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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↗

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↗

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↗

Evapotranspiration in Northern Eurasia: Impact of forcing uncertainties on terrestrial ecosystem model estimates

Abstract The ecosystems in Northern Eurasia (NE) play an important role in the global water cycle and the climate system. While evapotranspiration (ET) is a critical variable to understand this role, ET over this region remains largely unstudied. Using an improved version of the Terrestrial Ecosystem Model with five widely used forcing data sets, we examine the impact that uncertainties in climate forcing data have on the magnitude, variability, and dominant climatic drivers of ET for the period 1979–2008. Estimates of regional average ET vary in the range of 241.4–335.7 mm yr −1 depending on the choice of forcing data. This range corresponds to as much as 32% of the mean ET. Meanwhile, the spatial patterns of long‐term average ET across NE are generally consistent for all forcing data sets. Our ET estimates in NE are largely affected by uncertainties in precipitation ( P ), air temperature ( T ), incoming shortwave radiation ( R ), and vapor pressure deficit (VPD). During the growing season, the correlations between ET and each forcing variable indicate that T is the dominant factor in the north and P in the south. Unsurprisingly, the uncertainties in climate forcing data propagate as well to estimates of the volume of water available for runoff (here defined as P‐ET). While the Climate Research Unit data set is overall the best choice of forcing data in NE according to our assessment, the quality of these forcing data sets remains a major challenge to accurately quantify the regional water balance in NE.

Liu, Yaling↗

Effect of microstructure on fatigue crack propagation in additive manufactured nickel-based superalloy Haynes 282: an experiment and crystal plasticity study

Haynes 282 is a γ' precipitation-strengthened nickel-based superalloy known for its exceptional high-temperature creep resistance and excellent fabricability. Recent advancements in powder-bed fusion-based additive manufacturing (PBF-AM) have enabled the fabrication of Haynes 282 with accurate, site-specific control of the grain orientation and morphology at the microscale. This ability opens up new avenues for microstructure design, to improve the material’s fatigue crack resistance and service life. This paper investigates the fatigue crack growth behavior of hybrid microstructure Haynes 282 fabricated via PBF-AM. Previous experiments revealed a higher crack propagation rate in the coarse columnar-grained microstructural regions when compared against fine-grained areas. Here, a strain gradient crystal plasticity model was adapted to study the fracture-related mechanical fields at the crack tip in the two microstructures. The simulation results showed a consistent influence of grain structure and texture on crack propagation, as was seen in the experiment. The model analysis revealed higher crack propagation driving force along crack direction in the coarse-grained sharply textured microstructure and higher driving force for crack kinking in fine-grained more diffusely textured microstructure, which is ascribed to the combined effect of yield stress, hardening rate, texture and grain morphology. The presented modeling approach will facilitate the development of the AM-based accurate microstructure design by deepening the fundamental study in AM-specific microstructure-properties relations.

36 MATERIALS SCIENCE↗

Diabatic Eddy Forcing Increases Persistence and Opposes Propagation of the Southern Annular Mode in MERRA-2

Abstract As a dominant mode of jet variability on subseasonal time scales, the Southern Annular Mode (SAM) provides a window into how the atmosphere can produce internal oscillations on longer-than-synoptic time scales. While SAM’s existence can be explained by dry, purely barotropic theories, the time scale for its persistence and propagation is set by a lagged interaction between barotropic and baroclinic mechanisms, making the exact physical mechanisms challenging to identify and to simulate, even in latest generation models. By partitioning the eddy momentum flux convergence in MERRA-2 using an eddy–mean flow interaction framework, we demonstrate that diabatic processes (condensation and radiative heating) are the main contributors to SAM’s persistence in its stationary regime, as well as the key for preventing propagation in this regime. In SAM’s propagating regime, baroclinic and diabatic feedbacks also dominate the eddy–jet feedback. However, propagation is initiated by barotropic shifts in upper-level wave breaking and then sustained by a baroclinic response, leading to a roughly 60-day oscillation period. This barotropic propagation mechanism has been identified in dry, idealized models, but here we show evidence of this mechanism for the first time in reanalysis. The diabatic feedbacks on SAM are consistent with modulation of the storm-track latitude by SAM, altering the emission temperature and cloud cover over individual waves. Therefore, future attempts to improve the SAM time scale in models should focus on the storm-track location, as well as the roles of the cloud and moisture parameterizations. Significance Statement As they circumnavigate the planet, the tropospheric jet streams slowly drift north and south over about 30 days, longer than the normal limit of weather prediction. Understanding the source of this “memory” could improve our knowledge of how the atmosphere organizes itself and our ability to make long-term forecasts. Current theories have identified several possible internal atmospheric interactions responsible for this memory. Yet most of the theories for understanding the jets’ behavior assume that this behavior is only weakly influenced by atmospheric water vapor. We show that this assumption is not enough to understand jet persistence. Instead, clouds and precipitation are more important contributors in reanalysis data than internal “dry” mechanisms to this memory of the Southern Hemisphere jet.

54 ENVIRONMENTAL SCIENCES↗

Nonlinear ion modes in a strongly coupled plasma in the presence of nonthermal ion fluids and polarization force

The nonlinear propagation of ion-acoustic (IA) waves in a strongly coupled plasma system containing Maxwellian electrons and nonthermal ions has been theoretically and numerically investigated. The well-known reductive perturbation technique is used to derive both the Burgers and Korteweg−de Vries (KdV) equations. Their shock and solitary wave solutions have also been numerically analyzed in understanding localized electrostatic disturbances. It has been observed that the basic features (viz. polarity, amplitude, width, etc.) of IA waves are significantly modified by the effect of polarization force and other plasma parameters (e.g., the electron-to-ion number density ratio and ion-to-electron temperature ratio). This is a unique finding among all theoretical investigations made before, whose probable implications are discussed in this investigation. The implications of the results obtained from this investigation may be useful in understanding the wave propagation in both space and laboratory plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Self-focusing and defocusing of Gaussian laser beams in collisional underdense magnetized plasmas with considering the nonlinear ohmic heating and ponderomotive force effects

The propagation characteristics of a Gaussian laser beam in collisional magnetized plasma are investigated by considering the ponderomotive and ohmic heating nonlinearities. Here, by taking into account the effect of the external magnetic field, the second order differential equation of the dimensionless beam width parameter is solved numerically. Furthermore, the nonlinear dielectric permittivity of the mentioned plasma medium in the paraxial approximation and its dependence on the propagation characteristics of the Gaussian laser pulse is obtained, and its variation in terms of the dimensionless plasma length is analyzed at different initial normalized plasma and cyclotron frequencies. The results show that the dimensionless beam width parameter is strongly affected by the initial plasma frequency, magnetic strength, and laser pulse intensity. Furthermore, it is found that there exists a certain intensity value below which the laser pulse tends to self focus, while the beam diverges above of this value. In addition, the results confirm that, by increasing the plasma and cyclotron frequencies (plasma density and magnetic strength), the self-focusing effect can occur intensively.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Longitudinal Lorentz force on a subwavelength-diameter optical fiber

We analyze the longitudinal Lorentz forces that a propagating continuous-wave light exerts on a subwavelength-diameter optical fiber. Our theoretical results show that, during the propagating process, the guided light exerts no net time-averaged force on the fiber. Via numerical simulation, we find a significant overall pull force of 0.4 pN/mW acting on a 450-nm-diam fiber tip at a wavelength of 980 nm due to the scattering of the end face and a calculated force distribution reveals the feature of a near-field accumulation. Our results may be helpful to the configuration of optomechanical components or devices based on these fibers.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Repelling, binding, and oscillating of two-particle discrete-time quantum walks

In this paper, we investigate the effects of particle–particle interaction and static force on the propagation of probability distribution in two-particle discrete-time quantum walk, where the interaction and static force are expressed as a collision phase and a linear position-dependent phase, respectively. It is found that the interaction can lead to boson repelling and fermion binding. The static force also induces Bloch oscillation and results in a continuous transition from boson bunching to fermion anti-bunching. The interplays of particle–particle interaction, quantum interference, and Bloch oscillation provide a versatile framework to study and simulate many-particle physics via quantum walks.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The effect of plasma radius and profile on the development of self-modulation instability of electron bunches

Plasmas available for plasma wakefield accelerator experiments may have longitudinal and transverse density profiles that could affect the outcome of an experiment. This paper investigates the effect of plasmas with finite radius and inhomogeneous transverse density profiles on the wakefield excitation and the self-modulation instability (SMI) development in overdense plasmas. We focus here on the case of an electron bunch. Simulation results show that such plasmas generate larger focusing force for the propagating electron beam and therefore higher growth rate for the SMI. Although the initial accelerating field (E{sub z}) amplitude is lower in such plasmas, the increased focusing force can dominate the development trend of the SMI, i.e., larger saturated E{sub z} amplitude can be reached over similar plasma lengths.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Dust-acoustic waves in nonuniform dusty plasma in presence of polarization force

The effects of the dust density nonuniformity and the polarization force on linear propagation of the dust-acoustic waves in a nonuniform dusty plasma (consisting of electrons, ions, and arbitrarily charged dust particles) have been theoretically investigated. It has been shown that the linear dispersion properties of the dust-acoustic (DA) waves have been significantly modified by the dust density nonuniformity, dust polarity, and the polarization force. It is also found here that the phase speed of the DA waves is decreased by the effects of polarization force, and that their amplitude increases with the decrease of equilibrium dust number density. The different situations, which are relevant to different space and laboratory dusty plasmas, have been briefly discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗