Internal structure and swelling behaviour of in silico microgel particles

Microgels are soft colloids that, in virtue of their polymeric nature, can react to external stimuli such as temperature or pH by changing their size. The resulting swelling/deswelling transition can be exploited in fundamental research as well as for many diverse practical applications, ranging from art restoration to medicine. Such an extraordinary versatility stems from the complex internal structure of the individual microgels, each of which is a crosslinked polymer network. Here we employ a recently-introduced computational method to generate realistic microgel configurations and look at their structural properties, both in real and Fourier space, for several temperatures across the volume phase transition as a function of the crosslinker concentration and of the confining radius employed during the `in-silico' synthesis. We find that the chain-length distribution of the resulting networks can be analytically predicted by a simple theoretical argument. In addition, we find that our results are well-fitted to the fuzzy-sphere model, which correctly reproduces the density profile of the microgels under study

Information visualization for DNA microarray data analysis: A critical review

Graphical representation may provide effective means of making sense of the complexity and sheer volume of data produced by DNA microarray experiments that monitor the expression patterns of thousands of genes simultaneously. The ability to use ldquoabstractrdquo graphical representation to draw attention to areas of interest, and more in-depth visualizations to answer focused questions, would enable biologists to move from a large amount of data to particular records they are interested in, and therefore, gain deeper insights in understanding the microarray experiment results. This paper starts by providing some background knowledge of microarray experiments, and then, explains how graphical representation can be applied in general to this problem domain, followed by exploring the role of visualization in gene expression data analysis. Having set the problem scene, the paper then examines various multivariate data visualization techniques that have been applied to microarray data analysis. These techniques are critically reviewed so that the strengths and weaknesses of each technique can be tabulated. Finally, several key problem areas as well as possible solutions to them are discussed as being a source for future work

Modelos Bayesianos gráficos jerárquicos en psicología

El mejoramiento de los métodos gráficos en la investigación en psicología puede promover su uso y una mejor compresión de su poder de expresión. La aplicación de modelos Bayesianos gráficos jerárquicos se ha vuelto más frecuente en la investigación en psicología. El objetivo de este trabajo es introducir sugerencias para el mejoramiento de los modelos Bayesianos gráficos jerárquicos en psicología. Este conjunto de sugerencias se apoya en la descripción y comparación entre los dos enfoques principales con el uso de notación y pictogramas de distribución. Se concluye que la combinación de los aspectos relevantes de ambos puede mejorar el uso de los modelos Bayesianos gráficos jerárquicos en psicología.The improvement of graphical methods in psychological research can promote their use and a better comprehension of their expressive power. The application of hierarchical Bayesian graphical models has recently become more frequent in psychological research. The aim of this contribution is to introduce suggestions for the improvement of hierarchical Bayesian graphical models in psychology. This novel set of suggestions stems from the description and comparison between two main approaches concerned with the use of plate notation and distribution pictograms. It is concluded that the combination of relevant aspects of both models might improve the use of powerful hierarchical Bayesian graphical models in psychology.Fil: Campitelli, Guillermo Jorge. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Edith Cowan University; AustraliaFil: Macbeth, Guillermo Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Entre Ríos. Facultad de Ciencias de la Educación; Argentin

Multiscale molecular simulations of the formation and structure of polyamide membranes created by interfacial polymerization

Large scale molecular simu lations to model the formation of polyamide membranes have been carried out using a procedure that mimics experimental interfacial polymerization of trimesoyl chloride (TMC) and metaphenylene diamine (MPD) monomers. A coarse - grained representation of the m onomers has been developed to facilitate these simulations, which captures essential features of the stereochemistry of the monomers and of amide bonding between them. Atomic models of the membranes are recreated from the final coarse - grained representatio ns. Consistent with earlier treatments, membranes are formed through the growth and aggregation of oligomer clusters. The membranes are inhomogeneous, displaying opposing gradients of trapped carboxyl and amine side groups, local density variations, and r egions where the density of amide bonding is reduced as a result of the aggregation process. We observe the interfacial polymerization reaction is self - limiting and the simulated membranes display a thickness of 5 – 10 nm. They also display a surface roughn ess of 1 – 4 nm. Comparisons are made with recently published experimental results on the structure and chemistry of these membranes and some interesting similarities and differences are found

Flat-Band Ferromagnetism in Organic Polymers Designed by a Computer Simulation

By coupling a first-principles, spin-density functional calculation with an exact diagonalization study of the Hubbard model, we have searched over various functional groups for the best case for the flat-band ferromagnetism proposed by R. Arita et al. [Phys. Rev. Lett. {\bf 88}, 127202 (2002)] in organic polymers of five-membered rings. The original proposal (poly-aminotriazole) has turned out to be the best case among the materials examined, where the reason why this is so is identified here. We have also found that the ferromagnetism, originally proposed for the half-filled flat band, is stable even when the band filling is varied away from the half-filling. All these make the ferromagnetism proposed here more experimentally inviting.Comment: 11 pages, 13figure

Assortative mixing in close-packed spatial networks

Background In recent years, there is aroused interest in expressing complex systems as networks of interacting nodes. Using descriptors from graph theory, it has been possible to classify many diverse systems derived from social and physical sciences alike. In particular, folded proteins as examples of self-assembled complex molecules have also been investigated intensely using these tools. However, we need to develop additional measures to classify different systems, in order to dissect the underlying hierarchy. Methodology and Principal Findings In this study, a general analytical relation for the dependence of nearest neighbor degree correlations on degree is derived. Dependence of local clustering on degree is shown to be the sole determining factor of assortative versus disassortative mixing in networks. The characteristics of networks constructed from spatial atomic/molecular systems exemplified by self-organized residue networks built from folded protein structures and block copolymers, atomic clusters and well-compressed polymeric melts are studied. Distributions of statistical properties of the networks are presented. For these densely-packed systems, assortative mixing in the network construction is found to apply, and conditions are derived for a simple linear dependence. Conclusions Our analyses (i) reveal patterns that are common to close-packed clusters of atoms/molecules, (ii) identify the type of surface effects prominent in different close-packed systems, and (iii) associate fingerprints that may be used to classify networks with varying types of correlations

Recent Conceptual Consequences of Loop Quantum Gravity. Part II: Holistic Aspects

Based on the foundational aspects which have been discussed as consequences of ongoing research on loop quantum gravity in the first part of this paper, the holistic aspects of the latter are discussed in this second part, aiming at a consistent and systematic approach to eventually model a hierarchically ordered architecture of the world which is encompassing all of what there actually is. The idea is to clarify the explicit relationship between physics and philosophy on the one hand, and philosophy and the sciences in general, on the other. It is shown that the ontological determination of worldliness is practically identical with its epistemological determination so that the (scientific) activity of modelling and representing the world can be visualized itself as a (worldly) mode of being.Comment: 20 page