Emergence of highly-designable protein-backbone conformations in an off-lattice model

Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally suitable for design. Rather, certain structures are distinguished by unusually high designability: the number of amino-acid sequences for which they represent the unique ground state; sequences associated with such structures possess both robustness to mutation and thermodynamic stability. Here we report that highly designable backbone conformations also emerge in a realistic off-lattice model. The highly designable conformations of a chain of 23 amino acids are identified, and found to be remarkably insensitive to model parameters. While some of these conformations correspond closely to known natural protein folds, such as the zinc finger and the helix-turn-helix motifs, others do not resemble known folds and may be candidates for novel fold design.Comment: 7 figure

Exact solutions for a mean-field Abelian sandpile

We introduce a model for a sandpile, with N sites, critical height N and each site connected to every other site. It is thus a mean-field model in the spin-glass sense. We find an exact solution for the steady state probability distribution of avalanche sizes, and discuss its asymptotics for large N.Comment: 10 pages, LaTe

Interaction of Individual Skyrmions in Nanostructured Cubic Chiral Magnet

We report the direct evidence of field-dependent character of the interaction between individual magnetic skyrmions as well as between skyrmions and edges in B20-type FeGe nanostripes observed by means of high resolution Lorentz transmission electron microscopy. It is shown that above certain critical values of external magnetic field the character of such long-range skyrmion interactions change from attraction to repulsion. Experimentally measured equilibrium inter-skyrmion and skrymion-edge distances as function of applied magnetic field shows quantitative agreement with the results of micromagnetic simulations. Important role of demagnetizing fields and internal symmetry of three-dimensional magnetic skyrmions are discussed in details.Comment: accepted in PR

Superconducting correlations in ultra-small metallic grains

To describe the crossover from the bulk BCS superconductivity to a fluctuation-dominated regime in ultrasmall metallic grains, new order parameters and correlation functions, such as ``parity gap'' and ``pair-mixing correlation function'', have been recently introduced. In this paper, we discuss the small-grain behaviour of the Penrose-Onsager-Yang off-diagonal long-range order (ODLRO) parameter in a pseudo-spin representation. Relations between the ODLRO parameter and those mentioned above are established through analytical and numerical calculations.Comment: 7 pages, 1 figur

Structure Space of Model Proteins --A Principle Component Analysis

We study the space of all compact structures on a two-dimensional square lattice of size $N=6\times6$. Each structure is mapped onto a vector in $N$-dimensions according to a hydrophobic model. Previous work has shown that the designabilities of structures are closely related to the distribution of the structure vectors in the $N$-dimensional space, with highly designable structures predominantly found in low density regions. We use principal component analysis to probe and characterize the distribution of structure vectors, and find a non-uniform density with a single peak. Interestingly, the principal axes of this peak are almost aligned with Fourier eigenvectors, and the corresponding Fourier eigenvalues go to zero continuously at the wave-number for alternating patterns ($q=\pi$). These observations provide a stepping stone for an analytic description of the distribution of structural points, and open the possibility of estimating designabilities of realistic structures by simply Fourier transforming the hydrophobicities of the corresponding sequences.Comment: 14 pages, 12 figures, Conclusion has been modifie

Symmetry and designability for lattice protein models

Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a two-dimensional lattice protein model based on hydrophobicity, we find that those native structures that are encoded by the largest number of different sequences have high symmetry. However only certain symmetries are enhanced, e.g. x/y-mirror symmetry and $180^o$ rotation, while others are suppressed. If it takes a large number of mutations to destabilize the native state of a protein, then, by definition, the state is highly designable. Hence, our findings imply that insensitivity to mutation implies high symmetry. It appears that the relationship between designability and symmetry results because protein substructures are also designable. Native protein folds may therefore be symmetric because they are composed of repeated designable substructures.Comment: 13 pages, 10 figure

Nanoelectromechanical Resonator Arrays for Ultrafast, Gas-Phase Chromatographic Chemical Analysis

Miniaturized gas chromatography (GC) systems can provide fast, quantitative analysis of chemical vapors in an ultrasmall package. We describe a chemical sensor technology based on resonant nanoelectromechanical systems (NEMS) mass detectors that provides the speed, sensitivity, specificity, and size required by the microscale GC paradigm. Such NEMS sensors have demonstrated detection of subparts per billion (ppb) concentrations of a phosphonate analyte. By combining two channels of NEMS detection with an ultrafast GC front-end, chromatographic analysis of 13 chemicals was performed within a 5 s time window

Noise Stabilization of Self-Organized Memories

We investigate a nonlinear dynamical system which ``remembers'' preselected values of a system parameter. The deterministic version of the system can encode many parameter values during a transient period, but in the limit of long times, almost all of them are forgotten. Here we show that a certain type of stochastic noise can stabilize multiple memories, enabling many parameter values to be encoded permanently. We present analytic results that provide insight both into the memory formation and into the noise-induced memory stabilization. The relevance of our results to experiments on the charge-density wave material $NbSe_3$ is discussed.Comment: 29 pages, 6 figures, submitted to Physical Review

Nuclear Effects in Charmonium Production in QCD

It is shown that the nuclear shadowing of charmonium due to the modification of the nuclear parton distribution is similar in the factorization approach based on non relativistic QCD and in the color evaporation model. In the first model, a separate study of the color octet and color singlet contributions to the yields of the various charmonium states as well as the contributions of these states to the total $J/\Psi$ production is performed. It is found a clear $x_F$ dependence of these contributions which can reproduce experimental data for moderate $x_F$.Comment: 11 pages, 5 Postscript figure