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A finite micro-rotation material point method for micropolar solid and fluid dynamics with three-dimensional evolving contacts and free surfaces
This paper introduces an explicit material point method designed specifically for simulating the micropolar continuum dynamics in the finite deformation and finite microrotation regime. The material point method enables us to simulate large deformation problems while circumventing the potential mesh distortion without remeshing. To eliminate rotational motion damping and loss of angular momentum during the projection, we introduce the mapping for microinertia and angular momentum between particles and grids through the affine particle-in-cell approach. The microrotation and the curvature at each particle are updated through zero-order forward integration of the microgyration and its spatial gradient. We show that the microinertia and the angular momentum are conserved during the projections between particles and grids in our formulation. We verify the formulation and implementation by comparing with the analytical dispersion relation of micropolar waves under the small strain and small microrotation, as well as the analytical soliton solution for solids undergoing large deformation and large microrotation. Additionally we also demonstrate the capacity of the proposed computational framework to handle a wide spectrum of simulations that exhibit size effects in the geometrical nonlinear regime through three representative numerical examples, i.e., a cantilever beam torsion problem, a fragment-impact penetration problem, and a micropolar fluid discharging problem.
Superhydrophilicity of $α$-alumina surfaces results from tight binding of interfacial waters to specific aluminols
Understanding the microscopic driving force of water wetting is challenging and important for design of materials. The relations between structure, dynamics and hydrogen bonds of interfacial water can be investigated using molecular dynamics simulations. Here, contact angles at the alumina (0001) and ($11\bar{2}0$) surfaces are studied using both classical molecular dynamics simulations and experiments. To test the superhydrophilicity, the free energy cost of removing waters near the interfaces are calculated using the density fluctuations method. The strength of hydrogen bonds is determined by their lifetime and geometry. Both surfaces are superhydrophilic and the (0001) surface is more hydrophilic. Interactions between surfaces and interfacial waters promote a templating effect whereby the latter are aligned in a pattern that follows the underlying lattice of the surfaces. Translational and rotational dynamics of interfacial water molecules are slower than in bulk water. Hydrogen bonds between water and both surfaces are asymmetric, water-to-aluminol ones are stronger than aluminol-to-water ones. Molecular dynamics simulations eliminate the impacts of surface contamination when measuring contact angles and the results reveal the microscopic origin of the macroscopic superhydrophilicity of alumina surfaces: strong water-to-aluminol hydrogen bonds.
New Approach Methodology for Assessing Inhalation Risks of a Contact Respiratory Cytotoxicant: Computational Fluid Dynamics-Based Aerosol Dosimetry Modeling for Cross-Species and In Vitro Comparisons
Regulatory agencies are considering alternative approaches to assessing inhalation toxicity that utilizes in vitro studies with human cells and in silico modeling in lieu of additional animal studies. In support of this goal, computational fluid-particle dynamics models were developed to estimate site-specific deposition of inhaled aerosols containing the fungicide, chlorothalonil, in the rat and human for comparisons to prior rat inhalation studies and new human in vitro studies. Under bioassay conditions, the deposition was predicted to be greatest at the front of the rat nose followed by the anterior transitional epithelium and larynx corresponding to regions most sensitive to local contact irritation and cytotoxicity. For humans, simulations of aerosol deposition covering potential occupational or residential exposures (1–50 µm diameter) were conducted using nasal and oral breathing. Aerosols in the 1–5 µm range readily penetrated the deep region of the human lung following both oral and nasal breathing. Under actual use conditions (aerosol formulations >10 µm), the majority of deposited doses were in the upper conducting airways. Beyond the nose or mouth, the greatest deposition in the pharynx, larynx, trachea, and bronchi was predicted for aerosols in the 10–20 µm size range. Only small amounts of aerosols >20 µm penetrated past the pharyngeal region. Using the ICRP clearance model, local retained tissue dose metrics including maximal concentrations and areas under the curve were calculated for each airway region following repeated occupational exposures. These results are directly comparable with benchmark doses from in vitro toxicity studies in human cells leading to estimated human equivalent concentrations that reduce the reliance on animals for risk assessments.
Measuring Transverse Displacements Using Unmanned Aerial Systems Laser Doppler Vibrometer (UAS-LDV): Development and Field Validation
Measurement of bridge displacements is important for ensuring the safe operation of railway bridges. Traditionally, contact sensors such as Linear Variable Displacement Transducers (LVDT) and accelerometers have been used to measure the displacement of the railway bridges. However, these sensors need significant effort in installation and maintenance. Therefore, railroad management agencies are interested in new means to measure bridge displacements. This research focuses on mounting Laser Doppler Vibrometer (LDV) on an Unmanned Aerial System (UAS) to enable contact-free transverse dynamic displacement of railroad bridges. Researchers conducted three field tests by flying the Unmanned Aerial Systems Laser Doppler Vibrometer (UAS-LDV) 1.5 m away from the ground and measured the displacement of a moving target at various distances. The accuracy of the UAS-LDV measurements was compared to the Linear Variable Differential Transducer (LVDT) measurements. The results of the three field tests showed that the proposed system could measure non-contact, reference-free dynamic displacement with an average peak and root mean square (RMS) error for the three experiments of 10% and 8% compared to LVDT, respectively. Such errors are acceptable for field measurements in railroads, as the interest prior to bridge monitoring implementation of a new approach is to demonstrate similar success for different flights, as reported in the three results. This study also identified barriers for industrial adoption of this technology and proposed operational development practices for both technical and cost-effective implementation.
Molecular dynamics simulation study on the interfacial contact behavior between single-walled carbon nanotubes and nanowires
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Visualizing energy transfer between redox-active colloids
Redox-active colloids (RACs) represent a novel class of energy carriers that exchange electrical energy upon contact. Understanding contact-mediated electron transfer dynamics in RACs offers insights into physical contact events in colloidal suspensions and enables quantification of electrical energy transport in nonconjugated polymers. Redox-based electron transport was directly observed in monolayers of micron-sized RACs containing ethyl-viologen side groups via fluorescence microscopy through an unexpected nonlinear electrofluorochromism that is quantitatively coupled to the redox state of the colloid. Via imaging studies, using this electrofluorochromism, the apparent charge transfer diffusion coefficient D CT of the RAC was easily determined. The visualization of energy transport within suspensions of redox-active colloids was also demonstrated. Our work elucidates fundamental mechanisms of energy transport in colloidal systems, informs the development of next-generation redox flow batteries, and may inspire new designs of smart active soft matter including conductive polymers for applications ranging from electrochemical sensors and organic electronics to colloidal robotics.
Effect of interfacial vibrational coupling on surface wettability and water transport
Here, we report that the atomic-scale vibrational coupling at the solid-fluid interface can substantially alter the interfacial properties such as wettability and fluid slip. The wettability of water droplets on substrates subjected to various vibrational frequencies is studied using molecular dynamics simulation. The contact angle increases (i.e., becomes more hydrophobic) when the oscillation frequency of the substrate matches the intermolecular bending frequency of liquid water. We investigate the underlying mechanism by examining the dynamics of water molecules at the interface and find that the temporal contact between the solid and fluid is shorter when the frequencies match, resulting in weak solid-fluid adsorption. We further report that the vibrational match at the interface reduces wall-fluid friction and enhances water transport through the nanopore. Our findings demonstrate the importance of the atomic-scale vibrational coupling at the solid-fluid interface on the physicochemical behavior of nanodevices and biological nanochannels.
Full-field imaging learning machine (FILM)
A method of determining dynamic properties of a structure (linear or nonlinear) includes receiving spatio-temporal inputs, generating mode shapes and modal components corresponding to the spatio-temporal inputs using a trained deep complexity coding artificial neural network, and subsequently generating the dynamic properties by analyzing each modal component using a trained learning machine. A computing system for non-contact determination of dynamic properties of a structure includes a camera, a processor, and a memory including computer-executable instructions. When the instructions are executed, the system is caused to receive spatio-temporal image data, decompose the spatio-temporal image data into constituent manifold components using an autoencoder, and analyze the constituent manifold components using a trained learning machine to determine the dynamic properties.
Formation of transfermium elements in reactions with Pb 208
Within the Langevin framework, we investigate the dynamics of the fusion process for production of transfermium elements in reactions of Ca 48 , Ti 50 , Cr 54 , and Fe 58 with Pb 208 . After the reacting nuclei have made contact, the early dynamical stage is dominated by the dissipation of the initial radial kinetic energy, while the subsequent shape evolution is diffusive. The probability for surmounting the inner barrier and forming a compound system is obtained by simulating the evolution as a Metropolis random walk in a five-dimensional potential-energy landscape. Good agreement with the available data is obtained, especially for the maximal formation probability. Published by the American Physical Society 2024
Onset dynamics of air-water menisci on rock fracture surfaces
Information on menisci dynamics and equilibrium contact angles, θ e , is needed for modeling multiphase flow of fluids in geologic formations. The wettability of fracture faces is relevant to applications such as waterflooding in enhanced oil recovery and evaluation of caprock integrity for geologic carbon sequestration. We investigated the vertical capillary rise of air-water menisci on exposed fracture faces for a sandstone, a shale, and three granites. The experimental design approximated that employed in the Wilhelmy plate method. Replicate fracture faces were prepared by fracturing cylindrical rock cores using the Brazilian method and splitting the fractured cores apart along their fracture planes. Meniscus onset was imaged from a cross-sectional perspective using dynamic neutron radiography, and quantified with change point analysis. An existing model for meniscus onset fitted the experimental data very well (median R 2 = 0.96). Capillary rise was typified by t 2/3 scaling (where t is time), followed by a constant equilibrium height, z e . The average time taken for the menisci to reach z e was 0.39 s, with no differences between rock types. The menisci achieved a greater vertical extent on the fracture faces of the sedimentary rocks as compared to those of the granites. Apparent θ e values were calculated from the best fit estimates of z e using the Wilhelmy plate equation for a smooth and planar vertical surface. Despite the fractal roughness of some of the fracture faces, there was a significant linear relationship (R 2 = 0.80) between the apparent θ e values and intrinsic θ e values measured on polished surfaces of the same rocks using the sessile drop method. The regression equation indicated the apparent θ e values were consistently greater than the intrinsic values. This overestimation may be due to averaging of pixels at the air-water-solid interface, a required step in the image analysis. Further exploration of the range of applicability and measurement accuracy of this proposed new technique would be valuable.
Implementing contact angle boundary conditions for second-order Phase-Field models of wall-bounded multiphase flows
In the present work, a general formulation is proposed to implement the contact angle boundary conditions for the second-order Phase-Field models, which is applicable to N-phase (N ≥ 2) moving contact line problems. To remedy the issue of mass change due to the contact angle boundary condition, a source term or Lagrange multiplier is added to the original second-order Phase-Field models, which is determined by the consistent and conservative volume distribution algorithm so that the summation of the order parameters and the consistency of reduction are not influenced. To physically couple the proposed formulation to the hydrodynamics, especially for large-density-ratio problems, the consistent formulation is employed. The reduction-consistent conservative Allen-Cahn models are chosen as examples to illustrate the application of the proposed formulation. The numerical scheme that preserves the consistency and conservation of the proposed formulation is employed to demonstrate its effectiveness. Results produced by the proposed formulation are in good agreement with the exact and/or asymptotic solutions. The proposed method captures complex dynamics of moving contact line problems having large density ratios.
Systems dynamics and the uncertainties of diagnostics, testing and contact tracing for COVID-19
Not Available
Conductive Thin Films over Large Areas by Supramolecular Self-Assembly
We report a “one-step” method for preparing conductive thin films with cylindrical microdomains oriented normal to the surface over large areas using the supramolecular assembly of poly(styrene-block-4-vinylpyridine) (PS19-b-P4VP 5 ) and 5,10,15,20-tetrakis(4-hydroxyphenyl)-21H,23H-porphine (HOTPP). HOTPP interacts with the P4VP block by hydrogen bonding between the hydroxyl group of HOTPP and pyridine ring of PS 19 -b-P4VP 5 , forming cylindrical P4VP(HOTPP) domains having an average diameter of ~17 nm in a PS matrix. Here, dynamic light scattering, contact angle, and in situ grazing incidence small-angle X-ray scattering measurements show a morphological transition from spherical micelles in solution to cylindrical microdomains oriented normal to the substrate surface during the drying process. From the dependence of current on voltage, an average current of ~4.0 nA is found to pass through a single microdomain, pointing to a promising route for organic semiconductor device applications.
ENIGMA: Ecosystems and Networks Integrated with Genes and Molecular Assemblies. Final Report
ENIGMA research is performed at a very large scale involving collaborations between multiple research groups to address two major driving concepts: For any microbe, it is possible to discover efficiently the genetic determinants of adaptation to life in dynamic environments in contact with other living members of its ecology and reveal hidden functional phenomena that are only possible by using a systems biology approach; and for any environment, it is possible to predict the temporal changes in geochemistry and accompanying system behavior, for some length of time, given biogeochemical and physical inputs. These driving concepts also map directly to grand challenges the ENIGMA team has outlined: “Define the levels of biological organization most relevant to scaling from single cells to ecosystems and global cycles; capture how that organization varies in time and space; and identify critical interactions that dictate rates of carbon, nutrient, and energy transformation in different environments.”
Contact patterns in wild pigs ( Sus scrofa ) from GPS tracking reveal spatial and temporal dynamics of social behaviour
Wild pig ( Sus scrofa Linnaeus, 1758) social behaviour affects disease transmission and landscape-level population management. Recent research has incorporated analysis of social structure to better understand the risk of disease transmission in wild pigs, although the relationship between overall social structure of wild pigs remains unclear. Here, we seek to improve understanding of the spatial and temporal dynamics of wild pig social structure and contact rates to better inform management strategies. Using GPS tracking data, we measured home range overlap, and estimated contact rates of wild pigs at four study sites in the southern USA to identify pairwise social associations (i.e., contacts) based on synchronous movement. Contact rate was strongly associated with home range overlap, but exhibited substantial variation, especially at moderate levels of home range overlap. We found that female–female dyads had higher contact rates and longer duration phases of social association compared to female–male and male–male dyads. We found male–male dyads tended to experience social associations farther from their home range centers than female–female or female–male dyads. Social associations between wild pig dyads are highly dynamic in their spatial and temporal structure. Further, dyads with strong social associations still experience substantial time apart. Our findings highlight the challenges of predicting spatial and social associations in wild pig social pairs due to their dynamic social structure over space and time.
Efficient Scalable Contact Network Generation from Population Data
Modeling the contacts among a population is critical to understanding the dynamics of a disease outbreak. Contact networks, where nodes are individuals and edges are contacts among them, are used to represent these complex individual-level interactions. In this work, we are given the daily activity schedules of an urban population that represent the activity location and time of individuals in a population during a single twenty four hour period over multiple days. Using collocation to determine contact between individuals, our goal is to extract hourly contact networks from large-scale activity data. We improve upon the existing adjacency matrix-based method by implementing our custom sparse matrix multiplication algorithm. Starting with a Python implementation, we achieve a 1600x speed up in the computation with a fast custom designed sparse matrix multiplier algorithm implemented in the C++ language. This work is central to future parallel designs of the problem.
The Energetic Origins of Pi–Pi Contacts in Proteins
Accurate potential energy models of proteins must describe the many different types of noncovalent interactions that contribute to a protein’s stability and structure. Pi–pi contacts are ubiquitous structural motifs in all proteins, occurring between aromatic and nonaromatic residues and play a nontrivial role in protein folding and in the formation of biomolecular condensates. Guided by a geometric criterion for isolating pi–pi contacts from classical molecular dynamics simulations of proteins, we use quantum mechanical energy decomposition analysis to determine the molecular interactions that stabilize different pi–pi contact motifs. We find that neutral pi–pi interactions in proteins are dominated by Pauli repulsion and London dispersion rather than repulsive quadrupole electrostatics, which is central to the textbook Hunter–Sanders model. This results in a notable lack of variability in the interaction profiles of neutral pi–pi contacts even with extreme changes in the dielectric medium, explaining the prevalence of pi-stacked arrangements in and between proteins. We also find interactions involving pi-containing anions and cations to be extremely malleable, interacting like neutral pi–pi contacts in polar media and like typical ion–pi interactions in nonpolar environments. Like-charged pairs such as arginine–arginine contacts are particularly sensitive to the polarity of their immediate surroundings and exhibit canonical pi–pi stacking behavior only if the interaction is mediated by environmental effects, such as aqueous solvation.