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At least 145 records · Page 8

Dynamic basis of supercoiling-dependent DNA interrogation by Cas12a via R-loop intermediates

The sequence specificity and programmability of DNA binding and cleavage have enabled widespread applications of CRISPR-Cas12a in genetic engineering. As an RNA-guided CRISPR endonuclease, Cas12a engages a 20-base pair (bp) DNA segment by forming a three-stranded R-loop structure in which the guide RNA hybridizes to the DNA target. Here we use single-molecule torque spectroscopy to investigate the dynamics and mechanics of R-loop formation of two widely used Cas12a orthologs at base-pair resolution. We directly observe kinetic intermediates corresponding to a ~5 bp initial RNA-DNA hybridization and a ~17 bp intermediate preceding R-loop completion, followed by transient DNA unwinding that extends beyond the 20 bp R-loop. The complex multistate landscape of R-loop formation is ortholog-dependent and shaped by target sequence, mismatches, and DNA supercoiling. A four-state kinetic model captures essential features of Cas12a R-loop dynamics and provides a biophysical framework for understanding Cas12a activity and specificity.

59 BASIC BIOLOGICAL SCIENCES↗

Analytical integration of the tractions induced by non-singular dislocations on an arbitrary shaped triangular quadratic element

Here, an analytical model is proposed to evaluate the nodal force induced by a segment of dislocation upon an arbitrary shaped triangular element. This calculation is required in hybrid methods that associate dislocation dynamics to boundary or finite element to solve simultaneously the evolution of large ensembles of dislocations with complex boundary conditions. Nodal forces are defined as the triple integration of the unbalanced traction field induced by a straight dislocation upon the surface of the element. Following our previous approach (Queyreau et al 2014 Modelling Simul. Mater. Sci. Eng. 22 035004) on a simpler geometry and in the case of linear isotropic elasticity, triple integrals are solved by sequences of integration by parts that exhibit recurrence relations. The traction field is defined and finite everywhere even at the core of dislocations, thanks to the use of the non-singular stress expression formulated by Cai et al (2006 J. Mech. Phys. Solids 54 561–587). The nodal force expressions can be used when considering both a single convolution or double convolution of the Green's function with the core distribution. A solution is also proposed for the case of a semi-infinite segment through the study of the asymptotic behavior of the analytical expressions. The proposed approach is exact and very computationally efficient. The choice of an arbitrary shaped triangular element and quadratic shape functions allow the consideration of complex geometries and comply with automatic meshing procedures. These analytical expressions could also be employed to estimate dislocation interactions with interfaces.

42 ENGINEERING↗

Content-aware foveated camera for multi-target tracking

Modern image sensors deliver substantial space-time bandwidth, yet indiscriminate acquisition often overwhelms memory, computation, and downstream perception. We present a content-aware, multi-foveated camera that dynamically reallocates sensing and magnification to multiple regions of interest (ROIs). A phase-only spatial light modulator (SLM) serves as a solid-state, inertia-free beam-steering and lens element, enabling per-frame field-of-view (FOV) reconfiguration and content-aware target tracking. By interleaving frames across foveae, our system preserves a wide-FOV situational context while refreshing each ROI at high rates, thereby reducing data volume without degrading task performance. We constructed a prototype employing a single-SLM, single-sensor architecture and demonstrated its application in real-time multi-object tracking with dynamic ROI maintenance across multiple viewpoints. The approach offers a general pathway to integrate detection, tracking, and segmentation algorithms in the acquisition loop, shifting workload from post hoc processing to intelligent capture.

Zang, Zihan [Univ. of California, Los Angeles, CA ↗

Streamlined Loads Analysis of Floating Wind Turbines With Fiber Rope Mooring Lines

This paper presents an approach for more accurate yet relatively streamlined accounting for the nonlinear characteristics of synthetic fiber rope mooring lines for floating wind turbines. First, we select a minimal set of parameters that can efficiently approximate a mooring line material's quasi-static and dynamic stiffness characteristics. We also develop a set of baseline coefficients for different rope materials based on published product information and research papers. We then expand a quasi-static mooring model to include dynamic mooring line stiffness terms in a way that allows the nonlinear stiffness behavior of fiber ropes to be considered even in quasi-static analyses. For dynamic analysis, we have updated the model MoorDyn, coupled with OpenFAST, to work with the new dynamic mooring line stiffness terms. This includes the implementation of a new viscoelastic approach that allows the tension-strain relation of each mooring line segment to vary between two stiffness values, depending on the strain rate. After presenting the formulation of the approaches for modeling synthetic ropes, they are demonstrated on a floating wind turbine mooring system with taut polyester rope mooring lines. The results are compared with those of other approaches of similar fidelity, including the static-dynamic method and separate simulations with static and dynamic stiffness values. Comparing the results shows the ability of the new method to match the results of the previous methods in a more streamlined manner.

elasticity↗

Streamlined Loads Analysis of Floating Wind Turbines With Fiber Rope Mooring Lines: Preprint

This paper presents an approach for more accurate yet relatively streamlined accounting for the nonlinear characteristics of synthetic fiber rope mooring lines for floating wind turbines. First, we select a minimal set of parameters that can efficiently approximate a mooring line material's quasi-static and dynamic stiffness characteristics. We also develop a set of baseline coefficients for different rope materials based on published product information and research papers. We then expand a quasi-static mooring model to include dynamic mooring line stiffness terms in a way that allows the nonlinear stiffness behavior of fiber ropes to be considered even in quasi-static analyses. For dynamic analysis, we have updated the model MoorDyn, coupled with OpenFAST, to work with the new dynamic mooring line stiffness terms. This includes the implementation of a new viscoelastic approach that allows the tension-strain relation of each mooring line segment to vary between two stiffness values depending on the strain rate. After presenting the formulation of the approaches for modeling synthetic ropes, they are demonstrated on a floating wind turbine mooring system with taut polyester rope mooring lines. The results are compared with those of other approaches of similar fidelity including the static-dynamic method and separate simulations with static and dynamic stiffness values. Comparing the results shows the ability of the new method to match the results of the previous methods in a more streamlined manner.

elasticity↗

Exact enforcement of temporal continuity in sequential physics-informed neural networks

The use of deep learning methods in scientific computing represents a potential paradigm shift in engineering problem solving. One of the most prominent developments is Physics-Informed Neural Networks (PINNs), in which neural networks are trained to satisfy partial differential equations (PDEs). While this method shows promise, the standard version has been shown to struggle in accurately predicting the dynamic behavior of time-dependent problems. To address this challenge, methods have been proposed that decompose the time domain into multiple segments, employing a distinct neural network in each segment and directly incorporating continuity between them in the loss function of the minimization problem. In this work we introduce a method to exactly enforce continuity between successive time segments via a solution ansatz. This hard constrained sequential PINN (HCS-PINN) method is simple to implement and eliminates the need for any loss terms associated with temporal continuity. The method is tested for a number of benchmark problems involving both linear and non-linear PDEs. Examples include various first order time dependent problems in which traditional PINNs struggle, namely advection, Allen–Cahn, and Korteweg–de Vries equations. Furthermore, second and third order time-dependent problems are demonstrated via wave and Jerky dynamics examples, respectively. Notably, the Jerky dynamics problem is chaotic, making the problem especially sensitive to temporal accuracy. Finally, the numerical experiments conducted with the proposed method demonstrated superior convergence and accuracy over both traditional PINNs and the soft-constrained counterparts.

42 ENGINEERING↗

Structure-property relationship between lignin structures and properties of 3D-printed lignin composites

Lignin is a low-cost and renewable bioresource with a huge annual production promising to prepare sustainable materials. However, the poor interfacial adhesion between many lignin-polymer pairs deteriorates the mechanical performance of the composites, which seriously limits the application of lignin in 3D printing via fused depositional modeling. This work examined lignin-polyamide 12 (PA 12) intermolecular interactions (e.g., hydrogen bonding) to address the interface challenge. To realize this goal, the phenolic hydroxyl content was increased for a kraft softwood lignin using a LiBr/HBr demethylation procedure, increasing phenoxy content by 61.7%. Increased hydrogen bonding interactions between modified lignin (Pine-Lig-OH) and PA 12 demonstrated a significantly improved molten dynamic modulus by rheological analysis. Regarding mechanical properties, by adding 20 wt% of Pine-Lig-OH, the tensile strength and Young's modulus reached 46.6 MPa and 1.62 GPa, 30.2% and 33.9% higher than PA 12, respectively. Further morphological analysis proved the interfacial interactions are enhanced by showing the difference in the phase gaps. The dynamic mechanical analysis (DMA) supported the conclusion that Pine-Lig-OH could interact with polymer chains, alternating segmental movements due to the strong interaction. Here, this study presents a method to enhance lignin composite properties by promoting interactions with the polymer matrix through modified functional groups, guiding future lignin composite research.

36 MATERIALS SCIENCE↗

Automated bubble analysis of high-speed subcooled flow boiling images using U-net transfer learning and global optical flow

Capturing and analyzing the bubble dynamics is crucial to improving the understanding of boiling heat transfer mechanisms and predicting boiling heat transfer coefficient and boiling crisis. High speed video (HSV) imaging has been used for decades towards this end. Still, there is no universal approach to quantitatively analyze bubble dynamics from HSV images. In this study, we propose a data-driven post-processing approach to segment, track, and identify wall-attached vapor bubbles from HSV images of the boiling process in subcooled flow conditions. Firstly, we employ a transfer learning framework with a U-Net-based convolution neural network (CNN) architecture to detect and segment bubbles in HSV images of diverse contrast and surface texture using very little data (e.g., 10 images) for training. Then, we evaluate the trained CNN model with 100 ground-truth images, and the validation results show that the model accuracy and precision in detecting the optical footprint of bubbles are higher than 90%. Finally, we suggest a criterion to identify a condensing bubble based on the divergence of the bubble displacement, which is calculated from sequential segmented bubble images using a global optical flow code. Using this combination of machine learning and optical flow, we can identify nucleation sites and track the growth of bubbles nucleating at each site to quantify nucleation site density, nucleation frequency, and other fundamental boiling parameters. The proposed system is validated using results obtained on a special heater, which enables both infrared (IR) thermometry and HSV imaging on a metallic surface. We compare the fundamental boiling parameters obtained by the two different diagnostics. The results show good agreement. In conclusion, the difference between the measurements of nucleation site density, averaged nucleation frequency, and averaged growth time performed with the two techniques is always within ± 20% and mostly ± 10% of the values measured with IR thermometry.

42 ENGINEERING↗

Molecular mechanism of secreted amyloid-β precursor protein in binding and modulating GABABR1a

A recent phenomenal study discovered that the extension domain of secreted amyloid-β precursor protein (sAPP) can bind to the intrinsically disordered sushi 1 domain of the γ-aminobutyric acid type B receptor subunit 1a (GABA B R1a) and modulate its synaptic transmission. The work provided an important structural foundation for the modulation of GABA B R1a; however, the detailed molecular interaction mechanism, crucial for future drug design, remains elusive. Here, we further investigated the dynamical interactions between sAPP peptides and the natively unstructured sushi 1 domain using all-atom molecular dynamics simulations, for both the 17-residue sAPP peptide (APP 17-mer) and its minimally active 9 residue segment (APP 9-mer). We then explored mutations of the APP 9-mer with rigorous free energy perturbation (FEP) calculations. Our in silico mutagenesis studies revealed key residues (D4, W6, and W7) responsible for the binding with the sushi 1 domain. More importantly, one double mutation based on different vertebrate APP sequences from evolution exhibited a stronger binding (ΔΔG = -1.91 ± 0.66 kcal mol -1 ), indicating a potentially enhanced GABA B R1a modulator. These large-scale simulations may provide new insights into the binding mechanism between sAPP and the sushi 1 domain, which could open new avenues in the development of future GABA B R1a-specific therapeutics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Anomalous Retrograde Drifts in Obstructed Magnetron Microdischarges: a Consequence of a Field Reversal in the Anode Sheath?

The goal of this project was to carry out experiments at the Plasma Collaborative Research Facility (Princeton Plasma Physics Laboratory) aimed at confirming or refuting the hypothesis that an electric field reversal occurs in the near-anode region of a strongly obstructed planar magnetron microdischarges. Magnetron discharges are magnetized plasmas with E x B field topologies, and variants of such discharges are widely used in materials processing. The topologies are also similar to that of Hall thrusters used in space propulsion. Understanding the structure of these discharges will aid in developing reliable simulations that are intended to facilitate the further development of such technologies, as the field reversals, presumed to be due to strong axial-driven electron transport, provides further insight into transport properties. The possible existence of such a field reversal is hinted at because of the retrograde-propagating (i.e., negative E x B) spokes or gradient-driven drift instabilities seen in the high speed videos and segmented anode probing of the plasma. The presence of this field reversal should be reflected in the ion dynamics, particularly, in an ion drift towards the anode. The proposed experiments to be conducted at the PCRF are to characterize this anode-directed ion drift using state-of-the-art laser-induced fluorescence velocimetry. In particular, we seek to see if the near-anode ion velocity reverses direction when the external circuit is varied to alter the electron current demand imposed at the anode. Such an ion velocity reversal would confirm the mechanism, which is that the highly obstructed (small gapped) discharge produces strong axial gradients in plasma density, driving more electrons towards the anode then that demanded by the external circuit.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Activated relaxation in supercooled monodisperse atomic and polymeric WCA fluids: Simulation and ECNLE theory

Here, we combine simulation and Elastically Collective Nonlinear Langevin Equation (ECNLE) theory to study the activated relaxation in monodisperse atomic and polymeric Weeks–Chandler–Andersen (WCA) liquids over a wide range of temperatures and densities in the supercooled regime under isochoric conditions. By employing novel crystal-avoiding simulations, metastable equilibrium dynamics is probed in the absence of complications associated with size polydispersity. Based on a highly accurate structural input from integral equation theory, ECNLE theory is found to describe well the simulated density and temperature dependences of the alpha relaxation time of atomic fluids using a single system-specific parameter, a c , that reflects the nonuniversal relative importance of local cage and collective elastic barriers. For polymer fluids, the explicit dynamical effect of local chain connectivity is modeled at the fundamental dynamic free energy trajectory level based on a different parameter, N c , that quantifies the degree of intramolecular correlation of bonded segment activated barrier hopping. For the flexible chain model studied, a physically intuitive value of N c ≈ 2 results in good agreement between simulation and theory. A direct comparison between atomic and polymeric systems reveals that chain connectivity can speed up activated segmental relaxation due to weakening of equilibrium packing correlations but can slow down relaxation due to local bonding constraints. The empirical thermodynamic scaling idea for the alpha time is found to work well at high densities or temperatures but fails when both density and temperature are low. The rich and subtle behaviors revealed from simulation for atomic and polymeric WCA fluids are all well captured by ECNLE theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Subject-specific modeling framework for particle deposition using computational fluid dynamics

Quantifying particle deposition and dose in the respiratory tract requires a physiologically realistic representation and reproducible computational workflows. However, existing modeling frameworks, such as the International Commission on Radiological Protection (ICRP) compartmental models and the Multiple Path Particle Dosimetry (MPPD) tool, lack detailed deposition profiles and subject-specific capabilities. The combination of advances in computer vision algorithms applied to the respiratory tract and Computational Fluid and Particle Dynamics (CFPD) allows high-fidelity simulations of particle behavior in anatomically accurate geometries derived from individual CT scans. The segmentation, preprocessing, and file preparation task for a CFPD simulation was often time-consuming, and no prior studies to-date have yet presented a fully automated framework. This work presents a fully automated workflow to obtain individualized particle deposition profiles in the human respiratory tract. The pipeline starts with segmenting upper and lower airway geometries using morphological and deep learning-based methods, generating three-dimensional (3D) models from CT imaging data. Next, a series of algorithms are presented to quality check and prepare the 3D geometry for a CFD or CFPD simulation. The preprocessing step includes correcting geometric artifacts, enforcing a physically consistent mesh, and automatically identifying and capping multiple outlets, which is required for CFD/CFPD simulations. These processed models are then input into open-source (OpenFOAM) or commercial (StarCCM+) CFD solvers, where flow and transient particle transport equations — including turbulence and particle–wall interactions are solved under realistic breathing conditions. Finally, the resulting particle deposition profiles can be integrated with Monte Carlo radiation transport codes and state-of-the-art computational phantoms to assess organ-specific absorbed doses in scenarios of radioactive aerosol inhalation. The presented work streamlines respiratory tract segmentation, preprocessing for CFD/CFPD simulations, and integration with dose assessment workflows, reducing manual intervention and improving access to high-fidelity, subject-specific modeling. The high precision in predicted particle deposition and dose distributions can improve personalized treatment strategies in respiratory medicine and refine dose estimates for radiation protection.

AI↗

Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics

Lipid bilayers form the main matrix of functional cell membranes, and their dynamics underlie a host of physical and biological processes. Here we show that elastic membrane properties and collective molecular dynamics (MD) are related by the mean-square amplitudes (order parameters) and relaxation rates (correlation times) of lipid acyl chain motions. We performed all-atom MD simulations of liquid-crystalline bilayers that allow direct comparison with carbon-hydrogen (CH) bond relaxations measured with NMR spectroscopy. Previous computational and theoretical approaches have assumed isotropic relaxation, which yields inaccurate description of lipid chain dynamics and incorrect data interpretation. Instead, the new framework includes a fixed bilayer normal (director axis) and restricted anisotropic motion of the CH bonds in accord with their segmental order parameters, enabling robust validation of lipid force fields. Simulated spectral densities of thermally excited CH bond fluctuations exhibited well-defined spin-lattice (Zeeman) relaxations analogous to those in NMR measurements. Their frequency signature could be fit to a simple power-law function, indicative of nematic-like collective dynamics. Moreover, calculated relaxation rates scaled as the squared order parameters yielding an apparent K C modulus for bilayer bending. Our results show a strong correlation with K C values obtained from solid-state NMR studies of bilayers without and with cholesterol as validated by neutron spin-echo measurements of membrane elasticity. The simulations uncover a critical role of interleaflet coupling in membrane mechanics and thus provide important insights into molecular sites of emerging elastic properties within lipid bilayers.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling and Control Using Stochastic Distribution Control Theory for Intersection Traffic Flow

In this work, we investigated stochastic distribution control theory-based traffic signal optimization to achieve a smooth and uniform flow of vehicles through signalized intersections. In this context, the static and linear dynamic stochastic distribution models were developed to express the relationship between the signal timing and the traffic queue length together with its probability density function. Two stochastic distribution control algorithms were designed to control the signal timing at intersections such that the probability density function of the traffic queue of each intersection road segment is made as narrow and as small as possible. Also, a recursive input-output traffic queue estimation model was proposed, which is data-driven and dynamic in nature, to calculate real-time traffic queue length using traffic signal timings and loop-detector data. The control algorithms were evaluated for a one-signal corridor, two-signal corridor, and 2 x 2 network of signalized intersections. MATLAB simulation examples are provided to demonstrate the use of the proposed algorithms and comparison to the existing widely-used semi-actuated control has been made. Desired results were obtained.

97 MATHEMATICS AND COMPUTING↗

Relaxation Dynamics and Ion Conduction of Poly(Ethylene Carbonate/Ethylene Oxide) Copolymer-Based Electrolytes

Poly(ethylene carbonate/ethylene oxide) P(EC/EO) copolymer was synthesized from EC monomer as a new matrix component of solid polymer electrolytes (SPEs), and the correlation between polymer dynamics and ionic conductivity in the P(EC/EO)-based SPEs at various lithium salt weight fractions (w Li ) was investigated by dielectric spectroscopy, rheology, and molecular dynamics (MD) simulations. With the addition of lithium salt, the molecular motions at various scales (i.e., from local to segmental and global motion scales) were found to change as follows: (i) the local motion of P(EC/EO) was slightly accelerated, and at w Li ≥ 0.22, it was separated into two relaxation modes, one faster and the other slower than that of P(EC/EO), (ii) the segmental motion of P(EC/EO) became significantly slower with the addition of lithium salt, and (iii) the global terminal relaxation became slightly slower with the increase of w Li . Thus, the motion of P(EC/EO) at various scales in SPEs changed with different trends with increasing lithium salt. It was also found that the temperature dependence of the ionic conductivity was described by a Vogel–Fulcher–Tammann-type function, which was correlated with the segmental motion, as is known in other SPE systems. Furthermore, from MD simulations, lithium ions are coordinated with the EC units more likely and with a closer distance than EO units in P(EC/EO), and the coordination number of oxygens around one lithium ion was estimated as 6–7 at the distance of 0.30 nm. Here, these results suggest that the coordination structure of the oxygens around the lithium ion is slightly disrupted due to the presence of EC units compared to the chelating structure of pure PEO electrolytes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Stochastic Kinetics of Nanocatalytic Systems

Catalytic reaction events occurring on the surface of a nanoparticle constitute a complex stochastic process. Although advances in modern single-molecule experiments enable direct measurements of individual catalytic turnover events occurring on a segment of a single nanoparticle, we do not yet know how to measure the number of catalytic sites in each segment or how the catalytic turnover counting statistics and the catalytic turnover time distribution are related to the microscopic dynamics of catalytic reactions. Here, we address these issues by presenting a stochastic kinetics for nanoparticle catalytic systems. We propose a new experimental measure of the number of catalytic sites in terms of the mean and variance of the catalytic event count. By considering three types of nanocatalytic systems, we investigate how the mean, the variance, and the distribution of the catalytic turnover time depend on the catalytic reaction dynamics, the heterogeneity of catalytic activity, and communication among catalytic sites. This work enables accurate quantitative analyses of single-molecule experiments for nanocatalytic systems and enzymes with multiple catalytic sites.

Statistical Physics↗

Chain Flexibility and Structure of a Polyimide Copolymer: Revisiting the Freely Rotating Chain Model

Poly(4–4′-oxydiphenylene-pyromellitimide)-based polyimides─trade name Kapton─have wide-ranging engineering applications owing to their thermal and mechanical stability, but little is known about underlying chain-level characteristics. While theoretical models have conceptualized Kapton as inflexible polycyclic rods separated by freely rotating diphenyl ether hinge groups, the model’s core predictions remain untested and subtleties of the relaxation behavior are missed, which atomistic modeling can resolve. To these ends, we examine all-atom Kapton structures in crystalline and glassy amorphous configurations using a DFT-validated class II force field. Constructing amorphous configurations is challenging, as the fused-ring-containing backbone has slow relaxation dynamics and scaling suggestive of entanglements even in oligomers. In conclusion, we find larger backbone rearrangements of the linear polycyclic segments about ether groups that are consistent with the rod-hinge picture on the monomer scale, whereas a ring rotation analysis suggests partially flexible rod-like segments and involves multiple facile rotational relaxation modes.

Liesen, Nicholas T. [Lawrence Livermore National L↗

RhizoNet segments plant roots to assess biomass and growth for enabling self-driving labs

Abstract Flatbed scanners are commonly used for root analysis, but typical manual segmentation methods are time-consuming and prone to errors, especially in large-scale, multi-plant studies. Furthermore, the complex nature of root structures combined with noisy backgrounds in images complicates automated analysis. Addressing these challenges, this article introduces RhizoNet, a deep learning-based workflow to semantically segment plant root scans. Utilizing a sophisticated Residual U-Net architecture, RhizoNet enhances prediction accuracy and employs a convex hull operation for delineation of the primary root component. Its main objective is to accurately segment root biomass and monitor its growth over time. RhizoNet processes color scans of plants grown in a hydroponic system known as EcoFAB, subjected to specific nutritional treatments. The root detection model using RhizoNet demonstrates strong generalization in the validation tests of all experiments despite variable treatments. The main contributions are the standardization of root segmentation and phenotyping, systematic and accelerated analysis of thousands of images, significantly aiding in the precise assessment of root growth dynamics under varying plant conditions, and offering a path toward self-driving labs.

59 BASIC BIOLOGICAL SCIENCES↗