First-principles study of epitaxial strain in perovskites

Using an extension of a first-principles method developed by King-Smith and Vanderbilt [Phys. Rev. B {\bf 49}, 5828 (1994)], we investigate the effects of in-plane epitaxial strain on the ground-state structure and polarization of eight perovskite oxides: BaTiO$_3$, SrTiO$_3$, CaTiO$_3$, KNbO$_3$, NaNbO$_3$, PbTiO$_3$, PbZrO$_3$, and BaZrO$_3$. In addition, we investigate the effects of a nonzero normal stress. The results are shown to be useful in predicting the structure and polarization of perovskite oxide thin films and superlattices.Comment: 10 page

Current-Induced Spin Polarization in Gallium Nitride

Electrically generated spin polarization is probed directly in bulk GaN using Kerr rotation spectroscopy. A series of n-type GaN epilayers are grown in the wurtzite phase both by molecular beam epitaxy (MBE) and metalorganic chemical vapor deposition (MOCVD) with a variety of doping densities chosen to broadly modulate the transverse spin lifetime, T2*. The spin polarization is characterized as a function of electrical excitation energy over a range of temperatures. Despite weak spin-orbit interactions in GaN, a current-induced spin polarization (CISP) is observed in the material at temperatures of up to 200 K.Comment: 16 pages, 3 figure

The Multitude of Molecular Hydrogen Knots in the Helix Nebula

We present HST/NICMOS imaging of the H_2 2.12 \mu m emission in 5 fields in the Helix Nebula ranging in radial distance from 250-450" from the central star. The images reveal arcuate structures with their apexes pointing towards the central star. Comparison of these images with comparable resolution ground based images reveals that the molecular gas is more highly clumped than the ionized gas line tracers. From our images, we determine an average number density of knots in the molecular gas ranging from 162 knots/arcmin^2 in the denser regions to 18 knots/arcmin^2 in the lower density outer regions. Using this new number density, we estimate that the total number of knots in the Helix to be ~23,000 which is a factor of 6.5 larger than previous estimates. The total neutral gas mass in the Helix is 0.35 M_\odot assuming a mass of \~1.5x10^{-5} M_\odot for the individual knots. The H_2 intensity, 5-9x10^{-5} erg s^{-1} cm^{-2} sr^{-1}, remains relatively constant with projected distance from the central star suggesting a heating mechanism for the molecular gas that is distributed almost uniformly in the knots throughout the nebula. The temperature and H_2 2.12 \mu m intensity of the knots can be approximately explained by photodissociation regions (PDRs) in the individual knots; however, theoretical PDR models of PN under-predict the intensities of some knots by a factor of 10.Comment: 26 pages, 3 tables, 10 figures; AJ accepte

Solving the Klein-Gordon equation using Fourier spectral methods: A benchmark test for computer performance

The cubic Klein-Gordon equation is a simple but non-trivial partial differential equation whose numerical solution has the main building blocks required for the solution of many other partial differential equations. In this study, the library 2DECOMP&FFT is used in a Fourier spectral scheme to solve the Klein-Gordon equation and strong scaling of the code is examined on thirteen different machines for a problem size of 512^3. The results are useful in assessing likely performance of other parallel fast Fourier transform based programs for solving partial differential equations. The problem is chosen to be large enough to solve on a workstation, yet also of interest to solve quickly on a supercomputer, in particular for parametric studies. Unlike other high performance computing benchmarks, for this problem size, the time to solution will not be improved by simply building a bigger supercomputer.Comment: 10 page

Shortcuts in Stochastic Systems and Control of Biophysical Processes

The biochemical reaction networks that regulate living systems are all stochastic to varying degrees. The resulting randomness affects biological outcomes at multiple scales, from the functional states of single proteins in a cell to the evolutionary trajectory of whole populations. Controlling how the distribution of these outcomes changes over time-via external interventions like time-varying concentrations of chemical species-is a complex challenge. In this work, we show how counterdiabatic (CD) driving, first developed to control quantum systems, provides a versatile tool for steering biological processes. We develop a practical graph-theoretic framework for CD driving in discrete-state continuous-time Markov networks. Though CD driving is limited to target trajectories that are instantaneous stationary states, we show how to generalize the approach to allow for nonstationary targets and local control-where only a subset of system states is targeted. The latter is particularly useful for biological implementations where there may be only a small number of available external control knobs, insufficient for global control. We derive simple graphical criteria for when local versus global control is possible. Finally, we illustrate the formalism with global control of a genetic regulatory switch and local control in chaperone-assisted protein folding. The derived control protocols in the chaperone system closely resemble natural control strategies seen in experimental measurements of heat shock response in yeast and E. coli

Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model

During replication initiation, the core component of the helicase-the Mcm2-7 hexamer-is loaded on origin DNA as a double hexamer (DH). The two ring-shaped hexamers are staggered, leading to a kinked axial channel. How the origin DNA interacts with the axial channel is not understood, but the interaction could provide key insights into Mcm2-7 function and regulation. Here, we report the cryo-EM structure of the Mcm2-7 DH on dsDNA and show that the DNA is zigzagged inside the central channel. Several of the Mcm subunit DNA-binding loops, such as the oligosaccharide-oligonucleotide loops, helix 2 insertion loops, and presensor 1 (PS1) loops, are well defined, and many of them interact extensively with the DNA. The PS1 loops of Mcm 3, 4, 6, and 7, but not 2 and 5, engage the lagging strand with an approximate step size of one base per subunit. Staggered coupling of the two opposing hexamers positions the DNA right in front of the two Mcm2-Mcm5 gates, with each strand being pressed against one gate. The architecture suggests that lagging-strand extrusion initiates in the middle of the DH that is composed of the zinc finger domains of both hexamers. To convert the Mcm2-7 DH structure into the Mcm2-7 hexamer structure found in the active helicase, the N-tier ring of the Mcm2-7 hexamer in the DH-dsDNA needs to tilt and shift laterally. We suggest that these N-tier ring movements cause the DNA strand separation and lagging-strand extrusion

Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function

Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2-7 (minichromosome maintenance proteins 2-7) double hexamer. During S phase, each Mcm2-7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC-Cdc6 function to recruit a single Cdt1-Mcm2-7 heptamer to replication origins prior to Cdt1 release and ORC-Cdc6-Mcm2-7 complex formation, but how the second Mcm2-7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC-Cdc6-Mcm2-7 complex and an ORC-Cdc6-Mcm2-7-Mcm2-7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2-7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2-7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability

Soft modes of collective domain-wall vibrations in epitaxial ferroelectric thin films

Mechanical restoring forces acting on ferroelastic domain walls displaced from the equilibrium positions in epitaxial films are calculated for various modes of their cooperative translational oscillations. For vibrations of the domain-wall superlattice with the wave vectors corresponding to the center and boundaries of the first Brillouin zone, the soft modes are singled out that are distinguished by a minimum magnitude of the restoring force. It is shown that, in polydomain ferroelectric thin films, the soft modes of wall vibrations may create enormously large contribution to the film permittivity.Comment: 6 pages, 3 figure

Magnetotransport properties of a polarization-doped three-dimensional electron slab

We present evidence of strong Shubnikov-de-Haas magnetoresistance oscillations in a polarization-doped degenerate three-dimensional electron slab in an Al$_{x}$Ga$_{1-x}$N semiconductor system. The degenerate free carriers are generated by a novel technique by grading a polar alloy semiconductor with spatially changing polarization. Analysis of the magnetotransport data enables us to extract an effective mass of $m^{\star}=0.19 m_{0}$ and a quantum scattering time of $\tau_{q}= 0.3 ps$. Analysis of scattering processes helps us extract an alloy scattering parameter for the Al$_{x}$Ga$_{1-x}$N material system to be $V_{0}=1.8eV$