Multipole Vortex Blobs (MVB): Symplectic Geometry and Dynamics.
Ontology highlight
ABSTRACT:
SUBMITTER: Holm DD
PROVIDER: S-EPMC5479423 | biostudies-other | 2017
REPOSITORIES: biostudies-other
Similar Datasets
Project description:In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise because of (1) the transfer of torque between neighboring atoms and (2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In this study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives partial derivative D(m'm)(l)/partial derivative Omega. The force equations can be applied to electrostatic models based on atomic point multipoles or gaussian multipole charge density. Hydrogen-bonded dimers are used to test the intermolecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential. The electrostatic energies and forces are compared with their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, whereas geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models.
| S-EPMC2941241 | biostudies-literature
Project description:Localized surface plasmon resonance (LSPR) has been shown to exhibit a strong potential for nanoscale electromagnetic field manipulation beyond the diffraction limit. Particularly dark mode plasmons circumvent radiation loss and store the energy long in time, which raise the prospect of interesting plasmonics applications, for example biochemical sensing and nanoscale lasing. Here we theoretically investigate a method of exciting multipole plasmons, including dark modes, using normally incident light. By performing numerical calculations, we show that multipole plasmons in metal nanodisks can be selectively excited by circularly-polarized optical vortex beams. We study the electromagnetic fields of the beam cross-sections and their correspondence with the excited multipole plasmon modes with respect to spin and orbital angular momenta. The transfer of angular momentum between photons and plasmons is also discussed.
| S-EPMC4325316 | biostudies-literature
Project description:We recently developed a polarizable atomic multipole refinement method assisted by the AMOEBA force field for macromolecular crystallography. Compared to standard refinement procedures, the method uses a more rigorous treatment of x-ray scattering and electrostatics that can significantly improve the resultant information contained in an atomic model. We applied this method to high-resolution lysozyme and trypsin data sets, and validated its utility for precisely describing biomolecular electron density, as indicated by a 0.4-0.6% decrease in the R- and R(free)-values, and a corresponding decrease in the relative energy of 0.4-0.8 Kcal/mol/residue. The re-refinements illustrate the ability of force-field electrostatics to orient water networks and catalytically relevant hydrogens, which can be used to make predictions regarding active site function, activity, and protein-ligand interaction energies. Re-refinement of a DNA crystal structure generates the zigzag spine pattern of hydrogen bonding in the minor groove without manual intervention. The polarizable atomic multipole electrostatics model implemented in the AMOEBA force field is applicable and informative for crystal structures solved at any resolution.
| S-EPMC2884231 | biostudies-literature
Project description:Swimming animals need to generate propulsive force to overcome drag, regardless of whether they swim steadily or accelerate forward. While locomotion strategies for steady swimming are well characterized, far less is known about acceleration. Animals exhibit many different ways to swim steadily, but we show here that this behavioral diversity collapses into a single swimming pattern during acceleration regardless of the body size, morphology, and ecology of the animal. We draw on the fields of biomechanics, fluid dynamics, and robotics to demonstrate that there is a fundamental difference between steady swimming and forward acceleration. We provide empirical evidence that the tail of accelerating fishes can increase propulsive efficiency by enhancing thrust through the alteration of vortex ring geometry. Our study provides insight into how propulsion can be altered without increasing vortex ring size and represents a fundamental departure from our current understanding of the hydrodynamic mechanisms of acceleration. Our findings reveal a unifying hydrodynamic principle that is likely conserved in all aquatic, undulatory vertebrates.
| S-EPMC5748167 | biostudies-literature
Project description:Vortex rings can easily be generated in the laboratory or with homemade devices, but they have also been observed on volcanoes, since the eighteenth century. However, the physical conditions under which volcanic vortex rings form are still unknown. In order to better understand this phenomenon and provide clues on the dynamics of the volcanic vortex rings, we performed a series of finite element simulations to investigate which model configuration leads to the rings formation that best matches the field observations. Results show that the formation of volcanic vortex rings requires a combination of fast gas release from gas bubbles (slugs) at the top of the magma conduit and regularity in the shape of the emitting vent. Our findings offer important insights into the geometry of the uppermost portion of vortex-forming volcanic conduits. Volcanic vortex ring studies may form the basis for a cross-disciplinary assessment of the upper conduit dynamics of volcanic vents.
| S-EPMC9911723 | biostudies-literature
Project description:Vortices are archetypal objects that recur in the universe across the scale of complexity, from subatomic particles to galaxies and black holes. Their appearance is connected with spontaneous symmetry breaking and phase transitions. In Bose-Einstein condensates and superfluids, vortices are both point-like and quantized quasiparticles. We use a two-dimensional (2D) fluid of polaritons, bosonic particles constituted by hybrid photonic and electronic oscillations, to study quantum vortex dynamics. Polaritons benefit from easiness of wave function phase detection, a spinor nature sustaining half-integer vorticity, strong nonlinearity, and tuning of the background disorder. We can directly generate by resonant pulsed excitations a polariton condensate carrying either a full or half-integer vortex as initial condition and follow their coherent evolution using ultrafast imaging on the picosecond scale. The observations highlight a rich phenomenology, such as the spiraling of the half-vortex and the joint path of the twin charges of a full vortex, until the moment of their splitting. Furthermore, we observe the ordered branching into newly generated secondary couples, associated with the breaking of radial and azimuthal symmetries. This allows us to devise the interplay of nonlinearity and sample disorder in shaping the fluid and driving the vortex dynamics. In addition, our observations suggest that phase singularities may be seen as fundamental particles whose quantized events span from pair creation and recombination to 2D+t topological vortex strings.
| S-EPMC4672757 | biostudies-literature
Project description:Turbulence and coherent circulation structures, such as submesoscale and mesoscale eddies, convective plumes and Langmuir cells, play a critical role in shaping phytoplankton spatial distribution and population dynamics. We use a framework of advection-reaction-diffusion equations to investigate the effects of turbulent transport on the phytoplankton population growth and its spatial structure in a vertical two-dimensional vortex flow field. In particular, we focus on how turbulent flow velocities and sinking influence phytoplankton growth and biomass aggregation. Our results indicate that conditions in mixing and growth of phytoplankton can drive different vertical spatial structures in the mixed layer, with the depth of the mixed layer being a critical factor to allow coexistence of populations with different sinking speed. With increasing mixed layer depth, positive growth for sinking phytoplankton can be maintained with increasing turbulent flow velocities, allowing the apparently counter-intuitive persistence of fast sinking phytoplankton populations in highly turbulent and deep mixed layers. These dynamics demonstrate the role of considering advective transport within a turbulent vortex and can help to explain observed phytoplankton biomass during winter in the North Atlantic, where the overturn of deep convection has been suggested to play a critical role in phytoplankton survival.
| S-EPMC5721153 | biostudies-literature
Project description:Acoustic levitation in gaseous media provides a tool to process solid and liquid materials without the presence of surfaces such as container walls and hence has been used widely in chemical analysis, high-temperature processing, drop dynamics and bioreactors. To date high-density objects can only be acoustically levitated in simple standing-wave fields. Here we demonstrate the ability of a small number of peripherally placed sources to generate acoustic vortex fields and stably levitate a wide range of liquid and solid objects. The forces exerted by these acoustic vortex fields on a levitated water droplet are observed to cause a controllable deformation of the droplet and/or oscillation along the vortex axis. Orbital angular momentum transfer is also shown to rotate a levitated object rapidly and the rate of rotation can be controlled by the source amplitude. We expect this research can increase the diversity of acoustic levitation and expand the application of acoustic vortices.
| S-EPMC5540917 | biostudies-literature
Project description:Understanding the fluid-structure interaction is crucial for an optimal design and manufacturing of soft mesoscale materials. Multi-core emulsions are a class of soft fluids assembled from cluster configurations of deformable oil-water double droplets (cores), often employed as building-blocks for the realisation of devices of interest in bio-technology, such as drug-delivery, tissue engineering and regenerative medicine. Here, we study the physics of multi-core emulsions flowing in microfluidic channels and report numerical evidence of a surprisingly rich variety of driven non-equilibrium states (NES), whose formation is caused by a dipolar fluid vortex triggered by the sheared structure of the flow carrier within the microchannel. The observed dynamic regimes range from long-lived NES at low core-area fraction, characterised by a planetary-like motion of the internal drops, to short-lived ones at high core-area fraction, in which a pre-chaotic motion results from multi-body collisions of inner drops, as combined with self-consistent hydrodynamic interactions. The onset of pre-chaotic behavior is marked by transitions of the cores from one vortex to another, a process that we interpret as manifestations of the system to maximize its entropy by filling voids, as they arise dynamically within the capsule.
| S-EPMC7782531 | biostudies-literature
Project description:A vortex is a flow phenomenon that is very commonly observed in nature. More than a century, a vortex ring that forms during drop splashing has caught the attention of many scientists due to its importance in understanding fluid mixing and mass transport processes. However, the origin of the vortices and their dynamics remain unclear, mostly due to the lack of appropriate visualization methods. Here, with ultrafast X-ray phase-contrast imaging, we show that the formation of vortex rings originates from the energy transfer by capillary waves generated at the moment of the drop impact. Interestingly, we find a row of vortex rings along the drop wall, as demonstrated by a phase diagram established here, with different power-law dependencies of the angular velocities on the Reynolds number. These results provide important insight that allows understanding and modelling any type of vortex rings in nature, beyond just vortex rings during drop splashing.
| S-EPMC4569801 | biostudies-literature