No abstract

No abstract

Results are presented in the theory of the elastic rod model for DNA, among which are criteria enabling one to determine whether a calculated equilibrium configuration of a DNA segment is stable in the sense that it gives a local minimum to the sum of the segment's elastic energy and the potential of forces acting on it. The derived stability criteria are applicable to plasmids and to linear segments subject to strong anchoring end conditions. Their utility is illustrated with an example from the theory of configurations of the extranucleosomal loop of a DNA miniplasmid in a mononucleosome, with emphasis placed on the influence that nicking and ligation on one hand, and changes in the ratio of elastic coefficients on the other, have on the stability of equilibrium configurations. In that example, the configurations studied are calculated using an extension of the method of explicit solutions to cases in which the elastic rod modeling a DNA segment is considered impenetrable, and hence excluded volume effects and forces arising from self-contact are taken into account.

No abstract

A DNA polymer with hundreds or thousands of base pairs is modeled as a thin elastic rod. To find the equilibrium configurations and associated elastic energies as a function of linking number difference (ΔLk), a finite element scheme based on Kirchhoff’s rod theory is newly formulated so as to be able to treat self-contact. The numerical results obtained here agree well with those already published, both analytical and numerical, but a much more detailed picture emerges of the several equilibrium states which can exist for a given ΔLk. Of particular interest is the discovery of interwound states having odd integral values of the writhing number and very small twist energy. The existence of a noncircular cross section, inhomogeneous elastic constants, intrinsic curvature, and sequence-dependent bending and twisting can all be readily incorporated into the new formalism.

In order to enhance infrared light absorption in sub-bandgap transitions in an intermediate band solar cell, the scattered near-field potential from uncoated and coated metallic nanoparticles with a spheroidal shape is calculated with the electrostatic model. The absorption enhancement produced at the surface plasmon frequency of the nanoparticles can be of several orders of magnitude in some cases.Conventional single-gap solar cells cannot exploit photon energies below semiconductor bandgap energies. A promising concept to overcome this limitation is the intermediate band solar cell (IBSC), which reaches a detailed balance efficiency limit of 63.2% compared to 40.7% for singlegap cells. The IBSC can generate photocurrent from subbandgap photons, without voltage degradation, due to the existence of an electronic band-the intermediate band (IB)-within the semiconductor bandgap.The IB can be formed by the confined levels of a quantum dot (QD) array. Prototype IBSCs were fabricated with ten QD layers. However, the IB impact on the cell performance is still marginal, mainly due to the weak absorption coefficient associated to the QDs. One way of increasing this absorption is to grow more QD layers, but this introduces strain-induced dislocations that deteriorate the device performance. Procedures for reducing the strain are in development, ~ but this is still a challenging problem. In this contribution, an alternative procedure is studied that exploits the high near-field that can appear in the vicinity of metal nanoparticles (MNPs) sustaining surface plasmons. The inclusion of these particles close to QDs can amplify their absorption, allowing the replacement of several QD layers by a single one with MNPs. These MNPs might also induce defects but it is possible that the reduction of layers has an overall positive effect.When an electric plane-wave impinges on a particle much smaller than its wavelength the electric field induced inside the particle can be assumed uniform. This is the principle of electrostatic approximation (EA), valid only if the following conditions are simultaneously fulfilled:277T eq /\ s is obtained from Laplace equation (V-E = 0) whose solution is exact for ellipsoids with semiaxes a, b, and c. Due to the unpolarized na...

Configurations of protein-free DNA miniplasmids are calculated with the effects of impenetrability and self-contact forces taken into account by using exact solutions of Kirchhoff's equations of equilibrium for elastic rods of circular cross section. Bifurcation diagrams are presented as graphs of excess link, DeltaL, versus writhe, W, and the stability criteria derived in paper I of this series are employed in a search for regions of such diagrams that correspond to configurations that are stable, in the sense that they give local minima to elastic energy. Primary bifurcation branches that originate at circular configurations are composed of configurations with D(m) symmetry (m=2,3,...). Among the results obtained are the following. (i) There are configurations with C2 symmetry forming secondary bifurcation branches which emerge from the primary branch with m=3, and bifurcation of such secondary branches gives rise to tertiary branches of configurations without symmetry. (ii) Whether or not self-contact occurs, a noncircular configuration in the primary branch with m=2, called branch alpha, is stable when for it the derivative dDeltaL/dW, computed along that branch, is strictly positive. (iii) For configurations not in alpha, the condition dDeltaL/dW>0 is not sufficient for stability; in fact, each nonplanar contact-free configuration that is in a branch other than alpha is unstable. A rule relating the number of points of self-contact and the occurrence of intervals of such contact to the magnitude of DeltaL, which in paper I was found to hold for segments of DNA subject to strong anchoring end conditions, is here observed to hold for computed configurations of protein-free miniplasmids.

Explicit solutions to the equations of equilibrium in the theory of the elastic rod model for DNA are employed to develop a procedure for finding the configuration that minimizes the elastic energy of a minicircle in a mononucleosome with specified values of the minicircle size N in base pairs, the extent w of wrapping of DNA about the histone core particle, the helical repeat h(0)b of the bound DNA, and the linking number Lk of the minicircle. The procedure permits a determination of the set Y(N, w, h(0)b) of integral values of Lk for which the minimum energy configuration does not involve self-contact, and graphs of writhe versus w are presented for such values of Lk. For the range of N of interest here, 330 < N < 370, the set Y(N, w, h(0)b) is of primary importance: when Lk is not in Y(N, w, h(0)b), the configurations compatible with Lk have elastic energies high enough to preclude the occurrence of an observable concentration of topoisomer Lk in an equilibrium distribution of topoisomers. Equilibrium distributions of Lk, calculated by setting differences in the free energy of the extranucleosomal loop equal to differences in equilibrium elastic energy, are found to be very close to Gaussian when computed under the assumption that w is fixed, but far from Gaussian when it is assumed that w fluctuates between two values. The theoretical results given suggest a method by which one may calculate DNA-histone binding energies from measured equilibrium distributions of Lk.