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At least 577 records · Page 32

Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling

The CRISPR-Cas9 nuclease has been widely repurposed as a molecular and cell biology tool for its ability to programmably target and cleave DNA. Cas9 recognizes its target site by unwinding the DNA double helix and hybridizing a 20-nucleotide section of its associated guide RNA to one DNA strand, forming an R-loop structure. A dynamic and mechanical description of R-loop formation is needed to understand the biophysics of target searching and develop rational approaches for mitigating off-target activity while accounting for the influence of torsional strain in the genome. Here we investigate the dynamics of Cas9 R-loop formation and collapse using rotor bead tracking (RBT), a single-molecule technique that can simultaneously monitor DNA unwinding with base-pair resolution and binding of fluorescently labeled macromolecules in real time. By measuring changes in torque upon unwinding of the double helix, we find that R-loop formation and collapse proceed via a transient discrete intermediate, consistent with DNA:RNA hybridization within an initial seed region. Using systematic measurements of target and off-target sequences under controlled mechanical perturbations, we characterize position-dependent effects of sequence mismatches and show how DNA supercoiling modulates the energy landscape of R-loop formation and dictates access to states competent for stable binding and cleavage. Consistent with this energy landscape model, in bulk experiments we observe promiscuous cleavage under physiological negative supercoiling. The detailed description of DNA interrogation presented here suggests strategies for improving the specificity and kinetics of Cas9 as a genome engineering tool and may inspire expanded applications that exploit sensitivity to DNA supercoiling.

59 BASIC BIOLOGICAL SCIENCES↗

Acoustic emission from a growing crack

An analytical method is being developed to determine the signature of an acoustic emission waveform from a growing crack and the results of this analysis are compared to experimentally obtained values. Within the assumptions of linear elastic fracture mechanics, a two dimensional model is developed to examine a semi-infinite crack that, after propagating with a constant velocity, suddenly stops. The analytical model employs an integral equation method for the analysis of problems of dynamic fracture mechanics. The experimental procedure uses an interferometric apparatus that makes very localized absolute measurements with very high fidelity and without acoustically loading the specimen.

Jacobs, Laurence J.↗

Cooperative diffusion in body-centered cubic iron in Earth and super-Earths’ inner core conditions

Abstract The physical chemistry of iron at the inner-core conditions is key to understanding the evolution and habitability of Earth and super-Earth planets. Based on full first-principles simulations, we report cooperative diffusion along the longitudinally fast ⟨ 111 ⟩ directions of body-centered cubic (bcc) iron in temperature ranges of up to 2000–4000 K below melting and pressures of ∼300–4000 GPa. The diffusion is due to the low energy barrier in the corresponding direction and is accompanied by mechanical and dynamical stability, as well as strong elastic anisotropy of bcc iron. These findings provide a possible explanation for seismological signatures of the Earth’s inner core, particularly the positive correlation between P wave velocity and attenuation. The diffusion can also change the detailed mechanism of core convection by increasing the diffusivity and electrical conductivity and lowering the viscosity. The results need to be considered in future geophysical and planetary models and should motivate future studies of materials under extreme conditions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Dynamics of Variable Mass Systems

This report presents the results of an investigation of the effects of mass loss on the attitude behavior of spinning bodies in flight. The principal goal is to determine whether there are circumstances under which the motion of variable mass systems can become unstable in the sense that their transverse angular velocities become unbounded. Obviously, results from a study of this kind would find immediate application in the aerospace field. The first part of this study features a complete and mathematically rigorous derivation of a set of equations that govern both the translational and rotational motions of general variable mass systems. The remainder of the study is then devoted to the application of the equations obtained to a systematic investigation of the effect of various mass loss scenarios on the dynamics of increasingly complex models of variable mass systems. It is found that mass loss can have a major impact on the dynamics of mechanical systems, including a possible change in the systems stability picture. Factors such as nozzle geometry, combustion chamber geometry, propellant's initial shape, size and relative mass, and propellant location can all have important influences on the system's dynamic behavior. The relative importance of these parameters on-system motion are quantified in a way that is useful for design purposes.

Eke, Fidelis O.↗

DS-TIDE: Harnessing Dynamical Systems for Efficient Time-Independent Differential Equation Solving

Time-Independent Differential Equations (TIDEs) are central to modeling equilibrium behavior across a wide range of scientific and engineering domains, from electrostatics to porous media flow. Conventional numerical solvers offer reliable solutions but incur significant computational costs due to fine-grained discretization and iterative procedures. Machine learning-based approaches address this by replacing iterative solving processes with one-time inference; however, their sophisticated models require extensive training resources that often exceed those of traditional solvers. Consequently, designing a TIDE solver that achieves high accuracy, broad applicability, and exceptional computational efficiency remains a fundamental challenge. In this paper, we propose DS-TIDE, a novel hardware solver that is inspired by, and subsequently leverages, the intrinsic connection between Dynamical Systems (DS) and Differential Equations (DEs) to efficiently and accurately solve TIDEs. DS-TIDE employs a CMOS-compatible DS-based processor, whose physical states evolve under carefully designed DE-driven dynamics and naturally converge to equilibrium -- the solution of the target TIDE -- within ~1µs on a ~1-watt DS-TIDE processor. To enhance expressivity, DS-TIDE incorporates Heterogeneous Dynamics with Temporal Layering (HDTL), which solves TIDEs through a three-stage DS evolution -- conditioning, solving, and decoding -- each governed by specialized dynamics. The entire evolution process is analogous to an infinitely deep neural network temporally unrolled, offering the system the capability of representing complex equations. Furthermore, DS-TIDE is equipped with an on-device DS-DE Auto-Alignment mechanism that dynamically adapts intrinsic hardware dynamics within milliseconds, effectively aligning the system’s dynamics to diverse target DEs. Experimental results across TIDEs from a wide range of scientific and engineering domains demonstrate that DS-TIDE achieves ~10^3× speedup, ~10^5× energy savings, and competitive or superior accuracy compared to state-of-the-art numerical and ML-based solvers.

Liu, Chuan↗

A coarse-grain force field based on quantum mechanics (CGq FF) for molecular dynamics simulation of poly(ethylene glycol)- block -poly(ε-caprolactone) (PEG- b -PCL) micelles

In order to provide the means to predict from molecular dynamics (MD) simulations the structures of copolymer-based micelles in solution, we developed coarse grain force field (CGq FF) parameters for poly(ethylene glycol) (PEG) and for poly(ε-caprolactone) (PCL). A key advance here is the use of quantum mechanics to train the parameters describing the non-bonded (NB) interactions between the CG beads. The functional forms are the same as the MARTINI CG FF so standard MD codes can be used. Our CGq FF describes well the experimentally observed properties for the polymer–air and polymer–water interfaces, indicating the accuracy of the NB interactions. Additionally, the structural properties (density, radius of gyration ( R g ), and end-to-end distance ( h )) match both experiment and all atom (AA) simulations. We illustrate the application of this CGq FF by following the formation of a spherical micelle from 250 chains of PEG 23 - b -PCL 9 diblock copolymer, each block with molecular weight of 1000 Daltons (10 500 beads, corresponding to 123 250 atoms), in a water box with 119 139 water beads (426 553 water molecules).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Impact of substrates and quantum effects on exciton line shapes of 2D semiconductors at room temperature

Exciton resonances in monolayer transition-metal dichalcogenides (TMDs) provide exceptionally strong light–matter interaction at room temperature. Their spectral line shape is critical in the design of a myriad of optoelectronic devices, ranging from solar cells to quantum information processing. However, disorder resulting from static inhomogeneities and dynamical fluctuations can significantly impact the line shape. Many recent works experimentally evaluate the optical properties of TMD monolayers placed on a substrate and the line shape is typically linked directly to the material’s quality. Here, we highlight that the interference of the substrate and TMD reflections can strongly influence the line shape. We further show how basic, room-temperature reflection measurements allow investigation of the quantum mechanical exciton dynamics by systematically controlling the substrate reflection with index-matching oils. By removing the substrate contribution with properly chosen oil, we can extract the excitonic decay rates including the quantum mechanical dephasing rate. The results provide valuable guidance for the engineering of exciton line shapes in layered nanophotonic systems.

2D semiconductor↗

Numerical modeling and experimental validation of low velocity impact of woven GFRP/CFRP composites

Low-velocity impact of 2D woven glass fiber reinforced polymer (GFRP) and carbon fiber reinforced polymer (CFRP) composite laminates was studied experimentally and numerically. Hybrid laminates containing blocked layers of GFRP/CFRP/GFRP with all plies oriented at 0° were investigated. Relatively high impact energies were used to obtain full perforation of the laminate in a low-velocity impact setup. Numerical simulations were carried out using the in-house transient dynamics finite element code, Sierra/SM, developed at Sandia National Laboratories. A three-dimensional continuum damage model was used to describe the response of a woven composite ply. Two methods for handling delamination were considered and compared: (1) cohesive zone modeling and (2) continuum damage mechanics. The reduced model size achieved by omission of the cohesive zone elements produced acceptable results at reduced computational cost. Further, the comparison between different modeling techniques can be used to inform modeling decisions relevant to low velocity impact scenarios. The modeling was validated by comparing with the experimental results and showed good agreement in terms of predicted damage mechanisms and impactor velocity and force histories.

36 MATERIALS SCIENCE↗

The role of collective elasticity on activated structural relaxation, yielding, and steady state flow in hard sphere fluids and colloidal suspensions under strong deformation

In this work, we theoretically study the effect of external deformation on activated structural relaxation and aspects of the nonlinear mechanical response of glassy hard sphere fluids in the context of elastically collective nonlinear Langevin equation theory. This microscopic force-based approach describes activated relaxation as a coupled local–nonlocal event involving caging and longer range collective elasticity, with the latter becoming more important and ultimately dominant with increasing packing fraction under equilibrium conditions. The central new question we address is how this physical picture of activated relaxation, and the relative importance of local caging vs collective elasticity physics, depends on external deformation. Theoretical predictions are presented for deformation-induced enhancement of mobility, the onset of relaxation speed up at remarkably low values of stress, strain, or shear rate, apparent power law thinning of the steady state structural relaxation time and viscosity, a non-vanishing activation barrier in the shear thinning regime, an apparent Herschel–Bulkley form of the rate dependence of the steady state shear stress, exponential growth of different measures of a dynamic yield or flow stress with the packing fraction, and reduced fragility and dynamic heterogeneity under deformation. The results are contrasted with experiments and simulations, and qualitative or better agreement is found. An overarching conclusion is that deformation strongly reduces the importance of longer range collective elastic effects relative to the local caging aspect for most, but not all, physical questions, with deformation-dependent fragility and dynamic heterogeneity phenomena being qualitatively sensitive to collective elasticity. Overall, nonlinear rheology is predicted to be a more local problem than quiescent structural relaxation, albeit with deformation-modified activated processes still important.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Topological origin of phase separation in hydrated gels

Depending on their composition, hydrated gels can be homogeneous or phase-separated, which, in turn, affects their dynamical and mechanical properties. However, the nature of the structural features, if any, that govern the propensity for a given gel to phase-separate remains largely unknown. Here, we argue that the propensity for hydrated gels to phase-separate is topological in nature. We employ reactive molecular dynamics simulations to model the early-age precipitation of calcium–alumino–silicate–hydrate (Csingle bondAsingle bondSsingle bondH) gels with varying compositions, i.e., (CaO) 1.7 (Al 2 O 3 ) x (SiO 2 ) 1 – x (H 2 O) 3.7 + x . By adopting topological constraint theory, we investigate the structural origin of phase separation in hydrated gels. We report the existence of a homogeneous-to-phase-separated transition, wherein Si-rich (x ≤ 0.10) Csingle bondAsingle bondSsingle bondH gels are homogeneous, whereas Al-rich (x > 0.10) Csingle bondAsingle bondSsingle bondH gels tend to phase-separate. Furthermore, we demonstrate that this transition is correlated to a topological flexible-to-rigid transition within the atomic network. Finally, we reveal that the propensity for topologically-overconstrained gels to phase-separate arises from the existence of some internal stress within their atomic network, which acts as an energy penalty that drives phase separation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Penta-SiCN: A Highly Auxetic Monolayer

We report the negative Poisson’s (NPR) ratio in a two-dimensional (2D) material is a counterintuitive mechanical property that facilitates the development of nanoscale devices with sophisticated functionality. Inspired by the peculiar buckled lower-symmetric, trilayered geometry of pentagonal monolayers, we theoretically predict penta-SiCN, a ternary auxetic metallic monolayer with highly tunable NPR. The penta-SiCN is structurally, thermally, dynamically, and mechanically stable, and sustainable at and beyond room temperature with experimental feasibility. It possesses nontrivial geometrical and mechanical isotropy and relatively moderate thickness. Remarkably, the shorter and quasi sp3-hybridized C–N bond and the rigidity against the strain allow the monolayer to possess a high value of NPR (-0.136), even higher than that of black phosphorene, extendable up to -0.639 by 4% of biaxial stretching. On the other hand, the 2D Young’s modulus of 129.88 N/m decreases to 41.34 N/m at equivalent stretching, indicating relative softening and flexibility. Interestingly, a buckled-to-planar phase transition is identified at 10% biaxial strain before it suffers the fracture at 16%. Additionally, the strong optical anisotropy, absorbance (up to 6.51 x 105 cm -1 ), and presence of plasmon frequency demonstrate its potential application in optomechanical and plasmonics.

36 MATERIALS SCIENCE↗

An instrument for in situ characterization of powder spreading dynamics in powder-bed-based additive manufacturing processes

In powder-bed-based metal additive manufacturing (AM), the visualization and analysis of the powder spreading process are critical for understanding the powder spreading dynamics and mechanisms. Unfortunately, the high spreading speeds, the small size of the powder, and the opacity of the materials present a great challenge for directly observing the powder spreading behavior. In this study, we report a compact and flexible powder spreading system for in situ characterization of the dynamics of the powders during the spreading process by high-speed x-ray imaging. The system enables the tracing of individual powder movement within the narrow gap between the recoater and the substrate at variable spreading speeds from 17 to 322 mm/s. The instrument and method reported here provide a powerful tool for studying powder spreading physics in AM processes and for investigating the physics of granular material flow behavior in a confined environment.

47 OTHER INSTRUMENTATION↗

Numerical procedures for three-dimensional computational surface thermochemistry

Models and equations for surface thermochemistry and near-surface thermophysics of aerodynamically-heated thermal protection materials are reviewed, with particular emphasis on computational boundary conditions for surface mass and energy transfer. The surface energy and mass balances, coupled with an appropriate ablation or surface catalysis model, provide complete thermochemical boundary conditions for a true multidisciplinary solution of the fully coupled fluid-dynamics/solid mechanics problem. Practical approximate solutions can be obtained by using a detailed model with full thermophysics for either the solid or fluid phase amd a semianalytic method for the other half of the problem. A significant increase in the state-of-the-art in aerothermal computational fluid dynamics is possible by uniting CFD methodology with surface thermochemistry boundary conditions and the heat-balance-integral method.

Milos, Frank S.↗

Device-Level Multidimensional Thermal Dynamics With Implications for Current and Future Wide Bandgap Electronics

Researchers have been extensively studying wide-bandgap (WBG) semiconductor materials such as gallium nitride (GaN) with an aim to accomplish an improvement in size, weight, and power of power electronics beyond current devices based on silicon (Si). However, the increased operating power densities and reduced areal footprints of WBG device technologies result in significant levels of self-heating that can ultimately restrict device operation through performance degradation, reliability issues, and failure. Typically, self-heating in WBG devices is studied using a single measurement technique while operating the device under steady-state direct current measurement conditions. However, for switching applications, this steady-state thermal characterization may lose significance since the high power dissipation occurs during fast transient switching events. Therefore, it can be useful to probe the WBG devices under transient measurement conditions in order to better understand the thermal dynamics of these systems in practical applications. In this work, the transient thermal dynamics of an AlGaN/GaN high electron mobility transistor (HEMT) were studied using thermoreflectance thermal imaging and Raman thermometry. Also, the proper use of iterative pulsed measurement schemes such as thermoreflectance thermal imaging to determine the steady-state operating temperature of devices is discussed. These studies are followed with subsequent transient thermal characterization to accurately probe the self-heating from steady-state down to submicrosecond pulse conditions using both thermoreflectance thermal imaging and Raman thermometry with temporal resolutions down to 15 ns.

42 ENGINEERING↗

A Decentralized Market Mechanism for Energy Communities under Operating Envelopes

Here, we propose an operating envelopes (OEs) aware energy community market mechanism that dynamically charges/rewards its members based on two-part pricing. The OEs are imposed exogenously by a regulated distribution system operator (DSO) on the energy community's revenue meter and is subject to a generalized net energy metering (NEM) tariff design. By formulating the interaction of the community operator and its members as a Stackelberg game, we show that the proposed two-part pricing achieves a Nash equilibrium and maximizes the community's social welfare in a decentralized fashion while ensuring that the community's operation abides by the OEs. The market mechanism conforms with the cost-causation principle and guarantees community members a surplus level no less than their maximum surplus when they autonomously face the DSO. The dynamic and uniform community price is a monotonically decreasing function of the community's aggregate renewable generation. We also analyze the impact of exogenous parameters such as NEM rates and OEs on the value of joining the community. Lastly, through numerical studies, we showcase the community's welfare, and pricing, and compare its members' surplus to customers under the DSO's regime.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Enhanced accuracy through ensembling of randomly initialized auto-regressive models for dynamical systems

Computational mechanics simulations using traditional finite element methods (FEM) require prohibitively expensive computational resources for real-time engineering applications, design optimization, and digital twin implementations. While machine learning (ML) surrogate models offer significant computational speedups, autoregressive ML models for time-dependent mechanical systems suffer from error accumulation that compromises long-term prediction reliability - a critical concern for engineering applications where accuracy over extended time horizons is essential for safety and performance assessments. Here, we propose a deep ensemble framework specifically designed to address this challenge in computational mechanics applications, where multiple ML surrogate models with random weight initializations are trained in parallel and their predictions aggregated during inference. This approach leverages statistical diversity to maximize information gain from a fixed set of training data and to mitigate error propagation, while maintaining the computational efficiency that makes ML surrogates attractive for engineering practice. We validate the framework on three representative problems spanning critical areas of computational mechanics: stress field evolution in heterogeneous microstructures under complex loading (relevant to advanced materials design and composite analysis), planetary-scale shallow water dynamics (applicable to environmental and geotechnical engineering), and Gray-Scott reaction-diffusion systems (relevant to mass transport and chemical process engineering). Across all test cases, the ensemble approach demonstrates consistent error reduction of 15-33% compared to individual models. The codes for this work are available on GitHub (https://github.com/Graham-Brady-Research-Group/AutoregressiveEnsemble_SpatioTemporal_Evolution).

autoregressive prediction↗

Understanding multi-scale battery degradation with a macro-to-nano zoom through its hierarchy

Lithium-ion batteries (LIBs) feature structural and chemical complexities across a broad range of length scales. It is the hierarchy of the battery structure that determines its functionality. An in-depth understanding of the battery function, degradation, and failure mechanisms requires a thorough and systematic investigation from structural, chemical, mechanical, and dynamic perspectives. Here we present a macro-to-nano zoom through the hierarchy of a commercial 18650 type LIB using a suite of state-of-the-art X-ray microscopy techniques. Damage, deformation, and heterogeneity at different length scales are visualized and are associated with different degradation phenomena and mechanisms. Our results highlight the importance of the mechanical properties of the cathode material, which could impact both the immediate and the long-term cell behaviors significantly. While this study focuses on a commercial lithium cell with a standard configuration, our findings can be extrapolated and are applicable to the development of next-generation energy storage technology, e.g. solid-state batteries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗