Sequence heterogeneity and the dynamics of molecular motors

The effect of sequence heterogeneity on the dynamics of molecular motors is reviewed and analyzed using a set of recently introduced lattice models. First, we review results for the influence of heterogenous tracks such as a single-strand of DNA or RNA on the dynamics of the motors. We stress how the predicted behavior might be observed experimentally in anomalous drift and diffusion of motors over a wide range of parameters near the stall force and discuss the extreme limit of strongly biased motors with one-way hopping. We then consider the dynamics in an environment containing a variety of different fuels which supply chemical energy for the motor motion, either on a heterogeneous or on a periodic track. The results for motion along a periodic track are relevant to kinesin motors in a solution with a mixture of different nucleotide triphosphate fuel sources.Comment: To appear in a JPhys special issue on molecular motor

Theory of one-dimensional double-barrier quantum pump in two-frequency signal regime

A one-dimensional system with two $\delta$-like barriers or wells bi-chromaticaly oscillating at frequencies $\omega$ and $2\omega$ is considered. The alternating signal leads to the direct current across the structure (even in a symmetric system). The properties of this quantum pump are studied in a wide range of the system parameters.Comment: 4 pages, 5 figure

Molecular Motor of Double-Walled Carbon Nanotube Driven by Temperature Variation

An elegant formula for coordinates of carbon atoms in a unit cell of a single-walled nanotube (SWNT) is presented and a new molecular motor of double-walled carbon nanotube whose inner tube is a long (8,4) SWNT and outer tube a short (14,8) SWNT is constructed. The interaction between inner an outer tubes is analytically derived by summing the Lennard-Jones potentials between atoms in inner and outer tubes. It is proved that the molecular motor in a thermal bath exhibits a directional motion with the temperature variation of the bath.Comment: 9 pages, 4 figures, revtex

Noise-assisted classical adiabatic pumping in a symmetric periodic potential

We consider a classical overdamped Brownian particle moving in a symmetric periodic potential. We show that a net particle flow can be produced by adiabatically changing two external periodic potentials with a spatial and a temporal phase difference. The classical pumped current is found to be independent of the friction and to vanish both in the limit of low and high temperature. Below a critical temperature, adiabatic pumping appears to be more efficient than transport due to a constant external force.Comment: six pages, 3 figure

Optimal Self-Organization

We present computational and analytical results indicating that systems of driven entities with repulsive interactions tend to reach an optimal state associated with minimal interaction and minimal dissipation. Using concepts from non-equilibrium thermodynamics and game theoretical ideas, we generalize this finding to an even wider class of self-organizing systems which have the ability to reach a state of maximal overall ``success''. This principle is expected to be relevant for driven systems in physics like sheared granular media, but it is also applicable to biological, social, and economic systems, for which only a limited number of quantitative principles are available yet.Comment: This is the detailled revised version of a preprint on ``Self-Organised Optimality'' (cond-mat/9903319). For related work see http://www.theo2.physik.uni-stuttgart.de/helbing.html and http://angel.elte.hu/~vicsek

Two refreshing views of Fluctuation Theorems through Kinematics Elements and Exponential Martingale

In the context of Markov evolution, we present two original approaches to obtain Generalized Fluctuation-Dissipation Theorems (GFDT), by using the language of stochastic derivatives and by using a family of exponential martingales functionals. We show that GFDT are perturbative versions of relations verified by these exponential martingales. Along the way, we prove GFDT and Fluctuation Relations (FR) for general Markov processes, beyond the usual proof for diffusion and pure jump processes. Finally, we relate the FR to a family of backward and forward exponential martingales.Comment: 41 pages, 7 figures; version2: 45 pages, 7 figures, minor revisions, new results in Section

Regulation of membrane-type 1 matrix metalloproteinase expression by zonula occludens-2 in human lung cancer cells.

During tumor invasion, tumor epithelial cells acquire migratory and invasive properties involving important phenotypic alterations. Among these changes, one can observe reorganization or a loss of cell-cell adhesion complexes such as tight junctions (TJs). TJs are composed of transmembrane proteins (occludin, claudins) linked to the actin cytoskeleton through cytoplasmic adaptor molecules including those of the zonula occludens family (ZO-1, -2, -3). We here evaluated the potential role of ZO-2 in the acquisition of invasive properties by tumor cells. In vivo, we showed a decrease of ZO-2 expression in bronchopulmonary cancers, with a preferential localization in the cytoplasm. In addition, in vitro, the localization of ZO-2 varied according to invasive properties of tumor cells, with a cytoplasmic localization correlating with invasion. In addition, we demonstrated that ZO-2 inhibition increases invasive and migrative capacities of invasive tumor cells. This was associated with an increase of MT1-MMP. These results suggest that ZO-2, besides its structural role in tight junction assembly, can act also as a repressor of tumor progression through its ability to reduce the expression of tumor-promoting genes in invasive tumor cells

Différenciation des cellules souches embryonnaires humaines en cellules épithéliales respiratoires

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