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At least 919 records · Page 51

Onset of cavitation and vapor bubble development over hydrophilic and hydrophobic surfaces

Cavitation, the formation of vapor bubbles as the liquid pressure is reduced below the saturated vapor pressure, often requires a substantial negative relative pressure in a pure liquid. Classical nucleation theory (CNT) provides an estimate for the rate of cavitation but there is often a disconnect between the predictions at the molecular scale compared to observations at the macroscale. We report on mesoscale simulations of cavitation based on many-body dissipative particle dynamics (mDPD), a coarse-grained molecular dynamics (MD), which bridges the two scales. A liquid layer is confined between smooth planar walls at a constant temperature, while the pressure is reduced slowly by expanding the wall-bounded domain. The wetting properties of the liquid are determined by the parameters of the interaction potentials. With hydrophilic walls, homogeneous nucleation is observed in the liquid bulk. As a bubble forms and grows, it creates a strong pressure pulse and oscillations that cause other bubbles that may have formed slightly later to collapse. For a nearly neutral wall with a contact angle close to 90 ° , heterogeneous nucleation occurs at the walls at a smaller negative pressure and generates weaker pressure oscillations. With hydrophobic walls or seed particles, heterogeneous nucleation readily occurs, where fluctuations and the merger of transient surface bubbles are significant.

Science & Technology - Other Topics↗

PARA: A New Platform for the Rapid Assembly of gRNA Arrays for Multiplexed CRISPR Technologies

Multiplexed CRISPR technologies have great potential for pathway engineering and genome editing. However, their applications are constrained by complex, laborious and time-consuming cloning steps. In this research, we developed a novel method, PARA, which allows for the one-step assembly of multiple guide RNAs (gRNAs) into a CRISPR vector with up to 18 gRNAs. Here, we demonstrate that PARA is capable of the efficient assembly of transfer RNA/Csy4/ribozyme-based gRNA arrays. To aid in this process and to streamline vector construction, we developed a user-friendly PARAweb tool for designing PCR primers and component DNA parts and simulating assembled gRNA arrays and vector sequences.

59 BASIC BIOLOGICAL SCIENCES↗

Temperature dependence of nuclear quantum effects on liquid water via artificial neural network model based on SCAN meta-GGA functional

We investigate the temperature dependence of nuclear quantum effects (NQEs) on structural and dynamic properties of liquid water by training a neural network force field using first-principles molecular dynamics (FPMD) based on the strongly constrained and appropriately normed meta-generalized gradient approximation exchange-correlation approximation. The FPMD simulation based on density functional theory has become a powerful computational approach for studying a wide range of condensed phase systems. However, its large computational cost makes it difficult to incorporate NQEs in the simulation and investigate temperature dependence of various properties. To circumvent this difficulty, we use an artificial neural network model and employ the thermostatted ring polymer MD approach for studying the temperature dependence of NQEs on various properties. The NQEs generally bring the radial distribution functions closer to the experimental measurements. Translational diffusivity and rotational dynamics of water molecules are both slowed down by the NQEs. The competing inter-molecular and intra-molecular quantum effects on hydrogen bonds, as discussed by Habershon, Markland, and Manolopoulos [J. Chem. Phys. 131(2), 024501 (2019)], can explain the observed temperature dependence of the NQEs on the dynamical properties in our simulation.

Yao, Yi (ORCID:0000000299576979)↗

Investigation on the AgPt and AgPd hybrid alloy nanoparticles (HANPs) for the hybrid MoS 2 /ZnO/HANP UV photodetector application

We report hybrid photodetectors made of two or more nanomaterial components can offer the high potential for advanced photodetection applications with enhanced light absorption, improved efficiency and structural tunability. A hybrid UV photodetector (PD) configuration incorporating the plasmonic hybrid alloy nanoparticles (HANP), ZnO quantum dots (QDs) and MoS 2 nanoflakes, namely MoS2/ZnO/HANP PD, is demonstrated. The optimized MoS 2 /ZnO/HANP PD exhibits a high photocurrent of 5.66 mA at 0.34 mW/mm 2 under 385 nm illumination with two orders of improvement from the bare ZnO, which is one of the highest photocurrents by the ZnO-based PDs. It also demonstrates high figure-of-merits with the responsivity of 14,523 mA/W, detectivity of 8.13 x 10 11 jones, and external quantum efficiency (EQE) of 4,680 %, outperforming most of the ZnO-based hybrid architectures. The enhanced photoresponse is primarily attributed to the significantly enhanced hot electron generation by the AgPd HANPs and photocarrier collection through the ZnO QD layer. MoS 2 nanoflakes also provide additional photon absorption sites and boost the photo-carrier transfer process. HANPs are grown by adapting a dual-step solid-state dewetting process (SSD) approach and the superiority of AgPd HANPs is confirmed by systematic investigation, FDTD simulation and comparison of AgPt and AgPd HANPs.

MoS2↗

Modeling Dynamic Evolution of Oxygen Vacancies in Solid Oxide Materials

SOEC is a promising H 2 generation technology for mitigating climate change. Novel material design and optimization strategies, such as oxygen vacancy chemistries, can enhance SOEC efficiency. In this study, Monte Carlo-ReaxFF and eReaxFF simulations were used to study oxygen vacancies (O v ) and electron migration in BZY20 solid oxide material. Our results shows that O v migrate towards the surface, increasing surface O v concentration by 10%. Yttrium restricts electron mobility and functions as an electron trapping site, while Zr accelerates electron mobility and migration. These insights could improve solid-state electrolytes’ electrochemical performance in renewable energy applications.

13 HYDRO ENERGY↗

eReaxFF force field development for BaZr 0.8 Y 0.2 O 3-δ solid oxide electrolysis cells applications

The use of solid-oxide materials in electrocatalysis applications, especially in hydrogen-evolution reactions, is promising. However, further improvements are warranted to overcome the fundamental bottlenecks to enhancing the performance of solid-oxide electrolysis cells (SOECs), which is directly linked to the more-refined fundamental understanding of complex physical and chemical phenomena and mass exchanges that take place at the surfaces and in the bulk of electrocatalysis materials. Here, we developed an eReaxFF force field for barium zirconate doped with 20 mol% of yttrium, BaZr 0.8 Y 0.2 O 3-δ (BZY20) to enable a systematic, large-length-scale, and longer-timescale atomistic simulation of solid-oxide electrocatalysis for hydrogen generation. All parameters for the eReaxFF were optimized to reproduce quantum-mechanical (QM) calculations on relevant condensed phase and cluster systems describing oxygen vacancies, vacancy migrations, electron localization, water adsorption, water splitting, and hydrogen generation on the surfaces of the BZY20 solid oxide. Using the developed force field, we performed both zero-voltage (excess electrons absent) and non-zero-voltage (excess electrons present) molecular dynamics simulations to observe water adsorption, water splitting, proton migration, oxygen-vacancy migrations, and eventual hydrogen-production reactions. Based on investigations offered in the present study, we conclude that the eReaxFF force field-based approach can enable computationally efficient simulations for electron conductivity, electron leakage, and other non-zero-voltage effects on the solid oxide materials using the explicit-electron concept. Moreover, we demonstrate how the eReaxFF force field-based atomistic-simulation approach can enhance our understanding of processes in SOEC applications and potentially other renewable-energy applications.

08 HYDROGEN↗

"Oops, It didn't arm." - A Case Study of Two Automation Assisted Altitude Deviations

Altitude deviations are the most common pilot error reported to the Aviation Safety Reporting System. Last year, altitude deviations were reported to the ASRS at the rate of about one per hour. The reporting pilot's narrative is usually our only source of information about what happened in these incidents. In a recent line-oriented, simulator study, twenty-two airline crews flew a realistic, two-hour mission in a DC-9 and an MD-88 aircraft. This paper will describe and analyze two of the five altitude deviations that were observed during this study. The paper focuses on the flight crews' use (or misuse) of the autopilot and autothrottle during these incidents.

Plamer, Everett↗

Computational studies of Ras and PI3K

Until recently, experimental techniques in molecular cell biology have been the primary means to investigate biological risk upon space radiation. However, computational modeling provides an alternative theoretical approach, which utilizes various computational tools to simulate proteins, nucleotides, and their interactions. In this study, we are focused on using molecular mechanics (MM) and molecular dynamics (MD) to study the mechanism of protein-protein binding and to estimate the binding free energy between proteins. Ras is a key element in a variety of cell processes, and its activation of phosphoinositide 3-kinase (PI3K) is important for survival of transformed cells. Different computational approaches for this particular study are presented to calculate the solvation energies and binding free energies of H-Ras and PI3K. The goal of this study is to establish computational methods to investigate the roles of different proteins played in the cellular responses to space radiation, including modification of protein function through gene mutation, and to support the studies in molecular cell biology and theoretical kinetics models for our risk assessment project.

Ren, Lei↗

QMMM 2023: A program for combined quantum mechanical and molecular mechanical modeling and simulations

Combined quantum mechanical and molecular mechanical (QM/MM) methods play an important role in multiscale modeling and simulations. QMMM 2023 is a general-purpose program for single-point calculations, geometry optimizations, transition-state optimizations, and molecular dynamics (MD) at the QM/MM level. It calls a QM package and an MM package to perform the required single-level calculations and combines them into a QM/MM energy by a variety of schemes. QMMM 2023 supports GAMESS-US, Gaussian, and ORCA as QM packages and Tinker as the MM package. Four types of treatments are available for embedding the QM subsystem in the MM environment: mechanical embedding with gas-phase calculations of the QM region, electronic embedding that allows polarization of the QM region by the MM environment, polarizable embedding for mutual polarization of the QM and MM regions, and flexible embedding for both mutual polarization and partial charge transfer between the QM and MM regions. Boundaries between QM and MM regions that pass through covalent bonds can be treated by several methods, including the redistributed charge (RC) scheme, redistributed charge and dipole (RCD) scheme, balanced-RC scheme, balanced-RCD scheme, screened charge scheme that takes account of charge penetration effects, and smeared charge scheme that delocalizes the MM charges near the QM–MM boundary. Geometry optimization can be done using the optimizer implemented in QMMM 2023 or the Berny optimizer in Gaussian through external calls to Gaussian. Molecular dynamics simulations can be performed at the pure-MM level, pure-QM level, fixed-partitioning QM/MM level, and adaptive-partitioning QM/MM level. As a result, the adaptive-partitioning treatments permit on-the-fly relocation of the QM–MM boundary by dynamically reclassifying atoms or groups into the QM or MM subsystems.

97 MATHEMATICS AND COMPUTING↗

An Elevated Reservoir of Air Pollutants over the Mid-Atlantic States During the 2011 DISCOVER-AQ Campaign: Airborne Measurements and Numerical Simulations

During a classic heat wave with record high temperatures and poor air quality from July 18 to 23, 2011, an elevated reservoir of air pollutants was observed over and downwind of Baltimore, MD, with relatively clean conditions near the surface. Aircraft and ozonesonde measurements detected approximately 120 parts per billion by volume ozone at 800 meters altitude, but approximately 80 parts per billion by volume ozone near the surface. High concentrations of other pollutants were also observed around the ozone peak: approximately 300 parts per billion by volume CO at 1200 meters, approximately 2 parts per billion by volume NO2 at 800 meters, approximately 5 parts per billion by volume SO2 at 600 meters, and strong aerosol optical scattering (2 x 10 (sup 4) per meter) at 600 meters. These results suggest that the elevated reservoir is a mixture of automobile exhaust (high concentrations of O3, CO, and NO2) and power plant emissions (high SO2 and aerosols). Back trajectory calculations show a local stagnation event before the formation of this elevated reservoir. Forward trajectories suggest an influence on downwind air quality, supported by surface ozone observations on the next day over the downwind PA, NJ and NY area. Meteorological observations from aircraft and ozonesondes show a dramatic veering of wind direction from south to north within the lowest 5000 meters, implying that the development of the elevated reservoir was caused in part by the Chesapeake Bay breeze. Based on in situ observations, Community Air Quality Multi-scale Model (CMAQ) forecast simulations with 12 kilometers resolution overestimated surface ozone concentrations and failed to predict this elevated reservoir; however, CMAQ research simulations with 4 kilometers and 1.33 kilometers resolution more successfully reproduced this event. These results show that high resolution is essential for resolving coastal effects and predicting air quality for cities near major bodies of water such as Baltimore on the Chesapeake Bay and downwind areas in the Northeast.

ozone↗

Non-equilibrium critical scaling and universality in a quantum simulator

Universality and scaling laws are hallmarks of equilibrium phase transitions and critical phenomena. However, extending these concepts to non-equilibrium systems is an outstanding challenge. Despite recent progress in the study of dynamical phases, the universality classes and scaling laws for non-equilibrium phenomena are far less understood than those in equilibrium. In this work, using a trapped-ion quantum simulator with single-spin resolution, we investigate the non-equilibrium nature of critical fluctuations following a quantum quench to the critical point. We probe the scaling of spin fluctuations after a series of quenches to the critical Hamiltonian of a long-range Ising model. With systems of up to 50 spins, we show that the amplitude and timescale of the post-quench fluctuations scale with system size with distinct universal critical exponents, depending on the quench protocol. While a generic quench can lead to thermal critical behavior, we find that a second quench from one critical state to another (i.e. a double quench) results in a new universal non-equilibrium behavior, identified by a set of critical exponents distinct from their equilibrium counterparts. Our results demonstrate the ability of quantum simulators to explore universal scaling beyond equilibrium.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Geometric Delocalization in Two Dimensions

We demonstrate the existence of transient two-dimensional surfaces where a random-walking particle escapes to infinity in contrast to localization in standard flat two-dimensional space. We first prove that any rotationally symmetric two-dimensional membrane embedded in flat three-dimensional space cannot be transient. Then we formulate a criterion for the transience of a general asymmetric two-dimensional membrane. We use it to explicitly construct a class of transient two-dimensional manifolds with a nontrivial metric and height function but “zero average curvature,” which we dub “tablecloth manifolds.” The absence of the logarithmic infrared divergence of the Laplace-Beltrami operator in turn implies the absence of weak localization, nonexistence of bound states in shallow potentials, and breakdown of the Mermin-Wagner theorem and Kosterlitz-Thouless transition on the tablecloth manifolds, which may be realizable in both quantum simulators and corrugated two-dimensional materials.

Anderson localization↗

Open Circuit Switch Fault Management Method of a Multi-Phase Synchronous Buck Converter for EV Charging Application

Multi-phase synchronous buck converter (MSBC) is becoming popular for the electric vehicle (EV) charging application because of its higher efficiency, smaller passive component sizes, bidirectional power flow, and output current ripple reduction through interleaving. This converter also provides higher reliability than the traditional single phase converter since its modular structure enables fault tolerant operation. Fault management in the converter requires the detection of switch fault, shut down of the faulty phase, and reconfiguration of the PWM signals for the healthy phases to avoid circulating current and high output current ripple. In addition, it is desirable that the fault management method can be implemented using the micro-controller unit (MCU) or digital signal processor (DSP), which are widely used to control power converters. This paper presents a fault management method for detecting switch faults and reconfiguring healthy phases using a DSP. The method is validated through simulations and experiments using a commercial off-the-shelf power stack.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Spatio-Temporal Clustering of Seismicity Enabled by Off-Fault Plasticity

While significant progress has been made in understanding earthquake source processes in linear elastic domains, the effect of more realistic rheologies including plasticity is poorly understood. Here, in this work, we simulate the sequence of earthquake and aseismic slip of a 2D antiplane rate-and-state fault embedded in a full-space elastic-plastic bulk. We show that off-fault plasticity may lead to partial ruptures as well as temporal clustering of seismic events. Furthermore, the interaction of fault slip and off-fault plasticity results in pockets of slip deficit. While the energy dissipated through plastic deformation remains a small fraction of the total energy budget, its impact on the source characteristics is disproportionally large through the redistribution of stresses and viscous relaxation. Our results suggest a new mechanism of dynamic heterogeneity in earthquake physics that may have important implications on earthquake size distribution and energy budget.

58 GEOSCIENCES↗

AgMIP Regional Integrated Assessment of Agricultural Systems in Nioro, Senegal: Representative Agricultural Pathways, Climate, Crop and Economic Datasets

This paper describes the datasets that were used to implement an AgMIP Regional Integrated Assessment for the Nioro region of Senegal to assess the potential impacts of climate change on the principal agricultural system in the Senegal peanut basin and to assess adaptations of that system to climate change under current as well as future climate and socio-economic conditions. This dataset includes the Representative Agricultural Pathways developed for Nioro from 2000-2050; the climate data that were used to implement crop yield simulations; the data that were used to parameterize the DSSAT and APSIM crop models, including historical climate data and future climate scenarios; and the data that were used to parameterize the Tradeoff Analysis Model for Multi-dimensional Impact Assessment (TOAMD) economic simulation model, as well as simulated model outputs.

AgMIP↗