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

Deriving N-soliton solutions via constrained flows

The soliton equations can be factorized by two commuting x- and t-constrained flows. We propose a method to derive N-soliton solutions of soliton equations directly from the x- and t-constrained flows.Comment: 8 pages, AmsTex, no figures, to be published in Journal of Physics

Constructing N-soliton solution for the mKdV equation through constrained flows

Based on the factorization of soliton equations into two commuting integrable x- and t-constrained flows, we derive N-soliton solutions for mKdV equation via its x- and t-constrained flows. It shows that soliton solution for soliton equations can be constructed directly from the constrained flows.Comment: 10 pages, Latex, to be published in "J. Phys. A: Math. Gen.

Statistical Topography of Glassy Interfaces

Statistical topography of two-dimensional interfaces in the presence of quenched disorder is studied utilizing combinatorial optimization algorithms. Finite-size scaling is used to measure geometrical exponents associated with contour loops and fully packed loops. We find that contour-loop exponents depend on the type of disorder (periodic ``vs'' non-periodic) and they satisfy scaling relations characteristic of self-affine rough surfaces. Fully packed loops on the other hand are unaffected by disorder with geometrical exponents that take on their pure values.Comment: 4 pages, REVTEX, 4 figures included. Further information can be obtained from [email protected]

Classical Poisson structures and r-matrices from constrained flows

We construct the classical Poisson structure and $r$-matrix for some finite dimensional integrable Hamiltonian systems obtained by constraining the flows of soliton equations in a certain way. This approach allows one to produce new kinds of classical, dynamical Yang-Baxter structures. To illustrate the method we present the $r$-matrices associated with the constrained flows of the Kaup-Newell, KdV, AKNS, WKI and TG hierarchies, all generated by a 2-dimensional eigenvalue problem. Some of the obtained $r$-matrices depend only on the spectral parameters, but others depend also on the dynamical variables. For consistency they have to obey a classical Yang-Baxter-type equation, possibly with dynamical extra terms.Comment: 16 pages in LaTe

Enantiospecific Detection of Chiral Nanosamples Using Photoinduced Force

We propose a high-resolution microscopy technique for enantiospecific detection of chiral samples down to sub-100-nm size based on force measurement. We delve into the differential photoinduced optical force ΔF exerted on an achiral probe in the vicinity of a chiral sample when left and right circularly polarized beams separately excite the sample-probe interactive system. We analytically prove that ΔF is entangled with the enantiomer type of the sample enabling enantiospecific detection of chiral inclusions. Moreover, we demonstrate that ΔF is linearly dependent on both the chiral response of the sample and the electric response of the tip and is inversely related to the quartic power of probe-sample distance. We provide physical insight into the transfer of optical activity from the chiral sample to the achiral tip based on a rigorous analytical approach. We support our theoretical achievements by several numerical examples highlighting the potential application of the derived analytic properties. Lastly, we demonstrate the sensitivity of our method to enantiospecify nanoscale chiral samples with chirality parameter on the order of 0.01 and discuss how the sensitivity of our proposed technique can be further improved

Higher Order Potential Expansion for the Continuous Limits of the Toda Hierarchy

A method for introducing the higher order terms in the potential expansion to study the continuous limits of the Toda hierarchy is proposed in this paper. The method ensures that the higher order terms are differential polynomials of the lower ones and can be continued to be performed indefinitly. By introducing the higher order terms, the fewer equations in the Toda hierarchy are needed in the so-called recombination method to recover the KdV hierarchy. It is shown that the Lax pairs, the Poisson tensors, and the Hamiltonians of the Toda hierarchy tend towards the corresponding ones of the KdV hierarchy in continuous limit.Comment: 20 pages, Latex, to be published in Journal of Physics

Negaton and Positon solutions of the soliton equation with self-consistent sources

The KdV equation with self-consistent sources (KdVES) is used as a model to illustrate the method. A generalized binary Darboux transformation (GBDT) with an arbitrary time-dependent function for the KdVES as well as the formula for $N$-times repeated GBDT are presented. This GBDT provides non-auto-B\"{a}cklund transformation between two KdV equations with different degrees of sources and enable us to construct more general solutions with $N$ arbitrary $t$-dependent functions. By taking the special $t$-function, we obtain multisoliton, multipositon, multinegaton, multisoliton-positon, multinegaton-positon and multisoliton-negaton solutions of KdVES. Some properties of these solutions are discussed.Comment: 13 pages, Latex, no figues, to be published in J. Phys. A: Math. Ge