Bayesian ensemble refinement by replica simulations and reweighting

We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraint should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" (BioEn) method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.Comment: Paper submitted to The Journal of Chemical Physics (15 pages, 4 figures); updated references; expanded discussions of related formalisms, error treatment, and ensemble refinement with and without replicas; appendi

Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations

We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic and stochastic components of the peptide motion parametrized by an appropriate set of coarse variables. Techniques from traditional numerical analysis (Newton-Raphson, coarse projective integration) are thus enabled; these techniques help analyze important features of the free-energy landscape (coarse transition states, eigenvalues and eigenvectors, transition rates, etc.). Reverse integration of (irreversible) expected coarse variables backward in time can assist escape from free energy minima and trace low-dimensional free energy surfaces. To illustrate the ``coarse molecular dynamics'' approach, we combine multiple short (0.5-ps) replica simulations to map the free energy surface of the ``alanine dipeptide'' in water, and to determine the ~ 1/(1000 ps) rate of interconversion between the two stable configurational basins corresponding to the alpha-helical and extended minima.Comment: The article has been submitted to "The Journal of Chemical Physics.

Hydrodynamics of Diffusion in Lipid Membrane Simulations

By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon nanotubes in membranes. The resulting Oseen correction allows us to extract infinite-system diffusion coefficients and membrane surface viscosities from membrane simulations despite the logarithmic divergence of apparent diffusivities with increasing box width. The hydrodynamic theory of diffusion applies also to membranes with asymmetric leaflets and embedded proteins, and to a complex plasma-membrane mimetic

Scanner

An aerial vehicle rotating in gyroscopic fashion about one of its axes has an optical system which scans an area below the vehicle in determined relation to vehicle rotation. A sensing device is provided to sense the physical condition of the area of scan and optical means are associated to direct the physical intelligence received from the scan area to the sensing means. Means are provided to incrementally move the optical means through a series of steps to effect sequential line scan of the area being viewed keyed to the rotational rate of the vehicle

Pair diffusion, hydrodynamic interactions, and available volume in dense fluids

We calculate the pair diffusion coefficient D(r) as a function of the distance r between two hard-sphere particles in a dense monodisperse suspension. The distance-dependent pair diffusion coefficient describes the hydrodynamic interactions between particles in a fluid that are central to theories of polymer and colloid dynamics. We determine D(r) from the propagators (Green's functions) of particle pairs obtained from discontinuous molecular dynamics simulations. At distances exceeding 3 molecular diameters, the calculated pair diffusion coefficients are in excellent agreement with predictions from exact macroscopic hydrodynamic theory for large Brownian particles suspended in a solvent bath, as well as the Oseen approximation. However, the asymptotic 1/r distance dependence of D(r) associated with hydrodynamic effects emerges only after the pair distance dynamics has been followed for relatively long times, indicating non-negligible memory effects in the pair diffusion at short times. Deviations of the calculated D(r) from the hydrodynamic models at short distances r reflect the underlying many-body fluid structure, and are found to be correlated to differences in the local available volume. The procedure used here to determine the pair diffusion coefficients can also be used for single-particle diffusion in confinement with spherical symmetry.Comment: 6 pages, 5 figure

Resonant Scattering and Ly-alpha Radiation Emergent from Neutral Hydrogen Halos

With a state-of-the-art numerical method for solving the integral-differential equation of radiative transfer, we investigate the flux of the Ly$\alpha$ photon $\nu_0$ emergent from an optically thick halo containing a central light source. Our focus is on the time-dependent effects of the resonant scattering. We first show that the frequency distribution of photons in the halo are quickly approaching to a locally thermalized state around the resonant frequency, even when the mean intensity of the radiation is highly time-dependent. Since initial conditions are forgotten during the thermalization, some features of the flux, such as the two peak structure of its profile, actually are independent of the intrinsic width and time behavior of the central source, if the emergent photons are mainly from photons in the thermalized state. In this case, the difference $|\nu_{\pm}-\nu_0|$, where $\nu_{\pm}$ are the frequencies of the two peaks of the flux, cannot be less than $2$ times of Doppler broadening. We then study the radiative transfer in the case where the light emitted from the central source is a flash. We calculate the light curves of the flux from the halo. It shows that the flux is still a flash. The time duration of the flash for the flux, however, is independent of the original time duration of the light source but depends on the optical depth of the halo. Therefore, the spatial transfer of resonant photons is a diffusion process, even though it is not a purely Brownian diffusion. This property enables an optically thick halo to trap and store thermalized photons around $\nu_0$ for a long time after the cease of the central source emission. The photons trapped in the halo can yield delayed emission, of which the profile also shows typical two peak structure as that from locally thermalized photons. Possible applications of these results are addressed.Comment: 25 pages, 10 figures, accepted for publication in Ap

Vibrational and optical properties of MoS2_2: from monolayer to bulk

Molybdenum disulfide, MoS2, has recently gained considerable attention as a layered material where neighboring layers are only weakly interacting and can easily slide against each other. Therefore, mechanical exfoliation allows the fabrication of single and multi-layers and opens the possibility to generate atomically thin crystals with outstanding properties. In contrast to graphene, it has an optical gap of 1.9 eV. This makes it a prominent candidate for transistor and opto-electronic applications. Single-layer MoS$_2$ exhibits remarkably different physical properties compared to bulk MoS$_2$ due to the absence of interlayer hybridization. For instance, while the band gap of bulk and multi-layer MoS$_2$ is indirect, it becomes direct with decreasing number of layers. In this review, we analyze from a theoretical point of view the electronic, optical, and vibrational properties of single-layer, few-layer and bulk MoS$_2$. In particular, we focus on the effects of spin-orbit interaction, number of layers, and applied tensile strain on the vibrational and optical properties. We examine the results obtained by different methodologies, mainly ab initio approaches. We also discuss which approximations are suitable for MoS$_2$ and layered materials. The effect of external strain on the band gap of single-layer MoS$_2$ and the crossover from indirect to direct band gap is investigated. We analyze the excitonic effects on the absorption spectra. The main features, such as the double peak at the absorption threshold and the high-energy exciton are presented. Furthermore, we report on the phonon dispersion relations of single-layer, few-layer and bulk MoS$_2$. Based on the latter, we explain the behavior of the Raman-active $A_{1g}$ and $E^1_{2g}$ modes as a function of the number of layers

Ion Pair Potentials-of-Mean-Force in Water

Recent molecular simulation and integral equation results alkali-halide ion pair potentials-of-mean-force in water are discussed. Dielectric model calculations are implemented to check that these models produce that characteristic structure of contact and solvent-separated minima for oppositely charged ions in water under physiological thermodynamic conditions. Comparison of the dielectric model results with the most current molecular level information indicates that the dielectric model does not, however, provide an accurate description of these potentials-of-mean-force. We note that linear dielectric models correspond to modelistic implementations of second-order thermodynamic perturbation theory for the excess chemical potential of a distinguished solute molecule. Therefore, the molecular theory corresponding to the dielectric models is second-order thermodynamic perturbation theory for that excess chemical potential. The second-order, or fluctuation, term raises a technical computational issue of treatment of long-ranged interactions similar to the one which arises in calculation of the dielectric constant of the solvent. It is contended that the most important step for further development of dielectric models would be a separate assessment of the first-order perturbative term (equivalently the {\it potential at zero charge} ) which vanishes in the dielectric models but is generally nonzero. Parameterization of radii and molecular volumes should then be based of the second-order perturbative term alone. Illustrative initial calculations are presented and discussed.Comment: 37 pages and 8 figures. LA-UR-93-420