Extracting the underlying effective free energy landscape from single-molecule time series--local equilibrium states and their network

We present a new self-consistent procedure to construct a multidimensional effective free energy landscape from a scalar single molecule time series, when single molecules experience the landscape within a given timescale of "observation." The theory is based on a framework we recently developed to extract a set of local equilibrium states (LESs) and their network from a scalar time series, such as distance between dye molecules tagged in a biomolecule. We scrutinize the appropriateness of the assumptions of local equilibration and local detailed balance among LESs at the single molecule level within the given timescale, rather than postulating them a priori. The self-consistent procedure in this article incorporates the effect of local correlation of the system dynamics inside potential basins, and the effect of finiteness of the sampled data points in assigning the boundary between different LESs. We propose a new simple scheme to assign the dimensionality of the energy landscape from a single molecule time series. We also address the question of what the molecules actually "feel" from the underlying landscape at the single molecule level.     

Constrained dynamics and extraction of normal modes from ab initio molecular dynamics: application to ammonia

We present a methodology for extracting phonon data from ab initio Born-Oppenheimer molecular dynamics calculations of molecular crystals. Conventional ab initio phonon methods based on perturbations are difficult to apply to lattice modes because the perturbation energy is dominated by intramolecular modes. We use constrained molecular dynamics to eliminate the effect of bond bends and stretches and then show how trajectories can be used to isolate and define in particular, the eigenvalues and eigenvectors of modes irrespective of their symmetry or wave vector. This is done by k-point and frequency filtering and projection onto plane wave states. The method is applied to crystalline ammonia: the constrained molecular dynamics allows a significant speed-up without affecting structural or vibrational modes. All Gamma point lattice modes are isolated: the frequencies are in agreement with previous studies; however, the mode assignments are different.     

Infrared spectroscopy of small protonated water clusters at room temperature: an effective modes analysis

We perform infrared vibrational analysis on small protonated water clusters H(+)(H(2)O)(n), with n = 2, [ellipsis (horizontal)], 6, at room temperature. The absorption spectra are calculated based on classical trajectories obtained by the multistate empirical valence bond method. The analysis is carried out based on the effective modes analysis, which has been recently developed [Martinez et al., J. Chem. Phys. 125, 144106 (2006)] as generalization of the normal modes analysis. This technique enables us to decompose the full spectrum in maximally localized bands which are obtained by accounting for temperature and anharmonic effects. These effects are especially considered in the determination of the modes coupling. The spectra of the small clusters are interpreted by identifying the behavior of the excess charge, by understanding the role of hydrogen bonds, and by considering the effect of (micro-)solvation. Our results are presented by showing comparisons with other numerical methods and experimental measurements which are available in the literature.     

Helium clusters at finite temperature

An analysis of helium cluster properties at finite temperature using a phenomenological free energy density has been carried out. We have studied in detail the energetics and the density profile characteristics of hot drops of both helium isotopes containing 70, 112, 168, 240 and 330 atoms. A finite temperature mass formula including volume, surface and curvature terms has been derived.     

Bending dynamics of acetylene: new modes born in bifurcations of normal modes

Semiclassical techniques are used to analyze highly excited pure bending vibrational dynamics from spectra of C2H2. An analytic bifurcation approach is developed, based on critical points of a classical version of the quantum fitting Hamiltonian. At high energy four new types of anharmonic modes are born in bifurcations of the normal modes: local, orthogonal, precessional, and counter-rotator. Visual insight into their nature is obtained with the help of computer-generated three-dimensional animations. The connection between the local mode and the acetylene-vinylidene isomerization "reaction mode" is considered.     

Calculating intensities using effective Hamiltonians in terms of Coriolis-adapted normal modes

The calculation of rovibrational transition energies and intensities is often hampered by the fact that vibrational states are strongly coupled by Coriolis terms. Because it invalidates the use of perturbation theory for the purpose of decoupling these states, the coupling makes it difficult to analyze spectra and to extract information from them. One either ignores the problem and hopes that the effect of the coupling is minimal or one is forced to diagonalize effective rovibrational matrices (rather than diagonalizing effective rotational matrices). In this paper we apply a procedure, based on a quantum mechanical canonical transformation for deriving decoupled effective rotational Hamiltonians. In previous papers we have used this technique to compute energy levels. In this paper we show that it can also be applied to determine intensities. The ideas are applied to the ethylene molecule.     

Quantum dynamics through conical intersections: combining effective modes and quadratic couplings

We present a detailed study for the short-time dynamics through conical intersections in molecular systems related to the quadratic vibronic coupling (QVC) Hamiltonian [Müller, H.; K?ppel, H.; Cederbaum, L. S. New J. Chem. 1993, 17, 7-29] and the effective-mode formalism [Cederbaum, L. S.; Gindensperger, E.; Burghardt, I. Phys. Rev. Lett. 2005, 94, 113003]. Our approach is based on splitting the nuclear degrees of freedom of the whole system into system modes and environment modes. It was found that only three-effective environmental modes together with the system's modes are needed to describe the short-time dynamics of the complex system correctly. In addition, a detailed mathematical proof is given in the appendix to demonstrate that the exact cumulants are recovered up to the second order within the cumulant expansion of the autocorrelation function. The butatriene molecule is studied as an explicit showcase example to stress the viability of our proposed scheme and to compare with other systems.     

Hierarchy of effective modes for the dynamics through conical intersections in macrosystems

An extension of the effective-mode theory for the short-time dynamics through conical intersections in macrosystems [L. S. Cederbaum et al., Phys. Rev. Lett. 94, 113003 (2005)] is proposed. The macrosystem, containing a vast number of nuclear degrees of freedom (modes), is decomposed into a system part and an environment part. Only three effective modes are needed-together with the system's modes-to accurately calculate low resolution spectra and the short-time dynamics of the entire macrosystem. Here, the authors propose an iterative scheme to construct a hierarchy of additional triplets of effective modes. This naturally extends the effective-mode formulation. By taking into account more and more triplets, the dynamics are accurately predicted for longer and longer times, and more resolved spectra can be calculated. Numerical examples are presented, computed using various numbers of additional effective modes.     

Sedimentation equilibrium of suspensions of colloidal particles at finite concentrations

Equilibrium concentration profiles of non-dilute colloidal suspensions are calculated by means of the Carnahan-Starling expression for the osmotic compressibility of hard sphere liquids. The profiles depend on the average volume fraction of the suspension, , and on the field interaction parameter, ₀ (reciprocal of the Péclet number at infinite dilution). Profiles are computed for values of and ₀ typical of those encountered in sedimentation field-flow fractionation experiments. It is found that, in most cases, the volume fraction at the depletion wall is negligibly small and that the volume fraction at the accumulation wall ₀, depends on the ratio <>₀/₀ only. An inflexion point is found in the concentration profile if ₀ is larger than 0.13 whatever the value of ₀.     

Quantum dynamics through conical intersections in macrosystems: Combining effective modes and time-dependent Hartree

We address the nonadiabatic quantum dynamics of (macro)systems involving a vast number of nuclear degrees of freedom (modes) in the presence of conical intersections. The macrosystem is first decomposed into a system part carrying a few, strongly coupled modes, and an environment, comprising the remaining modes. By successively transforming the modes of the environment, a hierarchy of effective Hamiltonians for the environment can be constructed. Each effective Hamiltonian depends on a reduced number of effective modes, which carry cumulative effects. The environment is described by a few effective modes augmented by a residual environment. In practice, the effective modes can be added to the system’s modes and the quantum dynamics of the entire macrosystem can be accurately calculated on a limited time-interval. For longer times, however, the residual environment plays a role. We investigate the possibility to treat fully quantum mechanically the system plus a few effective environmental modes, augmented by the dynamics of the residual environment treated by the time-dependent Hartree (TDH) approximation. While the TDH approximation is known to fail to correctly reproduce the dynamics in the presence of conical intersections, it is shown that its use on top of the effective-mode formalism leads to much better results. Two numerical examples are presented and discussed; one of them is known to be a critical case for the TDH approximation.     

Molecular dynamics at constant pressure and temperature

Methods are discussed for generating by molecular dynamics isobaric-isoenthalpic, NPH, isochoric-isothermal, NVT, and isobaric-isothermal, NPT, ensembles. Andersen's constant-pressure method is reformulated so that the ensemble rather than the scaled system is directly calculated. Four constant-temperature schemes were considered. Two involve the addition of a stochastic collision term to the molecular trajectories. The Andersen method and a stochastic dynamics approach were examined. The latter employed a velocity damping term in addition to the random force. Two other methods employed uniform velocity scaling applied to all molecules. The NPT algorithm induces a transition to the dilute phase for a Lennard-Jones fluid in the spinodal region (p^* = 0.5, T^* = 1.28) of the phase diagram. The thermodynamic equivalence of the ensembles is demonstrated by long calculations of the chemical potential of Lennard-Jones states by the particle insertion method. The internal energy, pressure, constant volume and pressure specific heats, adiabatic compressibilities, pair radial distribution functions and self-diffusion coefficients are also evaluated. Only for second-order thermodynamic quantities is there evidence of an ensemble dependence.     

Optimized effective potentials from electron densities in finite basis sets

The Wu-Yang method for determining the optimized effective potential (OEP) and implicit density functionals from a given electron density is revisited to account for its ill-posed nature, as recently done for the direct minimization method for OEP's from a given orbital functional [T. Heaton-Burgess, F. A. Bulat, and W. Yang, Phys. Rev. Lett. 98, 256401 (2007)]. To address the issues on the general validity and practical applicability of methods that determine the Kohn-Sham (local) multiplicative potential in a finite basis expansion, a new functional is introduced as a regularized version of the original work of Wu and Yang. It is shown that the unphysical, highly oscillatory potentials that can be obtained when unbalanced basis sets are used are the controllable manifestation of the ill-posed nature of the problem. The new method ensures that well behaved potentials are obtained for arbitrary basis sets.     

Determining equilibrium constants for dimerization reactions from molecular dynamics simulations

With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations "via counting" become feasible for an increasing number of reactions. An example is the dimerization reaction of transmembrane alpha-helices. If an extended simulation of the two helices covers sufficiently many dimerization and dissociation events, their binding free energy is readily derived from the fraction of time during which the two helices are observed in dimeric form. Exactly how the correct value for the free energy is to be calculated, however, is unclear, and indeed several different and contradictory approaches have been used. In particular, results obtained via Boltzmann statistics differ from those determined via the law of mass action. Here, we develop a theory that resolves this discrepancy. We show that for simulation systems containing two molecules, the dimerization free energy is given by a formula of the form ΔG ∝ ln(P(1) /P(0) ). Our theory is also applicable to high concentrations that typically have to be used in molecular dynamics simulations to keep the simulation system small, where the textbook dilute approximations fail. It also covers simulations with an arbitrary number of monomers and dimers and provides rigorous error estimates. Comparison with test simulations of a simple Lennard Jones system with various particle numbers as well as with reference free energy values obtained from radial distribution functions show full agreement for both binding free energies and dimerization statistics.     

Josephson effect in superfluid atomic Fermi gases at finite temperature

By using Green's function method and linear response theory the Josephson effect of neutral fermions at finite temperature is investigated. Four different hyperfine states of the atoms are assumed to be trapped and to form two superfluids via the BCS-type of pairing. The Josephson effect can be realized by coupling the superfluids with two laser fields. The laser interaction is assumed to be a small perturbation and its effect is calculated using linear response theory. Both, single particle tunneling and the Josephson current, at finite temperature are calculated in Matsubara formalism.     

Symmetric-group algebraic variational solutions for Heisenberg models at finite temperature

The Heisenberg spin Hamiltonian for a collection of N spin-1/2 sites is viewed, as favored by Professor Matsen, to be an element of the group algebra of the symmetric group ??_N. Several computationally tractable, variational group–algebraic approximations for the finite-temperature density matrix are made so as to minimize the Gibb's free–energy functional. Relations to previous quite differently motivated approximations are identified, though improvements are noted with the present approach.     

Fluctuating charge normal modes: An algorithm for implementing molecular dynamics simulations with polarizable potentials

A new method for performing molecular dynamics simulations with fluctuating charge polarizable potentials is introduced. In fluctuating charge models, polarizability is treated by allowing the partial charges to be variables, with values that are coupled to charges on the same molecule as well as those on other molecules. The charges can be efficiently propagated in a molecular dynamics simulation using extended Lagrangian dynamics. By making a coordinate change from the charge variables to a set of normal mode charge coordinates for each molecule, a new method is constructed in which the normal mode charge variables uncouple from those on the same molecule. The method is applied to the TIP4P-FQ model of water and compared to other methods for implementing the dynamics. The methods are compared using different molecular dynamics time steps.     

Extracting the time scales of conformational dynamics from single-molecule single-photon fluorescence statistics

The quenching rate of a fluorophore attached to a macromolecule can be rather sensitive to its conformational state. The decay of the corresponding fluorescence lifetime autocorrelation function can therefore provide unique information on the time scales of conformational dynamics. The conventional way of measuring the fluorescence lifetime autocorrelation function involves evaluating it from the distribution of delay times between photoexcitation and photon emission. However, the time resolution of this procedure is limited by the time window required for collecting enough photons in order to establish this distribution with sufficient signal-to-noise ratio. Yang and Xie have recently proposed an approach for improving the time resolution, which is based on the argument that the autocorrelation function of the delay time between photoexcitation and photon emission is proportional to the autocorrelation function of the square of the fluorescence lifetime [Yang, H.; Xie, X. S. J. Chem. Phys. 2002, 117, 10965]. In this paper, we show that the delay-time autocorrelation function is equal to the autocorrelation function of the square of the fluorescence lifetime divided by the autocorrelation function of the fluorescence lifetime. We examine the conditions under which the delay-time autocorrelation function is approximately proportional to the autocorrelation function of the square of the fluorescence lifetime. We also investigate the correlation between the decay of the delay-time autocorrelation function and the time scales of conformational dynamics. The results are demonstrated via applications to a two-state model and an off-lattice model of a polypeptide.     

Extracting parameters for base-pair level models of DNA from molecular dynamics simulations

 A method is described to extract a complete set of sequence-dependent energy parameters for a rigid base-pair model of DNA from molecular dynamics (MD) simulations. The method is properly consistent with equilibrium statistical mechanics and leads to effective inertia parameters for the base-pair units as well as stacking and stiffness parameters for the base-pair junctions. We give explicit formulas that yield a complete set of base-pair model parameters in terms of equilibrium averages that can be estimated from a time series generated in an MD simulation. The expressions to be averaged depend strongly both on the choice of coordinates used to describe rigid-body orientations and on the choice of strain measures at each junction. Received: 12 July 2000 / Accepted: 5 January 2001 / Published online: 3 May 2001     

Thermal conductivity of molten alkali halides from equilibrium molecular dynamics simulations

The thermal conductivity of molten sodium chloride and potassium chloride has been computed through equilibrium molecular dynamics Green-Kubo simulations in the microcanonical ensemble (N,V,E). In order to access the temperature dependence of the thermal conductivity coefficient of these materials, the simulations were performed at five different state points. The form of the microscopic energy flux for ionic systems whose Coulombic interactions are calculated through the Ewald method is discussed in detail and an efficient formula is used by analogy with the methods used to evaluate the stress tensor in Coulombic systems. The results show that the Born-Mayer-Huggins-Tosi-Fumi potential predicts a weak negative temperature dependence for the thermal conductivity of NaCl and KCl. The simulation results are in agreement with part of the experimental data available in the literature with simulation values generally overpredicting the thermal conductivity by 10%-20%.