Superheat: An R package for creating beautiful and extendable heatmaps for visualizing complex data

The technological advancements of the modern era have enabled the collection of huge amounts of data in science and beyond. Extracting useful information from such massive datasets is an ongoing challenge as traditional data visualization tools typically do not scale well in high-dimensional settings. An existing visualization technique that is particularly well suited to visualizing large datasets is the heatmap. Although heatmaps are extremely popular in fields such as bioinformatics for visualizing large gene expression datasets, they remain a severely underutilized visualization tool in modern data analysis. In this paper we introduce superheat, a new R package that provides an extremely flexible and customizable platform for visualizing large datasets using extendable heatmaps. Superheat enhances the traditional heatmap by providing a platform to visualize a wide range of data types simultaneously, adding to the heatmap a response variable as a scatterplot, model results as boxplots, correlation information as barplots, text information, and more. Superheat allows the user to explore their data to greater depths and to take advantage of the heterogeneity present in the data to inform analysis decisions. The goal of this paper is two-fold: (1) to demonstrate the potential of the heatmap as a default visualization method for a wide range of data types using reproducible examples, and (2) to highlight the customizability and ease of implementation of the superheat package in R for creating beautiful and extendable heatmaps. The capabilities and fundamental applicability of the superheat package will be explored via three case studies, each based on publicly available data sources and accompanied by a file outlining the step-by-step analytic pipeline (with code).Comment: 26 pages, 10 figure

Magnetic Interactions in BiFeO3_3: a First-Principles Study

First-principles calculations, in combination with the four-state energy mapping method, are performed to extract the magnetic interaction parameters of multiferroic BiFeO$_3$. Such parameters include the symmetric exchange (SE) couplings and the Dzyaloshinskii-Moriya (DM) interactions up to second nearest neighbors, as well as the single ion anisotropy (SIA). All magnetic parameters are obtained not only for the $R3c$ structural ground state, but also for the $R3m$ and $R\bar{3}c$ phases in order to determine the effects of ferroelectricity and antiferrodistortion distortions, respectively, on these magnetic parameters. In particular, two different second-nearest neighbor couplings are identified and their origins are discussed in details. Moreover, Monte-Carlo (MC) simulations using a magnetic Hamiltonian incorporating these first-principles-derived interaction parameters are further performed. They result (i) not only in the accurate prediction of the spin-canted G-type antiferromagnetic structure and of the known magnetic cycloid propagating along a $$ direction, as well as their unusual characteristics (such as a weak magnetization and spin-density-waves, respectively); (ii) but also in the finding of another cycloidal state of low-energy and that awaits to be experimentally confirmed. Turning on and off the different magnetic interaction parameters in the MC simulations also reveal the precise role of each of them on magnetism

Evolution of shear-induced melting in dusty plasma

The spatiotemporal development of melting is studied experimentally in a 2D dusty plasma suspension. Starting with an ordered lattice, and then suddenly applying localized shear, a pair of counter-propagating flow regions develop. A transition between two melting stages is observed before a steady state is reached. Melting spreads with a front that propagates at the transverse sound speed. Unexpectedly, coherent longitudinal waves are excited in the flow region.Comment: 5 pages text, 3 figures, in press Physical Review Letters 2010

Filtration and transport of heavy metals in graphene oxide enabled sand columns

A fixed-bed sand column with graphene oxide (GO) layer was used to remove heavy metals (Cu(II) and Pb(II)) from an aqueous solution injected under steady flow. Due to the time constrained kinetic process of heavy metal sorption to GO, removal efficiency was affected by the injection flow rate. When injection flow rate changed from 1 to 5 mL min−1, the removal efficiency of the two metals decreased from 15.3% to 10.3% and from 26.7% to 19.0% for Cu(II) and Pb(II), respectively. Provided a fixed concentration of heavy metals in the injected flow, an increase in GO in column from 10 to 30 mg resulted in an sharp increase in the removal efficiency of Pb(II) from 26.7% to 40.5%. When Cu(II) and Pb(II) were applied simultaneously, the removal efficiency of the two metals was lower than when applied by individually. GO-sand column performance was much better for the removal of Pb(II) than for Cu(II) in each corresponding treatment. When breakthrough curve (BTC) data were simulated by the convection-dispersion-reaction (CDER) model, the fittings for Cu in every treatment were better than that of Pb in corresponding treatment. Considering the small amount of GO used to enable the sand columns that resulted in a great increase in k value, compared to the GO-free sand columns, the authors propose GO as an effective adsorption media in filters and reactive barriers to remove Pb(II) from flowing water

Local electronic structures on the superconducting interface LaAlO3/SrTiO3LaAlO_{3}/SrTiO_{3}

Motivated by the recent discovery of superconductivity on the heterointerface $LaAlO_{3}/SrTiO_{3}$, we theoretically investigate its local electronic structures near an impurity considering the influence of Rashba-type spin-orbit interaction (RSOI) originated in the lack of inversion symmetry. We find that local density of states near an impurity exhibits the in-gap resonance peaks due to the quasiparticle scattering on the Fermi surface with the reversal sign of the pairing gap caused by the mixed singlet and RSOI-induced triplet superconducting state. We also analyze the evolutions of density of states and local density of states with the weight of triplet pairing component determined by the strength of RSOI, which will be widely observed in thin films of superconductors with surface or interface-induced RSOI, or various noncentrosymmetric superconductors in terms of point contact tunneling and scanning tunneling microscopy, and thus reveal an admixture of the spin singlet and RSOI-induced triplet superconducting states.Comment: Phys. Rev. B 81, 144504 (2010)

Dynamical Monte Carlo investigation of spin reversals and nonequilibrium magnetization of single-molecule magnets

In this paper, we combine thermal effects with Landau-Zener (LZ) quantum tunneling effects in a dynamical Monte Carlo (DMC) framework to produce satisfactory magnetization curves of single-molecule magnet (SMM) systems. We use the giant spin approximation for SMM spins and consider regular lattices of SMMs with magnetic dipolar interactions (MDI). We calculate spin reversal probabilities from thermal-activated barrier hurdling, direct LZ tunneling, and thermal-assisted LZ tunnelings in the presence of sweeping magnetic fields. We do systematical DMC simulations for Mn$_{12}$ systems with various temperatures and sweeping rates. Our simulations produce clear step structures in low-temperature magnetization curves, and our results show that the thermally activated barrier hurdling becomes dominating at high temperature near 3K and the thermal-assisted tunnelings play important roles at intermediate temperature. These are consistent with corresponding experimental results on good Mn$_{12}$ samples (with less disorders) in the presence of little misalignments between the easy axis and applied magnetic fields, and therefore our magnetization curves are satisfactory. Furthermore, our DMC results show that the MDI, with the thermal effects, have important effects on the LZ tunneling processes, but both the MDI and the LZ tunneling give place to the thermal-activated barrier hurdling effect in determining the magnetization curves when the temperature is near 3K. This DMC approach can be applicable to other SMM systems, and could be used to study other properties of SMM systems.Comment: Phys Rev B, accepted; 10 pages, 6 figure

Periodic Modulation Effect on Self-Trapping of Two weakly coupled Bose-Einstein Condensates

With phase space analysis approach, we investigate thoroughly the self-trapping phenomenon for two weakly coupled Bose-Einstein condensates (BEC) in a symmetric double-well potential. We identify two kinds of self-trapping by their different relative phase behavior. With applying a periodic modulation on the energy bias of the system we find the occurrence of the self-trapping can be controlled, saying, the transition parameters can be adjusted effectively by the periodic modulation. Analytic expressions for the dependence of the transition parameters on the modulation parameters are derived for high and low frequency modulations. For an intermediate frequency modulation, we find the resonance between the periodic modulation and nonlinear Rabi oscillation dramatically affects the tunnelling dynamics and demonstrate many novel phenomena. Finally, we study the effects of many-body quantum fluctuation on self-trapping and discuss the possible experimental realization of the model.Comment: 7 pages, 11 figure