Polyelectrolyte Adsorption on Charged Substrate

The behavior of a polyelectrolyte adsorbed on a charged substrate of high-dielectric constant is studied by both Monte-Carlo simulation and analytical methods. It is found that in a low enough ionic strength medium, the adsorption transition is first-order where the substrate surface charge still keeps repulsive. The monomer density at the adsorbed surface is identified as the order parameter. It follows a linear relation with substrate surface charge density because of the electrostatic boundary condition at the charged surface. During the transition, the adsorption layer thickness remains finite. A new scaling law for the layer thickness is derived and verified by simulation.Comment: Proceedings of the 3rd Symposium on Slow Dynamics in Complex Systems, 3-8 November 2003, Sendai, Japa

Theory of Non-equilibrium Asymptotic State Thermodynamics: Interacting Ehrenfest Urn Ring as an Example

A generalized class of non-equilibrium state, called non-equilibrium asymptotic state (NEAS), is proposed. The NEAS is constructed within the framework of the Fokker-Planck equations in thermodynamic limit. Besides the usual equilibrium state and non-equilibrium steady state (NESS), the class of NEAS could also cover non-equilibrium periodic state (NEPS) in which its dynamics shows periodicity, non-equilibrium quasi-periodic state (NEQPS), and non-equilibrium chaotic state (NECS) in which its dynamics becomes chaotic. Based on the theory of NEAS thermodynamics, the corresponding thermodynamics of different NEAS could also be determined. Finally the interacting Ehrenfest urn ring model is used as an example to illustrate how different kinds of NEAS (equilibrium state, uniform NESS, non-uniform NESS, NEPS) in three-urn case are identified in our framework. In particular, the thermodynamics of NEPS and its phase transitions to other types of NEAS are studied

Non-equilibrium Dynamics and Phase Transitions in Potts model and Interacting Ehrenfest urn model

We show that the recently proposed interacting Ehrenfest M-urn model at equilibrium can be exactly mapped to a mean-field M-state Potts model. By exploiting this correspondence, we show that the M-state Potts model with M >= 3, with transition rates motivated by the non-equilibrium urn model, can exhibit rich non-equilibrium spin dynamics such as non-equilibrium steady states and non-equilibrium periodic states. Monte Carlo simulations of the 3-state Potts model are performed to demonstrate explicitly the first-order transitions for the equilibrium and non-equilibrium steady states, as well as the far-from-equilibrium periodic states.Comment: 18 pages, 6 figure

Scaling Theory of Polyelectrolyte Adsorption on Repulsive Charged Surface

We studied polyelectrolyte adsorption on a repulsive charged surface by scaling analysis. At low ionic strength and low surface charge density in which a single polyelectrolyte is able to be adsorbed onto the surface, different regimes in the phase diagram are identified. The possibility of multi-layer structure formed by polyelectrolytes of like charge is also investigated.Comment: 4 pages, 2 figure

The κB transcriptional enhancer motif and signal sequences of V(D)J recombination are targets for the zinc finger protein HIVEP3/KRC: a site selection amplification binding study

BACKGROUND: The ZAS family is composed of proteins that regulate transcription via specific gene regulatory elements. The amino-DNA binding domain (ZAS-N) and the carboxyl-DNA binding domain (ZAS-C) of a representative family member, named κB DNA binding and recognition component (KRC), were expressed as fusion proteins and their target DNA sequences were elucidated by site selection amplification binding assays, followed by cloning and DNA sequencing. The fusion proteins-selected DNA sequences were analyzed by the MEME and MAST computer programs to obtain consensus motifs and DNA elements bound by the ZAS domains. RESULTS: Both fusion proteins selected sequences that were similar to the κB motif or the canonical elements of the V(D)J recombination signal sequences (RSS) from a pool of degenerate oligonucleotides. Specifically, the ZAS-N domain selected sequences similar to the canonical RSS nonamer, while ZAS-C domain selected sequences similar to the canonical RSS heptamer. In addition, both KRC fusion proteins selected oligonucleoties with sequences identical to heptamer and nonamer sequences within endogenous RSS. CONCLUSIONS: The RSS are cis-acting DNA motifs which are essential for V(D)J recombination of antigen receptor genes. Due to its specific binding affinity for RSS and κB-like transcription enhancer motifs, we hypothesize that KRC may be involved in the regulation of V(D)J recombination

Malaria parasite translocon structure and mechanism of effector export.

The putative Plasmodium translocon of exported proteins (PTEX) is essential for transport of malarial effector proteins across a parasite-encasing vacuolar membrane into host erythrocytes, but the mechanism of this process remains unknown. Here we show that PTEX is a bona fide translocon by determining structures of the PTEX core complex at near-atomic resolution using cryo-electron microscopy. We isolated the endogenous PTEX core complex containing EXP2, PTEX150 and HSP101 from Plasmodium falciparum in the 'engaged' and 'resetting' states of endogenous cargo translocation using epitope tags inserted using the CRISPR-Cas9 system. In the structures, EXP2 and PTEX150 interdigitate to form a static, funnel-shaped pseudo-seven-fold-symmetric protein-conducting channel spanning the vacuolar membrane. The spiral-shaped AAA+ HSP101 hexamer is tethered above this funnel, and undergoes pronounced compaction that allows three of six tyrosine-bearing pore loops lining the HSP101 channel to dissociate from the cargo, resetting the translocon for the next threading cycle. Our work reveals the mechanism of P. falciparum effector export, and will inform structure-based design of drugs targeting this unique translocon

Establishment of a doxycycline-regulated cell line with inducible, doubly-stable expression of the wild-type p53 gene from p53-deleted hepatocellular carcinoma cells

p53 is important in the development of hepatocellular carcinoma (HCC) and in therapeutic approaches, but the mechanism whereby it inhibits HCC growth is still unclear. The aim of the present study was to establish a HCC cell system in which p53 levels can be regulated. Full-length wild-type p53 cDNA obtained by PCR was cloned into a retroviral response vector controlled by the tetracycline responsive element (RevTRE-p53). The regulatory vectors RevTet-Off and RevTRE-p53 were transfected into a packaging cell line, PT67. Hep3B cells in which the p53 gene was deleted were infected with RevTet-Off viral particles from the PT67. Three G418-resistant cell clones with high luciferase expression and low background were infected with RevTRE-p53. By screening dozens of RevTRE-p53-infected clones with hygromycin we identified the one with the highest expression of p53 and the lowest background after doxycycline treatment. The results showed that p53 expression in this cell clone could be simply turned on or off by removing or adding doxycycline. Furthermore, it was found that the level of p53 protein was negatively and sensitively related to the doxycycline concentration. In conclusion, we have established a HCC cell line in which p53 expression can be switched on or off and regulated in a dose- and time-dependent manner

Gaussian process machine learning-based surface extrapolation method for improvement of the edge effect in surface filtering

Filtering for signal and data is an important technology to reduce and/or remove noise signal for further extraction of desired information. However, it is well known that significant distortions may occur in the boundary areas of the filtered data because there is no sufficient data to be processed. This drawback largely affects the accuracy of topographic measurements and characterizations of precision freeform surfaces, such as freeform optics. To address this issue, a Gaussian process machine learning-based method is presented for extrapolation of the measured surface to an extended measurement area with high accuracy prior to filtering the surface. With the extrapolated data, the edge distortion can be effectively reduced. The effectiveness of this method was evaluated using both simulated and experimental data. Successful implementation of the proposed method not only addresses the issue in surface filtering but also provides a promising solution for numerous applications involving filtering processes

Intelligent Point-of-Interest Recommendation for Tourism Planning via Density-based Clustering and Genetic Algorithm

In recent years, geographic information service and relevant social media become more popular, some geographic point may interest people, e.g. scenic spot or famous store, naming as a point-of-interest (POI). However, the number of POI contributing by social media grows exponentially which causing a searching problem. How to recommend a POI to a user/tourist becomes a challenge. This study proposes an intelligent system using density-based clustering and genetic algorithm to recommend a POIs solution for tourism planning. Density-based clustering identifies candidate POIs. Skyline method decides a superior POI from candidate POIs by dominant of multiple attributes. Genetic algorithm optimizes the recommendation solution. The contribution is to get a tourism POI solution from a huge amount of candidate POIs based on user/tourist preferences. An experimental system implementation is in progress. In future, we will use open data from Google map and Foursquare to proof the proposed system mechanism effectiveness