Concise theory of chiral lipid membranes

A theory of chiral lipid membranes is proposed on the basis of a concise free energy density which includes the contributions of the bending and the surface tension of membranes, as well as the chirality and orientational variation of tilting molecules. This theory is consistent with the previous experiments [J.M. Schnur \textit{et al.}, Science \textbf{264}, 945 (1994); M.S. Spector \textit{et al.}, Langmuir \textbf{14}, 3493 (1998); Y. Zhao, \textit{et al.}, Proc. Natl. Acad. Sci. USA \textbf{102}, 7438 (2005)] on self-assembled chiral lipid membranes of DC$_{8,9}$PC. A torus with the ratio between its two generated radii larger than $\sqrt{2}$ is predicted from the Euler-Lagrange equations. It is found that tubules with helically modulated tilting state are not admitted by the Euler-Lagrange equations, and that they are less energetically favorable than helical ripples in tubules. The pitch angles of helical ripples are theoretically estimated to be about 0$^\circ$ and 35$^\circ$, which are close to the most frequent values 5$^\circ$ and 28$^\circ$ observed in the experiment [N. Mahajan \textit{et al.}, Langmuir \textbf{22}, 1973 (2006)]. Additionally, the present theory can explain twisted ribbons of achiral cationic amphiphiles interacting with chiral tartrate counterions. The ratio between the width and pitch of twisted ribbons is predicted to be proportional to the relative concentration difference of left- and right-handed enantiomers in the low relative concentration difference region, which is in good agreement with the experiment [R. Oda \textit{et al.}, Nature (London) \textbf{399}, 566 (1999)].Comment: 14 pages, 7 figure

Analyzing Single-Molecule Protein Transportation Experiments via Hierarchical Hidden Markov Models

To maintain proper cellular functions, over 50% of proteins encoded in the genome need to be transported to cellular membranes. The molecular mechanism behind such a process, often referred to as protein targeting, is not well understood. Single-molecule experiments are designed to unveil the detailed mechanisms and reveal the functions of different molecular machineries involved in the process. The experimental data consist of hundreds of stochastic time traces from the fluorescence recordings of the experimental system. We introduce a Bayesian hierarchical model on top of hidden Markov models (HMMs) to analyze these data and use the statistical results to answer the biological questions. In addition to resolving the biological puzzles and delineating the regulating roles of different molecular complexes, our statistical results enable us to propose a more detailed mechanism for the late stages of the protein targeting process

Can Electric Field Induced Energy Gaps In Metallic Carbon Nanotubes?

The low-energy electronic structure of metallic single-walled carbon nanotube (SWNT) in an external electric field perpendicular to the tube axis is investigated. Based on tight-binding approximation, a field-induced energy gap is found in all (n, n) SWNTs, and the gap shows strong dependence on the electric field and the size of the tubes. We numerically find a universal scaling that the gap is a function of the electric field and the radius of SWNTs, and the results are testified by the second-order perturbation theory in weak field limit. Our calculation shows the field required to induce a 0.1 ${\rm eV}$ gap in metallic SWNTs can be easily reached under the current experimental conditions. It indicates a kind of possibility to apply nanotubes to electric signal-controlled nanoscale switching devices

Instability and Periodic Deformation in Bilayer Membranes Induced by Freezing

The instability and periodic deformation of bilayer membranes during freezing processes are studied as a function of the difference of the shape energy between the high and the low temperature membrane states. It is shown that there exists a threshold stability condition, bellow which a planar configuration will be deformed. Among the deformed shapes, the periodic curved square textures are shown being one kind of the solutions of the associated shape equation. In consistency with recent expe rimental observations, the optimal ratio of period and amplitude for such a texture is found to be approximately equal to (2)^{1/2}\pi.Comment: 8 pages in Latex form, 1 Postscript figure. To be appear in Mod. Phys. Lett. B. 199

Analyzing Single-Molecule Protein Transportation Experiments via Hierarchical Hidden Markov Models

To maintain proper cellular functions, over 50% of proteins encoded in the genome need to be transported to cellular membranes. The molecular mechanism behind such a process, often referred to as protein targeting, is not well understood. Single-molecule experiments are designed to unveil the detailed mechanisms and reveal the functions of different molecular machineries involved in the process. The experimental data consist of hundreds of stochastic time traces from the fluorescence recordings of the experimental system. We introduce a Bayesian hierarchical model on top of hidden Markov models (HMMs) to analyze these data and use the statistical results to answer the biological questions. In addition to resolving the biological puzzles and delineating the regulating roles of different molecular complexes, our statistical results enable us to propose a more detailed mechanism for the late stages of the protein targeting process

Electric Current Focusing Efficiency in Graphene Electric Lens

In present work, we theoretically study the electron wave's focusing phenomenon in a single layered graphene pn junction(PNJ) and obtain the electric current density distribution of graphene PNJ, which is in good agreement with the qualitative result in previous numerical calculations [Science, 315, 1252 (2007)]. In addition, we find that for symmetric PNJ, 1/4 of total electric current radiated from source electrode can be collected by drain electrode. Furthermore, this ratio reduces to 3/16 in a symmetric graphene npn junction. Our results obtained by present analytical method provide a general design rule for electric lens based on negative refractory index systems.Comment: 13 pages, 7 figure

Dynamic disorder in receptor-ligand forced dissociation experiments

Recently experiments showed that some biological noncovalent bonds increase their lifetimes when they are stretched by an external force, and their lifetimes will decrease when the force increases further. Several specific quantitative models have been proposed to explain the intriguing transitions from the "catch-bond" to the "slip-bond". Different from the previous efforts, in this work we propose that the dynamic disorder of the force-dependent dissociation rate can account for the counterintuitive behaviors of the bonds. A Gaussian stochastic rate model is used to quantitatively describe the transitions observed recently in the single bond P-selctin glycoprotein ligand 1(PSGL-1)$-$P-selectin force rupture experiment [Marshall, {\it et al.}, (2003) Nature {\bf 423}, 190-193]. Our model agrees well to the experimental data. We conclude that the catch bonds could arise from the stronger positive correlation between the height of the intrinsic energy barrier and the distance from the bound state to the barrier; classical pathway scenario or {\it a priori} catch bond assumption is not essential.Comment: 4 pages, 2 figure

Area-Constrained Planar Elastica

We determine the equilibria of a rigid loop in the plane, subject to the constraints of fixed length and fixed enclosed area. Rigidity is characterized by an energy functional quadratic in the curvature of the loop. We find that the area constraint gives rise to equilibria with remarkable geometrical properties: not only can the Euler-Lagrange equation be integrated to provide a quadrature for the curvature but, in addition, the embedding itself can be expressed as a local function of the curvature. The configuration space is shown to be essentially one-dimensional, with surprisingly rich structure. Distinct branches of integer-indexed equilibria exhibit self-intersections and bifurcations -- a gallery of plots is provided to highlight these findings. Perturbations connecting equilibria are shown to satisfy a first order ODE which is readily solved. We also obtain analytical expressions for the energy as a function of the area in some limiting regimes.Comment: 23 pages, several figures. Version 2: New title. Changes in the introduction, addition of a new section with conclusions. Figure 14 corrected and one reference added. Version to appear in PR

Dimensional Crossover of Dilute Neon inside Infinitely Long Single-Walled Carbon Nanotubes Viewed from Specific Heats

A simple formula for coordinates of carbon atoms in a unit cell of a single-walled nanotube (SWNT) is presented and the potential of neon (Ne) inside an infinitely long SWNT is analytically derived under the assumption of pair-wise Lennard-Jones potential between Ne and carbon atoms. Specific heats of dilute Ne inside infinitely long (5, 5), (10, 10), (15, 15) and (20, 20) SWNT's are calculated at different temperatures. It is found that Ne inside four kinds of nanotubes exhibits 3-dimensional (3D) gas behavior at high temperature but different behaviors at low temperature: Ne inside (5, 5) nanotube behaves as 1D gas but inside (10, 10), (15, 15), and (20, 20) nanotubes behaves as 2D gas. Furthermore, at ultra low temperature, Ne inside (5, 5) nanotube still displays 1D behavior but inside (10, 10), (15, 15), and (20, 20) nanotubes behaves as lattice gas.Comment: 10 pages, 5 figure