Three dimensional structure from intensity correlations

We develop the analysis of x-ray intensity correlations from dilute ensembles of identical particles in a number of ways. First, we show that the 3D particle structure can be determined if the particles can be aligned with respect to a single axis having a known angle with respect to the incident beam. Second, we clarify the phase problem in this setting and introduce a data reduction scheme that assesses the integrity of the data even before the particle reconstruction is attempted. Finally, we describe an algorithm that reconstructs intensity and particle density simultaneously, thereby making maximal use of the available constraints.Comment: 17 pages, 9 figure

Isgur-Wise function in a QCD potential model with coulombic potential as perturbation

We study heavy light mesons in a QCD inspired quark model with the Cornell potential$-\frac{4\alpha_{S}}{3r}+br+c$. Here we consider the linear term $br$ as the parent and $-\frac{4\alpha_{S}}{3r}+c$ i.e.the Coloumbic part as the perturbation.The linear parent leads to Airy function as the unperturbed wavefunction. We then use the Dalgarno method of perturbation theory to obtain the total wavefunction corrected upto first order with Coulombic peice as the perturbation.With these wavefunctions, we study the Isgur-Wise function and calculate its slope and curvature.Comment: paper has been modified in Airy functions calculation upto o(r^3

Emergence of stable and fast folding protein structures

The number of protein structures is far less than the number of sequences. By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the sequence space. Even though the sequence space grows exponentially with N (the number of amino acids) we conjecture that the number of low energy compact structures only scales as ln N. This implies that many sequences must map onto countable number of basins in the structure space. The number of sequences for which a given fold emerges as a native structure is further reduced by the dual requirements of stability and kinetic accessibility. The factor that determines the dual requirement is related to the sequence dependent temperatures, T_\theta (collapse transition temperature) and T_F (folding transition temperature). Sequences, for which \sigma =(T_\theta-T_F)/T_\theta is small, typically fold fast by generically collapsing to the native-like structures and then rapidly assembling to the native state. Such sequences satisfy the dual requirements over a wide temperature range. We also suggest that the functional requirement may further reduce the number of sequences that are biologically competent. The scheme developed here for thinning of the sequence space that leads to foldable structures arises naturally using simple physical characteristics of proteins. The reduction in sequence space leading to the emergence of foldable structures is demonstrated using lattice models of proteins.Comment: latex, 18 pages, 8 figures, to be published in the conference proceedings "Stochastic Dynamics and Pattern Formation in Biological Systems

Dynamical Anomalous Subvarieties: Structure and Bounded Height Theorems

According to Medvedev and Scanlon, a polynomial $f(x)\in \bar{\mathbb Q}[x]$ of degree $d\geq 2$ is called disintegrated if it is not linearly conjugate to $x^d$ or $\pm C_d(x)$ (where $C_d(x)$ is the Chebyshev polynomial of degree $d$). Let $n\in\mathbb{N}$, let $f_1,\ldots,f_n\in \bar{\mathbb Q}[x]$ be disintegrated polynomials of degrees at least 2, and let $\varphi=f_1\times\ldots\times f_n$ be the corresponding coordinate-wise self-map of $({\mathbb P}^1)^n$. Let $X$ be an irreducible subvariety of $({\mathbb P}^1)^n$ of dimension $r$ defined over $\bar{\mathbb Q}$. We define the \emph{$\varphi$-anomalous} locus of $X$ which is related to the \emph{$\varphi$-periodic} subvarieties of $({\mathbb P}^1)^n$. We prove that the $\varphi$-anomalous locus of $X$ is Zariski closed; this is a dynamical analogue of a theorem of Bombieri, Masser, and Zannier \cite{BMZ07}. We also prove that the points in the intersection of $X$ with the union of all irreducible $\varphi$-periodic subvarieties of $({\mathbb P}^1)^n$ of codimension $r$ have bounded height outside the $\varphi$-anomalous locus of $X$; this is a dynamical analogue of Habegger's theorem \cite{Habegger09} which was previously conjectured in \cite{BMZ07}. The slightly more general self-maps $\varphi=f_1\times\ldots\times f_n$ where each $f_i\in \bar{\mathbb Q}(x)$ is a disintegrated rational map are also treated at the end of the paper.Comment: Minor mistakes corrected, slight reorganizatio

First and second order transition of frustrated Heisenberg spin systems

Starting from the hypothesis of a second order transition we have studied modifications of the original Heisenberg antiferromagnet on a stacked triangular lattice (STA-model) by the Monte Carlo technique. The change is a local constraint restricting the spins at the corners of selected triangles to add up to zero without stopping them from moving freely (STAR-model). We have studied also the closely related dihedral and trihedral models which can be classified as Stiefel models. We have found indications of a first order transition for all three modified models instead of a universal critical behavior. This is in accordance with the renormalization group investigations but disagrees with the Monte Carlo simulations of the original STA-model favoring a new universality class. For the corresponding x-y antiferromagnet studied before, the second order nature of the transition could also not be confirmed.Comment: 31 pages, 13 figures, to be published in Euro. J. Phys.