Perspectives on Pyroshock Attenuation in Cylindrical Space Structures with a Bulkhead.
Abstract not provided.
Lee, Daniel↗
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Interparticle spacing and structural ordering in superlattice PbS nanocrystal solids undergoing ligand exchange
Controlling the interparticle spacing in quantum dot (QD) thin films is the most readily accessible way to control transport rates between neighboring QDs and a critical component of device optimization. Here, we use X-ray scattering measurements to accurately measure the interparticle spacing in films of highly monodisperse lead sulfide (PbS) QDs that have undergone a variety of device-relevant ligand exchanges. We tabulate these values for use in simulations and data analysis. We find that monothiol and dithiol ligand species typically result in interparticle spacing values that are equal to the length of a single monothiol or dithiol ligand. Additionally, we find that spin-coating a thick film of QDs followed by a long-duration ligand exchange results in a more complete ligand exchange than spin-coating many thin layers with short-duration ligand exchanges in between. The former method also preserves a remarkable degree of the long-range ordering that was present in the film prior to ligand exchange. These results shed light on ways to produce highly-ordered QD solids with compact and functional ligands, which could lead to enhanced interdot coupling and transport phenomena.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Lagrangian space consistency relation for large scale structure
Consistency relations, which relate the squeezed limit of an (N+1)-point correlation function to an N-point function, are non-perturbative symmetry statements that hold even if the associated high momentum modes are deep in the nonlinear regime and astrophysically complex. Recently, Kehagias & Riotto and Peloso & Pietroni discovered a consistency relation applicable to large scale structure. We show that this can be recast into a simple physical statement in Lagrangian space: that the squeezed correlation function (suitably normalized) vanishes. This holds regardless of whether the correlation observables are at the same time or not, and regardless of whether multiple-streaming is present. Furthermore, the simplicity of this statement suggests that an analytic understanding of large scale structure in the nonlinear regime may be particularly promising in Lagrangian space.
79 ASTRONOMY AND ASTROPHYSICS↗
Space-Time Structured Plasma Waves
Electrostatic waves play a critical role in nearly every branch of plasma physics from fusion to advanced accelerators, to astro, solar, and ionospheric physics. The properties of planar electrostatic waves are fully determined by the plasma conditions, such as density, temperature, ionization state, or details of the distribution functions. Furthermore we demonstrate that electrostatic wave packets structured with space-time correlations can have properties that are independent of the plasma conditions. For instance, an appropriately structured electrostatic wave packet can travel at any group velocity, even backward with respect to its phase fronts, while maintaining a localized energy density. These linear, propagation-invariant wave packets can be constructed with or without orbital angular momentum by superposing natural modes of the plasma and can be ponderomotively excited by space-time structured laser pulses like the flying focus.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Dynamically generated momentum space shell structure of quarkyonic matter via an excluded volume model
The phase-space structure of zero-temperature quarkyonic matter is a Fermi sphere of quark matter surrounded by a shell of nucleonic matter. Here, we construct a quasiparticle model of quarkyonic matter based on the constituent quark model, where the quark and nucleon masses are related by $m_Q = m_N/N_c$, and $N_c$ is the number of quark colors. The region of occupied states is for quarks $k_Q < k_F/N_c$ and for nucleons $k_F < k_N < k_F + Δ$. We first consider the general problem of quarkyonic matter with hard-core nucleon interactions. We then specialize to a quasiparticle model where the hard-core nucleon interactions are accounted for by an excluded volume. In this model, we show that the nucleonic shell forms past some critical density related to the hard-core size and for large densities becomes a thin shell. We explore the basic features of such a model and argue this model has the semiquantitative behavior needed to describe neutron stars.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Complete fold annotation of the human proteome using a novel structural feature space
Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example. We demonstrate the utility of this method by predicting the folds of 34,330 human protein domains and showing that these predictions can yield useful insights into potential biological function, such as prediction of RNA-binding ability. Finally, our method can be applied to de novo fold prediction of entire proteomes and identify candidate novel fold families.
59 BASIC BIOLOGICAL SCIENCES↗
Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model
The brain produces diverse functions, from perceiving sounds to producing arm reaches, through the collective activity of populations of many neurons. Determining if and how the features of these exogenous variables (e.g., sound frequency, reach angle) are reflected in population neural activity is important for understanding how the brain operates. Often, high-dimensional neural population activity is confined to low-dimensional latent spaces. However, many current methods fail to extract latent spaces that are clearly structured by exogenous variables. This has contributed to a debate about whether or not brains should be thought of as dynamical systems or representational systems. Here, we developed a new latent process Bayesian regression framework, the orthogonal stochastic linear mixing model (OSLMM) which introduces an orthogonality constraint amongst time-varying mixture coefficients, and provide Markov chain Monte Carlo inference procedures. We demonstrate superior performance of OSLMM on latent trajectory recovery in synthetic experiments and show superior computational efficiency and prediction performance on several real-world benchmark data sets. We primarily focus on demonstrating the utility of OSLMM in two neural data sets: μ ECoG recordings from rat auditory cortex during presentation of pure tones and multi-single unit recordings form monkey motor cortex during complex arm reaching. We show that OSLMM achieves superior or comparable predictive accuracy of neural data and decoding of external variables (e.g., reach velocity). Most importantly, in both experimental contexts, we demonstrate that OSLMM latent trajectories directly reflect features of the sounds and reaches, demonstrating that neural dynamics are structured by neural representations. Together, these results demonstrate that OSLMM will be useful for the analysis of diverse, large-scale biological time-series datasets.
59 BASIC BIOLOGICAL SCIENCES↗
Non-resonant Raman optical activity from phase-space electronic structure theory
In order to model experimental non-resonant Raman optical activity, chemists must compute a host of second-order response tensors (e.g., the electric-dipole–magnetic-dipole polarizability) and their nuclear derivatives along a set of vibrational modes. While these response functions are almost always computed within a Born–Oppenheimer (BO) framework, here we provide a natural interpretation of the electric-dipole–magnetic-dipole polarizability within phase space electronic structure theory, a beyond-BO model whereby the electronic structure depends on nuclear momentum (P) in addition to nuclear position (R). By coupling to nuclear momentum, phase space electronic structure theory is able to capture the asymmetric response of the electronic properties to an external field, in so far as for a vibrating (non-stationary) molecule, $\frac{∂μ}{∂B}$≠$\frac{∂m}{∂F}$, where μ and m are the electrical linear and magnetic dipoles, and F and B are electric and magnetic fields. As an example, for a prototypical methyloxirane molecule, we show that phase space electronic structure theory is able to deliver a reasonably good match with experimental results in a manner that is formally invariant to gauge origin G 0 —provided that one uses a complete basis or, alternatively, gauge invariant atomic orbitals.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
ENERGY DISSIPATION AND LANDAU DAMPING IN TWO- AND THREE-DIMENSIONAL PLASMA TURBULENCE
Plasma turbulence is ubiquitous in space and astrophysical plasmas, playing an important role in plasma energization, but the physical mechanisms leading to dissipation of the turbulent energy remain to be definitively identified. Kinetic simulations in two dimensions (2D) have been extensively used to study the dissipation process. How the limitation to 2D affects energy dissipation remains unclear. This work provides a model of comparison between two- and three-dimensional (3D) plasma turbulence using gyrokinetic simulations; it also explores the dynamics of distribution functions during the dissipation process. It is found that both 2D and 3D nonlinear gyrokinetic simulations of a low-beta plasma generate electron velocity-space structures with the same characteristics as that of the linear Landau damping of Alfvén waves in a 3D linear simulation. The continual occurrence of the velocity-space structures throughout the turbulence simulations suggests that the action of Landau damping may be responsible for the turbulent energy transfer to electrons in both 2D and 3D, and makes possible the subsequent irreversible heating of the plasma through collisional smoothing of the velocity-space fluctuations. Although, in the 2D case where variation along the equilibrium magnetic field is absent, it may be expected that Landau damping is not possible, a common trigonometric factor appears in the 2D resonant denominator, leaving the resonance condition unchanged from the 3D case. The evolution of the 2D and 3D cases is qualitatively similar. However, quantitatively, the nonlinear energy cascade and subsequent dissipation is significantly slower in the 2D case.
79 ASTRONOMY AND ASTROPHYSICS↗
Relative importance of social factors, conspecific density, and forest structure on space use by the endangered Red-cockaded Woodpecker: A new consideration for habitat restoration
Understanding how the interplay between social behaviors and habitat structure influences space use is important for conservation of birds in restored habitat. We integrated fine-grained LiDAR-derived habitat data, spatial distribution of cavity trees, and spatially explicit behavioral observations in a multi-scale model to determine the relative importance of conspecific density, intraspecific interactions, and the distribution of cavities on space use by Red-cockaded Woodpeckers (Picoides borealis) on 2 sites in South Carolina, USA. We evaluated candidate models using information theoretic methods. Top scale-specific models included effects of conspecific density and number of cavity tree starts within 200 m of Red-cockaded Woodpecker foraging locations, and effects of the number of intraspecific interactions within 400 m of Red-cockaded Woodpecker foraging locations. The top multi-scale model for 22 of 34 Red-cockaded Woodpecker groups included covariates for the number of groups within 200 m of foraging locations and LiDARderived habitat with moderate densities of large pines (Pinus spp.) and minimal hardwood overstory. These results indicate distribution of neighboring groups was the most important predictor of space use once a minimal set of structural habitat thresholds was reached, and that placing recruitment clusters as little as 400 m from foraging partitions of neighboring groups may promote establishment of new breeding groups in unoccupied habitat. The presence of neighboring groups likely provides cues to foraging Red-cockaded Woodpeckers that facilitate prospecting prior to juvenile dispersal and, to a lesser extent, indicates high-quality forage resources. Careful consideration of local distribution of neighboring groups in potential habitat may improve managers’ ability to increase Red-cockaded Woodpecker density on restored landscapes and mitigate isolation of Red-cockaded Woodpecker groups, a problem that negatively affects fitness across the species’ range.
60 APPLIED LIFE SCIENCES↗
EFT of large scale structures in redshift space [On the EFT of large scale structures in redshift space]
Here, we further develop the description of redshift-space distortions within the effective field theory of large scale structures. First, we generalize the counterterms to include the effect of baryonic physics and primordial non-Gaussianity. Second, we evaluate the IR resummation of the dark matter power spectrum in redshift space. This requires us to identify a controlled approximation that makes the numerical evaluation straightforward and efficient. Third, we compare the predictions of the theory at one loop with the power spectrum from numerical simulations up to ℓ = 6. We find that the IR resummation allows us to correctly reproduce the baryon acoustic oscillation peak. The k reach—or, equivalently, the precision for a given k—depends on additional counterterms that need to be matched to simulations. Since the nonlinear scale for the velocity is expected to be longer than the one for the overdensity, we consider a minimal and a nonminimal set of counterterms. The quality of our numerical data makes it hard to firmly establish the performance of the theory at high wave numbers. Within this limitation, we find that the theory at redshift z = 0.56 and up to ℓ = 2 matches the data at the percent level approximately up to k~0.13 hMpc –1 or k~0.18 hMpc –1 , depending on the number of counterterms used, with a potentially large improvement over former analytical techniques.
79 ASTRONOMY AND ASTROPHYSICS↗
Automated characterization of spatial and dynamical heterogeneity in supercooled liquids via implementation of machine learning
Abstract A computational approach by an implementation of the principle component analysis (PCA) with K -means and Gaussian mixture (GM) clustering methods from machine learning algorithms to identify structural and dynamical heterogeneities of supercooled liquids is developed. In this method, a collection of the average weighted coordination numbers ( W C N s ‾ ) of particles calculated from particles’ positions are used as an order parameter to build a low-dimensional representation of feature (structural) space for K -means clustering to sort the particles in the system into few meso-states using PCA. Nano-domains or aggregated clusters are also formed in configurational (real) space from a direct mapping using associated meso-states’ particle identities with some misclassified interfacial particles. These classification uncertainties can be improved by a co-learning strategy which utilizes the probabilistic GM clustering and the information transfer between the structural space and configurational space iteratively until convergence. A final classification of meso-states in structural space and domains in configurational space are stable over long times and measured to have dynamical heterogeneities. Armed with such a classification protocol, various studies over the thermodynamic and dynamical properties of these domains indicate that the observed heterogeneity is the result of liquid–liquid phase separation after quenching to a supercooled state.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Nonlinear dust-acoustic structures in space plasmas with superthermal electrons, positrons, and ions
Some features of nonlinear dust-acoustic (DA) structures are investigated in a space plasma consisting of superthermal electrons, positrons, and positive ions in the presence of negatively charged dust grains with finite-temperature by employing a pseudo-potential technique in a hydrodynamic model. For this purpose, it is assumed that the electrons, positrons, and ions obey a kappa-like (κ) distribution in the background of adiabatic dust population. In the linear analysis, it is found that the dispersion relation yield two positive DA branches, i.e., the slow and fast DA waves. The upper branch (fast DA waves) corresponds to the case in which both (negatively charged) dust particles and (positively charged) ion species oscillate in phase with electrons and positrons. On the other hand, the lower branch (slow DA waves) corresponds to the case in which only dust particles oscillate in phase with electrons and positrons, while ion species are in antiphase with them. On the other hand, the fully nonlinear analysis shows that the existence domain of solitons and their characteristics depend strongly on the dust charge, ion charge, dust temperature, and the spectral index κ. It is found that the minimum/maximum Mach number increases as the spectral index κ increases. Also, it is found that only solitons with negative polarity can propagate and that their amplitudes increase as the parameter κ increases. Furthermore, the domain of Mach number shifts to the lower values, when the value of the dust charge Z{sub d} increases. Moreover, it is found that the Mach number increases with an increase in the dust temperature. Our analysis confirms that, in space plasmas with highly charged dusts, the presence of superthermal particles (electrons, positrons, and ions) may facilitate the formation of DA solitary waves. Particularly, in two cases of hydrogen ions H{sup +} (Z{sub i} = 1) and doubly ionized Helium atoms He{sup 2+} (Z{sub i} = 2), the mentioned results are the same. Additionally, the mentioned dusty plasma does not support DA solitons with positive polarity (compressive solitons). Furthermore, our analysis confirms that DA double layers cannot exist in such a system. Moreover, the positron density has not a considerable effect on the behavior of DA solitons in our model.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
CysLT1R receptor complex with Zafirlukast (P21 space group) structure (SFX@LCLS)
This dataset has overall quality of 2.4 Å (CC*=0.5), P1 space group and cell parameters 41.58, 68.56, 87.37, 76.33, 76.69, 81.19. Structure obtained from this data have been deposited under PDB ID 6RZ5. Data processing scripts are described in detail [here](https://gist.github.com/marinegor/96102c9b7ce87509a0832649d11ba927)
CXI↗
Magnetocaloric effect and magnetostructural coupling in Mn{sub 0.92}Fe{sub 0.08}CoGe compound
The structural properties of Mn{sub 0.92}Fe{sub 0.08}CoGe have been investigated in detail using synchrotron x-ray diffraction in zero and applied pressure (p = 0–10 GPa). A ferromagnetic transition occurs around T{sub C} = 300 K and a large magnetic-entropy change −ΔS{sub M} = 17.3 J/kg K detected at T{sub C} for a field change of ΔB = 5 T. The field dependence of −ΔS{sub M}{sup max} can be expressed as −ΔS{sub M}{sup max} ∝ B. At ambient temperature and pressure, Mn{sub 0.92}Fe{sub 0.08}CoGe exhibits a co-existence of the orthorhombic TiNiSi-type structure (space group Pnma) and hexagonal Ni{sub 2}In-type structure (space group P63/mmc). Application of external pressure drives a structure change from the orthorhombic TiNiSi-type structure to the hexagonal Ni{sub 2}In-type structure. A large anomaly in heat capacity around T{sub C} is detected and the Debye temperature θ{sub D} (=319(±10) K) has been derived from analyses of the low temperature heat capacity, T ≲ 10 K.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
On structural and lattice dynamic stability of LaF{sub 3} under high pressure: A first principle study
Structural and lattice dynamical stability of the LaF3 has been analyzed as a function of hydrostatic compression through first principle electronic band structure calculations. The comparison of enthalpies of various plausible structures calculated at various pressures suggests a phase transition from ambient condition tysonite structure (space group P-3c1) to a primitive orthorhombic structure (space group Pmmn) at a pressure of ∼19.5 GPa, in line with the experimental value of 16 GPa. Further, it is predicted that this phase will remain stable up to 100 GPa (the maximum pressure up to which calculations have been performed in the present work). The theoretically determined equation of state displays a good agreement with experimental data. Various physical quantities such as zero pressure equilibrium volume, bulk modulus, and pressure derivative of bulk modulus have been derived from the theoretically determined equation of state and compared with the available experimental data. Our lattice dynamic calculations correctly demonstrate that at zero pressure the tysonite structure is lattice dynamically stable whereas the Pmmn structure is unstable lattice dynamically. Further, at transition pressure the theoretically calculated phonon spectra clearly show that the Pmmn phase emerges as lattice dynamically stable phase whereas the tysonite structure becomes unstable dynamically, supporting our static lattice calculations.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Pressure-induced phase transitions of β-type pyrochlore CsTaWO 6
The β-type pyrochlore CsTaWO 6 was studied by synchrotron X-ray diffraction (XRD) and Raman scattering methods up to pressures of 43 GPa using a diamond anvil cell (DAC). With increasing pressure, the cubic pyrochlore in space group of Fd-3¯m with combining macron]m transforms to an orthorhombic structure (space group: Pnma) at 5.9 GPa and then to a monoclinic structure (space group: P2 1 /c) at ~18 GPa. The structural evolution in CsTaWO 6 is a continuous process and experimental results suggest that the initial cubic phase has a tetragonal distortion at ambient conditions. Both XRD and Raman measurements indicate that the pressure-induced phase transitions in CsTaWO 6 are reversible. Lastly, these results may provide a structural explanation of previous experimental resistivity measurement results for the isostructural superconductor K(Cs)Os 2 O 6 at high pressure conditions.
36 MATERIALS SCIENCE↗