Calibrated Langevin dynamics simulations of intrinsically disordered proteins

We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules. Our CG model includes repulsive steric, attractive hydrophobic, and electrostatic interactions between residues and is calibrated to a large collection of single-molecule fluorescence resonance energy transfer data on the inter-residue separations for 36 pairs of residues in five IDPs: $\alpha$-, $\beta$-, and $\gamma$-synuclein, the microtubule-associated protein $\tau$, and prothymosin $\alpha$. We find that our CG model is able to recapitulate the average inter-residue separations regardless of the choice of the hydrophobicity scale, which shows that our calibrated model can robustly capture the conformational dynamics of IDPs. We then employ our model to study the scaling of the radius of gyration with chemical distance in 11 known IDPs. We identify a strong correlation between the distance to the dividing line between folded proteins and IDPs in the mean charge and hydrophobicity space and the scaling exponent of the radius of gyration with chemical distance along the protein.Comment: 16 pages, 10 figure

Are better conducting molecules more rigid?

We investigate the electronic origin of the bending stiffness of conducting molecules. It is found that the bending stiffness associated with electronic motion, which we refer to as electro-stiffness, $\kappa_{e}$, is governed by the molecular orbital overlap $t$ and the gap width $u$ between HOMO and LUMO levels, and behaves as $\kappa_{e}\sim t^{2}/\sqrt{u^2+t^{2}}$. To study the effect of doping, we analyze the electron filling-fraction dependence on $\kappa_{e}$ and show that doped molecules are more flexible. In addition, to estimate the contribution of $\kappa_{e}$ to the total stiffness, we consider molecules under a voltage bias, and study the length contraction ratio as a function of the voltage. The molecules are shown to be contracted or dilated, with $\kappa_{e}$ increasing nonlinearly with the applied bias

Spontaneous Vortex Lattices in Quasi 2D Dipolar Spinor Condensates

Motivated by recent experiments\cite{BA}\cite{BB}, we study quasi 2D ferromagnetic condensates with various aspect ratios. We find that in zero magnetic field, dipolar energy generates a local energy minimum with all the spins lie in the 2D plane forming a row of {\em circular} spin textures with {\em alternating} orientation, corresponding to a packing of vortices of {\em identical} vorticity in different spin components. In a large magnetic field, the system can fall into a long lived dynamical state consisting of an array of elliptic and hyperbolic Mermin-Ho spin textures, while the true equilibrium is an uniaxial spin density wave with a single wave-vector along the magnetic field, and a wavelength similar to the characteristic length of the long lived vortex array state.Comment: 4 pages, 6 figure

Phase separation in the trapped spinor gases with anisotropic spin-spin interaction

We investigate the effect of the anisotropic spin-spin interaction on the ground state density distribution of the one dimensional spin-1 bosonic gases within a modified Gross-Pitaevskii theory both in the weakly interaction regime and in the Tonks-Girardeau (TG) regime. We find that for ferromagnetic spinor gas the phase separation occurs even for weak anisotropy of the spin-spin interaction, which becomes more and more obvious and the component of $m_F=0$ diminishes as the anisotropy increases. However, no phase separation is found for anti-ferromagnetic spinor gas in both regimes.Comment: 5pages, 4 figure

Identification of a WNT5A-Responsive Degradation Domain in the Kinesin Superfamily Protein KIF26B.

Noncanonical WNT pathways function independently of the β-catenin transcriptional co-activator to regulate diverse morphogenetic and pathogenic processes. Recent studies showed that noncanonical WNTs, such as WNT5A, can signal the degradation of several downstream effectors, thereby modulating these effectors' cellular activities. The protein domain(s) that mediates the WNT5A-dependent degradation response, however, has not been identified. By coupling protein mutagenesis experiments with a flow cytometry-based degradation reporter assay, we have defined a protein domain in the kinesin superfamily protein KIF26B that is essential for WNT5A-dependent degradation. We found that a human disease-causing KIF26B mutation located at a conserved amino acid within this domain compromises the ability of WNT5A to induce KIF26B degradation. Using pharmacological perturbation, we further uncovered a role of glycogen synthase kinase 3 (GSK3) in WNT5A regulation of KIF26B degradation. Lastly, based on the identification of the WNT5A-responsive domain, we developed a new reporter system that allows for efficient profiling of WNT5A-KIF26B signaling activity in both somatic and stem cells. In conclusion, our study identifies a new protein domain that mediates WNT5A-dependent degradation of KIF26B and provides a new tool for functional characterization of noncanonical WNT5A signaling in cells

Constant-size dynamic k-times anonymous authentication

Dynamic k-times anonymous authentication (k-TAA) schemes allow members of a group to be authenticated anonymously by application providers for a bounded number of times, where application providers can independently and dynamically grant or revoke access right to members in their own group. In this paper, we construct a dynamic k-TAA scheme with space and time complexities of O(log(k)) and a variant, in which the authentication protocol only requires constant time and space complexities at the cost of O(k) -sized public key. We also describe some tradeoff issues between different system characteristics. We detail all the zero-knowledge proof-of-knowledge protocols involved and show that our construction is secure in the random oracle model under the q-strong Diffie-Hellman assumption and q-decisional Diffie-Hellman inversion assumption. We provide a proof-of-concept implementation, experiment on its performance, and show that our scheme is practical

The reinforcing influence of recommendations on global diversification

Recommender systems are promising ways to filter the overabundant information in modern society. Their algorithms help individuals to explore decent items, but it is unclear how they allocate popularity among items. In this paper, we simulate successive recommendations and measure their influence on the dispersion of item popularity by Gini coefficient. Our result indicates that local diffusion and collaborative filtering reinforce the popularity of hot items, widening the popularity dispersion. On the other hand, the heat conduction algorithm increases the popularity of the niche items and generates smaller dispersion of item popularity. Simulations are compared to mean-field predictions. Our results suggest that recommender systems have reinforcing influence on global diversification.Comment: 6 pages, 6 figure

The dynamics of quantum phases in a spinor condensate

We discuss the quantum phases and their diffusion dynamics in a spinor-1 atomic Bose-Einstein condensate. For ferromagnetic interactions, we obtain the exact ground state distribution of the phases associated with the total atom number ($N$), the total magnetization (${\cal M}$), and the alignment (or hypercharge) ($Y$) of the system. The mean field ground state is stable against fluctuations of atom numbers in each of the spin components, and the phases associated with the order parameter for each spin components diffuse while dynamically recover the two broken continuous symmetries [U(1) and SO(2)] when $N$ and ${\cal M}$ are conserved as in current experiments. We discuss the implications to the quantum dynamics due to an external (homogeneous) magnetic field. We also comment on the case of a spinor-1 condensate with anti-ferromagnetic interactions.Comment: 5 figures, an extended version of cond-mat/030117

Infrared spectrum of the silicon hydride cation SiH_7^+

Silanium ions are an important class of hypervalent molecules, and the determination of their structure will yield insights into the nature of nonclassical bonding and provide a contrast to the bonding in carbonium ions. We report the infrared spectrum of the mass-selected silicon hydride cluster ion ^(28)SiH_7^+ detected by vibrational predissociation spectroscopy. Silanium ions were formed in a pulsed high pressure glow discharge and cooled by the subsequent supersonic expansion. Photodissociation spectra were obtained using a tandem time-of-flight mass spectrometer: (formula available in paper) ions were mass-selected and excited by a tunable infrared laser. The resulting photofragments were detected using a reflectron as a mass analyzer. We observed a vibrational band at 3865 cm^(-1), which was the only one observed from 3500 cm^(-1) to 4200 cm^(-1). This result suggests that the molecule might form a symmetric complex with the structure H_2⋅SiH_3^+⋅H_2, in contrast to the CH_7^+ which has the structure CH_5^+⋅H_2