Molecular elasticity and the geometric phase

We present a method for solving the Worm Like Chain (WLC) model for twisting semiflexible polymers to any desired accuracy. We show that the WLC free energy is a periodic function of the applied twist with period 4 pi. We develop an analogy between WLC elasticity and the geometric phase of a spin half system. These analogies are used to predict elastic properties of twist-storing polymers. We graphically display the elastic response of a single molecule to an applied torque. This study is relevant to mechanical properties of biopolymers like DNA.Comment: five pages, one figure, revtex, revised in the light of referee's comments, to appear in PR

Thermal Degradation of Adsorbed Bottle-Brush Macromolecules: Molecular Dynamics Simulation

The scission kinetics of bottle-brush molecules in solution and on an adhesive substrate is modeled by means of Molecular Dynamics simulation with Langevin thermostat. Our macromolecules comprise a long flexible polymer backbone with $L$ segments, consisting of breakable bonds, along with two side chains of length $N$, tethered to each segment of the backbone. In agreement with recent experiments and theoretical predictions, we find that bond cleavage is significantly enhanced on a strongly attractive substrate even though the chemical nature of the bonds remains thereby unchanged. We find that the mean bond life time decreases upon adsorption by more than an order of magnitude even for brush molecules with comparatively short side chains $N=1 \div 4$. The distribution of scission probability along the bonds of the backbone is found to be rather sensitive regarding the interplay between length and grafting density of side chains. The life time declines with growing contour length $L$ as $\propto L^{-0.17}$, and with side chain length as $\propto N^{-0.53}$. The probability distribution of fragment lengths at different times agrees well with experimental observations. The variation of the mean length $L(t)$ of the fragments with elapsed time confirms the notion of the thermal degradation process as a first order reaction.Comment: 15 pages, 7 figure

Thermal Fluctuations of Elastic Filaments with Spontaneous Curvature and Torsion

We study the effects of thermal flucutations on thin elastic filaments with spontaneous curvature and torsion. We derive analytical expressions for the orientational correlation functions and for the persistence length of helices, and find that this length varies non-monotonically with the strength of thermal fluctuations. In the weak fluctuation regime, the persistence length of a spontaneously twisted helix has three resonance peaks as a function of the twist rate. In the limit of strong fluctuations, all memory of the helical shape is lost.Comment: 1 figur

Localization and Capacitance Fluctuations in Disordered Au Nano-junctions

Nano-junctions, containing atomic-scale gold contacts between strongly disordered leads, exhibit different transport properties at room temperature and at low temperature. At room temperature, the nano-junctions exhibit conductance quantization effects. At low temperatures, the contacts exhibit Coulomb-Blockade. We show that the differences between the room-temperature and low temperature properties arise from the localization of electronic states in the leads. The charging energy and capacitance of the nano-junctions exhibit strong fluctuations with applied magnetic field at low temperature, as predicted theoretically.Comment: 20 pages 8 figure

Theory of strong inelastic co-tunneling

We develop a theory of the conductance of a quantum dot connected to two leads by single-mode quantum point contacts. If the contacts are in the regime of perfect transmission, the conductance shows no Coulomb blockade oscillations as a function of the gate voltage. In the presence of small reflection in both contacts, the conductance develops small Coulomb blockade oscillations. As the temperature of the system is lowered, the amplitude of the oscillations grows, and eventually sharp periodic peaks in conductance are formed. Away from the centers of the peaks the conductance vanishes at low temperatures as $T^2$, in agreement with the theory of inelastic co-tunneling developed for the weak-tunneling case. Conductance near the center of a peak can be studied using an analogy with the multichannel Kondo problem. In the case of symmetric barriers, the peak conductance at $T\to 0$ is of the order of $e^2/\hbar$. In the asymmetric case, the peak conductance vanishes linearly in temperature.Comment: 22 pages, 4 figures, uses REVTEX 3.0, epsf.sty and multicol.st

Higher-Order Results for the Relation between Channel Conductance and the Coulomb Blockade for Two Tunnel-Coupled Quantum Dots

We extend earlier results on the relation between the dimensionless tunneling channel conductance $g$ and the fractional Coulomb blockade peak splitting $f$ for two electrostatically equivalent dots connected by an arbitrary number $N_{\text{ch}}$ of tunneling channels with bandwidths $W$ much larger than the two-dot differential charging energy $U_{2}$. By calculating $f$ through second order in $g$ in the limit of weak coupling ($g \rightarrow 0$), we illuminate the difference in behavior of the large-$N_{\text{ch}}$ and small-$N_{\text{ch}}$ regimes and make more plausible extrapolation to the strong-coupling ($g \rightarrow 1$) limit. For the special case of $N_{\text{ch}}=2$ and strong coupling, we eliminate an apparent ultraviolet divergence and obtain the next leading term of an expansion in $(1-g)$. We show that the results we calculate are independent of such band structure details as the fraction of occupied fermionic single-particle states in the weak-coupling theory and the nature of the cut-off in the bosonized strong-coupling theory. The results agree with calculations for metallic junctions in the $N_{\text{ch}} \rightarrow \infty$ limit and improve the previous good agreement with recent two-channel experiments.Comment: 27 pages, 1 RevTeX file with 4 embedded Postscript figures. Uses eps

Conformational transitions of heteropolymers in dilute solutions

In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are transformed to a form containing only the mean squared distances between pairs of monomers. These equations are further expressed in terms of instantaneous gradients of the variational free energy. The method allowed us to study exhaustively the stability and conformational structure of some periodic and random aperiodic sequences. A typical phase diagram of a fairly long amphiphilic heteropolymer chain is found to contain phases of the extended coil, the homogeneous globule, the micro-phase separated globule, and a large number of frustrated states, which result in conformational phases of the random coil and the frozen globule. We have also found that for a certain class of sequences the frustrated phases are suppressed. The kinetics of folding from the extended coil to the globule proceeds through non-equilibrium states possessing locally compacted, but partially misfolded and frustrated, structure. This results in a rather complicated multistep kinetic process typical of glassy systems.Comment: 15 pages, RevTeX, 20 ps figures, accepted for publication in Phys. Rev.

Thermodynamics and structure of self-assembled networks

We study a generic model of self-assembling chains which can branch and form networks with branching points (junctions) of arbitrary functionality. The physical realizations include physical gels, wormlike micells, dipolar fluids and microemulsions. The model maps the partition function of a solution of branched, self-assembling, mutually avoiding clusters onto that of a Heisenberg magnet in the mathematical limit of zero spin components. The model is solved in the mean field approximation. It is found that despite the absence of any specific interaction between the chains, the entropy of the junctions induces an effective attraction between the monomers, which in the case of three-fold junctions leads to a first order reentrant phase separation between a dilute phase consisting mainly of single chains, and a dense network, or two network phases. Independent of the phase separation, we predict the percolation (connectivity) transition at which an infinite network is formed that partially overlaps with the first-order transition. The percolation transition is a continuous, non thermodynamic transition that describes a change in the topology of the system. Our treatment which predicts both the thermodynamic phase equilibria as well as the spatial correlations in the system allows us to treat both the phase separation and the percolation threshold within the same framework. The density-density correlation correlation has a usual Ornstein-Zernicke form at low monomer densities. At higher densities, a peak emerges in the structure factor, signifying an onset of medium-range order in the system. Implications of the results for different physical systems are discussed.Comment: Submitted to Phys. Rev.

Quantum state engineering with Josephson-junction devices

We review recent theoretical and experimental progress in quantum state engineering with Josephson junction devices. The concepts of quantum computing have stimulated an increased activity in the field. Either charges or phases (fluxes) of the Josephson systems can be used as quantum degrees of freedom, and their quantum state can be manipulated coherently by voltage and current pulses. They thus can serve as qubits, and quantum logic gates can be performed. Their phase coherence time, which is limited, e.g., by the electromagnetic fluctuations in the control circuit, is long enough to allow a series of these manipulations. The quantum measurement process performed by a single-electron transistor, a SQUID, or further nanoelectronic devices is analyzed in detail.Comment: An article prepared for Reviews of Modern Physics, 46 pages, 23 figure