8,454 research outputs found
Regularized Born-Oppenheimer molecular dynamics
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
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 -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
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
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