Spectrins in Axonal Cytoskeletons: Dynamics Revealed by Extensions and Fluctuations

The macroscopic properties, the properties of individual components and how those components interact with each other are three important aspects of a composited structure. An understanding of the interplay between them is essential in the study of complex systems. Using axonal cytoskeleton as an example system, here we perform a theoretical study of slender structures that can be coarse-grained as a simple smooth 3-dimensional curve. We first present a generic model for such systems based on the fundamental theorem of curves. We use this generic model to demonstrate the applicability of the well-known worm-like chain (WLC) model to the network level and investigate the situation when the system is stretched by strong forces (weakly bending limit). We specifically studied recent experimental observations that revealed the hitherto unknown periodic cytoskeleton structure of axons and measured the longitudinal fluctuations. Instead of focusing on single molecules, we apply analytical results from the WLC model to both single molecule and network levels and focus on the relations between extensions and fluctuations. We show how this approach introduces constraints to possible local dynamics of the spectrin tetramers in the axonal cytoskeleton and finally suggests simple but self-consistent dynamics of spectrins in which the spectrins in one spatial period of axons fluctuate in-sync.Comment: 18 pages, 4 figure

Helical structures from an isotropic homopolymer model

We present Monte Carlo simulation results for square-well homopolymers at a series of bond lengths. Although the model contains only isotropic pairwise interactions, under appropriate conditions this system shows spontaneous chiral symmetry breaking, where the chain exists in either a left- or a right-handed helical structure. We investigate how this behavior depends upon the ratio between bond length and monomer radius.Comment: 10 pages, 3 figures, accepted for publication by Physical Review Letter

Multistability of free spontaneously-curved anisotropic strips

Multistable structures are objects with more than one stable conformation, exemplified by the simple switch. Continuum versions are often elastic composite plates or shells, such as the common measuring tape or the slap bracelet, both of which exhibit two stable configurations: rolled and unrolled. Here we consider the energy landscape of a general class of multistable anisotropic strips with spontaneous Gaussian curvature. We show that while strips with non-zero Gaussian curvature can be bistable, strips with positive spontaneous curvature are always bistable, independent of the elastic moduli, strips of spontaneous negative curvature are bistable only in the presence of spontaneous twist and when certain conditions on the relative stiffness of the strip in tension and shear are satisfied. Furthermore, anisotropic strips can become tristable when their bending rigidity is small. Our study complements and extends the theory of multistability in anisotropic shells and suggests new design criteria for these structures.Comment: 20 pages, 10 figure

Theory of pressure acoustics with boundary layers and streaming in curved elastic cavities

The acoustic fields and streaming in a confined fluid depend strongly on the acoustic boundary layer forming near the wall. The width of this layer is typically much smaller than the bulk length scale set by the geometry or the acoustic wavelength, which makes direct numerical simulations challenging. Based on this separation in length scales, we extend the classical theory of pressure acoustics by deriving a boundary condition for the acoustic pressure that takes boundary-layer effects fully into account. Using the same length-scale separation for the steady second-order streaming, and combining it with time-averaged short-range products of first-order fields, we replace the usual limiting-velocity theory with an analytical slip-velocity condition on the long-range streaming field at the wall. The derived boundary conditions are valid for oscillating cavities of arbitrary shape and wall motion as long as the wall curvature and displacement amplitude are both sufficiently small. Finally, we validate our theory by comparison with direct numerical simulation in two examples of two-dimensional water-filled cavities: The well-studied rectangular cavity with prescribed wall actuation, and the more generic elliptical cavity embedded in an externally actuated rectangular elastic glass block.Comment: 18 pages, 5 figures, pdfLatex, RevTe

Measure of phonon-number moments and motional quadratures through infinitesimal-time probing of trapped ions

A method for gaining information about the phonon-number moments and the generalized nonlinear and linear quadratures in the motion of trapped ions (in particular, position and momentum) is proposed, valid inside and outside the Lamb-Dicke regime. It is based on the measurement of first time derivatives of electronic populations, evaluated at the motion-probe interaction time t=0. In contrast to other state-reconstruction proposals, based on measuring Rabi oscillations or dispersive interactions, the present scheme can be performed resonantly at infinitesimal short motion-probe interaction times, remaining thus insensitive to decoherence processes.Comment: 10 pages. Accepted in JPhys

The Generalization of the Decomposition of Functions by Energy Operators

This work starts with the introduction of a family of differential energy operators. Energy operators ($Psi_R^+$, $Psi_R^-$) were defined together with a method to decompose the wave equation in a previous work. Here the energy operators are defined following the order of their derivatives ($Psi_k^+$, $Psi_k^-$, k = {0,1,2,..}). The main part of the work is to demonstrate that for any smooth real-valued function f in the Schwartz space ($S^-(R)$), the successive derivatives of the n-th power of f (n in Z and n not equal to 0) can be decomposed using only $Psi_k^+$ (Lemma) or with $Psi_k^+$, $Psi_k^-$ (k in Z) (Theorem) in a unique way (with more restrictive conditions). Some properties of the Kernel and the Image of the energy operators are given along with the development. Finally, the paper ends with the application to the energy function.Comment: The paper was accepted for publication at Acta Applicandae Mathematicae (15/05/2013) based on v3. v4 is very similar to v3 except that we modified slightly Definition 1 to make it more readable when showing the decomposition with the families of energy operator of the derivatives of the n-th power of

Vortex and translational currents due to broken time-space symmetries

We consider the classical dynamics of a particle in a $d=2,3$-dimensional space-periodic potential under the influence of time-periodic external fields with zero mean. We perform a general time-space symmetry analysis and identify conditions, when the particle will generate a nonzero averaged translational and vortex currents. We perform computational studies of the equations of motion and of corresponding Fokker-Planck equations, which confirm the symmetry predictions. We address the experimentally important issue of current control. Cold atoms in optical potentials and magnetic traps are among possible candidates to observe these findings experimentally.Comment: 4 pages, 2 figure

Interface-mediated interactions: Entropic forces of curved membranes

Particles embedded in a fluctuating interface experience forces and torques mediated by the deformations and by the thermal fluctuations of the medium. Considering a system of two cylinders bound to a fluid membrane we show that the entropic contribution enhances the curvature-mediated repulsion between the two cylinders. This is contrary to the usual attractive Casimir force in the absence of curvature-mediated interactions. For a large distance between the cylinders, we retrieve the renormalization of the surface tension of a flat membrane due to thermal fluctuations.Comment: 11 pages, 5 figures; final version, as appeared in Phys. Rev.

On the differential geometry of curves in Minkowski space

We discuss some aspects of the differential geometry of curves in Minkowski space. We establish the Serret-Frenet equations in Minkowski space and use them to give a very simple proof of the fundamental theorem of curves in Minkowski space. We also state and prove two other theorems which represent Minkowskian versions of a very known theorem of the differential geometry of curves in tridimensional Euclidean space. We discuss the general solution for torsionless paths in Minkowki space. We then apply the four-dimensional Serret-Frenet equations to describe the motion of a charged test particle in a constant and uniform electromagnetic field and show how the curvature and the torsions of the four-dimensional path of the particle contain information on the electromagnetic field acting on the particle.Comment: 10 pages. Typeset using REVTE

Application of the level-set method to the implicit solvation of nonpolar molecules

A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model (Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. {\bf 104}, 527 (2006) and J. Chem.\Phys. {\bf 124}, 084905 (2006)). In the level-set method, a possible solute-solvent interface is represented by the zero level-set (i.e., the zero level surface) of a level-set function and is eventually evolved into the equilibrium solute-solvent interface. The evolution law is determined by minimization of a solvation free energy {\it functional} that couples both the interfacial energy and the van der Waals type solute-solvent interaction energy. The surface evolution is thus an energy minimizing process, and the equilibrium solute-solvent interface is an output of this process. The method is implemented and applied to the solvation of nonpolar molecules such as two xenon atoms, two parallel paraffin plates, helical alkane chains, and a single fullerene $C_{60}$. The level-set solutions show good agreement for the solvation energies when compared to available molecular dynamics simulations. In particular, the method captures solvent dewetting (nanobubble formation) and quantitatively describes the interaction in the strongly hydrophobic plate system