A Finite-Size Scaling Study of a Model of Globular Proteins

Grand canonical Monte Carlo simulations are used to explore the metastable fluid-fluid coexistence curve of the modified Lennard-Jones model of globular proteins of ten Wolde and Frenkel (Science, v277, 1975 (1997)). Using both mixed-field finite-size scaling and histogram reweighting methods, the joint distribution of density and energy fluctuations is analyzed at coexistence to accurately determine the critical-point parameters. The subcritical coexistence region is explored using the recently developed hyper-parallel tempering Monte Carlo simulation method along with histogram reweighting to obtain the density distributions. The phase diagram for the metastable fluid-fluid coexistence curve is calculated in close proximity to the critical point, a region previously unattained by simulation.Comment: 17 pages, 10 figures, 2 Table

Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins

Without invoking the Markov approximation, we derive formulas for vibrational energy relaxation (VER) and dephasing for an anharmonic system oscillator using a time-dependent perturbation theory. The system-bath Hamiltonian contains more than the third order coupling terms since we take a normal mode picture as a zeroth order approximation. When we invoke the Markov approximation, our theory reduces to the Maradudin-Fein formula which is used to describe VER properties of glass and proteins. When the system anharmonicity and the renormalization effect due to the environment vanishes, our formulas reduce to those derived by Mikami and Okazaki invoking the path-integral influence functional method [J. Chem. Phys. 121 (2004) 10052]. We apply our formulas to VER of the amide I mode of a small amino-acide like molecule, N-methylacetamide, in heavy water.Comment: 16 pages, 5 figures, 5 tables, submitted to J. Chem. Phy

Instantaneous Pair Theory for High-Frequency Vibrational Energy Relaxation in Fluids

Notwithstanding the long and distinguished history of studies of vibrational energy relaxation, exactly how it is that high frequency vibrations manage to relax in a liquid remains somewhat of a mystery. Both experimental and theoretical approaches seem to say that there is a natural frequency range associated with intermolecular motions in liquids, typically spanning no more than a few hundred cm^{-1}. Landau-Teller-like theories explain how a solvent can absorb any vibrational energy within this "band", but how is it that molecules can rid themselves of superfluous vibrational energies significantly in excess of these values? We develop a theory for such processes based on the idea that the crucial liquid motions are those that most rapidly modulate the force on the vibrating coordinate -- and that by far the most important of these motions are those involving what we have called the mutual nearest neighbors of the vibrating solute. Specifically, we suggest that whenever there is a single solvent molecule sufficiently close to the solute that the solvent and solute are each other's nearest neighbors, then the instantaneous scattering dynamics of the solute-solvent pair alone suffices to explain the high frequency relaxation. The many-body features of the liquid only appear in the guise of a purely equilibrium problem, that of finding the likelihood of particularly effective solvent arrangements around the solute. These results are tested numerically on model diatomic solutes dissolved in atomic fluids (including the experimentally and theoretically interesting case of I_2 in Xe). The instantaneous pair theory leads to results in quantitative agreement with those obtained from far more laborious exact molecular dynamics simulations.Comment: 55 pages, 6 figures Scheduled to appear in J. Chem. Phys., Jan, 199

Quantum trajectories for the realistic measurement of a solid-state charge qubit

We present a new model for the continuous measurement of a coupled quantum dot charge qubit. We model the effects of a realistic measurement, namely adding noise to, and filtering, the current through the detector. This is achieved by embedding the detector in an equivalent circuit for measurement. Our aim is to describe the evolution of the qubit state conditioned on the macroscopic output of the external circuit. We achieve this by generalizing a recently developed quantum trajectory theory for realistic photodetectors [P. Warszawski, H. M. Wiseman and H. Mabuchi, Phys. Rev. A_65_ 023802 (2002)] to treat solid-state detectors. This yields stochastic equations whose (numerical) solutions are the ``realistic quantum trajectories'' of the conditioned qubit state. We derive our general theory in the context of a low transparency quantum point contact. Areas of application for our theory and its relation to previous work are discussed.Comment: 7 pages, 2 figures. Shorter, significantly modified, updated versio

Broadband noise decoherence in solid-state complex architectures

Broadband noise represents a severe limitation towards the implementation of a solid-state quantum information processor. Considering common spectral forms, we propose a classification of noise sources based on the effects produced instead of on their microscopic origin. We illustrate a multi-stage approach to broadband noise which systematically includes only the relevant information on the environment, out of the huge parametrization needed for a microscopic description. We apply this technique to a solid-state two-qubit gate in a fixed coupling implementation scheme.Comment: Proceedings of Nobel Symposium 141: Qubits for Future Quantum Informatio

Scanning Quantum Decoherence Microscopy

The use of qubits as sensitive magnetometers has been studied theoretically and recent demonstrated experimentally. In this paper we propose a generalisation of this concept, where a scanning two-state quantum system is used to probe the subtle effects of decoherence (as well as its surrounding electromagnetic environment). Mapping both the Hamiltonian and decoherence properties of a qubit simultaneously, provides a unique image of the magnetic (or electric) field properties at the nanoscale. The resulting images are sensitive to the temporal as well as spatial variation in the fields created by the sample. As an example we theoretically study two applications of this technology; one from condensed matter physics, the other biophysics. The individual components required to realise the simplest version of this device (characterisation and measurement of qubits, nanoscale positioning) have already been demonstrated experimentally.Comment: 11 pages, 5 low quality (but arXiv friendly) image

Density-Functional Theory of Quantum Freezing: Sensitivity to Liquid-State Structure and Statistics

Density-functional theory is applied to compute the ground-state energies of quantum hard-sphere solids. The modified weighted-density approximation is used to map both the Bose and the Fermi solid onto a corresponding uniform Bose liquid, assuming negligible exchange for the Fermi solid. The required liquid-state input data are obtained from a paired phonon analysis and the Feynman approximation, connecting the static structure factor and the linear response function. The Fermi liquid is treated by the Wu-Feenberg cluster expansion, which approximately accounts for the effects of antisymmetry. Liquid-solid transitions for both systems are obtained with no adjustment of input data. Limited quantitative agreement with simulation indicates a need for further improvement of the liquid-state input through practical alternatives to the Feynman approximation.Comment: IOP-TeX, 21 pages + 7 figures, to appear, J. Phys.: Condens. Matte

Translationally invariant nonlinear Schrodinger lattices

Persistence of stationary and traveling single-humped localized solutions in the spatial discretizations of the nonlinear Schrodinger (NLS) equation is addressed. The discrete NLS equation with the most general cubic polynomial function is considered. Constraints on the nonlinear function are found from the condition that the second-order difference equation for stationary solutions can be reduced to the first-order difference map. The discrete NLS equation with such an exceptional nonlinear function is shown to have a conserved momentum but admits no standard Hamiltonian structure. It is proved that the reduction to the first-order difference map gives a sufficient condition for existence of translationally invariant single-humped stationary solutions and a necessary condition for existence of single-humped traveling solutions. Other constraints on the nonlinear function are found from the condition that the differential advance-delay equation for traveling solutions admits a reduction to an integrable normal form given by a third-order differential equation. This reduction also gives a necessary condition for existence of single-humped traveling solutions. The nonlinear function which admits both reductions defines a two-parameter family of discrete NLS equations which generalizes the integrable Ablowitz--Ladik lattice.Comment: 24 pages, 4 figure

Normal form for travelling kinks in discrete Klein-Gordon lattices

We study travelling kinks in the spatial discretizations of the nonlinear Klein--Gordon equation, which include the discrete $\phi^4$ lattice and the discrete sine--Gordon lattice. The differential advance-delay equation for travelling kinks is reduced to the normal form, a scalar fourth-order differential equation, near the quadruple zero eigenvalue. We show numerically non-existence of monotonic kinks (heteroclinic orbits between adjacent equilibrium points) in the fourth-order equation. Making generic assumptions on the reduced fourth-order equation, we prove the persistence of bounded solutions (heteroclinic connections between periodic solutions near adjacent equilibrium points) in the full differential advanced-delay equation with the technique of center manifold reduction. Existence and persistence of multiple kinks in the discrete sine--Gordon equation are discussed in connection to recent numerical results of \cite{ACR03} and results of our normal form analysis

The density functional theory of classical fluids revisited

We reconsider the density functional theory of nonuniform classical fluids from the point of view of convex analysis. From the observation that the logarithm of the grand-partition function $\log \Xi [\phi]$ is a convex functional of the external potential $\phi$ it is shown that the Kohn-Sham free energy ${\cal A}[\rho]$ is a convex functional of the density $\rho$. $\log \Xi [\phi]$ and ${\cal A}[\rho]$ constitute a pair of Legendre transforms and each of these functionals can therefore be obtained as the solution of a variational principle. The convexity ensures the unicity of the solution in both cases. The variational principle which gives $\log \Xi [\phi]$ as the maximum of a functional of $\rho$ is precisely that considered in the density functional theory while the dual principle, which gives ${\cal A}[\rho]$ as the maximum of a functional of $\phi$ seems to be a new result.Comment: 10 page