Radiographic areal density measurements on the OMEGA EP laser system.

We describe two orthogonal radiography geometries at the OMEGA EP laser facility, which we refer to as side-on and face-on radiography. This setup can be used to determine quantitative information about the areal densities in solid, particulate, or liquid samples. We show sample images from these two different platforms that use the radiography diagnostic, one of material microjetting by the Richtmeyer-Meshkov instability and one of a deforming tin sample by the Rayleigh-Taylor instability, demonstrating the versatile applicability of such measurements in the field of high-energy density physics. The analytical methodology behind the quantitative Rayleigh-Taylor face-on radiography is also demonstrated and can be applied to other types of samples.

Observations of grain-boundary phase transformations in an elemental metal.

The theory of grain boundary (the interface between crystallites, GB) structure has a long history1 and the concept of GBs undergoing phase transformations was proposed 50 years ago2,3. The underlying assumption was that multiple stable and metastable states exist for different GB orientations4-6. The terminology 'complexion' was recently proposed to distinguish between interfacial states that differ in any equilibrium thermodynamic property7. Different types of complexion and transitions between complexions have been characterized, mostly in binary or multicomponent systems8-19. Simulations have provided insight into the phase behaviour of interfaces and shown that GB transitions can occur in many material systems20-24. However, the direct experimental observation and transformation kinetics of GBs in an elemental metal have remained elusive. Here we demonstrate atomic-scale GB phase coexistence and transformations at symmetric and asymmetric [Formula: see text] tilt GBs in elemental copper. Atomic-resolution imaging reveals the coexistence of two different structures at Σ19b GBs (where Σ19 is the density of coincident sites and b is a GB variant), in agreement with evolutionary GB structure search and clustering analysis21,25,26. We also use finite-temperature molecular dynamics simulations to explore the coexistence and transformation kinetics of these GB phases. Our results demonstrate how GB phases can be kinetically trapped, enabling atomic-scale room-temperature observations. Our work paves the way for atomic-scale in situ studies of metallic GB phase transformations, which were previously detected only indirectly9,15,27-29, through their influence on abnormal grain growth, non-Arrhenius-type diffusion or liquid metal embrittlement.

MS-STEM-FEM: A parallelized multi-slice fluctuation TEM simulation tool.

Atomic configurations of glassy or amorphous materials containing medium-range order (MRO) may be identified by comparing fluctuation transmission electron microscopy (FTEM) measurements to FTEM simulations obtained using model configurations. Candidate model sizes have traditionally been much thinner than the samples measured experimentally, and publicly available FTEM simulation software has until now omitted microscope parameters, dynamical scattering, and the phase of the diffracted electron wave. We introduce MS-STEM-FEM, an open-source software package for simulating FTEM experiments using established multi-slice TEM simulation techniques to emulate experiment more closely by incorporating microscope parameters and simulating electron scattering and propagation as a complex valued wave. Simulations using established models are compared with results of experimental STEM-FEM to validate the software. Several statistical measures of diffraction are implemented and their responses to model features are compared. Dynamical scattering is found to be less influential than the variety of crystallite orientations which occur in thicker models. Simulations of variable resolution microscopy confirm that cumulative intensity of the FTEM signal decreases with reduced model MRO and increased coherence volume. Advantageous model scaling characteristics and efficient processor performance scaling are demonstrated, along with a study of convergence with respect to pertinent simulation parameters to identify accuracy requirements.

Predicting phase behavior of grain boundaries with evolutionary search and machine learning.

The study of grain boundary phase transitions is an emerging field until recently dominated by experiments. The major bottleneck in the exploration of this phenomenon with atomistic modeling has been the lack of a robust computational tool that can predict interface structure. Here we develop a computational tool based on evolutionary algorithms that performs efficient grand-canonical grain boundary structure search and we design a clustering analysis that automatically identifies different grain boundary phases. Its application to a model system of symmetric tilt boundaries in Cu uncovers an unexpected rich polymorphism in the grain boundary structures. We find new ground and metastable states by exploring structures with different atomic densities. Our results demonstrate that the grain boundaries within the entire misorientation range have multiple phases and exhibit structural transitions, suggesting that phase behavior of interfaces is likely a general phenomenon.

Shear viscosity for dense plasmas by equilibrium molecular dynamics in asymmetric Yukawa ionic mixtures.

We present molecular dynamics (MD) calculations of shear viscosity for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and inertial confinement fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100-500 eV and a number density of 10^{25} ions/cc. The motion of 30,000-120,000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction; the electrons are not simulated explicitly. Shear viscosity is calculated using the Green-Kubo approach with an integral of the shear stress autocorrelation function, a quantity calculated in the equilibrium MD simulations. We systematically study different mixtures through a series of simulations with increasing fraction of the minority high-Z element (Ar) in the D-Ar plasma mixture. In the more weakly coupled plasmas, at 500 eV and low Ar fractions, results from MD compare very well with Chapman-Enskog kinetic results. In the more strongly coupled plasmas, the kinetic theory does not agree well with the MD results. We develop a simple model that interpolates between classical kinetic theories at weak coupling and the Murillo Yukawa viscosity model at higher coupling. This hybrid kinetics-MD viscosity model agrees well with the MD results over the conditions simulated, ranging from moderately weakly coupled to moderately strongly coupled asymmetric plasma mixtures.

Diffusivity in asymmetric Yukawa ionic mixtures in dense plasmas.

In this paper we present molecular dynamics (MD) calculations of the interdiffusion coefficient for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and inertial confinement fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100-500 eV and a number density ∼10(25) ions/cm(3). The motion of 30,000-120,000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction; the electrons are not simulated explicitly. The species diffusivity is then calculated using the Green-Kubo approach using an integral of the interdiffusion current autocorrelation function, a quantity calculated in the equilibrium MD simulations. Our MD simulation results show that a widely used expression relating the interdiffusion coefficient with the concentration-weighted sum of self-diffusion coefficients overestimates the interdiffusion coefficient. We argue that this effect due to cross-correlation terms in velocities is characteristic of asymmetric mixed plasmas. Comparison of the MD results with predictions of kinetic theories also shows a discrepancy with MD giving effectively a larger Coulomb logarithm.

Self-diffusivity and interdiffusivity of molten aluminum-copper alloys under pressure, derived from molecular dynamics.

We use molecular dynamics (MD) to simulate diffusion in molten aluminum-copper (AlCu) alloys. The self-diffusivities and Maxwell-Stefan diffusivities are calculated for AlCu mixtures using the Green-Kubo formulas at temperatures from 1000 to 4000 K and pressures from 0 to 25 GPa, along with additional points at higher temperatures and pressures. The diffusivities are corrected for finite-size effects. The Maxwell-Stefan diffusivity is compared to the diffusivity calculated from the self-diffusivities using a generalization of the Darken equation. We find that the effects of cross-correlation are small. Using the calculated self-diffusivities, we have assessed whether dilute hard-sphere and dilute Lennard-Jones models apply to the molten mixture. Neither of the two dilute gas diffusivities describes the diffusivity in molten Al and Cu. We report generalized analytic models for the self-diffusivities and interdiffusivity (mutual diffusivity) that fit the MD results well. The MD-derived transport coefficients are in good agreement with the available experimental data. We also report MD calculations of the viscosity and an analytic fit to those results. The ionic thermal conductivity is discussed briefly.

Time-dependent measure of a nanoscale force-pulse driven by the axonemal dynein motors in individual live sperm cells.

Nanoscale mechanical forces generated by motor proteins are crucial to normal cellular and organismal functioning. The ability to measure and exploit such forces is important to developing motile biomimetic nanodevices powered by biological motors for nanomedicine. Axonemal dynein motors positioned inside the sperm flagellum drive microtubule sliding and give rise to rhythmic beating. This force-generating action pushes the sperm cell through viscous media. Here we report new nanoscale information on how the propulsive force is generated by the sperm flagellum and how this force varies over time. Using a modified atomic force microscope, single-cell recordings reveal discrete approximately 50-ms pulses oscillating with amplitude 9.8 +/- 2.6 nN independent of pulse frequency (3.5-19.5 Hz). The average work carried out by each cell is 4.6 x 10(-16) J per pulse, equivalent to the hydrolysis of approximately 5500 molecules of adenosine triphosphate. The mechanochemical coupling at each active dynein head is approximately 2.2 pN per adenosine triphosphate molecule and approximately 3.9 pN per dynein arm. From the clinical editor: In this paper, nanoscale mechanical forces generated by axonemal dynein motors derived from sperm flagellum are examined and reported. These motor proteins are crucial to normal cellular and organismal functioning. The ability to measure and exploit such forces is important to developing motile biomimetic nanodevices powered by biological motors for nanomedicine.

Using alloying to promote the subtle rhombohedral phase transition in vanadium.

Recently it has been suggested theoretically and discovered experimentally that pressure can induce body-centered cubic vanadium to transition to a rhombohedral phase. Here we show using density functional theory calculations that alloying can affect the same transition, and in particular alloying can increase the stability of the rhombohedral phase, reducing the pressure needed to induce the transition. These calculations are full supercell calculations, as opposed to the virtual crystal approximation and other approximate schemes that neglect atomic relaxation and local bonding effects. These results suggest a way in which alloying provides a means of designing this class of exotic phases to be more robust.

Nonlinearly additive forces in multivalent ligand binding to a single protein revealed with force spectroscopy.

We present evidence of multivalent interactions between a single protein molecule and multiple carbohydrates at a pH where the protein can bind four ligands. The evidence is based not only on measurements of the force required to rupture the bonds formed between concanavalin A (ConA) and alpha-D-mannose but also on an analysis of the polymer-extension force curves to infer the polymer architecture that binds the protein to the cantilever and the ligands to the substrate. We find that although the rupture forces for multiple carbohydrate connections to a single protein are larger than the rupture force for a single connection, they do not scale additively with increasing number. Specifically, the most common rupture forces are approximately 46, 68, and 85 pN at a loading rate of 650 +/- 25 pN/s, which we argue corresponds to 1, 2, and 3 ligands being pulled simultaneously from a single protein as corroborated by an analysis of the linkage architecture. As in our previous work polymer tethers allow us to discriminate between specific and nonspecific binding. We analyze the binding configuration (i.e., serial vs parallel connections) through fitting the polymer stretching data with modified wormlike chain (WLC) models that predict how the effective stiffness of the tethers is affected by multiple connections. This analysis establishes that the forces we measure are due to single proteins interacting with multiple ligands, the first force spectroscopy study that establishes single-molecule multivalent binding unambiguously.

The AFM measured force required to rupture the dithiolate linkage of thioctic acid to gold is less than the rupture force of a simple gold-alkyl thiolate bond.

We show with atomic force microscopy that thioctic acid, a spatially constrained system with two sulfur linkages to gold, is less stable to tensile stress than a thiolate with a single attachment to gold. The force required to remove the dithiolate-linked thioctic acid was 0.31+/-0.13 nN, whereas the force required to remove a simple thiolate from the gold substrate was 1.05+/-0.29 nN. These results suggest that SAMs of densely packed or polypodal thiols may be substantially less stable under tensile stress than previously recognized and that the additional thiolate linkages may not only fail to increase the overall strength of attachment but could actually reduce it.

The structure of the cubic coincident site lattice rotation group.

This work is intended to be a mathematical underpinning for the field of grain-boundary engineering and its relatives. The inter-relationships within the set of rotations producing coincident site lattices in cubic crystals are examined in detail. Besides combining previously established but widely scattered results into a unified context, the present work details newly developed representations of the group structure in terms of strings of generators (based on quaternionic number theory, and including uniqueness proofs and rules for algebraic manipulation) as well as an easily visualized topological network model. Important results that were previously obscure or not universally understood (e.g. the Sigma combination rule governing triple junctions) are clarified in these frameworks. The methods also facilitate several general observations, including the very different natures of twin-limited structures in two and three dimensions, the inadequacy of the Sigma combination rule to determine valid quadruple nodes, and a curious link between allowable grain-boundary assignments and the four-color map theorem. This kind of understanding is essential to the generation of realistic statistical models of grain-boundary networks (particularly in twin-dominated systems) and is especially applicable to the field of grain-boundary engineering.

Force spectroscopy of the double-tethered concanavalin-A mannose bond.

We present the measurement of the force required to rupture a single protein-sugar bond using a methodology that provides selective discrimination between specific and nonspecific binding events and helps verify the presence of a single functional molecule on the atomic force microscopy tip. In particular, the interaction force between a polymer-tethered concanavalin-A protein (ConA) and a similarly tethered mannose carbohydrate was measured as 47 +/- 9 pN at a bond loading rate of approximately 10 nN/s. Computer simulations of the polymer molecular configurations were used to determine the angles that the polymers could sweep out during binding and, in conjunction with mass spectrometry, used to separate the angular effects from the effects due to a distribution of tether lengths. We find that when using commercially available polymer tethers that vary in length from 19 to 29 nm, the angular effects are relatively small and the rupture distributions are dominated by the 10-nm width of the tether length distribution. In all, we show that tethering both a protein and its ligand allows for the determination of the single-molecule bond rupture force with high sensitivity and includes some validation for the presence of a single-tethered functional molecule on the atomic force microscopy tip.

Equilibrium model of bimodal distributions of epitaxial island growth.

We present a nanostructure diagram for use in designing heteroepitaxial systems of quantum dots. The nanostructure diagram is computed using a new equilibrium statistical physics model and predicts the island size and shape distributions for a range of combinations of growth temperature and amount of deposited material. The model is applied to Ge on Si(001), the archetype for bimodal island growth, and the results compare well with data from atomic force microscopy of Ge/Si islands grown by chemical vapor deposition.

Combining constitutive materials modeling with atomic force microscopy to understand the mechanical properties of living cells.

The goal of this work is to study the properties of living cells and cell membranes by using atomic force microscopy. During atomic force microscopy (AFM) measurement, there is a strong mechanical coupling between the AFM tip and the cell. The purpose of this paper is to present a model of the overall mechanical response of the cell that allows us to separate out the mechanical response of the cell from the local surface interactions we wish to quantify. These local interactions include recognition (or binding) events between molecules bound to an AFM tip (e.g., an antibody) and molecules or receptors on the cell surface (e.g., the respective antigen). The computational model differs from traditional Hertzian contact models by explicitly taking into account the mechanics of the biomembrane and cytoskeleton. The model also accounts for the mechanical response of the living cell during arbitrary deformation. The indentation of a bovine sperm cell is used to test the validity of this model, and further experiments are proposed to fully parameterize the model.