Using sketch-map coordinates to analyze and bias molecular dynamics simulations

When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.

Simplifying the representation of complex free-energy landscapes using sketch-map

A new scheme, sketch-map, for obtaining a low-dimensional representation of the region of phase space explored during an enhanced dynamics simulation is proposed. We show evidence, from an examination of the distribution of pairwise distances between frames, that some features of the free-energy surface are inherently high-dimensional. This makes dimensionality reduction problematic because the data does not satisfy the assumptions made in conventional manifold learning algorithms We therefore propose that when dimensionality reduction is performed on trajectory data one should think of the resultant embedding as a quickly sketched set of directions rather than a road map. In other words, the embedding tells one about the connectivity between states but does not provide the vectors that correspond to the slow degrees of freedom. This realization informs the development of sketch-map, which endeavors to reproduce the proximity information from the high-dimensionality description in a space of lower dimensionality even when a faithful embedding is not possible.

One-Pot, High-Yield Synthesis of Convex Au Octahedra by H2O2 - Mediated Process In Solution Phase

A simple, non-seeding and high-yield synthesis of convex gold octahedra with size of ca. 50 nm in aqueous solution is described. The octahedral nanoparticles were systematically prepared by reduction of HAuCl4 using ascorbic acid (AA) in the presence of cetyltrimethylammonium bromide (CTAB) as the stabilizing surfactant while concentrations of Au3+ were fixed. The synthesizing process is especially different to other wet synthesis of metallic nanoparticles because it is mediated by H2O2. Mechanism of the H2O2 – mediated process will be described in details. The gold octahedra were shown to be single crystals with all 8 faces belonging to {111} family. Moreover, the single crystalline particles also showed attractive optical properties towards LSPR that should find uses as labels for microscopic imaging, materials for colorimetric biosensings, or nanosensor developments.

Amplitude modulated signal transmission through a phase conjugating lens

Free space transmission of an on-off modulated sinusoidal signal through a phase conjugating lens (PCL) is theoretically examined using a combined time/frequency domain approach. The on-off keyed (OOK) signal is generated by a dipole antenna located in the far-field zone of the lens. The PCL consists of a dual layer of antenna elements interconnected via phase conjugating circuitry. We demonstrate that electromagnetic interference between antenna elements creates spatially localised areas of good-quality reception and zones where the signal is significantly denigrated by interference. Next, it is shown that destructive interference and packet desynchronisation effects critically depend on bit rate. It is also shown that a circular concave lens can be used to produce high-quality signal reception in a given direction while suppressing signal reception in all other directions. The effect that the bandwidth of the phase conjugating unit has on the transmitted signal properties for the cases of high and low bit rate OOK modulation are studied and a signal quality characterisation scheme is proposed which uses cross-correlation. The results of the study yields understanding of the performance of phase conjugating arrays under OOK modulation. The work suggests a novel approach for realising a secure communication wireless system.

Reflection and Transmission at a Phase Discontinuous Interface

In this paper we extend the derivation of the modified form Snells's law that occurs when an additional phase profile is introduced at the material interface. We show that this permits electromagnetic (EM) beam steering, negative refraction and retrodirective action opportunities for such engineered surfaces even if they are immersed in a uniform dielectric. Simple expressions for the retrodirected and negatively refracted beams are derived along with the propagation conditions that occur at the boundary interface inside the critical angle range. It is also demonstrated how the transmission and reflected power levels are affected by the additional phase taper introduced at the surface.

Two-Ray Modeling of Recombination Effects in the Presence of a Phase Conjugation Array

This article describes by means of a simple model how signal recombination effects behave under the influence of phase conjugating retrodirective array (RDA) technology. A two-ray ground reflection model is used to predict the operational advantages of RDA technology in multipath rich environments. The simulation results show that advantageous signal recombination occurs due to automatic self-phasing. As the number of elements in the RDA increases, the fading effect normally observed due to out of phase multipath signal is mitigated to the extent that the system approaches that of one operating in a free space environment. © 2013 Wiley Periodicals, Inc. Microwave Opt Technol Lett 55:1987–1989, 2013

Scaling of the entanglement spectrum near quantum phase transitions

The entanglement spectrum describing quantum correlations in many-body systems has been recently recognized as a key tool to characterize different quantum phases, including topological ones. Here we derive its analytically scaling properties in the vicinity of some integrable quantum phase transitions and extend our studies also to nonintegrable quantum phase transitions in one-dimensional spin models numerically. Our analysis shows that, in all studied cases, the scaling of the difference between the two largest nondegenerate Schmidt eigenvalues yields with good accuracy critical points and mass scaling exponents.

High-contrast imaging search for planets and brown dwarfs around the most massive stars in the solar neighborhood

There has been a long-standing discussion in the literature as to whether core accretion or disk instability is the dominant mode of planet formation. Over the last decade, several lines of evidence have been presented showing that core accretion is most likely the dominant mechanism for the close-in population of planets probed by radial velocity and transits. However, this does not by itself prove that core accretion is the dominant mode for the total planet population, since disk instability might conceivably produce and retain large numbers of planets in the far-out regions of the disk. If this is a relevant scenario, then the outer massive disks of B-stars should be among the best places for massive planets and brown dwarfs to form and reside. In this study, we present high-contrast imaging of 18 nearby massive stars of which 15 are in the B2-A0 spectral-type range and provide excellent sensitivity to wide companions. By comparing our sensitivities to model predictions of disk instability based on physical criteria for fragmentation and cooling, and using Monte Carlo simulations for orbital distributions, we find that ~85% of such companions should have been detected in our images on average. Given this high degree of completeness, stringent statistical limits can be set from the null-detection result, even with the limited sample size. We find that

Estimating Stellar Radial Velocity Variability from Kepler and GALEX: Implications for the radial velocity confirmation of exoplanets.

We cross match the GALEX and Kepler surveys to create a unique dataset with both ultraviolet (UV) measurements and highly precise photometric variability measurements in the visible light spectrum. As stellar activity is driven by magnetic field modulations, we have used UV emission from the magnetically heated gas in the stellar atmosphere to serve as our proxy for the more well-known stellar activity indicator, R' HK . The R' HK approximations were in turn used to estimate the level of astrophysical noise expected in radial velocity (RV) measurements and these were then searched for correlations with photometric variability. We find significant scatter in our attempts to estimate RV noise for magnetically active stars, which we attribute to variations in the phase and strength of the stellar magnetic cycle that drives the activity of these targets. However, for stars we deem to be magnetically quiet, we do find a clear correlation between photometric variability and estimated levels of RV noise (with variability up to ~10 m s–1). We conclude that for these quiet stars, we can use photometric measurements as a proxy to estimate the RV noise expected. As a result, the procedure outlined in this paper may help select targets best-suited for RV follow-up necessary for planet confirmation.

Spectroscopic Observations of SN 2012fr: A Luminous Normal Type Ia Supernova with Early High Velocity Features and Late Velocity Plateau

We present 65 optical spectra of the Type Ia supernova SN 2012fr, of which 33 were obtained before maximum light. At early times SN 2012fr shows clear evidence of a high-velocity feature (HVF) in the Si II 6355 line which can be cleanly decoupled from the lower velocity "photospheric" component. This Si II 6355 HVF fades by phase -5; subsequently, the photospheric component exhibits a very narrow velocity width and remains at a nearly constant velocity of v~12,000 km/s until at least 5 weeks after maximum brightness. The Ca II infrared (IR) triplet exhibits similar evidence for both a photospheric component at v~12,000 km/s with narrow line width and long velocity plateau, as well as a high-velocity component beginning at v~31,000 km/s two weeks before maximum. SN 2012fr resides on the border between the "shallow silicon" and "core-normal" subclasses in the Branch et al. (2009) classification scheme, and on the border between normal and "high-velocity" SNe Ia in the Wang et al. (2009a) system. Though it is a clear member of the "low velocity gradient" (LVG; Benetii et al., 2005) group of SNe Ia and exhibits a very slow light-curve decline, it shows key dissimilarities with the overluminous SN 1991T or SN 1999aa subclasses of SNe Ia. SN 2012fr represents a well-observed SN Ia at the luminous end of the normal SN Ia distribution, and a key transitional event between nominal spectroscopic subclasses of SNe Ia.

Nonlinear optics from an ab initio approach by means of the dynamical Berry phase: Application to second- and third-harmonic generation in semiconductors

We present an ab initio real-time-based computational approach to study nonlinear optical properties in condensed matter systems that is especially suitable for crystalline solids and periodic nanostructures. The equations of motion and the coupling of the electrons with the external electric field are derived from the Berry-phase formulation of the dynamical polarization [Souza et al., Phys. Rev. B 69, 085106 (2004)]. Many-body effects are introduced by adding single-particle operators to the independent-particle Hamiltonian. We add a Hartree operator to account for crystal local effects and a scissor operator to correct the independent particle band structure for quasiparticle effects. We also discuss the possibility of accurately treating excitonic effects by adding a screened Hartree-Fock self-energy operator. The approach is validated by calculating the second-harmonic generation of SiC and AlAs bulk semiconductors: an excellent agreement is obtained with existing ab initio calculations from response theory in frequency domain [Luppi et al., Phys. Rev. B 82, 235201 (2010)]. We finally show applications to the second-harmonic generation of CdTe and the third-harmonic generation of Si. 

Thermotropic phase boundaries in classic ferroelectrics

High-performance piezoelectrics are lead-based solid solutions that exhibit a so-called morphotropic phase boundary, which separates two competing phases as a function of chemical composition; as a consequence, an intermediate low-symmetry phase with a strong piezoelectric effect arises. In search for environmentally sustainable lead-free alternatives that exhibit analogous characteristics, we use a network of competing domains to create similar conditions across thermal inter-ferroelectric transitions in simple, lead-free ferroelectrics such as BaTiO 3 and KNbO 3. Here we report the experimental observation of thermotropic phase boundaries in these classic ferroelectrics, through direct imaging of low-symmetry intermediate phases that exhibit large enhancements in the existing nonlinear optical and piezoelectric property coefficients. Furthermore, the symmetry lowering in these phases allows for new property coefficients that exceed all the existing coefficients in both parent phases. Discovering the thermotropic nature of thermal phase transitions in simple ferroelectrics thus presents unique opportunities for the design of 'green' high-performance materials.

Can a carbon nano-coating resist metallic phase transformation in silicon substrate during nanoimpact?

Nanomechanical response of a silicon specimen coated with a sp3 crystalline carbon coating (1.8 nm thickness) was investigated using MD simulation. A sharp conical rigid tip was impacted at the speed of 50 m/sec up to a depth of ~80% of the coating thickness. Unlike pure silicon specimen, no metallic phase transformation was observed i.e. a thin coating was able to resist Si-I to Si-II metallic phase transformation signifying that the coating could alter the stress distribution and thereby the contact tribology of the substrate. The stress state of the system, radial distribution function and the load-displacement curve were all aligned with above observations

Near Field Enhancement and Subwavelength Imaging Using Resonantly Loaded Apertures

It is demonstrated that the electromagnetic (EM) transmission through a subwavelength or non-resonant aperture in a conductive screen can be dramatically enhanced by loading it with folded metallic strips exhibiting resonant properties. When illuminated by an EM plane wave these loaded apertures enable very tight, subwavelength, collimation of the EM power in the near field zone. We propose planar and quasi-planar resonant insertion geometries that should allow, for the first time, two-dimensional dual-polarization subwavelength field confinement along with ability to focus both electric and magnetic fields. The proposed technique for resonance transmission enhancement and near field confinement forms a basis for a new class of microwave near field imaging probe with subwavelength resolution capable of operating over a wide range of imaging distances (0.05–$0.25lambda$). Measurement results demonstrate the possibility of high contrast (more than 3 dB in amplitude and 40 degrees in phase) near field subwavelength imaging of 2D and 3D resonant and non-resonant metallic and dielectric targets in free space and in moderately lossy layered media.

Monodomain strained ferroelectric PbTiO(3) thin films: Phase transition and critical thickness study

This work demonstrates that instead of paraelectric PbTiO(3), completely c-oriented ferroelectric PbTiO(3) thin films were directly grown on (001)-SrTiO(3) substrates by pulsed-laser deposition with thickness up to 340 nm at a temperature well above the Curie temperature of bulk PbTiO(3). The influence of laser-pulse frequency, substrate-surface termination on growth, and functional properties were studied using x-ray diffraction, transmission electron microscopy, and piezoresponse force microscopy. At low growth rates (frequency 8 Hz) a domains were formed for film thickness above 20-100 nm. Due to coherency strains the Curie temperature (T(c)) of the monodomain films was increased approximately by 350 degrees C with respect to the T(c) of bulk PbTiO(3) even for 280-nm-thick films. Nonetheless, up to now this type of growth mode has been considered unlikely to occur since the Matthews-Blakeslee (MB) model already predicts strain relaxation for films having a thickness of only similar to 10 nm. However, the present work disputes the applicability of the MB model. It clarifies the physical reasons for the large increase in T(c) for thick films, and it is shown that the experimental results are in good agreement with the predictions based on the monodomain model of Pertsev et al. [Phys. Rev. Lett. 80, 1988 (1998)].