arXiv subjects

A. R. Bishop

Publications and source records attributed to A. R. Bishop.

At least 127 records · Page 7Linked to original sources

arXiv2003

Structurally specific thermal fluctuations identify functional sites for DNA transcription

We report results showing that thermally-induced openings of double stranded DNA coincide with the location of functionally relevant sites for transcription. Investigating both viral and bacterial DNA gene promoter segments, we found that the most probable opening occurs at the transcription start site. Minor openings appear to be related to other regulatory sites. Our results suggest that coherent thermal fluctuations play an important role in the initiation of transcription. Essential elements of the dynamics, in addition to sequence specificity, are nonlinearity and entropy, provided by local base-pair constraints.

cond-mat.soft↗

arXiv2003

Atomic scale lattice distortions and domain wall profiles

We present an atomic scale theory of lattice distortions using strain related variables and their constraint equations. Our approach connects constrained {\it atomic length} scale variations to {\it continuum} elasticity and describes elasticity at several length scales. We apply the approach to a two-dimensional square lattice with a monatomic basis, and find the elastic deformations and hierarchical atomic relaxations in the vicinity of a domain wall between two different homogeneous strain states. We clarify the microscopic origin of gradient terms, some of which are included phenomenologically in Ginzburg-Landau theory, by showing that they are anisotropic.

cond-mat.mtrl-sci↗

arXiv2003

Atomic scale elastic textures coupled to electrons in superconductors

We present an atomic scale theory of lattice distortions using strain related variables and their constraint equations. Our approach connects constrained atomic length scale variations to continuum elasticity and describes elasticity at all length scales. We apply the general approach to a two-dimensional square lattice with a monatomic basis, and find the atomic scale elastic textures around a structural domain wall and a single defect, as exemplary textures. We clarify the microscopic origin of gradient terms, some of which are included phenomenologically in Landau-Ginzburg theory. The obtained elastic textures are used to investigate the effects of elasticity-driven lattice deformation on the nanoscale electronic structure in superconductor by solving the Bogliubov-de Gennes equations with the electronic degrees of freedom coupled to the lattice ones. It is shown that the order parameter is depressed in the regions where the lattice deformation takes place. The calculated local density of states suggests the electronic structure is strongly modulated as a response to the lattice deformation-- the elasticity propagates the electronic response over long distances. In particular, it is possible for the trapping of low-lying quasiparticle states around the defects. These predictions could be directly tested by STM experiments in superconducting materials.

cond-mat.supr-con↗

arXiv2003

Competing interactions of spin and lattice in the Kondo lattice model

The magnetic properties of a system of coexisting localized spins and conduction electrons are investigated within an extended version of the one dimensional Kondo lattice model in which effects stemming from the electron-lattice and on-site Coulomb interactions are explicitly included. After bosonizing the conduction electrons, is it observed that intrinsic inhomogeneities with the statistical scaling properties of a Griffiths phase appear, and determine the spin structure of the localized impurities. The appearance of the inhomogeneities is enhanced by appropriate phonons and acts destructively on the spin ordering. The inhomogeneities appear on well defined length scales, can be compared to the formation of intrinsic mesoscopic metastable patterns which are found in two-fluid systems.

cond-mat.str-el↗

arXiv2003

Vibrational edge modes in intrinsically inhomogeneous doped transition metal oxides

By applying an unrestriced Hartree-Fock approximation and a Random Phase approximation to multiband Peierls-Hubbard Hamiltonians, we determine the phonon mode structure in models of transition metal oxides in the presence of intrinsic nanoscale inhomogeneities induced by hole doping. We identify low frequency $local$ vibrational modes pinned to the interface between regions of distinct electronic structure and separated in frequency from the band of extended phonons. A major characteristic of these ``edge'' modes is that their energy is essentially insensitive to the doping level, while their intensity increases with the density of interfaces (and thus doping level). We argue that the presence of such modes is a typical feature of systems with phase separation, including cuprates, nickelates, manganites, and bismuthates. We specifically address the experimental signatures of these modes in lattice inelastic neutron scattering.

cond-mat.str-el↗

arXiv2003

Elasticity-Driven Nanoscale Electronic Structure in Superconductors

The effects of long-range anisotropic elastic deformations on electronic structure in superconductors are analyzed within the framework of the Bogoliubov-de Gennes equations. Cases of twin boundaries and isolated defects are considered as illustrations. We find that the superconducting order parameter is depressed in the regions where pronounced lattice deformation occurs. The calculated local density of states suggests that the electronic structure is strongly modulated in response to lattice deformations, and propagates to longer distances. In particular, this allows the trapping of low-lying quasiparticle states around defects. Some of our predictions can be directly tested by STM experiments.

cond-mat.supr-con↗

arXiv2003

A Novel Mechanism for Superfluidity Breakdown in Weakly Coupled Bose-Einstein Condensates

This paper has been withdrawn by the authors. The authors have now written two separate papers, one theoretical (A. Smerzi, A. Trombettoni, P. G. Kevrekidis, and A. R. Bishop Phys. Rev. Lett. 89, 170402 (2002)) and one experimental (F. S. Cataliotti, L. Fallani, F. Ferlaino, C. Fort, P. Maddaloni, and M. Inguscio New Journal of Physics 5, 71 (2003)).

cond-mat.soft↗

arXiv2003

Dark-in-Bright Solitons in Bose-Einstein Condensates with Attractive Interactions

We demonstrate a possibility to generate localized states in effectively one-dimensional Bose-Einstein condensates with a negative scattering length in the form of a dark soliton in the presence of an optical lattice (OL) and/or a parabolic magnetic trap. We connect such structures with twisted localized modes (TLMs) that were previously found in the discrete nonlinear Schr{ö}dinger equation. Families of these structures are found as functions of the OL strength, tightness of the magnetic trap, and chemical potential, and their stability regions are identified. Stable bound states of two TLMs are also found. In the case when the TLMs are unstable, their evolution is investigated by means of direct simulations, demonstrating that they transform into large-amplitude fundamental solitons. An analytical approach is also developed, showing that two or several fundamental solitons, with the phase shift $π$ between adjacent ones, may form stable bound states, with parameters quite close to those of the TLMs revealed by simulations. TLM structures are found numerically and explained analytically also in the case when the OL is absent, the condensate being confined only by the magnetic trap.

cond-mat.soft↗

arXiv2003

Elasticity-driven Nanoscale Texturing in Complex Electronic Materials

Finescale probes of many complex electronic materials have revealed a non-uniform nanoworld of sign-varying textures in strain, charge and magnetization, forming meandering ribbons, stripe segments or droplets. We introduce and simulate a Ginzburg-Landau model for a structural transition, with strains coupling to charge and magnetization. Charge doping acts as a local stress that deforms surrounding unit cells without generating defects. This seemingly innocuous constraint of elastic `compatibility', in fact induces crucial anisotropic long-range forces of unit-cell discrete symmetry, that interweave opposite-sign competing strains to produce polaronic elasto-magnetic textures in the composite variables. Simulations with random local doping below the solid-solid transformation temperature reveal rich multiscale texturing from induced elastic fields: nanoscale phase separation, mesoscale intrinsic inhomogeneities, textural cross-coupling to external stress and magnetic field, and temperature-dependent percolation. We describe how this composite textured polaron concept can be valuable for doped manganites, cuprates and other complex electronic materials.

cond-mat.mtrl-sci↗

arXiv2003

Long-range Charger transfer in DNA through Polaron Diffusion

Recent experimental evidence shows that the pi-orbitals along the stacking of base pairs can facilitate the long-range charge transfer in DNA. Proton motion in the base pair hydrogen bonds has also been found to affect the transfer rate. To explain this behavior we propose a model considering interactions of doped charges with hydrogen bonds and vibrations in DNA. The charge trapped by either protons or vibrations can cause structural distortions leading to polaron formation. By further considering polaron diffusion in DNA we find that the charge transfer rate derived from the diffusion coefficient is in agreement with the experimental results.

cond-mat.mtrl-sci↗

arXiv2003

Feedback Loops Between Fields and Underlying Space Curvature: an Augmented Lagrangian Approach

We demonstrate a systematic implementation of coupling between a scalar field and the geometry of the space (curve, surface, etc.) which carries the field. This naturally gives rise to a feedback mechanism between the field and the geometry. We develop a systematic model for the feedback in a general form, inspired by a specific implementation in the context of molecular dynamics (the so-called Rahman-Parrinello molecular dynamics, or RP-MD). We use a generalized Lagrangian that allows for the coupling of the space's metric tensor (the first fundamental form) to the scalar field, and add terms motivated by RP-MD. We present two implementations of the scheme: one in which the metric is only time-dependent [which gives rise to ordinary differential equation (ODE) for its temporal evolution], and one with spatio-temporal dependence [wherein the metric's evolution is governed by a partial differential equation (PDE)]. Numerical results are reported for the (1+1)-dimensional model with a nonlinearity of the sine-Gordon type.

nlin.PS↗

arXiv2003

Domain Walls in Two-Component Dynamical Lattices

We introduce domain-wall (DW) states in the bimodal discrete nonlinear Schr{ö}dinger equation, in which the modes are coupled by cross phase modulation (XPM). By means of continuation from various initial patterns taken in the anti-continuum (AC) limit, we find a number of different solutions of the DW type, for which different stability scenarios are identified. In the case of strong XPM coupling, DW configurations contain a single mode at each end of the chain. The most fundamental solution of this type is found to be always stable. Another solution, which is generated by a different AC pattern, demonstrates behavior which is unusual for nonlinear dynamical lattices: it is unstable for small values of the coupling constant $C$ (which measures the ratio of the nonlinearity and coupling lengths), and becomes stable at larger $C$. Stable bound states of DWs are also found. DW configurations generated by more sophisticated AC patterns are identified as well, but they are either completely unstable, or are stable only at small values of $C$. In the case of weak XPM, a natural DW solution is the one which contains a combination of both polarizations, with the phase difference between them 0 and $π$ at the opposite ends of the lattice. This solution is unstable at all values of $C$, but the instability is very weak for large $C$, indicating stabilization as the continuum limit is approached. The stability of DWs is also verified by direct simulations, and the evolution of unstable DWs is simulated too; in particular, it is found that, in the weak-XPM system, the instability may give rise to a moving DW.

nlin.PS↗

arXiv2003

Dynamics and Melting of Stripes, Crystals, and Bubbles with Quenched Disorder

Two-dimensional systems in which there is a competition between long-range repulsion and short range attraction exhibit a remarkable variety of patterns such as stripes, bubbles, and labyrinths. Such systems include magnetic films, Langmuir monolayers, polymers, gels, water-oil mixtures, and two-dimensional electron systems. In many of these systems quenched disorder from the underlying substrate may be present. We examine the dynamics and stripe formation in the presence of both an applied dc drive and quenched disorder. When the disorder strength exceeds a critical value, an applied dc drive can induce a dynamical stripe ordering transition to a state that is more ordered than the originating undriven, unpinned pattern.

cond-mat.soft↗

arXiv2002

Effect of FET geometry on charge ordering of transition metal oxides

We examine the effect of an FET geometry on the charge ordering phase diagram of transition metal oxides using numerical simulations of a semiclassical model including long-range Coulomb fields, resulting in nanoscale pattern formation. We find that the phase diagram is unchanged for insulating layers thicker than approximately twice the magnetic correlation length. For very thin insulating layers, the onset of a charge clump phase is shifted to lower values of the strength of the magnetic dipolar interaction, and intermediate diagonal stripe and geometric phases can be suppressed. Our results indicate that, for sufficiently thick insulating layers, charge injection in an FET geometry can be used to experimentally probe the intrinsic charge ordering phases in these materials.

cond-mat.mes-hall↗

arXiv2002

Ferroelastic Dynamics and Strain Compatibility

We derive underdamped evolution equations for the order-parameter (OP) strains of a ferroelastic material undergoing a structural transition, using Lagrangian variations with Rayleigh dissipation, and a free energy as a polynomial expansion in the $N=n+N_{op}$ symmetry-adapted strains. The $N_{op}$ strain equations are structurally similar in form to the Lagrange-Rayleigh 1D strain dynamics of Bales and Gooding (BG), with `strain accelerations' proportional to a Laplacian acting on a sum of the free energy strain derivative and frictional strain force. The tensorial St. Venant's elastic compatibility constraints that forbid defects, are used to determine the n non-order-parameter strains in terms of the OP strains, generating anisotropic and long-range OP contributions to the free energy, friction and noise. The {\it same} OP equations are obtained by either varying the displacement vector components, or by varying the N strains subject to the $N_c$ compatibility constraints. A Fokker-Planck equation, based on the BG dynamics with noise terms, is set up. The BG dynamics corresponds to a set of nonidentical nonlinear (strain) oscillators labeled by wavevector $\vec{k}$, with competing short- and long-range couplings. The oscillators have different `strain-mass' densities $ρ(k) \sim 1/k^2$ and dampings $\sim 1/ρ(k) \sim k^2$, so the lighter large-k oscillators equilibrate first, corresponding to earlier formation of smaller-scale oriented textures. This produces a sequential-scale scenario for post-quench nucleation, elastic patterning, and hierarchical growth. (Continued ...)

cond-mat.mtrl-sci↗

arXiv2002

Polarized Magnetic Wire Induced by Tunneling Through a Magnetic Impurity

Using the zero mode method we compute the conductance of a wire consisting of a magnetic impurity coupled to two Luttinger liquid leads characterized by the Luttinger exponent $α(\leq 1)$. We find for resonance conditions, in which the Fermi energy of the leads is close to a single particle energy of the impurity, the conductance as a function of temperature is $G \sim \frac{e^2}{h} (T/T_F)^{2(α-2)}$, whereas for off-resonance conditions the conductance is $G \sim \frac{e^2}{h} (T/T_F)^{2(α-1)}$. By applying a gate voltage and/or a magnetic field, one of the spin components can be in resonance while the other is off-resonance causing a strong asymmetry between the spin-up and spin-down conductances.

cond-mat.str-el↗

arXiv2002

Thermal diffusion of supersonic solitons in an anharmonic chain of atoms

We study the non-equilibrium diffusion dynamics of supersonic lattice solitons in a classical chain of atoms with nearest-neighbor interactions coupled to a heat bath. As a specific example we choose an interaction with cubic anharmonicity. The coupling between the system and a thermal bath with a given temperature is made by adding noise, delta-correlated in time and space, and damping to the set of discrete equations of motion. Working in the continuum limit and changing to the sound velocity frame we derive a Korteweg-de Vries equation with noise and damping. We apply a collective coordinate approach which yields two stochastic ODEs which are solved approximately by a perturbation analysis. This finally yields analytical expressions for the variances of the soliton position and velocity. We perform Langevin dynamics simulations for the original discrete system which fully confirm the predictions of our analytical calculations, namely noise-induced superdiffusive behavior which scales with the temperature and depends strongly on the initial soliton velocity. A normal diffusion behavior is observed for very low-energy solitons where the noise-induced phonons also make a significant contribution to the soliton diffusion.

cond-mat.soft↗

arXiv2002

Ground state properties of ferromagnetic metal/conjugated polymer interfaces

We theoretically investigate the ground state properties of ferromagnetic metal/conjugated polymer interfaces. The work is partially motivated by recent experiments in which injection of spin polarized electrons from ferromagnetic contacts into thin films of conjugated polymers was reported. We use a one-dimensional nondegenerate Su-Schrieffer-Heeger (SSH) Hamiltonian to describe the conjugated polymer and one-dimensional tight-binding models to describe the ferromagnetic metal. We consider both a model for a conventional ferromagnetic metal, in which there are no explicit structural degrees of freedom, and a model for a half-metallic ferromagnetic colossal magnetoresistance (CMR) oxide which has explicit structural degrees of freedom. The Fermi energy of the magnetic metallic contact is adjusted to control the degree of electron transfer into the polymer. We investigate electron charge and spin transfer from the ferromagnetic metal to the organic polymer, and structural relaxation near the interface. Bipolarons are the lowest energy charge state in the bulk polymer for the nondegenerate SSH model Hamiltonian. As a result electrons (or holes) transferred into the bulk of the polymer form spinless bipolarons. However, there can be spin density in the polymer localized near the interface.

cond-mat.mtrl-sci↗