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At least 55 records · Page 3

Reduced dynamic complexity allows structure elucidation of an excited state of KRAS G13D

Localized dynamics of RAS, including regions distal to the nucleotide-binding site, is of high interest for elucidating the mechanisms by which RAS proteins interact with effectors and regulators and for designing inhibitors. Among several oncogenic mutants, methyl relaxation dispersion experiments reveal highly synchronized conformational dynamics in the active (GMPPNP-bound) KRAS G13D , which suggests an exchange between two conformational states in solution. Methyl and 31 P NMR spectra of active KRAS G13D in solution confirm a two-state ensemble interconverting on the millisecond timescale, with a major Pγ atom peak corresponding to the dominant State 1 conformation and a secondary peak indicating an intermediate state different from the known State 2 conformation recognized by RAS effectors. High-resolution crystal structures of active KRAS G13D and KRAS G13D -RAF1 RBD complex provide snapshots of the State 1 and 2 conformations, respectively. We use residual dipolar couplings to solve and cross-validate the structure of the intermediate state of active KRAS G13D , showing a conformation distinct from those of States 1 and 2 outside the known flexible switch regions. The dynamic coupling between the conformational exchange in the effector lobe and the breathing motion in the allosteric lobe is further validated by a secondary mutation in the allosteric lobe, which affects the conformational population equilibrium.

59 BASIC BIOLOGICAL SCIENCES↗

Inviscid analysis of jet injection between two moving streams

An analytical method is developed for determining the flow interaction when a two-dimensional jet is injected between two moving streams. The jet is flowing out of channel and is turned as it enters between the external streams. The local velocity variation resulting from the flow interaction provides a static pressure variation along the jet bounding streamlines that is a priori unknown. Hense, the flow must be obtained by coupling the three flow regions (the jet and the free stream on either side) along the jet boundaries. Both external streams have the same total pressure, which is different from that in the jet. The solution is for the condition that the total pressure in the jet does not differ from the free-stream value by a large amount compared with the free-stream dynamic head. Results are given for the shape of the jet boundaries for various injection configurations.

Goldstein, M. E.↗

Thermodynamic modeling of countercurrent chemical looping reverse water gas shift process for redox material screening

The reverse water gas shift (RWGS) reaction is a key pathway for CO 2 utilization, particularly within Power-to-X process chains aimed at sustainable fuel and chemical production. Countercurrent chemical looping (CL-RWGS) using non-stoichiometric oxides can overcome equilibrium limitations of conventional RWGS reactors, enabling significantly higher CO 2 conversions. However, modeling the limiting performance of such systems is challenging due to their multiphase nature and coupled spatial and temporal variation in chemical composition. In this work, we present a discretized batch equilibrium model that simulates CL-RWGS reactors as a series of localized equilibrium exchanges between gas and solid elements. The model is numerically stable, computationally efficient, and free of kinetic source terms, making it well-suited for parametric studies and system-level integration. It is validated against established convection–diffusion models and shown to predict reasonable upper bounds on experimental results. Application of the model to a range of oxygen carrier materials identifies cerium–zirconium solid solutions, particularly Ce 0.80 Zr 0.20 O 2 , as a promising class offering superior oxygen storage characteristics compared to state-of-the-art La 0.6 Sr 0.4 FeO 3 . This framework provides a robust platform for materials screening, reactor sizing, and performance optimization in chemical looping systems. The model implementation is available as open-source software to support further research and development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Emittance bounds for transient radiative cooling of a scattering rectangular region

Transient cooling was analyzed for a two-dimensional gray rectangular region that emits, absorbs, and isotropically scatters radiation. The region, initially at uniform temperature, is placed in surroundings at a much lower temperature. The cooling analysis yields two simultaneous equations for the transient temperature and scattering source function distributions. The region starts to cool with the medium at uniform temperature. For this condition, the local emittance around the perimeter was obtained by a numerical solution of the radiative equations, and the rate of heat loss from the entire medium was evaluated. As cooling continues, the emissive ability decreases because of the lower temperatures in the outer regions of the rectangle. Based on some previous work, a lower limit for the transient overall emittance was found by obtaining a similarity solution. For some ranges of optical thickness and scattering albedo, the lower limit is only a small amount below the initial emittance. For these conditions, the initial emittance can be used to compute the entire transient resulting in a considerable simplification.

Siegel, Robert↗

Boundary-consistent B-spline filtering schemes and application to high-fidelity simulations of turbulence

A filtering operation, based on B-spline discretizations, is introduced to target weakly growing mesh-scale oscillations that can arise in high-fidelity turbulence simulations. This is a spectral regularization that can be described using the singular values of a banded matrix operator, with the filtering strength set by a scalar- or vector-valued penalty parameter. The penalty parameter can be specified though it can also be advantageously selected to minimize the generalized cross validation (GCV) measure of distance between the pre- and post-filtered solutions. Efficient algorithms are developed to compute both the scalar and vector penalty parameters. The B-spline filter has a sharper localization to high-wavenumber than compact or explicit filters of the same stencil width and is demonstrated for solutions of the Burgers' equation, decaying Burgers' turbulence, and compressible Navier–Stokes turbulent channel flow. Furthermore, these simulations confirm the scheme's numerical stability and ability to narrowly target the high wavenumber components of numerical solutions. An advantage over finite-difference filters is that these B-spline filters are stable on bounded domains and even preserve formal order of accuracy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Effect of magnetospheric convection on thermal plasma in the inner magnetosphere

The effects of E x B convection on the distribution of plasma parameters in the inner magnetosphere have been examined. Analytical solutions describing density distributions along convective trajectories in the equatorial plane have been found. These solutions suggest the following dependence of plasma concentration n on the magnetic field B along convective trajectories: n proportional to B(exp alpha), where the parameter alpha varies between alpha is less than or = between 4/3 and 2. The alpha = 2 case corresponds to disregarding transport parallel to B. The lower bound alpha = 4/3 describes the situation when parallel transport dominates over convective motions perpendicular to B. A solution has also been obtained describing the effect of convection on diffusive equilibrium profiles in the dayside plasmasphere. In addition, ion temperature variations due to adiabatic effects associated with plasma convection have been analyzed in detail. Convective drifts lead to ion temperature anisotropies with the value and sign of the anisotropy contingent on density and temperature variations, local time, and the location of the convective trajectory with respect to the location of the plasmapause. We have also found that convective motions lead to a substantial exchange of energy between the ionosphere and the plasmasphere through electron heat fluxes.

Khazanov, G. V.↗

The formation of sharp edges in planetary rings by nearby satellites

Equations are derived which govern the shapes of the perturbed streamlines near the 'sharp edge' boundaries between regions of high and low planetary ring optical depth; these are maintained by the shepherd satellites, which transfer angular momentum to and from ring particles. The results obtained by these equations' solution with a simple numerical model, whose parameters resemble those of the Encke division, are found to faithfully reproduce the sharp edges bounding the division; they imply that the ring thickness in the unperturbed regions far from the edges is of the order of 10 m, and that the angle-averaged surface density varies on a much shorter radial length scale than that over which the satellite torque is applied. This feature's relationship to the local reversal of angular momentum viscous transport, in the most strongly perturbed regions, is demonstrated.

Borderies, Nicole↗

Definitive IGRF models for 1945, 1950, 1955, and 1960

Definitive internal geomagnetic field models are obtained for the epochs 1945, 1950, 1955, and 1960, with the solution including local biases for the fixed observatories. In order to derive a priori models for the epochs, the International Geomagnetic Reference Field (12/83) model (based on Magsat data) was projected backward in time using a spline fit to annual secular-variation models. An uncertainty model was developed which included estimates of the effects of crustal and core fields not represented by the model. Differences between biases from year to year are found to be within the predicted bounds.

Langel, R. A.↗

Bifurcation Analysis Using Rigorous Branch and Bound Methods

For the study of nonlinear dynamic systems, it is important to locate the equilibria and bifurcations occurring within a specified computational domain. This paper proposes a new approach for solving these problems and compares it to the numerical continuation method. The new approach is based upon branch and bound and utilizes rigorous enclosure techniques to yield outer bounding sets of both the equilibrium and local bifurcation manifolds. These sets, which comprise the union of hyper-rectangles, can be made to be as tight as desired. Sufficient conditions for the existence of equilibrium and bifurcation points taking the form of algebraic inequality constraints in the state-parameter space are used to calculate their enclosures directly. The enclosures for the bifurcation sets can be computed independently of the equilibrium manifold, and are guaranteed to contain all solutions within the computational domain. A further advantage of this method is the ability to compute a near-maximally sized hyper-rectangle of high dimension centered at a fixed parameter-state point whose elements are guaranteed to exclude all bifurcation points. This hyper-rectangle, which requires a global description of the bifurcation manifold within the computational domain, cannot be obtained otherwise. A test case, based on the dynamics of a UAV subject to uncertain center of gravity location, is used to illustrate the efficacy of the method by comparing it with numerical continuation and to evaluate its computational complexity.

Smith, Andrew P.↗

Free Energy and Flexibility Analysis of Autoinhibited Human BRAF

The RAF serine/threonine protein kinases function as direct effectors of RAS in the intracellular transmission of extracellular growth signals, and they are key targets for drug discovery, given the high incidence of oncogenic mutations in RAF and other components of this signaling pathway. In its inactive state, RAF is held in an autoinhibited conformation in the cytosol through a combination of intramolecular interactions and binding to a regulatory 14−3−3 protein dimer. Activation of RAF is initiated by its interaction with membrane-localized GTP-bound RAS, which induces conformational changes that release RAF from its autoinhibited state. However, the molecular mechanisms governing RAF activation remain incomplete, largely due to the challenges in experimentally capturing the intermediate conformational states in this process. To address this gap, we developed a comprehensive all-atom model of BRAF based on existing cryo-EM structures. Using this model, we performed extensive molecular dynamics simulations to evaluate the stability and free energy landscape of autoinhibited BRAF in solution. Our analysis reveals conformational flexibility within the autoinhibited complex, suggesting that this dynamic behavior may play a role in facilitating BRAF activation upon engagement with the membrane-bound RAS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The mechanism driving a solid–solid phase transition in a biomacromolecular crystal

A solid-solid phase transition (SSPT) occurs between distinguishable crystalline forms. Because of its importance in application and theory in material science and condensed matter physics, SSPT has been studied most extensively in metallic alloys, inorganic salt or small organic molecular crystals, but much less so in biomacromolecular crystals. In general, the mechanism of SSPT at atomic and molecular levels is not well understood. Here, we describe the ordered molecular rearrangements in biomacromolecular crystals of the adenine riboswitch (riboA) aptamer using real-time serial crystallography and solution atomic force microscopy (AFM). The large, ligand-induced conformational changes drive the initial phase transition from the apo unit cell (AUC) to the trans unit cell 1 (TUC1). During this transition, coaxial stacking of P1 duplexes becomes the dominant packing interface, whereas P2-P2 interactions are almost completely disrupted, resulting in “floating” layers of molecules. The coupling points in TUC1 and their local conformational flexibility allow the molecules to reorganize to achieve the more densely packed and energetically favorable bound unit cell (BUC). Our study thus reveals the interplay between the conformational changes and the crystal phases—the underlying mechanism that drives the phase transition. Using polarized video microscopy (PVM) to monitor the SSPT in small crystals at high ligand concentration, we have identified the time window during which the major conformational changes take place, and simulated the in crystallo kinetics. Together, these results provide the spatiotemporal information necessary for informing time-resolved crystallography (TRX) experiments. Moreover, this study illustrates a practical approach to characterize SSPT in transparent crystals.

36 MATERIALS SCIENCE↗

Earthquake-induced impact of base-isolated buildings: theory, numerical modeling, and design solutions

Earthquake shaking more intense than that used to size the horizontal clearance between a base–isolated building and near–rigid perimeter moat wall will result in hard impact, producing high–frequency, high–amplitude acceleration response in the structure and supported equipment. Herein this paper provides a design solution for the damaging effects of hard impact by installing a compliant engineered element in the load path between the base–isolated building and the moat wall, resulting in soft impact and a much smaller acceleration response. The engineered element assumed herein is a commercial–off–the–shelf marine fender with mechanical properties determined by physical testing. The attachment of a flexible engineered element, with well–defined stiffness and damping, to a near–rigid moat wall, simplifies the numerical modeling of the building–moat wall system and eliminates the need to bound the lateral stiffness of the wall for impact calculations. The simple model of the engineered element can be implemented in commercial finite element codes. Theory is developed for two–sided impact of a single–degree–of–freedom oscillator. Analytical solutions are derived for the shifted first–mode frequency of the impacted oscillator and for its free–vibration response. The shifted first–mode frequency is a function of the composite lateral stiffness of the isolator–engineered element assembly and its earthquake–induced displacement. Local peaks in the spectral response of the impacted oscillator form at odd integer multiples of the shifted first–mode frequency. The analytical solutions can be used to verify, in part, the numerical model used for impact analysis.

42 ENGINEERING↗

Upwind second-order difference schemes and applications in unsteady aerodynamic flows

Explicit second-order upwind difference schemes in combination with spatially symmetric schemes can produce larger stability bounds and better numerical resolution than symmetric schemes alone. However, if conservation form is essential, a special operator is required for transition between schemes. An operational approach has been devised for deriving transition operators so that strict conservation and local consistency are maintained. Various aspects of hybrid schemes are studied numerically for model linear and nonlinear equations. To demonstrate the utility of combining two different algorithms, MacCormack's explicit, noncentered, second-order method is combined with a completely upwind version, and numerical solutions of the Euler equations are obtained for two-dimensional, transonic flows with embedded supersonic regions and shock waves. The general utility of the operational approach for combining schemes is emphasized by deriving a second-order conservative scheme for the steady transonic small-disturbance potential equation.

Warming, R. F.↗

Discovering Planetary Nebula Geometries: Explorations with a Hierarchy of Models

Astronomical objects known as planetary nebulae (PNe) consist of a shell of gas expelled by an aging medium-sized star as it makes its transition from a red giant to a white dwarf. In many cases this gas shell can be approximately described as a prolate ellipsoid. Knowledge of the physics of ionization processes in this gaseous shell enables us to construct a model in three dimensions (3D) called the Ionization-Bounded Prolate Ellipsoidal Shell model (IBPES model). Using this model we can generate synthetic nebular images, which can be used in conjunction with Hubble Space Telescope (HST) images of actual PNe to perform Bayesian model estimation. Since the IBPES model is characterized by thirteen parameters, model estimation requires the search of a 13-dimensional parameter space. The 'curse of dimensionality,' compounded by a computationally intense forward problem, makes forward searches extremely time-consuming and frequently causes them to become trapped in local solutions. We find that both the speed and of the search can be improved by judiciously reducing the dimensionality of the search space. Our basic approach employs a hierarchy of models of increasing complexity that converges to the IBPES model. Earlier studies establish that a hierarchical sequence converges more quickly, and to a better solution, than a search relying only on the most complex model. Here we report results for a hierarchy of five models. The first three models treat the nebula as a 2D image, while the last two models explore its characteristics as a 3D object and enable us to characterize the physics of the nebula. This five-model hierarchy is applied to HST images of ellipsoidal PNe to estimate their geometric properties and gas density profiles.

Huyser, Karen A.↗

GTOC9: Methods and Results from the Jet Propulsion Laboratory Team

The removal of 123 pieces of debris from the Sunsynchronous LEO environment is accomplished by a 10-spacecraft campaign wherein the spacecraft, flying in succession over an 8-yr period, rendezvous with a series of the debris objects, delivering a de-orbit package at each one before moving on to the next object by means of impulsive manoeuvres. This was the GTOC9 problem, as posed by the European Space Agency. The methods used by the Jet Propulsion Laboratory team are described, along with the winning solution found by the team. Methods include branch-and-bound searches that exploit the natural nodal drift to compute long chains of rendezvous with debris objects, beam searches for synthesising campaigns, ant colony optimisation, and a genetic algorithm. Databases of transfers between all bodies on a fine time grid are made, containing an easyto- compute yet accurate estimate of the transfer V . Lastly, a final non-linear programming optimisation is performed to ensure the trajectories meet all the constraints and are locally optimal in initial mass.

Sims, Jon↗

Fault geometries and extension in the Valles Marineris, Mars

The central troughs of the Valles Marineris system on Mars are generally regarded to be of tectonic origin because they are linear and bounded by faults. Their radial orientation to the Tharsis rise suggests that at least their incipient formation was influenced by the formation of the rise, but the exact role of Tharsis is not yet well understood. Collapse and erosion may have significantly modified the original tectonic troughs. To better understand the magnitude and mechanism of crustal extension across the Valles Marineris, the attitudes of trough-wall faults that parallel the long axes of the troughs were studied. Our results will help to determine if the extension is related to the Tharsis rise, to a local arch along which the troughs lie, or to other mechanisms. Fault-plane attitudes were obtained by performing a photogrammetric study of fault traces in the walls of Candor and Melas Chasmata. If the exposed wall faults are not major trough-bounding faults, it is assumed that these major faults are buried at the base of the walls and have similar geometries to the exposed faults. Three dimensional coordinates of several points along each fault trace were obtained and three-point solutions to their geometries were constructed. As expected, the results show that the faults dip toward the interior of the troughs, suggesting that they are indeed normal faults associated with trough formation.

Chadwick, D. J.↗

An approach to the development of numerical algorithms for first order linear hyperbolic systems in multiple space dimensions: The constant coefficient case

Two methods for developing high order single step explicit algorithms on symmetric stencils with data on only one time level are presented. Examples are given for the convection and linearized Euler equations with up to the eighth order accuracy in both space and time in one space dimension, and up to the sixth in two space dimensions. The method of characteristics is generalized to nondiagonalizable hyperbolic systems by using exact local polynominal solutions of the system, and the resulting exact propagator methods automatically incorporate the correct multidimensional wave propagation dynamics. Multivariate Taylor or Cauchy-Kowaleskaya expansions are also used to develop algorithms. Both of these methods can be applied to obtain algorithms of arbitrarily high order for hyperbolic systems in multiple space dimensions. Cross derivatives are included in the local approximations used to develop the algorithms in this paper in order to obtain high order accuracy, and improved isotropy and stability. Efficiency in meeting global error bounds is an important criterion for evaluating algorithms, and the higher order algorithms are shown to be up to several orders of magnitude more efficient even though they are more complex. Stable high order boundary conditions for the linearized Euler equations are developed in one space dimension, and demonstrated in two space dimensions.

Goodrich, John W.↗

Smart-Divert Powered Descent Guidance to Avoid the Backshell Landing Dispersion Ellipse

A smart-divert capability has been added into the Powered Descent Guidance (PDG) software originally developed for Mars pinpoint and precision landing. The smart-divert algorithm accounts for the landing dispersions of the entry backshell, which separates from the lander vehicle at the end of the parachute descent phase and prior to powered descent. The smart-divert PDG algorithm utilizes the onboard fuel and vehicle thrust vectoring to mitigate landing error in an intelligent way: ensuring that the lander touches down with minimum- fuel usage at the minimum distance from the desired landing location that also avoids impact by the descending backshell. The smart-divert PDG software implements a computationally efficient, convex formulation of the powered-descent guidance problem to provide pinpoint or precision-landing guidance solutions that are fuel-optimal and satisfy physical thrust bound and pointing constraints, as well as position and speed constraints. The initial smart-divert implementation enforced a lateral-divert corridor parallel to the ground velocity vector; this was based on guidance requirements for MSL (Mars Science Laboratory) landings. This initial method was overly conservative since the divert corridor was infinite in the down-range direction despite the backshell landing inside a calculable dispersion ellipse. Basing the divert constraint instead on a local tangent to the backshell dispersion ellipse in the direction of the desired landing site provides a far less conservative constraint. The resulting enhanced smart-divert PDG algorithm avoids impact with the descending backshell and has reduced conservatism.

Carson, John M.↗