Efficient multiple time scale molecular dynamics: using colored noise thermostats to stabilize resonances

Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by resonances between the fast and slow modes. In this paper we show that this problem can be alleviated by using a simple colored noise thermostatting scheme which selectively targets the high frequency modes in the system. For two sample problems, flexible water and solvated alanine dipeptide, we demonstrate that this allows the use of large outer time steps while still obtaining accurate sampling and minimizing the perturbation of the dynamics. Furthermore, this approach is shown to be comparable to constraining fast motions, thus providing an alternative to molecular dynamics with constraints.Comment: accepted for publication by the Journal of Chemical Physic

High Velocity Line Emission in the NLR of NGC 4151

Narrow-band imaging of the nuclear region of NGC 4151 with the Hubble Space Telescope is presented. The filter bandpasses isolate line emission in various high velocity ranges in several ions. Slitless and long-slit spectra of the region with the Space Telescope Imaging Spectrograph also indicate the locations of high velocity gas. These emission regions are faint and are interspersed among the bright emission clouds seen in direct images. They have radial velocities up to 1400 km/s relative to the nucleus, and are found in both approach and recession on both sides of the nucleus. This contrasts strongly with the bright emission line clouds which have been discussed previously as showing bidirectional outflow with velocities within 400 km/s of the nucleus. We discuss the possible connections of the high velocity material with the radio jet and the nuclear radiation.Comment: 12 pages plus 6 figures, to be published in A

Kinosternon subrubrum subrubrum (Eastern Mud Turtle) Predator Escape

Known avian predators of Kinosternon subrubrum include crows and eagles (Ernst et al. 1994. Turtles of the United States and Canada, Smithsonian Inst. Press, Washington, DC; Mitchell 1994. The Reptiles of Virginia, Smithsonian Inst. Press, Washington, DC)..

High-Pressure Synthesis of a Pentazolate Salt

The pentazolates, the last all-nitrogen members of the azole series, have been notoriously elusive for the last hundred years despite enormous efforts to make these compounds in either gas or condensed phases. Here we report a successful synthesis of a solid state compound consisting of isolated pentazolate anions N5-, which is achieved by compressing and laser heating cesium azide (CsN3) mixed with N2 cryogenic liquid in a diamond anvil cell. The experiment was guided by theory, which predicted the transformation of the mixture at high pressures to a new compound, cesium pentazolate salt (CsN5). Electron transfer from Cs atoms to N5 rings enables both aromaticity in the pentazolates as well as ionic bonding in the CsN5 crystal. This work provides a critical insight into the role of extreme conditions in exploring unusual bonding routes that ultimately lead to the formation of novel high nitrogen content species

Local structural studies of Ba1−x_{1-x}Kx_xFe2_2As2_2 using atomic pair distribution function analysis

Systematic local structural studies of Ba$_{1-x}$K$_x$Fe$_2$As$_2$ system are undertaken at room temperature using atomic pair distribution function (PDF) analysis. The local structure of the Ba$_{1-x}$K$_x$Fe$_2$As$_2$ is found to be well described by the long-range structure extracted from the diffraction experiments, but with anisotropic atomic vibrations of the constituent atoms ($U_{11}$ = $U_{22} \ne U_{33}$). The crystal unit cell parameters, the FeAs$_4$ tetrahedral angle and the pnictogen height above the Fe-plane are seen to show systematic evolution with K doping, underlining the importance of the structural changes, in addition to the charge doping, in determining the properties of Ba$_{1-x}$K$_x$Fe$_2$As$_2$

Two-dimensional Nanolithography Using Atom Interferometry

We propose a novel scheme for the lithography of arbitrary, two-dimensional nanostructures via matter-wave interference. The required quantum control is provided by a pi/2-pi-pi/2 atom interferometer with an integrated atom lens system. The lens system is developed such that it allows simultaneous control over atomic wave-packet spatial extent, trajectory, and phase signature. We demonstrate arbitrary pattern formations with two-dimensional 87Rb wavepackets through numerical simulations of the scheme in a practical parameter space. Prospects for experimental realizations of the lithography scheme are also discussed.Comment: 36 pages, 4 figure

Mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution.

Elucidating the spectrum of epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) states in clinical samples promises insights on cancer progression and drug resistance. Using mass cytometry time-course analysis, we resolve lung cancer EMT states through TGFβ-treatment and identify, through TGFβ-withdrawal, a distinct MET state. We demonstrate significant differences between EMT and MET trajectories using a computational tool (TRACER) for reconstructing trajectories between cell states. In addition, we construct a lung cancer reference map of EMT and MET states referred to as the EMT-MET PHENOtypic STAte MaP (PHENOSTAMP). Using a neural net algorithm, we project clinical samples onto the EMT-MET PHENOSTAMP to characterize their phenotypic profile with single-cell resolution in terms of our in vitro EMT-MET analysis. In summary, we provide a framework to phenotypically characterize clinical samples in the context of in vitro EMT-MET findings which could help assess clinical relevance of EMT in cancer in future studies