Strategies for Optimize Off-Lattice Aggregate Simulations

We review some computer algorithms for the simulation of off-lattice clusters grown from a seed, with emphasis on the diffusion-limited aggregation, ballistic aggregation and Eden models. Only those methods which can be immediately extended to distinct off-lattice aggregation processes are discussed. The computer efficiencies of the distinct algorithms are compared.Comment: 6 pages, 7 figures and 3 tables; published at Brazilian Journal of Physics 38, march, 2008 (http://www.sbfisica.org.br/bjp/files/v38_81.pdf

Cities: continuity, transformation, and emergence

Cities can be regarded as the quintessential example of complexity. Insofar as we can define a hidden hand determining their morphology, this is based on the glue that stitches together the actions of individuals and organizations who build the city from the ground-up, so-to-speak. When general systems theory entered the lexicon of science in the mid- 20th century, cities were regarded as being excellent examples of systems with interactions between basic elements that demonstrated the slogan of the field: the ‘whole is greater than the sum of the parts’. Since then, as complexity theory has evolved to embrace systems theory and as temporal dynamics has come onto the agenda, cities once again have been used to illustrate basic themes: global organization from local action, emergent morphology from simple spatial decision, temporal order at global levels from volatile, seemingly random change at the level of individual decision-making, evolution and progress through coevolution, competition, and endless variety. Here we will sketch these ideas with respect to cities illustrating particularly three key ideas which involve the tension between continuously changing systems, qualitative transformations, and radical change based on emergent properties of the whole. Our analysis has many implications for a new theory of urban planning which is built from the bottom up, rather than from the top down which is the traditional way in which such interventions are currently carried out in the name of making better cities. Contemporary problems such as ethnic segregation, urban sprawl, traffic congestion, urban decline, and regeneration are all informed by the perspective on complexity theory that we bring to bear here

Helix vs. Sheet Formation in a Small Peptide

Segments with the amino acid sequence EKAYLRT appear in natural occurring proteins both in $\alpha$-helices and $\beta$-sheets. For this reason, we have use this peptide to study how secondary structure formation in proteins depends on the local environment. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. Results in gas phase are compared with that in an implicit solvent. We find that both in gas phase and solvated EKAYLRT forms an $\alpha$-helix when not interacting with other molecules. However, in the vicinity of a $\beta$-strand, the peptide forms a $\beta$-strand. Because of this change in secondary structure our peptide may provide a simple model for the $\alpha \to \beta$ transition that is supposedly related to the outbreak of Prion diseases and similar illnesses.Comment: to appear in Physical Review

Extended hydrodynamics from Enskog's equation for a two-dimensional system general formalism

Balance equations are derived from Enskog's kinetic equation for a two-dimensional system of hard disks using Grad's moment expansion method. This set of equations constitute an extended hydrodynamics for moderately dense bi-dimensional fluids. The set of independent hydrodynamic fields in the present formulations are: density, velocity, temperature {\em and also}--following Grad's original idea--the symmetric and traceless pressure tensor $p_{ij}$ and the heat flux vector $\mathbf q^{k}$. An approximation scheme similar in spirit to one made by Grad in his original work is made. Once the hydrodynamics is derived it is used to discuss the nature of a simple one-dimensional heat conduction problem. It is shown that, not too far from equilibrium, the nonequilibrium pressure in this case only depends on the density, temperature and heat flux vector.Comment: :9 pages, 1 figure, This will appear in J. Stat. Phys. with minor corrections and corresponds to Ref[9] of cond-mat/050710

Effect of dicationic ionic liquids on lyotropic liquid crystals formed by a binary system composed of Triton-X 100 and water

In this work, binary mixtures of a non-ionic surfactant (Triton X-100) and water were studied with concentrations of 30%wt H2O, showing, lamellar mesophase at temperatures below 10oC. Different dicationic ionic liquids were used for doping these mesophases: 1,n-bis(3-methylimidazolium-1-yl)alkane, 1,n-bis(1-methylpyrrolidinium-1-yl)alkane and 1,n-bis(pyridinium-N-yl)alkane dibromide, where n = 6 and 8. Polarized Optical Microscopy and Small-Angle X-ray Scattering were used for identifying the mesophases and the influence of different dicationic ionic liquids on the lyotropic liquid crystals phase transitions. The addition of dicationic ionic liquids to the lyotropic liquid crystals samples led to changes in transition temperature and in mesophase structure itself (such as characteristic distances)

Detection and Molecular Characterization of Giardia and Cryptosporidium spp. Circulating in Wild Small Mammals from Portugal

Simple Summary Wild small mammals can be a veterinary and public health concern, because they can act as reservoir hosts for numerous pathogens and potentially transmit them to humans, domestic animals and other wildlife species. This study represents the first investigation of the diarrhea-causing parasites Cryptosporidium spp. and Giardia spp. in wild rodents and shrews from Portugal. Cryptosporidium spp. was rarely and Giardia was frequently detected in the feces of the analyzed species, with the southwestern water voles (Arvicola sapidus) and Lusitanian pine voles (Microtus lusitanicus) showing the highest infection rates of Giardia spp. Genetic characterization based on common genomic marker sequences revealed the rodent-adapted Giardia microti and potentially zoonotic Cryptosporidium muris as the only circulating species. These findings suggest the limited role of wild rodents and shrews as natural sources of human infections in Portugal regarding the investigated parasites. Moreover, the host ranges of Giardia and Cryptosporidium spp. were extended and the obtained genetic sequences of Giardia microti are useful for future comparative studies. From the One-Heath perspective, this study helps to understand the epidemiology of Giardia spp. and Cryptosporidium spp. in wildlife. Cryptosporidium spp. and Giardia spp. are important diarrhea-causing protozoan parasites worldwide that exhibit broad host ranges. Wild small mammals can harbor host-adapted and potentially zoonotic species of both parasites. The aim of this study was to investigate Cryptosporidium spp. and Giardia spp. in wild rodents and shrews in Portugal, focusing on the protist's occurrence and genetic diversity. Molecular screening by PCR at the small subunit (SSU) rRNA gene locus of 290 fecal samples from wood mice (Apodemus sylvaticus), southwestern water voles (Arvicola sapidus), Cabrera's voles (Microtus cabrerae), Lusitanian pine voles (Microtus lusitanicus), Algerian mice (Mus spretus) and greater white-toothed shrews (Crocidura russula) in Northeast Portugal revealed the low occurrence of Cryptosporidium spp. (1%) and high occurrence of Giardia spp. (32.8%). The analysis revealed that species was the only significant factor associated with the increasing probability of Giardia spp. infection, with the highest prevalence reported in southwestern water voles and Lusitanian pine voles. Cryptosporidium and Giardia species determination at the SSU rRNA gene locus revealed C. muris and G. microti as the only circulating species, respectively. Subtyping of the glutamate dehydrogenase (gdh) and beta-giardin (bg) genes provided evidence of the high genetic diversity within the G. microti clade. This study suggests that rodent-adapted G. microti occurs to a large extent in cricetid hosts and supports the limited role of wild rodents and shrews as natural sources of human infections in Northeast Portugal regarding the investigated parasites. Moreover, this is the first record of G. microti in southwestern water voles, Lusitanian pine voles, Algerian mice, wood mice and Cabrera's voles and C. muris in Cabrera's voles. Finally, this study improves the database of sequences relevant for the sequence typing of G. microti strains and provides new insights about the epidemiology of Giardia spp. and Cryptosporidium spp. in wild rodents and shrews, two parasite genera of high importance for public and animal health