Editorial: Response to cardiac resynchronization therapy

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A non-perturbative analysis of symmetry breaking in two-dimensional phi^4 theory using periodic field methods

We describe the generalization of spherical field theory to other modal expansion methods. The main approach remains the same, to reduce a d-dimensional field theory into a set of coupled one-dimensional systems. The method we discuss here uses an expansion with respect to periodic-box modes. We apply the method to phi^4 theory in two dimensions and compute the critical coupling and critical exponents. We compare with lattice results and predictions via universality and the two-dimensional Ising model.Comment: 12 pages, 4 figures, version to appear in Physics Letters

Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes

A general approach for calculating spectral and optical properties of pigment-protein complexes of known atomic structure is presented. The method, that combines molecular dynamics simulations, quantum chemistry calculations and statistical mechanical modeling, is demonstrated by calculating the absorption and circular dichroism spectra of the B800-B850 BChls of the LH2 antenna complex from Rs. molischianum at room temperature. The calculated spectra are found to be in good agreement with the available experimental results. The calculations reveal that the broadening of the B800 band is mainly caused by the interactions with the polar protein environment, while the broadening of the B850 band is due to the excitonic interactions. Since it contains no fitting parameters, in principle, the proposed method can be used to predict optical spectra of arbitrary pigment-protein complexes of known structure.Comment: ReVTeX4, 11 pages, 9 figures, submitted to J. Chem. Phy

Calculating potentials of mean force and diffusion coefficients from nonequilibirum processes without Jarzynski's equality

In general, the direct application of the Jarzynski equality (JE) to reconstruct potentials of mean force (PMFs) from a small number of nonequilibrium unidirectional steered molecular dynamics (SMD) paths is hindered by the lack of sampling of extremely rare paths with negative dissipative work. Such trajectories, that transiently violate the second law, are crucial for the validity of JE. As a solution to this daunting problem, we propose a simple and efficient method, referred to as the FR method, for calculating simultaneously both the PMF U(z) and the corresponding diffusion coefficient D(z) along a reaction coordinate z for a classical many particle system by employing a small number of fast SMD pullings in both forward (F) and time reverse (R) directions, without invoking JE. By employing Crook's transient fluctuation theorem (that is more general than JE) and the stiff spring approximation, we show that: (i) the mean dissipative work W_d in the F and R pullings are equal, (ii) both U(z) and W_d can be expressed in terms of the easily calculable mean work of the F and R processes, and (iii) D(z) can be expressed in terms of the slope of W_d. To test its viability, the FR method is applied to determine U(z) and D(z) of single-file water molecules in single-walled carbon nanotubes (SWNTs). The obtained U(z) is found to be in very good agreement with the results from other PMF calculation methods, e.g., umbrella sampling. Finally, U(z) and D(z) are used as input in a stochastic model, based on the Fokker-Planck equation, for describing water transport through SWNTs on a mesoscopic time scale that in general is inaccessible to MD simulations.Comment: ReVTeX4, 13 pages, 6 EPS figures, Submitted to Journal of Chemical Physic

Phase Fluctuations and Pseudogap Properties: Influence of Nonmagnetic Impurities

The presence of nonmagnetic impurities in a 2D ``bad metal'' depresses the superconducting Berezinskii-Kosterlitz-Thouless transition temperature, while leaving the pairing energy scale unchanged. Thus the region of the pseudogap non-superconducting phase, where the modulus of the order parameter is non-zero but its phase is random, and which opens at the pairing temperature is substantially bigger than for the clean system. This supports the premise that fluctuations in the phase of the order parameter can in principle describe the pseudogap phenomena in high-$T_c$ materials over a rather wide range of temperatures and carrier densities. The temperature dependence of the bare superfluid density is also discussed.Comment: 11 pages, LaTeX, 1 EPS figure; final version to appear in Low.Temp.Phy

Pairing Fluctuation Theory of Superconducting Properties in Underdoped to Overdoped Cuprates

We propose a theoretical description of the superconducting state of under- to overdoped cuprates, based on the short coherence length of these materials and the associated strong pairing fluctuations. The calculated $T_c$ and the zero temperature excitation gap $\Delta(0)$, as a function of hole concentration $x$, are in semi-quantitative agreement with experiment. Although the ratio $T_c/\Delta(0)$ has a strong $x$ dependence, different from the universal BCS value, and $\Delta(T)$ deviates significantly from the BCS prediction, we obtain, quite remarkably, quasi-universal behavior, for the normalized superfluid density $\rho_s(T)/\rho_s(0)$ and the Josephson critical current $I_c(T)/I_c(0)$, as a function of $T/T_c$. While experiments on $\rho_s(T)$ are consistent with these results, future measurements on $I_c(T)$ are needed to test this prediction.Comment: 4 pages, 3 figures, REVTeX, submitted to Phys. Rev. Let

Comment on "Is the nonlinear Meissner effect unobservable?"

In a recent Letter (Phys. Rev. Lett. 81, p.5640 (1998), cond-mat/9808249 v3), it was suggested that nonlocal effects may prevent observation of the nonlinear Meissner effect in YBCO. We argue that this claim is incorrect with regards to measurements of the nonlinear transverse magnetic moment, and that the most likely reason for a null result lies elsewhere.Comment: 1 pag

Kinetic Monte Carlo and Cellular Particle Dynamics Simulations of Multicellular Systems

Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of cell aggregates as bioink particles. Computer simulations based on Metropolis Monte Carlo (MMC) algorithms were successful in explaining and predicting the resulting stationary structures (corresponding to the lowest adhesion energy state). Here we present two alternatives to the MMC approach for modeling cellular motion and self-assembly: (1) a kinetic Monte Carlo (KMC), and (2) a cellular particle dynamics (CPD) method. Unlike MMC, both KMC and CPD methods are capable of simulating the dynamics of the cellular system in real time. In the KMC approach a transition rate is associated with possible rearrangements of the cellular system, and the corresponding time evolution is expressed in terms of these rates. In the CPD approach cells are modeled as interacting cellular particles (CPs) and the time evolution of the multicellular system is determined by integrating the equations of motion of all CPs. The KMC and CPD methods are tested and compared by simulating two experimentally well known phenomena: (1) cell-sorting within an aggregate formed by two types of cells with different adhesivities, and (2) fusion of two spherical aggregates of living cells.Comment: 11 pages, 7 figures; submitted to Phys Rev

Chaos in Andreev Billiards

A new type of classical billiard - the Andreev billiard - is investigated using the tangent map technique. Andreev billiards consist of a normal region surrounded by a superconducting region. In contrast with previously studied billiards, Andreev billiards are integrable in zero magnetic field, {\it regardless of their shape}. A magnetic field renders chaotic motion in a generically shaped billiard, which is demonstrated for the Bunimovich stadium by examination of both Poincar\'e sections and Lyapunov exponents. The issue of the feasibility of certain experimental realizations is addressed.Comment: ReVTeX3.0, 4 pages, 3 figures appended as postscript file (uuencoded with uufiles

Algorithm for obtaining the gradient expansion of the local density of states and the free energy of a superconductor

We present an efficient algorithm for obtaining the gauge-invariant gradient expansion of the local density of states and the free energy of a clean superconductor. Our method is based on a new mapping of the semiclassical linearized Gorkov equations onto a pseudo-Schroedinger equation for a three-component wave-function psi(x), where one component is directly related to the local density of states. Because psi(x) satisfies a linear equation of motion, successive terms in the gradient expansion can be obtained by simple linear iteration. Our method works equally well for real and complex order parameter, and in the presence of arbitrary external fields. We confirm a recent calculation of the fourth order correction to the free energy by Kosztin, Kos, Stone and Leggett [Phys. Rev. B 58, 9365 (1998)], who obtained a discrepancy with an earlier result by Tewordt [Z. Phys. 180, 385 (1964)]. We also give the fourth order correction to the local density of states, which has not been published before.Comment: 12 preprint pages, added remark concerning Eilenberger equation, accepted for publication in Phys. Rev.