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Although it is a central question in biology, how cell shape controls intracellular dynamics largely remains an open question. Here, we show that the shape of Arabidopsis pavement cells creates a stress pattern that controls microtubule orientation, which then guides cell wall reinforcement. Live- imaging, combined with modeling of cell mechanics, shows that microtubules align along the maximal te

Abstract in UndeterminedBackground: For 2-dye microarray platforms, some missing values may arise from an un-measurably low RNA expression in one channel only. Information of such "one-channel depletion" is so far not included in algorithms for imputation of missing values.Results: Calculating the mean deviation between imputed values and duplicate controls in five datasets, we show that KNN-based

Single-file diffusion is a theoretically challenging many-body problem where the calculation of even the simplest observables, e.g. mean square displacement, for a tracer particle requires an elaborate mathematical machinery. There is therefore a need for simple approaches which provide intuitive understandings and predict qualitatively correct behaviours. Here we put forward a scaling-type method

Background: Proteases of human pathogens are becoming increasingly important drug targets, hence it is necessary to understand their substrate specificity and to interpret this knowledge in practically useful ways. New methods are being developed that produce large amounts of cleavage information for individual proteases and some have been applied to extract cleavage rules from data. However, the

Strong plasmonic-molecular resonance coupling occurs between noble metal nanocrystals and organic adsorbates when the plasmonic resonance is degenerate with the molecular one. This interaction forms the basis for many fundamental studies and practical applications. We describe here the first direct measurement of the resonance coupling on single gold nanorods. The dark-field scattering technique i

The protein folding problem is addressed focussing on the hydro- phobicity patterns in the amino acid sequences and structures. Both real and model proteins are investigated. The hydrophobicity pattern of real proteins is probed in two ways. First, it is asked which binary pattern is most conserved within groups of related proteins. Not unexpectedly, the most conserved patterns are strongly corre

We present and investigate an extension of the classical random graph to a general class of inhomogeneous random graph models, where vertices come in different types, and the probability of realizing an edge depends on the types of its terminal vertices. This approach provides a general framework for the analysis of a large class of models. The generic phase structure is derived using generating f

Using an atomic model with a simplified-sequence-based potential, the folding properties of several different peptides are studied. Both alpha-helical (Trp cage, F-s) and beta-sheet(GB1p, GB1m2, GB1m3, Betanova, LLM) peptides are considered. The model is able to fold these different peptides for one and the same choice of;parameters, and the melting behaviour of the peptides (folded population aga

A diffusion process on complex networks is introduced in order to uncover their large-scale topological structures. This is achieved by focusing on the slowest decaying diffusive modes of the network. The proposed procedure is applied to real-world networks like a friendship network of known modular structure, and an Internet routing network. For the friendship network, its known structure is well

This paper presents a first study of the pseudoscalar meson masses to two loops, or next-to-next-to-leading order, within the supersymmetric formulation of partially quenched chiral perturbation theory (PQchiPT). The expression for the pseudoscalar meson mass in the case of three valence and three sea quarks with equal masses, but different from each other, is given to O(p(6)), along with a numeri

Recent experiments have identified peptides that adhere to GaAs and Si surfaces. Here, we use all-atom Monte Carlo simulations with implicit solvent to investigate the behavior in aqueous solution of four such peptides, all with 12 residues. At room temperature, we find that all four peptides are largely unstructured, which is consistent with experimental data. At the same time, we find that one o

A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Go approximation, which ignores non-native interactions. We find that the collapse transition is considerably more abrupt for the protein A sequence than fo

A summary of recent progress in Chiral Perturbation Theory (ChPT) at the two-loop level is given. A short introduction to ChPT is included, along with an explanation of the usefulness of developing ChPT for partially quenched QCD. Further, our recent work in partially quenched ChPT is reviewed, and a few comments are given on older work in mesonic ChPT at the two-loop level. In particular, we quot

Using simple sequence-based potentials, the folding properties of a designed three-helix-bundle protein, an alpha-helix and a beta-hairpin are studied. The three-helix-bundle protein is modelled using 5-6 atoms per amino acid and is found to undergo a first-order-like folding transition in which chain collapse and helix formation cannot be separated, which is in-accord with experimental data. The

How the molecular programs of differentiated cells develop as cells transit from multipotency through lineage commitment remains unexplored. This reflects the inability to access cells undergoing commitment or located in the immediate vicinity of commitment boundaries. It remains unclear whether commitment constitutes a gradual process, or else represents a discrete transition. Analyses of in vitr

While pattern formation is studied in various areas of biology, little is known about the noise leading to variations between individual realizations of the pattern. One prominent example for de novo pattern formation in plants is the patterning of trichomes on Arabidopsis leaves, which involves genetic regulation and cell-to-cell communication. These processes are potentially variable due to, e.g