3-dimensional Gravity from the Turaev-Viro Invariant

We study the $q$-deformed su(2) spin network as a 3-dimensional quantum gravity model. We show that in the semiclassical continuum limit the Turaev-Viro invariant obtained recently defines naturally regularized path-integral $\grave{\rm a}$ la Ponzano-Regge, In which a contribution from the cosmological term is effectively included. The regularization dependent cosmological constant is found to be ${4\pi^2\over k^2} +O(k^{-4})$, where $q^{2k}=1$. We also discuss the relation to the Euclidean Chern-Simons-Witten gravity in 3-dimension.Comment: 11page

Polymer Release out of a Spherical Vesicle through a Pore

Translocation of a polymer out of curved surface or membrane is studied via mean first passage time approach. Membrane curvature gives rise to a constraint on polymer conformation, which effectively drives the polymer to the outside of membrane where the available volume of polymer conformational fluctuation is larger. Considering a polymer release out of spherical vesicle, polymer translocation time $\tau$ is changed to the scaling behavior $\tau\sim L^2$ for $R<R_G$, from $\tau\sim L^3$ for $R\gg R_G$, where $L$ is the polymer contour length and $R$, $R_G$ are vesicle radius and polymer radius of gyration respectively. Also the polymer capture into a spherical budd is studied and possible apparatus for easy capture is suggested.Comment: 14 pages RevTeX, 6 postscript figures, published in Phys. Rev. E 57, 730 (1998

Quantum Zeno Effect Explains Magnetic-Sensitive Radical-Ion-Pair Reactions

Chemical reactions involving radical-ion pairs are ubiquitous in biology, since not only are they at the basis of the photosynthetic reaction chain, but are also assumed to underlie the biochemical magnetic compass used by avian species for navigation. Recent experiments with magnetic-sensitive radical-ion pair reactions provided strong evidence for the radical-ion-pair magnetoreception mechanism, verifying the expected magnetic sensitivities and chemical product yield changes. It is here shown that the theoretical description of radical-ion-pair reactions used since the 70's cannot explain the observed data, because it is based on phenomenological equations masking quantum coherence effects. The fundamental density matrix equation derived here from basic quantum measurement theory considerations naturally incorporates the quantum Zeno effect and readily explains recent experimental observations on low- and high-magnetic-field radical-ion-pair reactions.Comment: 10 pages, 5 figure

Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations

Formation of bacteriorhodopsin (bR) from apoprotein and retinal has been studied experimentally, but the actual pathway, including the point of entry, is little understood. Molecular dynamics simulations provide a surprisingly clear prediction. A window between bR helices E and F in the transmembrane part of the protein can be identified as an entry point for retinal. Steered molecular dynamics, performed by applying a series of external forces in the range of 200–1000 pN over a period of 0.2 ns to retinal, allows one to extract this chromophore from bR once the Schiff base bond to Lys216 is cleaved. Extraction proceeds until the retinal tail forms a hydrogen bond network with Ala144, Met145, and Ser183 side groups lining the exit/entry window. The manipulation induces a distortion with a fitted root mean square deviation of coordinates (ignoring retinal, water, and hydrogen atoms) of less than 1.9 A by the time the retinal carbonyl reaches the protein surface. The forces needed to extract retinal are due to friction and do not indicate significant potential barriers. The simulations therefore suggest a pathway for the binding of retinal. Water molecules are found to play a crucial role in the binding process

Fluctuation-Driven Molecular Transport in an Asymmetric Membrane Channel

Channel proteins, that selectively conduct molecules across cell membranes, often exhibit an asymmetric structure. By means of a stochastic model, we argue that channel asymmetry in the presence of non-equilibrium fluctuations, fueled by the cell's metabolism as observed recently, can dramatically influence the transport through such channels by a ratchet-like mechanism. For an aquaglyceroporin that conducts water and glycerol we show that a previously determined asymmetric glycerol potential leads to enhanced inward transport of glycerol, but for unfavorably high glycerol concentrations also to enhanced outward transport that protects a cell against poisoning.Comment: REVTeX4, 4 pages, 3 figures; Accepted for publication in Phys. Rev. Let

Symmetric angular momentum coupling, the quantum volume operator and the 7-spin network: a computational perspective

A unified vision of the symmetric coupling of angular momenta and of the quantum mechanical volume operator is illustrated. The focus is on the quantum mechanical angular momentum theory of Wigner's 6j symbols and on the volume operator of the symmetric coupling in spin network approaches: here, crucial to our presentation are an appreciation of the role of the Racah sum rule and the simplification arising from the use of Regge symmetry. The projective geometry approach permits the introduction of a symmetric representation of a network of seven spins or angular momenta. Results of extensive computational investigations are summarized, presented and briefly discussed.Comment: 15 pages, 10 figures, presented at ICCSA 2014, 14th International Conference on Computational Science and Application