physical properties of liquid crystals and the molecular structures of the constituent molecules, and reports molecular mechanics calculations designed to provide a predictive and interpretative basis for structure/property relationships in liquid crystals. The calculations are of the minimum energy configurations of dimers of interacting liquid crystal molecules, and the geometry of the dimers, relative orientation of molecular dipoles and the extent of parallel correlation are related to liquid crystal properties. A large number of structural types are examined and the results discussed in terms of dipole correlation, apolar angular correlation, chiral twist sense and transition temperatures of liquid crystals.     

Crystal structure of a dimerization domain of human Caprin-2: similar overall dimeric fold but different molecular surface properties to that of human Caprin-1

Abstract

Human Caprin-1 and Caprin-2 are prototypic members of the caprin (cytoplasmic activation/proliferation-associated protein) protein family. Vertebrate caprin proteins contain two highly conserved homologous regions (HR1 and HR2) and C-terminal RGG motifs. Drosophila caprin (dCaprin) shares HR1 and RGG motifs but lacks HR2. Caprin-1 and Caprin-2 have important and non-redundant functions. The detailed molecular mechanisms of their actions remain largely unknown. Previously, we determined the crystal structure of a ～120-residue fragment of Caprin-1 within the HR1 region. The structure has a novel all α-helical fold that self-associates to form a homodimer. In this study, the crystal structure of a corresponding fragment from Caprin-2 is reported. The Caprin-2 fragment has similar protein fold and dimeric structure as that of the Caprin-1 fragment. Structural comparison reveals that the molecular interactions mediating homodimerization of Caprin-1 and Caprin-2 are largely conserved in the two systems. Structural-modelling study of the corresponding dCaprin fragment indicates that dCaprin may also adopt a similar dimeric structure. The presence of a dimerization domain within HR1 may represent an evolutionarily conserved feature of the caprin protein family. Interestingly, while Caprin-1 and Caprin-2 adopt similar overall dimeric structures, the two structures have quite different molecular surface properties. In the Caprin-1 dimeric structure, some of the surface areas are known or suspected to function as binding sites for Carpin-1-interacting proteins. The different surface properties of the caprin dimeric structures may dictate their intermolecular interaction with specific protein partners.

Communicated by Ramaswamy H. Sarma.     

An exploratory technique for measuring fertility norms

Abstract

In an attempt to remedy inherent weaknesses in traditional methods of fertility norm measurement, the evaluative dimension of the semantic differential is used to measure such norms among college women at two Southern universities. The instrument was designed to gauge the covert evaluative response elicited in people who observe behaviors relevant to norms which they have internalized. Variations in evaluations of hypothetical couples representing the parities zero through seven are associated with the race, religious preference, religiosity, and future work orientations of respondents. The significance of differences in the relative configurations of norms is determined by a special model of analysis of variance, and subgroups are compared with respect to the intensity of the norms they hold.     

A Monte Carlo Study of Ring Polymers in Disordered Systems

Abstract

We study the properties of ring polymers in disordered systems using a Monte Carlo algorithm. The algorithm is used to generate a ring on a two dimensional lattice, and the disorder is represented by the random dilution of the lattice. We show how the ring undergoes a cross-over from obeying self avoiding statistics at low concentrations of disorder, to behaving like a branched polymer as the concentration of disorder is increased. We find a scaling behavior to characterize this cross-over phenomenon. We further show how this scaling behavior is also present in another class of problems, namely two dimensional vesicles subjected to a pressure differential.     

Solution Structure of a GAAG Tetraloop in Helix 6 of SRP RNA from Pyrococcus furiosus

The NMR structure of a 12-mer RNA derived from the helix 6 of SRP RNA from Pyrococcus furiosus, whose loop-closing base pair is U:G, was determined, and the structural and thermodynamic properties of the RNA were compared with those of a mutant RNA with the C:G closing base pair. Although the structures of the two RNAs are similar to each other and adopt the GNRR motif, the conformational stabilities are significantly different to each other. It was suggested that weaker stacking interaction of the GAAG loop with the U:G closing base pair in 12-mer RNA causes the lower conformational stability.     

Addressing water quality in water footprinting: current status,methods and limitations

Purpose

In contrast to water consumption, water pollution has gained less attention in water footprinting so far. Unlike water scarcity impact assessment, on which a consensus has recently been achieved, there is no agreement on how to address water quality deterioration in water footprinting. This paper provides an overview of existing water footprint methods to calculate impacts associated with water pollution and discusses their strengths and limitations using an illustrative example.

Methods

The methods are described and applied to a case study for the wastewater generated in textile processing. The results for two scenarios with different water quality parameters are evaluated against each other and the water scarcity footprint (WSF). Finally, methodological aspects, strengths and limitations of each method are analysed and discussed and recommendations for the methods application are provided.

Results and discussion

Two general impact assessment approaches exist to address water quality in water footprinting: the Water Degradation Footprint (WDF) calculates the impacts associated with the propagation of released pollutants in the environment and their uptake by the population and ecosystem, while the Water Availability Footprint (WAF) quantifies the impacts related to the water deprivation, when polluted water cannot be used. Overall, seven methods to consider water quality in water footprinting were identified, which rely upon one or a combination of WDF, WAF and WSF. Methodological scopes significantly vary regarding the inventory requirements and provided results (a single-score or several impact categories). The case study demonstrated that the methods provide conflicting results concerning which scenario is less harmful with regard to the water pollution.

Conclusions

This paper provides a review of the water pollution assessment methods in water footprinting and analyses their modelling choices and resulting effects on the WF. With regard to the identified inconsistencies, we reveal the urgent need for a guidance for the methods application to provide robust results and allow a consistent evaluation of the water quality in water footprinting.

     

A Molecular Dynamics Investigation of Chain Conformational Changes In Compressed Bilayers

Abstract

The conformations of the chains constituting the hydrophilic component of alkyl monolayers and bilayers are investigated by performing molecular dynamics atomistic simulations on these systems at different temperatures. Several monitoring techniques are used to reveal the chain conformations, including atom pair radial distribution functions, evolutions of the torsional angles over thousands of timesteps, frequency distributions of the torsionl angles and ‘snapshot’ plots of the atomic configurations. These methods consistently testify to the stability of the trans (fully extended) character of the strain-free alkyl chains up to room temperature. The chains retain much of this conformation even when the layers are compressed by the application of pressure, to which the chains respond by ‘folding’ at the ends attaching them to the substrate planes while maintaining directions which are mainly normal to these planes. A non-zero gap between the layers is also maintained. A pressure of about 50 kbar abruptly causes all motion in the chains to cease, resulting in a highly ordered lattice structure.