Nanoindentation of virus capsids in a molecular model

A molecular-level model is used to study the mechanical response of empty cowpea chlorotic mottle virus (CCMV) and cowpea mosaic virus (CPMV) capsids. The model is based on the native structure of the proteins that consitute the capsids and is described in terms of the C-alpha atoms. Nanoindentation by a large tip is modeled as compression between parallel plates. Plots of the compressive force versus plate separation for CCMV are qualitatively consistent with continuum models and experiments, showing an elastic region followed by an irreversible drop in force. The mechanical response of CPMV has not been studied, but the molecular model predicts an order of magnitude higher stiffness and a much shorter elastic region than for CCMV. These large changes result from small structural changes that increase the number of bonds by only 30% and would be difficult to capture in continuum models. Direct comparison of local deformations in continuum and molecular models of CCMV shows that the molecular model undergoes a gradual symmetry breaking rotation and accommodates more strain near the walls than the continuum model. The irreversible drop in force at small separations is associated with rupturing nearly all of the bonds between capsid proteins in the molecular model while a buckling transition is observed in continuum models.Comment: 18 figure

Degree of entanglement as a physically ill-posed problem: The case of entanglement with vacuum

We analyze an example of a photon in superposition of different modes, and ask what is the degree of their entanglement with vacuum. The problem turns out to be ill-posed since we do not know which representation of the algebra of canonical commutation relations (CCR) to choose for field quantization. Once we make a choice, we can solve the question of entanglement unambiguously. So the difficulty is not with mathematics, but with physics of the problem. In order to make the discussion explicit we analyze from this perspective a popular argument based on a photon leaving a beam splitter and interacting with two two-level atoms. We first solve the problem algebraically in Heisenberg picture, without any assumption about the form of representation of CCR. Then we take the $\infty$-representation and show in two ways that in two-mode states the modes are maximally entangled with vacuum, but single-mode states are not entangled. Next we repeat the analysis in terms of the representation of CCR taken from Berezin's book and show that two-mode states do not involve the mode-vacuum entanglement. Finally, we switch to a family of reducible representations of CCR recently investigated in the context of field quantization, and show that the entanglement with vacuum is present even for single-mode states. Still, the degree of entanglement is here difficult to estimate, mainly because there are $N+2$ subsystems, with $N$ unspecified and large.Comment: This paper is basically a reply to quant-ph/0507189 by S. J. van Enk and to the remarks we got from L. Vaidman after our preliminary quant-ph/0507151. Version accepted in Phys. Rev.

Multiple Concentric Cylinder Model (MCCM) user's guide

A user's guide for the computer program mccm.f is presented. The program is based on a recently developed solution methodology for the inelastic response of an arbitrarily layered, concentric cylinder assemblage under thermomechanical loading which is used to model the axisymmetric behavior of unidirectional metal matrix composites in the presence of various microstructural details. These details include the layered morphology of certain types of ceramic fibers, as well as multiple fiber/matrix interfacial layers recently proposed as a means of reducing fabrication-induced, and in-service, residual stress. The computer code allows efficient characterization and evaluation of new fibers and/or new coating systems on existing fibers with a minimum of effort, taking into account inelastic and temperature-dependent properties and different morphologies of the fiber and the interfacial region. It also facilitates efficient design of engineered interfaces for unidirectional metal matrix composites

Properties of the solvation force of a two-dimensional Ising strip in scaling regimes

We consider d=2 Ising strip with surface fields acting on boundary spins. Using the properties of the transfer matrix spectrum we identify two pseudotransition temperatures and show that they satisfy similar scaling relations as expected for real transition temperatures in strips with d>2. The solvation force between the boundaries of the strip is analysed as a function of temperature, surface fields and the width of the strip. For large widths the solvation force can be described by scaling functions in three different regimes: in the vicinity of the critical wetting temperature of 2D semi-infinite system, in the vicinity of the bulk critical temperature, and in the regime of weak surface fields where the critical wetting temperature tends towards the bulk critical temperature. The properties of the relevant scaling functions are discussed

Basic Twist Quantization of the Exceptional Lie Algebra G_2

We present the formulae for twist quantization of $g_2$, corresponding to the solution of classical YB equation with support in the 8-dimensional Borel subalgebra of $g_2$. The considered chain of twists consists of the four factors describing the four steps of quantization: Jordanian twist, the two twist factors extending Jordanian twist and the deformed Jordanian or in second variant additional Abelian twist. The first two steps describe as well the $sl(3)$ quantization. The coproducts are calculated for each step in explicite form, and for that purpose we present new formulas for the calculation of similarity transformations on tensor product. We introduce new basic generators in universal enveloping algebra $U(g_2)$ which provide nonlinearities in algebraic sector maximally simplifying the deformed coproducts.Comment: LaTeX, aps, jmp class, 24 pages. Minor changes, the version in press in JM