A non-equilibrium dynamic mechanism for the allosteric effect

Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may function by modifying the nonequilibrium protein dynamics. The theory predicts that an enzyme under the new mechanism has different temperature dependence, waiting time distribution of the turnover cycle, and dynamic fluctuation patterns with and without effector. Experimental tests of the theory are proposed.Comment: accepted by Phys. Rev. Lett. Major revisions were made to fit the style. 4 pages, 2 figure

Low-field microwave absorption in epitaxial La-Sr-Mn-O films resulting from the angle-tuned ferromagnetic resonance in the multidomain state

We studied magnetic-field induced microwave absorption in 100-200 nm thick La$_{0.7}$Sr$_{0.3}$MnO$_{3}$ films on SrTiO$_{3}$ substrate and found a low-field absorption with a very peculiar angular dependence: it appears only in the oblique field and is absent both in the parallel and in the perpendicular orientations. We demonstrate that this low-field absorption results from the ferromagnetic resonance in the multidomain state (domain-mode resonance). Its unusual angular dependence arises from the interplay between the parallel component of the magnetic field that drives the film into multidomain state and the perpendicular field component that controls the domain width through its effect on domain wall energy. The low-field microwave absorption in the multidomain state can be a tool to probe domain structure in magnetic films with in-plane magnetization.Comment: 9 pages, 9 Figure

Automatic generation of generalised regular factorial designs

Open Access for this article was paid for by the French Research Agency (ANR), project Escapade (ANR-12-AGRO-0003).The R package planor enables the user to search for, and construct, factorial designs satisfying given conditions. The user specifies the factors and their numbers of levels, the factorial terms which are assumed to be non-zero, and the subset of those which are to be estimated. Both block and treatment factors can be allowed for, and they may have either fixed or random effects, as well as hierarchy relationships. The designs are generalised regular designs, which means that each one is constructed by using a design key and that the underlying theory is that of finite abelian groups. The main theoretical results and algorithms on which planor is based are developed and illustrated, with the emphasis on mathematical rather than programming details. Sections 3–5 are dedicated to the elementary case, when the numbers of levels of all factors are powers of the same prime. The ineligible factorial terms associated with users’ specifications are defined and it is shown how they can be used to search for a design key by a backtrack algorithm. Then the results are extended to the case when different primes are involved, by making use of the Sylow decomposition of finite abelian groups. The proposed approach provides a unified framework for a wide range of factorial designs.Publisher PDFPeer reviewe

An information-bearing seed for nucleating algorithmic self-assembly

Self-assembly creates natural mineral, chemical, and biological structures of great complexity. Often, the same starting materials have the potential to form an infinite variety of distinct structures; information in a seed molecule can determine which form is grown as well as where and when. These phenomena can be exploited to program the growth of complex supramolecular structures, as demonstrated by the algorithmic self-assembly of DNA tiles. However, the lack of effective seeds has limited the reliability and yield of algorithmic crystals. Here, we present a programmable DNA origami seed that can display up to 32 distinct binding sites and demonstrate the use of seeds to nucleate three types of algorithmic crystals. In the simplest case, the starting materials are a set of tiles that can form crystalline ribbons of any width; the seed directs assembly of a chosen width with >90% yield. Increased structural diversity is obtained by using tiles that copy a binary string from layer to layer; the seed specifies the initial string and triggers growth under near-optimal conditions where the bit copying error rate is 17 kb of sequence information. In sum, this work demonstrates how DNA origami seeds enable the easy, high-yield, low-error-rate growth of algorithmic crystals as a route toward programmable bottom-up fabrication

Spin wave resonances in La_{0.7}Sr_{0.3}MnO_{3} films: measurement of spin wave stiffness and anisotropy field

We studied magnetic field dependent microwave absorption in epitaxial La$_{0.7}$Sr$_{0.3}$MnO$_{3}$ films using an X-band Bruker ESR spectrometer. By analyzing angular and temperature dependence of the ferromagnetic and spin-wave resonances we determine spin-wave stiffness and anisotropy field. The spin-wave stiffness as found from the spectrum of the standing spin-wave resonances in thin films is in fair agreement with the results of inelastic neutron scattering studies on a single crystal of the same composition [Vasiliu-Doloc et al., J. Appl. Phys. \textbf{83}, 7343 (1998)].Comment: 15 pages, 7 figures (now figure captions are included

Two Gap State Density in MgB2_{2}: A True Bulk Property or A Proximity Effect?

We report on the temperature dependence of the quasiparticle density of states (DOS) in the simple binary compound MgB2 directly measured using scanning tunneling microscope (STM). To achieve high quality tunneling conditions, a small crystal of MgB2 is used as a tip in the STM experiment. The ``sample'' is chosen to be a 2H-NbSe2 single crystal presenting an atomically flat surface. At low temperature the tunneling conductance spectra show a gap at the Fermi energy followed by two well-pronounced conductance peaks on each side. They appear at voltages V$_{S}\simeq \pm 3.8$ mV and V$_{L}\simeq \pm 7.8$ mV. With rising temperature both peaks disappear at the Tc of the bulk MgB2, a behavior consistent with the model of two-gap superconductivity. The explanation of the double-peak structure in terms of a particular proximity effect is also discussed.Comment: 4 pages, 3 figure

Nonresonant microwave absorption in epitaxial La-Sr-Mn-O films and its relation to colossal magnetoresistance

We study magnetic-field-dependent nonresonant microwave absorption and dispersion in thin La$_{0.7}$Sr$_{0.3}$MnO$_{3}$ films and show that it originates from the colossal magnetoresistance. We develop the model for magnetoresistance of a thin ferromagnetic film in oblique magnetic field. The model accounts fairly well for our experimental findings, as well as for results of other researchers. We demonstrate that nonresonant microwave absorption is a powerful technique that allows contactless measurement of magnetic properties of thin films, including magnetoresistance, anisotropy field and coercive field.Comment: 20 pages, 11 figure

A core genetic module : the Mixed Feedback Loop

The so-called Mixed Feedback Loop (MFL) is a small two-gene network where protein A regulates the transcription of protein B and the two proteins form a heterodimer. It has been found to be statistically over-represented in statistical analyses of gene and protein interaction databases and to lie at the core of several computer-generated genetic networks. Here, we propose and mathematically study a model of the MFL and show that, by itself, it can serve both as a bistable switch and as a clock (an oscillator) depending on kinetic parameters. The MFL phase diagram as well as a detailed description of the nonlinear oscillation regime are presented and some biological examples are discussed. The results emphasize the role of protein interactions in the function of genetic modules and the usefulness of modelling RNA dynamics explicitly.Comment: To be published in Physical Review

Scale-free Networks from Optimal Design

A large number of complex networks, both natural and artificial, share the presence of highly heterogeneous, scale-free degree distributions. A few mechanisms for the emergence of such patterns have been suggested, optimization not being one of them. In this letter we present the first evidence for the emergence of scaling (and smallworldness) in software architecture graphs from a well-defined local optimization process. Although the rules that define the strategies involved in software engineering should lead to a tree-like structure, the final net is scale-free, perhaps reflecting the presence of conflicting constraints unavoidable in a multidimensional optimization process. The consequences for other complex networks are outlined.Comment: 6 pages, 2 figures. Submitted to Europhysics Letters. Additional material is available at http://complex.upc.es/~sergi/software.ht