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At least 19 records

Mapping mechanical force propagation through biomolecular complexes

In this paper, we employ single-molecule force spectroscopy with an atomic force microscope (AFM) and steered molecular dynamics (SMD) simulations to reveal force propagation pathways through a mechanically ultrastable multidomain cellulosome protein complex. We demonstrate a new combination of network-based correlation analysis supported by AFM directional pulling experiments, which allowed us to visualize stiff paths through the protein complex along which force is transmitted. Finally, the results implicate specific force-propagation routes nonparallel to the pulling axis that are advantageous for achieving high dissociation forces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Range and strength of mechanical interactions of force dipoles in elastic fiber networks

Mechanical forces generated by myosin II molecular motors drive diverse cellular processes, most notably shape change, division and locomotion. These forces may be transmitted over long range through the cytoskeletal medium – a disordered, viscoelastic network of biopolymers. The resulting cell size scale force chains can in principle mediate mechanical interactions between distant actomyosin units, leading to self-organized structural order in the cell cytoskeleton. Inspired by such force transmission through elastic structures in the cytoskeleton, we consider a percolated fiber lattice network, where fibers are represented as linear elastic elements that can both bend and stretch, and the contractile activity of myosin motors is represented by force dipoles. Then, by using a variety of metrics, we show how two such contractile force dipoles interact with each other through their mutual mechanical deformations of the elastic fiber network. As a prelude to two-dipole interactions, we quantify how forces propagate through the network from a single anisotropic force dipole by analyzing clusters of nodes connected by highly strained bonds, as well as through the decay rate of strain energy with distance from a force dipole. We show that predominant fiber bending screens out force propagation, resulting in reduced and strongly network configuration-dependent dipole interactions. On the other hand, stretching-dominated networks support longer-ranged inter-dipole interactions that recapitulate the predictions of linear elasticity theory. By characterizing the differences between tensile and compressive force propagation in the fiber network, we show how inter-dipole interaction depends on the dipoles’ mutual separation and orientation. The resulting elastic interaction energy may mediate a force between multiple distant dipoles, leading to their self-organization into ordered configurations. In conclusion, this provides a potential pathway for active mechanical force-driven structural order in elastic biopolymer networks.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The potential of high-frequency forced pulsed water jet for nuclear decommissioning - 15367

Forced Pulse Water Jetting (FPWJ) has been demonstrated in other works as a credible and consistent method for removing coatings or otherwise preparing surfaces across numerous industries. Its applicability to the nuclear industry as a powerful tool for decommissioning and waste treatment has only recently being recognized and underpinning study is required before any deployment can be considered. Use of FPWJ within the nuclear sector for decommissioning and waste treatment, requires a different degree of surface finish to achieve a decontamination effect or an assured performance. This necessitates a greater erosion of the base metal than in other industries. The addition of a Forced Pulse Modulation Unit (FPMU) to a high pressure water jetting system offers performance shifts akin to the differences between High Pressure (HP) and Ultra High Pressure (UHP) water jets. Trials have been undertaken in a controlled environment to establish the number of cycles to achieve a given mass loss and or depth of penetration that would otherwise provide decontamination of mostly flat or simple geometry surfaces using a robotic arm for consistency and safety. It has also been shown that metalwork can be readily penetrated without risk of explosion, for example to allow draining of a gas cylinder. Most nuclear facilities have a plethora of pipe systems spanning various diameters. A considerable portion of the UK Sellafield site has 2 inch bore pipe. The FPMU technology is being adapted to consider applications in enclosed systems, such as decontamination of pipes. Exploratory works to date show there to be many physical attributes that influence performance that include, standoff of the jet, established propagated forced pulse jet length, interference from resultant water spray and angle of attack. Comparatively small changes to these parameters can have a profound effect on performance. The process is capable of removing 10's microns to several mms of metal progressively and repeatedly. This enables a credible potential treatment of plant and equipment at Intermediate Level Waste and High Level Waste thresholds. In considering this as a treatment method, a balance between performance, cost and environmental impact of effluents must be made and will be studied further during future active trials. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

The effects of different types of additives on growth of biomineral phases investigated by in situ atomic force microscopy

In this study, interactions between different types of additives with specific crystal surfaces of mineral phases found in biominerals were investigated at nanometer and micrometer scales by in situ atomic force microscopy (AFM). Firstly, the inhibitory effect of magnesium ion (Mg 2+ ) and that of a peptide molecule, L-aspartic acid 6mer (L-Asp 6 ) on the growth of a fast growing [-10-1] step on the (-101) face of calcium oxalate monohydrate (COM) crystal are quantitatively compared by the step speed data. Differences in the inhibitory effect are explained based on a De Yoreo model of step kinetics in detail. The step speed data show that Mg 2+ had a little inhibitory effect on the growth of the [-10-1] step, approaching a limiting value of about 15% reduction in the step speed, whereas L-Asp 6 was substantially more effective in inhibiting the step growth with an ability to stop the growth completely. Secondly, the effects of a protein molecule, bovine serum albumin (BSA) and a pseudo protein-like organic particle PSPMA 30 -PDPA 47 micelle on the growth of calcite on its {104} faces are compared. Both BSA and PSPMA 30 -PDPA 47 micelle temporarily pinned the passing steps without or negligibly inhibiting the step growth overall. The BSA molecule remained at the crystal surface without incorporation into the crystal because the steps passed through it, pushing it up and out. However, in contrast to the BSA, the micelle was incorporated into the crystal by the passing steps. In conclusion, these results together with other relevant studies suggest that the decisive factor in determining for macromolecules to be incorporated into growing minerals or to remain intact on the mineral surface with no incorporation is the magnitude of binding strength of the macromolecules to the growing step against the step’s propagation force.

36 MATERIALS SCIENCE↗

Space Situational Awareness for Python

SSAPy is a python package allowing for fast and precise orbital modeling. SSAPy is designed with speed and accuracy in mind and offers the following capabilities: - A variety of integrators, including Runge-Kutta, SciPy, SGP4, etc. - Customizable force propagation models, including a variety of Earth gravity models, lunar gravity, radiation pressure, etc. - Multiple-hypothesis tracking (MHT) UCT linker - Vectorized computations - Short arc probabilistic orbit determination - Conjunction probability estimation - Uncertainty quantification - Monte Carlo data fusion - Support for multiple coordinate frames (with coordinate frame conversions)

Schlafly, Edward↗

SSAPy - Space Situational Awareness for Python

SSAPy is a fast and flexible orbit modeling and analysis tool for orbits spanning from low-Earth into the cislunar regime. Orbits can be flexibly specified from common input formats such as Keplerian elements or two-line element (TLE) data files. SSAPy allows users to model satellites and specify parameters such as satellite area, mass, and drag coefficients. SSAPy includes a customizable force-propagation with a range of Earth, Lunar, radiation, atmospheric, and maneuvering models. SSAPy makes use of various community integration methods and can calculate time-evolved orbital quantities, including satellite magnitudes and state vectors. Users can specify various space- and ground-based observation models with support for multiple coordinate and reference frames. SSAPy also supports orbit analysis and propagation methods such as multiple hypothesis tracking and has built-in uncertainty quantification. The majority of SSAPy’s methods are vectorized and parallelizable, allowing for effective use of high-performance computer (HPC) systems. Finally, SSAPy has plotting functionality, allowing users to visualize orbits and trajectories. Examples are shown in Figure 1 and Figure 2.

97 MATHEMATICS AND COMPUTING↗

Initiated chemical vapor deposited nanoadhesive for bonding National Ignition Facility's targets

Currently, the target fabrication scientists in National Ignition Facility Directorate at Lawrence Livermore National Laboratory (LLNL) is studying the propagation force resulted from laser impulses impacting a target. To best study this, they would like the adhesive used to glue the target substrates to be as thin as possible. The main objective of this research project is to create adhesive glue bonds for NIF’s targets that are ≤ 1 μm thick. Polyglycidylmethacrylate (PGMA) thin films were coated on various substrates using initiated chemical vapor deposition (iCVD). Film quality studies using white light interferometry reveal that the iCVD PGMA films were smooth. The coated substrates were bonded at 150 °C under vacuum, with low inflow of Nitrogen. Success in bonding most of NIF’s mock targets at thicknesses ≤ 1 μm indicates that our process is feasible in bonding the real targets. Key parameters that are required for successful bonding were concluded from the bonding results. They include inert bonding atmosphere, sufficient contact between the PGMA films, and smooth substrates. Average bond strength of 0.60 MPa was obtained from mechanical shearing tests. The bonding failure mode of the sheared interfaces was observed to be cohesive. Future work on this project will include reattempt to bond silica aerogel to iCVD PGMA coated substrates, stabilize carbon nanotube forests with iCVD PGMA coating, and kinetics study of PGMA thermal crosslinking.

36 MATERIALS SCIENCE↗

Outflow of chromospheric emission features from the rim of a sunspot

In viewing a 16 mm movie made from a time sequence of spectroheliograms, some of these emission features are found to move outward from the rim of the sunspot until they are eventually lost in the small plage. There are two interpretations for the streaming of the magnetic features. It is possible that kinks in the line of force propagate along a horizontal extension of the penumbral magnetic field. Alternatively, fragments of the sunspot magnetic field are carried away by the photospheric velocity field.

Liu, S.-Y.↗

Dynamics of Sheared Granular Materials

This work focuses on the properties of sheared granular materials near the jamming transition. The project currently involves two aspects. The first of these is an experiment that is a prototype for a planned ISS (International Space Station) flight. The second is discrete element simulations (DES) that can give insight into the behavior one might expect in a reduced-g environment. The experimental arrangement consists of an annular channel that contains the granular material. One surface, say the upper surface, rotates so as to shear the material contained in the annulus. The lower surface controls the mean density/mean stress on the sample through an actuator or other control system. A novel feature under development is the ability to 'thermalize' the layer, i.e. create a larger amount of random motion in the material, by using the actuating system to provide vibrations as well control the mean volume of the annulus. The stress states of the system are determined by transducers on the non-rotating wall. These measure both shear and normal components of the stress on different size scales. Here, the idea is to characterize the system as the density varies through values spanning dense almost solid to relatively mobile granular states. This transition regime encompasses the regime usually thought of as the glass transition, and/or the jamming transition. Motivation for this experiment springs from ideas of a granular glass transition, a related jamming transition, and from recent experiments. In particular, we note recent experiments carried out by our group to characterize this type of transition and also to demonstrate/ characterize fluctuations in slowly sheared systems. These experiments give key insights into what one might expect in near-zero g. In particular, they show that the compressibility of granular systems diverges at a transition or critical point. It is this divergence, coupled to gravity, that makes it extremely difficult if not impossible to characterize the transition region in an earth-bound experiment. In the DE modeling, we analyze dynamics of a sheared granular system in Couette geometry in two (2D) and three (3D) space dimensions. Here, the idea is to both better understand what we might encounter in a reduced-g environment, and at a deeper level to deduce the physics of sheared systems in a density regime that has not been addressed by past experiments or simulations. One aspect of the simulations addresses sheared 2D system in zero-g environment. For low volume fractions, the expected dynamics of this type of system is relatively well understood. However, as the volume fraction is increased, the system undergoes a phase transition, as explained above. The DES concentrate on the evolution of the system as the solid volume fraction is slowly increased, and in particular on the behavior of very dense systems. For these configurations, the simulations show that polydispersity of the sheared particles is a crucial factor that determines the system response. Figures 1 and 2 below, that present the total force on each grain, show that even relatively small (10 %) nonuniformity of the size of the grains (expected in typical experiments) may lead to significant modifications of the system properties, such as velocity profiles, temperature, force propagation, and formation shear bands. The simulations are extended in a few other directions, in order to provide additional insight to the experimental system analyzed above. In one direction, both gravity, and driving due to vibrations are included. These simulations allow for predictions on the driving regime that is required in the experiments in order to analyze the jamming transition. Furthermore, direct comparison of experiments and DES will allow for verification of the modeling assumptions. We have also extended our modeling efforts to 3D. The (preliminary) results of these simulations of an annular system in zero-g environment will conclude the presentation.

Kondic, Lou↗

Breakdown of vertically propagating two-dimensional gravity waves forced by orography

The propagation of orographic gravity waves into an atmosphere with exponentially decreasing density is simulated with a two-dimensional, nonlinear, time-dependent numerical model. After the stationary wave is established over the mountain, the model predicts that wave breaking causes a large reduction of the vertical momentum flux in the flow, not only at levels where wave breaking is present, but also far below the lowest occurrence of overturning. More than half of the decrease in momentum flux is explained by the presence of large amplitude, downward propagating waves, which are generated in regions of wave breaking. The downward propagating waves appear almost simultaneously with overturning, and have nonzero phase speeds, suggesting a strongly nonlinear generation mechanism that depends on local wave properties. The generation of these downward propagating waves is a robust process, insensitive to mountain height, mountain width, or density scale height. These results have important implications for observational studies of orographically generated waves as well as for schemes that seek to parameterize the effects of orogoraphy in large-scale models.

Bacmeister, Julio T.↗

Observations of Martian tides over two annual cycles

The first four diurnal surface pressure harmonics have been analyzed over major portions of two Martian annual cycles (Mars years) at the two Viking lander sites. The diurnal harmonics of surface wind have also been analyzed at one of the sites. Since the atmospheric tides have previously been shown to provide a good indication of Martian global dust storms, these results provide a basis for comparing dust storm activity in the two years. Two global dust storms occurred during the first year. During the second year, there was only one major storm, and it closely followed the pattern of the first storm of the first year. A significant feature of the results is the brief, but nearly complete, vanishing of the diurnal pressure tide at the onset of one of the global dust storms. It is proposed that this may have been due to interference between the normal westward-propagating diurnal tide and a topographically forced eastward propagating tide, and that the latter may have helped initiate the global storm.

Leovy, C. B.↗

A study of the force-field equation for the propagation of galactic cosmic rays

A new development is given of the solution of the equation of the force-field approximation for the propagation of galactic cosmic rays in the interplanetary region. It leads to simpler methods for determining the force-field parameters. A method is given for determining the separable diffusion coefficient from observations of galactic electron spectrum and near-earth electron spectra; it is shown that this diffusion coefficient is not unique but may have a periodic-like dependence upon rigidity; and the method is used to obtain diffusion coefficients for 1965 and 1968. Approximate formulae relating small changes in intensity and diffusion coefficient are developed and some applications of these noted; in one it is shown that the form of, and changes in, diffusion coefficient deduced previously for a neutron monitor event during June-September 1969 are unnecessarily constrained and therefore probably not correct.

Gleeson, L. J.↗

A quantitative quantum-chemical analysis tool for the distribution of mechanical force in molecules

The promising field of mechanochemistry suffers from a general lack of understanding of the distribution and propagation of force in a stretched molecule, which limits its applicability up to the present day. In this article, we introduce the JEDI (Judgement of Energy DIstribution) analysis, which is the first quantum chemical method that provides a quantitative understanding of the distribution of mechanical stress energy among all degrees of freedom in a molecule. The method is carried out on the basis of static or dynamic calculations under the influence of an external force and makes use of a Hessian matrix in redundant internal coordinates (bond lengths, bond angles, and dihedral angles), so that all relevant degrees of freedom of a molecule are included and mechanochemical processes can be interpreted in a chemically intuitive way. The JEDI method is characterized by its modest computational effort, with the calculation of the Hessian being the rate-determining step, and delivers, except for the harmonic approximation, exact ab initio results. We apply the JEDI analysis to several example molecules in both static quantum chemical calculations and Born-Oppenheimer Molecular Dynamics simulations in which molecules are subject to an external force, thus studying not only the distribution and the propagation of strain in mechanically deformed systems, but also gaining valuable insights into the mechanochemically induced isomerization of trans-3,4-dimethylcyclobutene to trans,trans-2,4-hexadiene. The JEDI analysis can potentially be used in the discussion of sonochemical reactions, molecular motors, mechanophores, and photoswitches as well as in the development of molecular force probes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Granular Contact Forces: Proof of "Self-Ergodicity" by Generalizing Boltzmann's Stosszahlansatz and H Theorem

Ergodicity is proved for granular contact forces. To obtain this proof from first principles, this paper generalizes Boltzmann's stosszahlansatz (molecular chaos) so that it maintains the necessary correlations and symmetries of granular packing ensembles. Then it formally counts granular contact force states and thereby defines the proper analog of Boltzmann's H functional. This functional is used to prove that (essentially) all static granular packings must exist at maximum entropy with respect to their contact forces. Therefore, the propagation of granular contact forces through a packing is a truly ergodic process in the Boltzmannian sense, or better, it is self-ergodic. Self-ergodicity refers to the non-dynamic, internal relationships that exist between the layer-by-layer and column-by-column subspaces contained within the phase space locus of any particular granular packing microstate. The generalized H Theorem also produces a recursion equation that may be solved numerically to obtain the density of single particle states and hence the distribution of granular contact forces corresponding to the condition of self-ergodicity. The predictions of the theory are overwhelmingly validated by comparison to empirical data from discrete element modeling.

Metzger, Philip T.↗

Binding partner- and force-promoted changes in αE-catenin conformation probed by native cysteine labeling

Adherens Junctions (AJs) are cell-cell adhesion complexes that sense and propagate mechanical forces by coupling cadherins to the actin cytoskeleton via β-catenin and the F-actin binding protein αE-catenin. When subjected to mechanical force, the cadherin•catenin complex can tightly link to F-actin through αE-catenin, and also recruits the F-actin-binding protein vinculin. In this study, labeling of native cysteines combined with mass spectrometry revealed conformational changes in αE-catenin upon binding to the E-cadherin•β-catenin complex, vinculin and F-actin. A method to apply physiologically meaningful forces in solution revealed force-induced conformational changes in αE-catenin when bound to F-actin. Comparisons of wild-type αE-catenin and a mutant with enhanced vinculin affinity using cysteine labeling and isothermal titration calorimetry provide evidence for allosteric coupling of the N-terminal β-catenin-binding and the middle (M) vinculin-binding domain of αE-catenin. Cysteine labeling also revealed possible crosstalk between the actin-binding domain and the rest of the protein. The data provide insight into how binding partners and mechanical stress can regulate the conformation of full-length αE-catenin, and identify the M domain as a key transmitter of conformational changes.

59 BASIC BIOLOGICAL SCIENCES↗