Synthesis of dynamic systems using FORMA: FORTRAN Matrix Analysis. Volume 1: Methodology
Synthesis of structural dynamic systems using digital computer and FORMA(FORTRAN Matrix Analysis)
Wohlen, R. L.↗
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Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry
Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading proteins implicated in diseases. A key step in this process is the formation of a ternary complex where a heterobifunctional molecule induces proximity of an E3 ligase to a protein of interest (POI), thus facilitating ubiquitin transfer to the POI. In this work, we characterize 3 steps in the TPD process. (1) We simulate the ternary complex formation of SMARCA2 bromodomain and VHL E3 ligase by combining hydrogen-deuterium exchange mass spectrometry with weighted ensemble molecular dynamics (MD). (2) We characterize the conformational heterogeneity of the ternary complex using Hamiltonian replica exchange simulations and small-angle X-ray scattering. (3) We assess the ubiquitination of the POI in the context of the full Cullin-RING Ligase, confirming experimental ubiquitinomics results. Differences in degradation efficiency can be explained by the proximity of lysine residues on the POI relative to ubiquitin.
59 BASIC BIOLOGICAL SCIENCES↗
Simulation of linear mechanical systems
A dynamics and controls analyst is typically presented with a structural dynamics model and must perform various input/output tests and design control laws. The required time/frequency simulations need to be done many times as models change and control designs evolve. This paper examines some simple ways that open and closed loop frequency and time domain simulations can be done using the special structure of the system equations usually available. Routines were developed to run under Pro-Matlab in a mixture of the Pro-Matlab interpreter and FORTRAN (using the .mex facility). These routines are often orders of magnitude faster than trying the typical 'brute force' approach of using built-in Pro-Matlab routines such as bode. This makes the analyst's job easier since not only does an individual run take less time, but much larger models can be attacked, often allowing the whole model reduction step to be eliminated.
Sirlin, S. W.↗
Ultrafast time-resolved x-ray absorption spectroscopy of ionized urea and its dimer through ab initio nonadiabatic dynamics
Investigating the early dynamics of chemical systems following ionization is essential for our understanding of radiation damage. However, experimental as well as theoretical investigations are very challenging due to the complex nature of these processes. Time-resolved x-ray absorption spectroscopy on a femtosecond timescale, in combination with appropriate simulations, is able to provide crucial insights into the ultrafast processes that occur upon ionization due to its element-specific probing nature. In this theoretical study, we investigate the ultrafast dynamics of valence-ionized states of urea and its dimer employing Tully's fewest switches surface hopping approach using Koopmans' theorem to describe the ionized system. We demonstrate that following valence ionization through a pump pulse, the time-resolved x-ray absorption spectra at the carbon, nitrogen, and oxygen K-edges reveal rich insights into the dynamics. Excited states of the ionized system give rise to time-delayed blueshifts in the x-ray absorption spectra as a result of electronic relaxation dynamics through nonadiabatic transitions. Moreover, our statistical analysis reveals specific structural dynamics in the molecule that induce time-dependent changes in the spectra. For the urea monomer, we elucidate the possibility to trace effects of specific molecular vibrations in the time-resolved x-ray absorption spectra. For the urea dimer, where ionization triggers a proton transfer reaction, we show how the x-ray absorption spectra can reveal specific details on the progress of proton transfer.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Structural considerations of folded protein import through the chloroplast TOC/ TIC translocons
Protein import into chloroplasts is carried out by the protein translocons at the outer and inner envelope membranes (TOC and TIC). Detailed structures for these translocons are lacking, with only a low-resolution TOC complex structure available. Recently, we showed that the TOC/TIC translocons can import folded proteins, a rather unique feat for a coupled double membrane system. In this work we also determined the maximum functional TOC/TIC pore size to be 30–35 Å. Here, we discuss how such large pores could form and compare the structural dynamics of the pore-forming Toc75 subunit to its bacterial/mitochondrial Omp85 family homologs. We put forward structural models that can be empirically tested and also briefly review the pore dynamics of other protein translocons with known structures.
59 BASIC BIOLOGICAL SCIENCES↗
Operando Electrochemical Liquid-Cell Scanning Transmission Electron Microscopy (EC-STEM) Studies of Evolving Cu Nanocatalysts for CO 2 Electroreduction
The design and synthesis of nanocatalysts with well-defined sizes, compositions, and structures have revolutionized our accessibility to tunable catalyst activity and selectivity for a variety of energy-related electrochemical reactions. Nonetheless, establishing structure-(re)activity correlations requires the understanding of the dynamic evolution of pristine nanocatalysts and the identification of their active states under operating conditions. We previously communicated the operando observation of Cu nanocatalysts evolving into active metallic Cu nanograins for CO 2 electroreduction (Yang et al. Nature 2023, 614, 262–269). Here, we expand our discussion to the technical capabilities and further research applications of operando electrochemical liquid-cell scanning transmission electron microscopy (EC-STEM), which enables quantitative electrochemistry while tracking dynamic structural evolution of sub-10 nm Cu nanocatalysts. The coexistent H 2 bubbles, often disruptive to operando spectroscopy, are an effective approach to create a thin-liquid layer that significantly improves spatial resolution while remaining electrochemically accessible to Cu nanocatalysts. Operando four-dimensional (4D) STEM in liquids provides insights into the complex structure of active polycrystalline metallic Cu nanograins. With continuous technical developments, we anticipate that operando EC-STEM will evolve into a powerful electroanalytical method to advance our understanding of a variety of nanoscale electrocatalysts at solid/liquid interfaces.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural optimization in the dynamics response regime - A computational approach.
Structural optimization of designs with requirements including restrictions on structure dynamic response and characteristics
Fox, R. L.↗
Structural optimization in the dynamics response regime - A computational approach
Structural optimization of designs with requirements including restrictions on structure dynamic response and characteristics
Fox, R. L.↗
Dynamics and control of hypersonic vehicles - The integration challenge for the 1990's
The dynamic characteristics of hypersonic vehicles are reviewed, with special attention to the interactions between the airframe, engine, and structural dynamics. Based on a preliminary investigation of the dynamics of a generic vehicle configuration similar to the X-30 with Scramjet propulsion, an assessment of these interactions is presented. The control effectors include aerodynamic pitch-control surfaces, as well as engine fuel flow and diffuser area ratio. The study configuration is statically instable in pitch, and exhibits strong airframe/engine/elastic coupling in the attitude dynamics and engine responses. This strong coupling will require a highly integrated airframe-engine control system, and the performance of the attitude control system will be contingent upon the ability to adequately deal with the structural aeroelastic response and engine dynamics.
Schmidt, David K.↗
How Silica Surface Chemistry Modulates Interfacial Water: Insights from Machine Learning Molecular Dynamics
Controlling water structure and dynamics at silica interfaces are central to a wide range of technologies, including protective oxide layers for solar water splitting and nanoporous membranes. In this work, we develop a machine learning interatomic potential, trained via active learning, to achieve ab initio accuracy for water confined between hydroxylated silica surfaces over a range of silanol coverages and slit widths. We find that partially hydroxylated surfaces (50 and 75% OH) support stronger water−surface hydrogen bonding and more extended interfacial density profiles than fully hydroxylated (100% OH) surfaces, indicating that increasing OH coverage does not necessarily strengthen interfacial hydrogenbond networks. Translational diffusion decreases approximately linearly with slit width and OH coverage, whereas rotational dynamics respond nonlinearly. In particular, at the smallest slit width of 5 Å, 75% OH coverage produces an enhanced local tetrahedral ordered interfacial network that strongly suppresses reorientation, while 100% coverage yields a crowded, disordered interfacial layer that also hinders rotation. In contrast, the 50% OH coverage is sufficiently sparse that it does not markedly alter water structure or dynamics under confinement. These results show that coupled control of pore size and surface chemistry enables nonlinear tuning of interfacial water structure and transport, providing a design strategy for optimizing porous silica for either enhanced interfacial stability and controlled reactivity or rapid and selective transport.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Liquid-like solid-state diffusion of lithium ions in super-halide-rich argyrodite
The development of solid electrolytes with high ionic conductivity is essential for advancing safer, high-energy-density solid-state batteries, where lithium site distribution in the sublattice strongly affects ion transport. Here, we report a super-halide-rich argyrodite, Li 5.3 PS 4.3 Cl 1.7 , with remarkable room-temperature ionic conductivity (11.4 ± 0.7 mS cm -1 ) due to population of two additional interstitial lithium sites induced by vacancy redistribution. Prominent lithium density between lithium sites and elevated atomic displacement parameters indicate liquid-like diffusive behavior resembling sublattice melting. Combining electrochemical impedance spectroscopy, pulsed-field gradient NMR, and T 1 relaxation methods, we demonstrate that the augmented conductivity partly arises from a low energy barrier (0.08 eV) at the local scale, attributed to a three-site lithium distribution that drives correlated lithium dynamics. This work advances our understanding of the structure-dynamics interplay in super-halide-rich argyrodites, and highlighting their potential as solid-state battery electrolytes in cells with a coated single-crystal NMC82 cathode that achieve 170 mAh/g capacity at a 0.2 C rate .
25 ENERGY STORAGE↗
Ultrafast-induced coherent acoustic phonons in the two-dimensional magnet CrSBr
Magnetism in two-dimensional (2D) van der Waals (vdW) crystals offers promising new directions for low-dimensional physics and devices. In this work, mega-electron volt (MeV) ultrafast electron diffraction was employed to investigate the ultrafast atomic dynamics of a novel, 2D vdW magnetic single-crystal CrSBr. Femtosecond (fs) optical pump pulses excited non-equilibrium atomic displacements shown to be coherent acoustic phonons (CAPs). Phonon frequencies were extracted by analyzing oscillations of different Bragg peak (BP) intensities and were determined to be GHz acoustic disturbances that propagated as strain waves. Phonon modes exhibit anisotropy with respect to the a and b crystal axes. Subharmonic phonon frequencies were also observed, and this provided a signature of nonlinear oscillatory coupling between the laser-induced pumping phonon frequency and secondary phonon frequencies. Thus, CrSBr was found to serve as a nonlinear phononic frequency converter. The ultrafast time dependence of the Bragg intensity was simulated by incorporating an oscillating deviation parameter ansatz into expressions for the dynamical scattering intensity yielded excellent modeling of the ultrafast structural dynamics of the photo-excited 2D crystal. Our work provides a foundation for exploring how fs light pulses can influence phonon dynamics in materials with strong spin-lattice coupling. These results suggest that CAPs can match the magnon frequencies and show the promise of CrSBr for use in optical-to-microwave transducers and phononic devices.
43 PARTICLE ACCELERATORS↗
Structural optimization using optimality criteria methods
Optimality criteria methods take advantage of some concepts as those of statically determinate or indeterminate structures, and certain variational principles of structural dynamics, to develop efficient algorithms for the sizing of structures that are subjected to stiffness-related constraints. Some of the methods and iterative strategies developed over the last decade for calculations of the Lagrange multipliers in stressand displacement-limited problems, as well as for satisfying the appropriate optimality criterion, are discussed. The application of these methods are illustrated by solving problems with stress and displacement constraints.
Khot, N. S.↗
Control Law Design in a Computational Aeroelasticity Environment
A methodology for designing active control laws in a computational aeroelasticity environment is given. The methodology involves employing a systems identification technique to develop an explicit state-space model for control law design from the output of a computational aeroelasticity code. The particular computational aeroelasticity code employed in this paper solves the transonic small disturbance aerodynamic equation using a time-accurate, finite-difference scheme. Linear structural dynamics equations are integrated simultaneously with the computational fluid dynamics equations to determine the time responses of the structure. These structural responses are employed as the input to a modern systems identification technique that determines the Markov parameters of an "equivalent linear system". The Eigensystem Realization Algorithm is then employed to develop an explicit state-space model of the equivalent linear system. The Linear Quadratic Guassian control law design technique is employed to design a control law. The computational aeroelasticity code is modified to accept control laws and perform closed-loop simulations. Flutter control of a rectangular wing model is chosen to demonstrate the methodology. Various cases are used to illustrate the usefulness of the methodology as the nonlinearity of the aeroelastic system is increased through increased angle-of-attack changes.
Newsom, Jerry R.↗
A Multi-Mode Blade Damping Control using Shunted Piezoelectric Transducers with Active Feedback Structure
The Structural Dynamics and. Mechanics branch (RXS) is developing smart adaptive structures to improve fan blade damping at resonances using piezoelectric (PE) transducers. In this presentation, only one shunted PE transducer was used to demonstrate active control of multi-mode blade resonance damping on a titanium alloy (Ti-6A1-4V) flat plate model, regardless of bending, torsion, and 2-stripe modes. This work would have a significant impact on the conventional passive shunt damping world because the standard feedback control design tools can now be used to design and implement electric shunt for vibration control. In other words, the passive shunt circuit components using massive inductors and. resistors for multi-mode resonance control can be replaced with digital codes. Furthermore, this active approach with multi patches can simultaneously control several modes in the engine operating range. Dr. Benjamin Choi presented the analytical and experimental results from this work at the Propulsion-Safety and. Affordable Readiness (P-SAR) Conference in March, 2009.
Choi, Benjamin↗
Stage Separation Failure: Model Based Diagnostics and Prognostics
Safety of the next-generation space flight vehicles requires development of an in-flight Failure Detection and Prognostic (FD&P) system. Development of such system is challenging task that involves analysis of many hard hitting engineering problems across the board. In this paper we report progress in the development of FD&P for the re-contact fault between upper stage nozzle and the inter-stage caused by the first stage and upper stage separation failure. A high-fidelity models and analytical estimations are applied to analyze the following sequence of events: (i) structural dynamics of the nozzle extension during the impact; (ii) structural stability of the deformed nozzle in the presence of the pressure and temperature loads induced by the hot gas flow during engine start up; and (iii) the fault induced thrust changes in the steady burning regime. The diagnostic is based on the measurements of the impact torque. The prognostic is based on the analysis of the correlation between the actuator signal and fault-induced changes in the nozzle structural stability and thrust.
Luchinsky, Dmitry↗
Method and System for Predicting Rocket Nozzle Deformation During Engine Start-Up and Shut-Down Transients
Computational fluid dynamics (CFD) computations are performed at time increments using structural properties of the nozzle and flow properties of combustion products flowing through the nozzle. Each CFD computation accounts for movement of the wall geometry of the rocket nozzle due to the flowfield. Structural dynamics computations are performed at each time increment using the CFD computations in order to describe the movement of the wall geometry. Mesh dynamics computations at each time increment redefine the flowfield to account for the movement of the wall geometry. The mesh dynamics computations are based on a spring analogy process. The computations are iterated to solution convergence at each time increment with results being output to an output device.
Wang, Ten-See↗
Excited-state vibronic coherences and intramolecular charge transfer dynamics of the photoinactive cyanobacteriochrome NpF2164g5
We have characterized the excited-state structural dynamics that follow optical excitation of the photoinactive cyanobacteriochrome (CBCR) NpF2164g5 to determine the first events along the photoisomerization reaction coordinate of the phycocyanobilin (PCB) chromophore in red-to-green photoactive CBCRs. Within 25 fs of photoexcitation to the first excited singlet state, S1, a cross peak begins to develop below the diagonal of the broadband two-dimensional electronic spectrum (2DES) owing to the formation of a twisted conformation of the PCB chromophore with an enhanced intramolecular charge-transfer (ICT) character. Excited-state coherent wavepacket motions, including a torsion of the methine bridge between rings C and D and the carbon–hydrogen out-of-plane (HOOP) wagging vibration, are rapidly damped as the cross peak forms. This finding supports an assignment of the torsional and HOOP modes to the reaction coordinate of a coherent nonadiabatic mechanism. The ICT process is accompanied by an ultrafast Stokes shift and rapidly damped oscillations at the torsional mode’s frequency, which are sensed by measurements of the energy gap of the cross peak using its first moment with respect to the detection frequency axis of the 2DES spectrum. Furthermore, these results have the further implication that polar side chains of nearby amino acid residues in the binding site of the PCB chromophore can manipulate the barrier height for photoisomerization in red-to-green photoactive CBCRs and in phytochromes by redistributing the π-electron density along the methine bridge between the C and D rings.
Charge transfer↗