Persistence length of a polyelectrolyte in salty water: a Monte-Carlo study

We address the long standing problem of the dependence of the electrostatic persistence length $l_e$ of a flexible polyelectrolyte (PE) on the screening length $r_s$ of the solution within the linear Debye-Huckel theory. The standard Odijk, Skolnick and Fixman (OSF) theory suggests $l_e \propto r_s^2$, while some variational theories and computer simulations suggest $l_e \propto r_s$. In this paper, we use Monte-Carlo simulations to study the conformation of a simple polyelectrolyte. Using four times longer PEs than in previous simulations and refined methods for the treatment of the simulation data, we show that the results are consistent with the OSF dependence $l_e \propto r_s^2$. The linear charge density of the PE which enters in the coefficient of this dependence is properly renormalized to take into account local fluctuations.Comment: 7 pages, 6 figures. Various corrections in text and reference

Low-temperature specific heat in hydrogenated and Mn-doped La(Fe, Si)(13)

It is now well established that the paramagnetic-to-ferromagnetic transition in the magnetocaloric La(FeSi)13 is a cooperative effect involving spin, charge, and lattice degrees of freedom. However, the influence of this correlated behavior on the ferromagnetic state is as yet little studied. Here we measure the specific heat at low temperatures in a systematic set of LaFexMnySiz samples, with and without hydrogen, to extract the Sommerfeld coefficient, the Debye temperature, and the spin-wave stiffness. Substantial and systematic changes in magnitude of the Sommerfeld coefficient are observed with Mn substitution and introduction of hydrogen, showing that over and above the changes to the density of states at the Fermi energy there are significant enhanced d-band electronic interactions at play. The Sommerfeld coefficient is found to be 90–210mJmol−1K−2, unusually high compared to that expected from band-structure calculations. The Debye temperature determined from the specific heat measurement is insensitive to Mn and Si doping but increases when hydrogen is introduced into the system. The Sommerfeld coefficient is reduced in magnetic field for all compositions that have a measurable spin-wave contribution. These results move our understanding of the cooperative effects forward in this important and interesting class of materials significantly and provide a basis for future theoretical development

Discrete molecular dynamics simulations of peptide aggregation

We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet structure. This structure has an inter-strand distance of 0.48 nm and an inter-sheet distance of 1.0 nm, which agree with experimental observations. In this model, the hydrogen bond interactions give rise to the inter-strand spacing in beta-sheets, while the Go interactions among side chains make beta-strands parallel to each other and allow beta-sheets to pack into layers. The aggregates also contain free edges which may allow for further aggregation of model peptides to form elongated fibrils.Comment: 15 pages, 8 figure

A Model Ground State of Polyampholytes

The ground state of randomly charged polyampholytes is conjectured to have a structure similar to a necklace, made of weakly charged parts of the chain, compacting into globules, connected by highly charged stretched `strings'. We suggest a specific structure, within the necklace model, where all the neutral parts of the chain compact into globules: The longest neutral segment compacts into a globule; in the remaining part of the chain, the longest neutral segment (the 2nd longest neutral segment) compacts into a globule, then the 3rd, and so on. We investigate the size distributions of the longest neutral segments in random charge sequences, using analytical and Monte Carlo methods. We show that the length of the n-th longest neutral segment in a sequence of N monomers is proportional to N/(n^2), while the mean number of neutral segments increases as sqrt(N). The polyampholyte in the ground state within our model is found to have an average linear size proportional to sqrt(N), and an average surface area proportional to N^(2/3).Comment: 8 two-column pages. 5 eps figures. RevTex. Submitted to Phys. Rev.

Model Revision from Temporal Logic Properties in Computational Systems Biology

International audienceSystems biologists build models of bio-molecular processes from knowledge acquired both at the gene and protein levels, and at the phenotype level through experiments done in wildlife and mutated organisms. In this chapter, we present qualitative and quantitative logic learning tools, and illustrate how they can be useful to the modeler. We focus on biochemical reaction models written in the Systems Biology Markup Language SBML, and interpreted in the Biochemical Abstract Machine BIOCHAM. We first present a model revision algorithm for inferring reaction rules from biological properties expressed in temporal logic. Then we discuss the representations of kinetic models with ordinary differential equations (ODEs) and with stochastic logic programs (SLPs), and describe a parameter search algorithm for finding parameter values satisfying quantitative temporal properties. These methods are illustrated by a simple model of the cell cycle control, and by an application to the modelling of the conditions of synchronization in period of the cell cycle by the circadian cycle

Molecular Dynamics Simulation Study of Interaction between Model Rough Hydrophobic Surfaces

We study some aspects of hydrophobic interaction between molecular rough and flexible model surfaces. The model we use in this work is based on a model we used previously (Eun, C.; Berkowitz, M. L. J. Phys. Chem. B 2009, 113, 13222-13228), when we studied the interaction between model patches of lipid membranes. Our original model consisted of two graphene plates with attached polar headgroups; the plates were immersed in a water bath. The interaction between such plates can be considered as an example of a hydrophilic interaction. In the present work we modify our previous model by removing the charge from the zwitterionic headgroups. As a result of this procedure, the plate character changes; it becomes hydrophobic. By separating the total interaction (or potential of mean force, PMF) between plates into the direct and the water-mediated interactions we observe that the latter changes from repulsive to attractive, clearly emphasizing the important role of water as a medium. We also investigate the effect of roughness and flexibility of the headgroups on the interaction between plates and observe that roughness enhances the character of the hydrophobic interaction. The presence of a dewetting transition in a confined space between charge-removed plates confirms that the interaction between plates is strongly hydrophobic. In addition, we notice that there is a shallow local minimum in the PMF in case of charge-removed plates. We find that this minimum is associated with the configurational changes that flexible headgroups undergo, as the two plates are brought together.Comment: 27 pages, 9 figure

Using a logical model to predict the growth of yeast

<p>Abstract</p> <p>Background</p> <p>A logical model of the known metabolic processes in <it>S. cerevisiae </it>was constructed from iFF708, an existing Flux Balance Analysis (FBA) model, and augmented with information from the KEGG online pathway database. The use of predicate logic as the knowledge representation for modelling enables an explicit representation of the structure of the metabolic network, and enables logical inference techniques to be used for model identification/improvement.</p> <p>Results</p> <p>Compared to the FBA model, the logical model has information on an additional 263 putative genes and 247 additional reactions. The correctness of this model was evaluated by comparison with iND750 (an updated FBA model closely related to iFF708) by evaluating the performance of both models on predicting empirical minimal medium growth data/essential gene listings.</p> <p>Conclusion</p> <p>ROC analysis and other statistical studies revealed that use of the simpler logical form and larger coverage results in no significant degradation of performance compared to iND750.</p

Development and implementation of clinical guidelines : an artificial intelligence perspective

Clinical practice guidelines in paper format are still the preferred form of delivery of medical knowledge and recommendations to healthcare professionals. Their current support and development process have well identified limitations to which the healthcare community has been continuously searching solutions. Artificial intelligence may create the conditions and provide the tools to address many, if not all, of these limitations.. This paper presents a comprehensive and up to date review of computer-interpretable guideline approaches, namely Arden Syntax, GLIF, PROforma, Asbru, GLARE and SAGE. It also provides an assessment of how well these approaches respond to the challenges posed by paper-based guidelines and addresses topics of Artificial intelligence that could provide a solution to the shortcomings of clinical guidelines. Among the topics addressed by this paper are expert systems, case-based reasoning, medical ontologies and reasoning under uncertainty, with a special focus on methodologies for assessing quality of information when managing incomplete information. Finally, an analysis is made of the fundamental requirements of a guideline model and the importance that standard terminologies and models for clinical data have in the semantic and syntactic interoperability between a guideline execution engine and the software tools used in clinical settings. It is also proposed a line of research that includes the development of an ontology for clinical practice guidelines and a decision model for a guideline-based expert system that manages non-compliance with clinical guidelines and uncertainty.This work is funded by national funds through the FCT – Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project PEst-OE/EEI/UI0752/2011"

Personality profiles of cultures: aggregate personality traits

Personality profiles of cultures can be operationalized as the mean trait levels of culture members. College students from 51 cultures rated an individual from their country whom they knew well (N = 12, 156). Aggregate scores on Revised NEO Personality Inventory scales generalized across age and gender groups, approximated the individual-level Five-Factor Model, and correlated with aggregate self-report personality scores and other culture-level variables. Results were not attributable to national differences in economic development or to acquiescence. Geographical differences in scale variances and mean levels were replicated, with Europeans and Americans generally scoring higher in Extraversion than Asians and Africans. Findings support the rough scalar equivalence of NEO-PI-R factors and facets across cultures, and suggest that aggregate personality profiles provide insight into cultural differences