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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Multi-level Force-dependent Allosteric Enhancement of αE-catenin Binding to F-actin by Vinculin

Classical cadherins are transmembrane proteins whose extracellular domains link neighboring cells, and whose intracellular domains connect to the actin cytoskeleton via β-catenin and α-catenin. The cadherin-catenin complex transmits forces that drive tissue morphogenesis and wound healing. In addition, tension-dependent changes in αE-catenin conformation enables it to recruit the actin-binding protein vinculin to cell-cell junctions, which contributes to junctional strengthening. How and whether multiple cadherin-complexes cooperate to reinforce cell-cell junctions in response to load remains poorly understood. Here, we used single-molecule optical trap measurements to examine how multiple cadherin-catenin complexes interact with F-actin under load, and how this interaction is influenced by the presence of vinculin. We show that force oriented toward the (-) end of the actin filament results in mean lifetimes 3-fold longer than when force was applied towards the barbed (+) end. We also measured force-dependent actin binding by a quaternary complex comprising the cadherin-catenin complex and the vinculin head region, which cannot itself bind actin. Binding lifetimes of this quaternary complex increased as additional complexes bound F-actin, but only when load was oriented toward the (-) end. In contrast, the cadherin-catenin complex alone did not show this form of cooperativity. Furthermore, these findings reveal multi-level, force-dependent regulation that enhances the strength of the association of multiple cadherin/catenin complexes with F-actin, conferring positive feedback that may strengthen the junction and polarize F-actin to facilitate the emergence of higher-order cytoskeletal organization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fluctuations and Pinning for Individually Manipulated Skyrmions

We numerically examine the dynamics of individually dragged skyrmions interacting simultaneously with an array of other skyrmions and quenched disorder. For drives just above depinning, we observe a broadband noise signal with a 1/ f characteristic, while at higher drives, narrowband or white noise appears. Even in the absence of quenched disorder, the threshold force that must be applied to translate the driven skyrmion is finite due to elastic interactions with other skyrmions. The depinning threshold increases as the strength of the quenched disorder is raised. Above the depinning force, the skyrmion moves faster in the presence of quenched disorder than in a disorder-free system since the pinning sites prevent other skyrmions from being dragged along with the driven skyrmion. For strong pinning, we find a stick-slip motion of the driven skyrmion which produces a telegraph noise signature. The depinning threshold increases monotonically with skyrmion density in the absence of quenched disorder, but when pinning is present, the depinning threshold changes nonmonotonically with skyrmion density, and there are reentrant pinned phases due to a competition between pinning induced by the quenched disorder and that produced by the elastic interactions of the skyrmion lattice.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Impact of three-body forces on elastic nucleon-nucleus scattering observables

In a previous series of papers we investigated the domain of applicability of chiral potentials to the construction of a microscopic optical potential (OP) for elastic nucleon-nucleus scattering. The OP was derived at the first order of the spectator expansion of the Watson multiple scattering theory and its final expression was a folding integral between the nucleon-nucleon ( N N ) t matrix and the nuclear density of the target. In the calculations N N and three-nucleon ( 3 N ) chiral interactions were used for the target density and only the N N interaction for the N N t matrix. The purpose of this study is to achieve another step towards the calculation of a more consistent OP introducing the 3 N force also in the dynamic part of the OP. The full treatment of the 3 N interaction is beyond our present capabilities. Thus, here it is approximated with a density dependent N N interaction obtained after the averaging over the Fermi sphere. In practice, in our model the 3 N force acts as a medium correction of the bare N N interaction used to calculate the t matrix. Even if the 3 N force is treated in an approximate way, this method naturally extends our previous model of the OP and allows a direct comparison of our present and previous results. We consider as case studies the elastic scattering of nucleons off C 12 and O 16 . We present results for the differential cross section and the spin observables for different values of the projectile energy. From the comparison with the experimental data and with the results of our previous model we assess the importance of the 3 N interaction in the dynamic part of the OP. Conclusions: Our analysis indicates that the contribution of the 3 N force in the t matrix is small for the differential cross section and it is sizable for the spin observables, in particular, for the analyzing power. We find that the two-pion exchange term is the major contributor to the 3 N force. A chiral expansion order-by-order analysis of the scattering observables confirms the convergence of our results at the next-to-next-to-next-to-leading-order, as already established in our previous work.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

System and method for voltage-based real-time micro-object position control with the aid of a digital computer

The system and method described allow for real-time control over positioning of a micro-object. A movement of at least one micro-object suspended in a medium can be induced by a generation of one or more forces by electrodes proximate to the micro-object. Prior to inducing the movement, a simulation is used to develop a model describing a parameter of an interaction between each of the electrodes and the micro-object. A function describing the forces generated by an electrode and an extent of the movement induced due to the forces is generated using the model. The function is used to design closed loop policy control scheme for moving the micro-object towards a desired position. The position of the micro-object is tracked and taken into account when generating voltage patterns in the scheme.

Matei, Ion↗
DOE OSTI2026

Substantial Diel Changes of Cloud Adjustments to Aerosols in Ship‐Tracks

Clouds adjust their albedo, amount and liquid water path to anthropogenic aerosols, and produce a climate forcing. Such cloud adjustments are complex functions of both environmental conditions and interaction time. However, direct observations of temporal changes in cloud adjustments are limited. Here, we develop a method to show observational evidence of substantial diel changes in cloud adjustments within ship-tracks. Polluted clouds experiencing extended nighttime exposure exhibit higher increases in cloud fraction while liquid-water path adjustments follow a non-monotonic evolution. The higher cloud fraction increase persists through daytime. Such diel variations likely stem from diel changes in solar heating and background cloud precipitation, and are important because nighttime changes persist and affect solar radiation during the day. Accounting for diel variations produces a stronger aerosol forcing, by −0.1 ∼−0.4 W⁢m −2 . Our approach reveals how the temporal evolution of cloud adjustments can have important implications for aerosol-cloud interactions.

Yuan, Tianle [NASA Goddard Space Flight Center (GS↗
DOE OSTI2020

Multi-Scale Simulation of Wind Farm Performance during a Frontal Passage

Predicting the response of wind farms to changing flow conditions is necessary for optimal design and operation. Here in this work, simulation and analysis of a frontal passage through a utility scale wind farm is achieved for the first time using a seamless multi-scale modeling approach. A generalized actuator disk (GAD) wind turbine model is used to represent turbine–flow interaction, and results are compared to novel radar observations during the frontal passage. The Weather Research and Forecasting (WRF) model is employed with a nested grid setup that allows for coupling between multi-scale atmospheric conditions and turbine response. Starting with mesoscale forcing, the atmosphere is dynamically downscaled to the region of interest, where the interaction between turbulent flows and individual wind turbines is simulated with 10 m grid spacing. Several improvements are made to the GAD model to mimic realistic turbine operation, including a yawing capability and a power output calculation. Ultimately, the model is able to capture both the dynamics of the frontal passage and the turbine response; predictions show good agreement with observed background velocity, turbine wake structure, and power output after accounting for a phase shift in the mesoscale forcing. This study demonstrates the utility of the WRF-GAD model framework for simulating wind farm performance under complex atmospheric conditions.

17 WIND ENERGY↗
DOE OSTI2020

Finite-size effects on the self-force

Electromagnetic and linear gravitational radiation do not solely propagate on the null cone in 3 + 1 dimensions in curved spacetimes, contrary to their well-known behavior in flat spacetime. Their additional propagation inside the null cone is known as the tail effect. A compact body will produce a signal whose tail will interact with its future worldline, thus producing a tail-induced self-force. In this work, we present new results for the tail-induced scalar, electromagnetic, and gravitational self-force for a test mass in orbit around a central mass, including effects from the internal structure of that body.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

Linearly scaling and almost Hamiltonian dielectric continuum molecular dynamics simulations through fast multipole expansions

Hamiltonian Dielectric Solvent (HADES) is a recent method [S. Bauer et al., J. Chem. Phys. 140, 104103 (2014)] which enables atomistic Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric solvent continua. Such simulations become rapidly impractical for large proteins, because the computational effort of HADES scales quadratically with the number N of atoms. If one tries to achieve linear scaling by applying a fast multipole method (FMM) to the computation of the HADES electrostatics, the Hamiltonian character (conservation of total energy, linear, and angular momenta) may get lost. Here, we show that the Hamiltonian character of HADES can be almost completely preserved, if the structure-adapted fast multipole method (SAMM) as recently redesigned by Lorenzen et al. [J. Chem. Theory Comput. 10, 3244-3259 (2014)] is suitably extended and is chosen as the FMM module. By this extension, the HADES/SAMM forces become exact gradients of the HADES/SAMM energy. Their translational and rotational invariance then guarantees (within the limits of numerical accuracy) the exact conservation of the linear and angular momenta. Also, the total energy is essentially conserved—up to residual algorithmic noise, which is caused by the periodically repeated SAMM interaction list updates. These updates entail very small temporal discontinuities of the force description, because the employed SAMM approximations represent deliberately balanced compromises between accuracy and efficiency. The energy-gradient corrected version of SAMM can also be applied, of course, to MD simulations of all-atom solvent-solute systems enclosed by periodic boundary conditions. However, as we demonstrate in passing, this choice does not offer any serious advantages.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation

The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute “obstacles” and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as “buffers” that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events occurring in crowded cellular environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1999

Effective Forces Between Colloidal Particles

Colloidal suspensions have proven to be excellent model systems for the study of condensed matter and its phase behavior. Many of the properties of colloidal suspensions can be investigated with a systematic variation of the characteristics of the systems and, in addition, the energy, length and time scales associated with them allow for experimental probing of otherwise inaccessible regimes. The latter property also makes colloidal systems vulnerable to external influences such as gravity. Experiments performed in micro-ravity by Chaikin and Russell have been invaluable in extracting the true behavior of the systems without an external field. Weitz and Pusey intend to use mixtures of colloidal particles with additives such as polymers to induce aggregation and form weak, tenuous, highly disordered fractal structures that would be stable in the absence of gravitational forces. When dispersed in a polarizable medium, colloidal particles can ionize, emitting counterions into the solution. The standard interaction potential in these charged colloidal suspensions was first obtained by Derjaguin, Landau, Verwey and Overbeek. The DLVO potential is obtained in the mean-field linearized Poisson-Boltzmann approximation and thus has limited applicability. For more precise calculations, we have used ab initio density functional theory. In our model, colloidal particles are charged hard spheres, the counterions are described by a continuum density field and the solvent is treated as a homogeneous medium with a specified dielectric constant. We calculate the effective forces between charged colloidal particles by integrating over the solvent and counterion degrees of freedom, taking into account the direct interactions between the particles as well as particle-counterion, counterion-counterion Coulomb, counterion entropic and correlation contributions. We obtain the effective interaction potential between charged colloidal particles in different configurations. We evaluate two- and three-body forces in the bulk as well as study the influence of soft walls. We qualitatively explain the effects of the walls on the forces and demonstrate that many-body effects are negligible in our system. With adjustments in the parameters, the DLVO pair-potential can describe the results quantitatively. Besides electrostatic interactions, entropic depletion effects that arise from (hard-core) exclusion play an important role in determining the behavior of multi-component colloidal suspensions. A standard theory for depletion forces is due to Asakura and Oosawa and is based on the ideal gas approximation. To go beyond this approximation, we have studied entropic forces in molecular dynamics simulations of systems of hard spheres (the effects of the solvent have been ignored). The effective depletion forces for these systems can be found either from equilibrium distribution functions or from direct momentum transfer calculations. Our results obtained by either method show qualitative differences from the Asakura-Oosawa forces, indicating a longer range, higher value at contact and most importantly a more complicated structure, comprising of several maxima and minima. Our calculations include the determination of effective forces between two spheres, a hard sphere and a wall, and the behavior of a hard sphere near a step-edge and a corner. We also demonstrate that such entropic forces do not necessarily satisfy pairwise additivity.

Tehver, Riina↗
NASA NTRS1989

The effect of exhaust plume/afterbody interaction on installed scramjet performance

An upwind implicit Navier-Stokes code has been used to study hypersonic exhaust plume/afterbody flow fields. It is found that afterbody forces varied linearly with the nozzle exit pressure for moderately underexpanded jets, and that exhaust gases with low isentropic exponents (gamma) contribute up to 25 percent more force than high-gamma exhaust gases. Highly underexpanded jets are shown to create a strong plume shock, and the interaction of this shock with the afterbody produces a complicated pattern of crossflow separation.

Edwards, T. A.↗
DOE OSTI2012

Novel Cooperative Interactions and Structural Ordering in H[subscript 2]S-H[subscript 2]

Hydrogen sulfide (H{sub 2}S) and hydrogen (H{sub 2}) crystallize into a 'guest-host' structure at 3.5 GPa and, at the initial formation pressure, the rotationally disordered component molecules exhibit weak van der Waals-type interactions. With increasing pressure, hydrogen bonding develops and strengthens between neighboring H{sub 2}S molecules, reflected in a pronounced drop in S-H vibrational stretching frequency and also observed in first-principles calculations. At 17 GPa, an ordering process occurs where H{sub 2}S molecules orient themselves to maximize hydrogen bonding and H{sub 2} molecules simultaneously occupy a chemically distinct lattice site. Intermolecular forces in the H{sub 2}S+H{sub 2} system may be tuned with pressure from the weak hydrogen-bonding limit to the ordered hydrogen-bonding regime, resulting in a novel clathrate structure stabilized by cooperative interactions.

08 HYDROGEN↗
DOE OSTI2014

Nature of the effective interaction between dendrimers

We have performed fully atomistic classical molecular dynamics simulations to calculate the effective interaction between two polyamidoamine dendrimers. Using the umbrella sampling technique, we have obtained the potential of mean force (PMF) between the dendrimers and investigated the effects of protonation level and dendrimer size on the PMF. Our results show that the interaction between the dendrimers can be tuned from purely repulsive to partly attractive by changing the protonation level. The PMF profiles are well-fitted by the sum of an exponential and a Gaussian function with the weight of the exponential function dominating over that of the Gaussian function. This observation is in disagreement with the results obtained in previous analytic [C. Likos, M. Schmidt, H. Löwen, M. Ballauff, D. Pötschke, and P. Lindner, Macromolecules 34, 2914 (2001)] and coarse-grained simulation [I. Götze, H. Harreis, and C. Likos, J. Chem. Phys. 120, 7761 (2004)] studies which predicted the effective interaction to be Gaussian.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Local nonlinear rf forces in inhomogeneous magnetized plasmas

The local nonlinear forces induced by radio frequency (rf) waves are derived in inhomogeneous magnetized plasmas, where the inhomogeneity exists in the rf fields, in the static magnetic field as well as in the equilibrium density and temperature. The local parallel force is completely resonant, but a novel component dependent on those inhomogeneities is obtained as the result of the inhomogeneous transport of parallel resonant-absorbed momentum by the nonlinear perpendicular drift flux. In the local poloidal force, the component induced by the inhomogeneity of rf power absorption is also confirmed and it can be recognized as the residual effect from the incomplete cancellation between the rate of the diamagnetic poloidal momentum gain and the Lorentz force due to the radial diffusion-like flux. The compact expression for radial force is also obtained for the first time, whose nonresonant component is expressed as the sum of the ponderomotive force on particles and the gradients of the nonresonant perpendicular pressure and of the nonresonant momentum flux due to the finite temperature effect. Numerical calculations in a 1-D slab model show that the resonant component dependent on the inhomogeneities may be significant when the ion absorption dominates the resonant wave-particle interaction. A quantitative estimation shows that the novel component in the parallel force is important to understand the experiments of the ion-cyclotron-frequency mode-conversion flow drive.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
NASA NTRS2003

SPARC-IGAC Symposium on Climate-Chemistry Interactions. Climate Feedback by Water Vapor in the Tropical Upper Troposphere

The strong greenhouse forcing by atmospheric water vapor is expected to play an important role in shaping the direction of any future changes in climate. We present calculations that provide a new perspective on the sensitivity of upper tropospheric water vapor to changes in surface temperature. Equilibrium states of our atmospheric model show unambiguously that as the surface warms, changes in the vertical distribution and temperature of detraining air parcels from tropical convection lead to higher water vapor mixing ratios in the upper troposphere. However, the increase in mixing ratio is not as large as the increase in saturation mixing ratio due to warmer environmental temperatures, so that the relative humidity decreases. Our analysis suggests that models that maintain a fixed relative humidity are likely overestimating the magnitude of the water vapor feedback.

Dessler, A. E.↗
DOE OSTI2023

Quantifying uncertainties due to irreducible three-body forces in deuteron-nucleus reactions

Deuteron-induced nuclear reactions are an essential tool for probing the structure of nuclei as well as astrophysical information such as (n, γ) cross sections. The deuteron-nucleus system is typically described within a Faddeev three-body model consisting of a neutron (n), a proton (p), and the target nucleus (A) interacting through pairwise phenomenological potentials. While Faddeev techniques enable the exact description of the three-body dynamics, their predictive power is limited in part by the omission of irreducible neutron-proton-nucleus three-body force (n–p–A 3BF). Here, our goal is to quantify systematic uncertainties stemming from the reduction of deuteron-nucleus (d + A) dynamics to a picture of three pointlike nuclear clusters interacting via pairwise nucleon-nucleus forces, using as testing grounds d + α scattering and the 6 Li ground state. We particularly focus on quantifying uncertainties arising from the full antisymmetrization of the (A + 2)-body system with the target nucleus fixed in its ground state. We adopt the ab initio no-core shell model coupled with the resonating group method (NCSM/RGM) to compute microscopic n–α and p–α interactions, and use them in a three-body description of the d + α system by means of momentum-space Faddeev-type equations. Simultaneously, we also carry out ab initio calculations of d + α scattering and 6 Li ground state by means of six-body NCSM/RGM calculations to serve as a benchmark for the three-body model predictions given by the Faddeev calculations. By comparing the Faddeev and NCSM/RGM results, we show that the irreducible n–p–α 3BF has a non-negligible effect on bound state and scattering observables alike. Specifically, the Faddeev approach yields a 6 Li ground state that is approximately 600 keV shallower than the one obtained with the NCSM/RGM. Additionally, the Faddeev calculations for d + α scattering yield a 3 + resonance that is located approximately 400 keV higher in energy compared to the NCSM/RGM result. The shape of the d + α angular distributions computed using the two approaches also differ, owing to the discrepancy in the predictions of the 3 + resonance energy. The Faddeev three-body model predictions for d + α scattering and 6 Li using microscopic n–α and p–α potentials differ from those computed microscopically with the NCSM/RGM. These discrepancies are due to the n–p–α 3BF, which arises from two-nucleon exchange terms in the microscopic d–α interaction and are not accounted for in the three-body model Faddeev calculations. This study lays the foundation for future parametrizations of the 3BF due to Pauli exclusion principle effects in improved three-body calculations of deuteron-induced reactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Substituent and Heteroatom Effects on π–π Interactions: Evidence That Parallel-Displaced π-Stacking is Not Driven by Quadrupolar Electrostatics

Stacking interactions are a recurring motif in supramolecular chemistry and biochemistry, where a persistent theme is a preference for parallel-displaced aromatic rings rather than face-to-face π-stacking. This is usually explained in terms of quadrupole–quadrupole interactions between the arene moieties but that interpretation is inconsistent with accurate calculations, which reveal that the quadrupolar picture is qualitatively wrong. At typical π-stacking distances, quadrupolar electrostatics may differ in sign from an exact calculation based on charge densities of the interacting arenes. We apply symmetry-adapted perturbation theory to dimers composed of substituted benzene and various aromatic heterocycles, which display a wide range of electrostatic interactions, and we investigate the interplay of Pauli repulsion, dispersion, and electrostatics as it pertains to parallel-displaced π-stacking. Profiles of energy components along cofacial slip-stacking coordinates support a prominent role for the “van der Waals model” (dispersion in competition with Pauli repulsion), even for polar monomers where electrostatic interactions are significant. While electrostatic interactions are necessary to explain the optimal face-to-face π-stacking distance and to account for the relative orientation of one polar arene with respect to another, we find no evidence to support continued invocation of quadrupolar electrostatics as a basis for π-stacking. Our results suggest that a driving force for offset-stacking exists even in the absence of electrostatic interactions. Consequently, tuning electrostatics via functionalization does not guarantee that slip-stacking can be avoided. This has implications for rational design of soft materials and other supramolecular architectures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

The Role of Three-Nucleon Forces and Many-Body Processes in Nuclear Pairing

We present microscopic valence-shell calculations of pairing gaps in the calcium isotopes, focusing on the role of three-nucleon (3N) forces and manybody processes. In most cases, we find a reduction in pairing strength when the leading chiral 3N forces are included, compared to results with lowmomentum two-nucleon (NN) interactions only. This is in agreement with a recent energy density functional study. At the NN level, calculations that include particle particle and hole hole ladder contributions lead to smaller pairing gaps compared with experiment. When particle hole contributions as well as the normal-ordered one- and two-body parts of 3N forces are consistently included to third order, we find reasonable agreement with experimental three-point mass differences. This highlights the important role of 3N forces and manybody processes for pairing in nuclei. Finally, we relate pairing gaps to the evolution of nuclear structure in neutron-rich calcium isotopes and study the predictions for the 2+ excitation energies, in particular for 54Ca.

Holt, Jason D.↗

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