8,454 research outputs found

    Regularized Born-Oppenheimer molecular dynamics

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    While the treatment of conical intersections in molecular dynamics generally requires nonadiabatic approaches, the Born-Oppenheimer adiabatic approximation is still adopted as a valid alternative in certain circumstances. In the context of Mead-Truhlar minimal coupling, this paper presents a new closure of the nuclear Born-Oppenheimer equation, thereby leading to a molecular dynamics scheme capturing geometric phase effects. Specifically, a semiclassical closure of the nuclear Ehrenfest dynamics is obtained through a convenient prescription for the nuclear Bohmian trajectories. The conical intersections are suitably regularized in the resulting nuclear particle motion and the associated Lorentz force involves a smoothened Berry curvature identifying a loop-dependent geometric phase. In turn, this geometric phase rapidly reaches the usual topological index as the loop expands away from the original singularity. This feature reproduces the phenomenology appearing in recent exact nonadiabatic studies, as shown explicitly in the Jahn-Teller problem for linear vibronic coupling. Likewise, a newly proposed regularization of the diagonal correction term is also shown to reproduce quite faithfully the energy surface presented in recent nonadiabatic studies.Comment: Third version with minor changes. To appear in Phys. Rev.

    Hydrodynamic Flows on Curved Surfaces: Spectral Numerical Methods for Radial Manifold Shapes

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    We formulate hydrodynamic equations and spectrally accurate numerical methods for investigating the role of geometry in flows within two-dimensional fluid interfaces. To achieve numerical approximations having high precision and level of symmetry for radial manifold shapes, we develop spectral Galerkin methods based on hyperinterpolation with Lebedev quadratures for L2L^2-projection to spherical harmonics. We demonstrate our methods by investigating hydrodynamic responses as the surface geometry is varied. Relative to the case of a sphere, we find significant changes can occur in the observed hydrodynamic flow responses as exhibited by quantitative and topological transitions in the structure of the flow. We present numerical results based on the Rayleigh-Dissipation principle to gain further insights into these flow responses. We investigate the roles played by the geometry especially concerning the positive and negative Gaussian curvature of the interface. We provide general approaches for taking geometric effects into account for investigations of hydrodynamic phenomena within curved fluid interfaces.Comment: 14 figure

    Mobility Measurements Probe Conformational Changes in Membrane Proteins due to Tension

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    The function of membrane-embedded proteins such as ion channels depends crucially on their conformation. We demonstrate how conformational changes in asymmetric membrane proteins may be inferred from measurements of their diffusion. Such proteins cause local deformations in the membrane, which induce an extra hydrodynamic drag on the protein. Using membrane tension to control the magnitude of the deformations and hence the drag, measurements of diffusivity can be used to infer--- via an elastic model of the protein--- how conformation is changed by tension. Motivated by recent experimental results [Quemeneur et al., Proc. Natl. Acad. Sci. USA, 111 5083 (2014)] we focus on KvAP, a voltage-gated potassium channel. The conformation of KvAP is found to change considerably due to tension, with its `walls', where the protein meets the membrane, undergoing significant angular strains. The torsional stiffness is determined to be 26.8 kT at room temperature. This has implications for both the structure and function of such proteins in the environment of a tension-bearing membrane.Comment: Manuscript: 4 pages, 4 figures. Supplementary Material: 8 pages, 1 figur
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