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At least 775 records · Page 43

Defining the Mechanism of Proton Pumping in Heme-Copper Oxidases

During this award, progress was made in two distinct areas of science, one was within the context of bioinorganic chemistry and another in the context of biomimetic, small molecule chemistry. The overarching goals of this work was to understand the fundamental mechanistic drivers for biological reactions specifically, proton transfer reactions. In the biochemical sphere, this goal was investigated through investigation of the bacterial proton pump, ubiquinol oxidase (UbO). Further work in the bioinorganic space was completed in collaboration with the Bandarian group on a novel natural peptide product. While in the biomimetic space, this work was explored through a computational collaborative study with the Riordan group relating to proton coupled electron transfers in iron complexes as relating to the heme active site in proton pumping enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Space Charge Simulations of High Intensity Proton Beams in the AGS Booster

Computer simulation studies have been performed to understand the beam behavior and to explore intensity limitations of proton beams in the AGS Booster at higher beam intensities. During the 100 GeV polarized proton operations of RHIC Run 2024, sPHENIX operated in modes with a crossing angle at collisions in order to mitigate beam-beam effects. Three different running modes were employed: (a) sPHENIX operated with a negative (-2 mrad) crossing angle, and STAR operated with 0 mrad. Both experiments were brought into collisions at the start of the store. (b) sPHENIX was brought into collisions with 0 mrad first. Then STAR was brought into collisions after the beam-beam parameter from sPHENIX reduced to below $10 \times 10^{-3}$. (c) sPHENIX operated with a positive (+1.5 mrad) crossing angle, and STAR operated with 0 mrad. Both experiments were brought into collisions at the start of the store. The collisions with a crossing angle of up to $\pm 2$ mrad, as in running modes (a) and (c), lead to large Piwinski angle in the new sPHENIX detector, which reduces luminosity if other parameters are unchanged. There are two ways to compensate the reduction in luminosity: squeeze $\beta^{*}$ if there is sufficient dynamic aperture, or increase the injected beam intensity. The first part of polarized proton operation during RHIC Run 2024 was dedicated to increasing the intensity. Different configurations were tested with crossing angle and lattice adjustments on RHIC. At the same time, new injector configurations were developed and tested in an effort to push for both higher intensity and better quality of the beam injected into RHIC. When the beam intensity is increased, space charge is a concern particularly in the lower energy stages of acceleration, such as during the injection and the early part of the Booster cycle, which could become a dominant effect in limiting the intensity of the beam that can be delivered to RHIC.

43 PARTICLE ACCELERATORS↗

OC6 Phase Ia: CFD Simulations of the Free-Decay Motion of the DeepCwind Semisubmersible

Currently, the design of floating offshore wind systems is primarily based on mid-fidelity models with empirical drag forces. The tuning of the model coefficients requires data from either experiments or high-fidelity simulations. As part of the OC6 (Offshore Code Comparison Collaboration, Continued, with Correlation, and unCertainty (OC6) is a project under the International Energy Agency Wind Task 30 framework) project, the present investigation explores the latter option. A verification and validation study of computational fluid dynamics (CFD) models of the DeepCwind semisubmersible undergoing free-decay motion is performed. Several institutions provided CFD results for validation against the OC6 experimental campaign. The objective is to evaluate whether the CFD setups of the participants can provide valid estimates of the hydrodynamic damping coefficients needed by mid-fidelity models. The linear and quadratic damping coefficients and the equivalent damping ratio are chosen as metrics for validation. Large numerical uncertainties are estimated for the linear and quadratic damping coefficients; however, the equivalent damping ratios are more consistently predicted with lower uncertainty. Some difference is observed between the experimental and CFD surge-decay motion, which is caused by mechanical damping not considered in the simulations that likely originated from the mooring setup, including a Coulomb-friction-type force. Overall, the simulations and the experiment show reasonable agreement, thus demonstrating the feasibility of using CFD simulations to tune mid-fidelity models.

17 WIND ENERGY↗

Shear Band Formation in Thin-Film Multilayer Columns Under Compressive Loading: A Mechanistic Study

Micro-pillar compression is a popular experimental technique used for characterizing the mechanical behavior of nano- and micro-laminates. The compressive stress–strain response of the column-shaped thin-film composite can be measured, and the deformation and damage features can be revealed by post-test cross-section microscopy. The development of plastic instability in the form of localized strain concentration (shear bands), leading to eventual failure, is frequently observed. In the present study, a computational approach is used to illustrate the commonality of shear band formation from a continuum standpoint. Systematic finite element analyses are conducted, showing that the strain field tends to become localized once plastic yielding commences. Distinct shear offsets of the layered structure can be revealed from the numerical model, which is similar to those observed in experiments. The actual appearance of shear bands depends on the materials’ constitutive behavior and precise geometries. Post-yield strain hardening reduces the propensity of shear band formation, while strain softening enhances it. Imperfections such as the undulated layer geometry, as well as the frictional characteristics between the specimen and test apparatus, can also influence the shear band morphology and overall stress–strain response.

finite element modeling↗

On the hardness of learning ground state entanglement of geometrically local Hamiltonians

Characterizing the entanglement structure of ground states of local Hamiltonians is a fundamental problem in quantum information. In this work we study the computational complexity of this problem, given the Hamiltonian as input. Our main result is that to show it is cryptographically hard to determine if the ground state of a geometrically local, polynomially gapped Hamiltonian on qudits (d=O(1)) has near-area law vs near-volume law entanglement. This improves prior work of Bouland et al. (arXiv:2311.12017) showing this for non-geometrically local Hamiltonians. In particular we show this problem is roughly factoring-hard in 1D, and LWE-hard in 2D. Our proof works by constructing a novel form of public-key pseudo-entanglement which is highly space-efficient, and combining this with a modification of Gottesman and Irani's quantum Turing machine to Hamiltonian construction. Our work suggests that the problem of learning so-called "gapless" quantum phases of matter might be intractable.

Computational Complexity (cs.CC)↗

A First Step Towards Quantum Simulating Jet Evolution in a Dense Medium

The fast development of quantum technologies over the last decades has offered a glimpse to a future where the quantum properties of multi particle systems might be more fully understood. In particular, quantum computing might prove crucial to explore many aspects of high energy physics unaccessible to classical methods. In this talk, we will describe how one can use digital quantum computers to study the evolution of QCD jets in quark gluons plasmas. We construct a quantum circuit to study single particle evolution in a dense QCD medium. Focusing on the jet quenching parameter $\hat{q}$, we present some early numerical results for a small quantum circuit. Future extensions of this strategy are also addressed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

CryoEM structures of the human CLC-2 voltage-gated chloride channel reveal a ball-and-chain gating mechanism

CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different tissues. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated by hyperpolarization, rather than depolarization, of the plasma membrane. The molecular basis for the divergence in polarity of voltage gating among closely related homologs has been a long-standing mystery, in part because few CLC channel structures are available. Here, we report cryoEM structures of human CLC-2 at 2.46 – 2.76 Å, in the presence and absence of the selective inhibitor AK-42. AK-42 binds within the extracellular entryway of the Cl – -permeation pathway, occupying a pocket previously proposed through computational docking studies. In the apo structure, we observed two distinct conformations involving rotation of one of the cytoplasmic C-terminal domains (CTDs). In the absence of CTD rotation, an intracellular N-terminal 15-residue hairpin peptide nestles against the TM domain to physically occlude the Cl – -permeation pathway. This peptide is highly conserved among species variants of CLC-2 but is not present in other CLC homologs. Previous studies suggested that the N-terminal domain of CLC-2 influences channel properties via a “ball-and-chain” gating mechanism, but conflicting data cast doubt on such a mechanism, and thus the structure of the N-terminal domain and its interaction with the channel has been uncertain. Through electrophysiological studies of an N-terminal deletion mutant lacking the 15-residue hairpin peptide, we support a model in which the N-terminal hairpin of CLC-2 stabilizes a closed state of the channel by blocking the cytoplasmic Cl – -permeation pathway.

59 BASIC BIOLOGICAL SCIENCES↗

Residential Battery Modeling for Control-Oriented Techno-Economic Studies: Preprint

Electrochemical batteries, which serve as electric energy storage devices, are becoming increasingly popular among residential buildings that incorporate solar photovoltaic (PV) systems to help meet their energy needs. Battery economics are affected by performance degradation over time, and managing this degradation can help extend the battery's lifespan. The tradeoff between operational costs/benefits and managing battery degradation is of significant research interest. One of the key factors for assessing battery degradation is the dispatch strategy used to control the charging and discharging of the battery. Conventional dispatch strategies typically use simple rule-based methods, and these overly aggressive charging/discharging cycles can significantly reduce a battery’s life span. Our research seeks to develop optimized dispatch strategies for grid-connected PV homes with a goal of extending battery life while simultaneously taking into consideration utility costs and occupant comfort. To achieve this goal, we adapted lithium-ion battery life- and cyclic-degradation models for use in high-fidelity building simulations, so whole-building and grid-interactive controllers can dispatch the batteries along with other flexible loads. With the help of a co-simulation platform, we performed a simulation study to compute the optimized dispatch strategies for relevant operating conditions brought about by changing geographical locations, weather conditions, and utility pricing. Comparing the optimized strategies with the conventional strategies resulted in a >50% decrease in capacity degradation and >10% average reduction in operational costs during the months of January and July in Fort Collins, Colorado; Phoenix, Arizona; and Portland, Oregon.

30 DIRECT ENERGY CONVERSION↗

MODELLING FIBER ORIENTATION DURING ADDITIVE MANUFACTURING COMPRESSION MOLDING PROCESSES

The production of high-performance thermoplastic composites reinforced with short carbon fibers can be achieved by a novel “additive manufacturing-compression molding” technique. An advantage of such combination is two-fold: controlled fiber orientation in additive manufacturing and less void content by compression molding. In this study, a computational fluid dynamics model has been developed to predict the behavior of printed layers during fiber-reinforced thermoplastic extrusion and subsequent compression molding. The fiber orientation was modelled with a simple quadratic closure model. The interaction between the fibers is included using a rotary diffusion coefficient which becomes significant in concentrated regimes. Finally, the second order orientation tensor is coupled with the momentum equation as an anisotropic part of the stress term. The effect of processing parameters on the behavior of printed layers was investigated to determine the favorable printing scenarios. The developed numerical model enables design of high-performance composites with tunable mechanical properties.

Seta, Berin↗

Preliminary analysis of TREAT free-field experiments using OpenMC

This work analyses activation calculations for dosimetry materials during a steady-state irradiation in the Transient Reactor Test (TREAT) reactor core. Hence, we developed a workflow based on the Monte Carlo code OpenMC alongside a custom depletion solver. The irradiation-induced activity as a function of time is computed, and several sensitivity studies are performed to evaluate uncertainty. This study has shown activity computations are sensitive to flux amplitude, irradiation time, atoms quantity and microscopic cross sections. Stochastic uncertainties have been propagated to evaluate the activity uncertainty for each dosimetry material. Most uncertainties are below our target of 3%, which demonstrates OpenMC as a powerful predictive and analysis tool. The precise results obtained through this newly developed computation scheme will be used in future experiments to characterize quantities of interest when operating the TREAT reactor in new configurations.

61 - RADIATION PROTECTION AND DOSIMETRY↗

Modelling drug adsorption in metal–organic frameworks: the role of solvent

Solvent plays a key role in biological functions, catalysis, and drug delivery. Metal–organic frameworks (MOFs) due to their tunable functionalities, porosities and surface areas have been recently used as drug delivery vehicles. To investigate the effect of solvent on drug adsorption in MOFs, we have performed integrated computational and experimental studies in selected biocompatible MOFs, specifically, UiO-AZB, HKUST-1 (or CuBTC) and NH 2 -MIL-53(Al). The adsorption of three drugs, namely, 5-fluorouracil (5-FU), ibuprofen (IBU), and hydroxyurea (HU) were performed in the presence and absence of the ethanol. Our computational predictions, at 1 atmospheric pressure, showed a reasonable agreement with experimental studies performed in the presence of ethanol. We find that in the presence of ethanol the drug molecules were adsorbed at the interface of solvent and MOFs. Moreover, the computationally calculated adsorption isotherms suggested that the drug adsorption was driven by electrostatic interactions at lower pressures (<10 –4 Pa). Our computational predictions in the absence of ethanol were higher compared to those in the presence of ethanol. The MOF–adsorbate interaction (U HA ) energy decreased with decrease in the size of a drug molecule in all three MOFs at all simulated pressures. At high pressure the interaction energy increases with increase in the MOFs pore size as the number of molecules adsorbed increases. Thus, our research shows the important role played by solvent in drug adsorption and suggests that it is critical to consider solvent while performing computational studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Insights into grain boundary energy structure-property relationships by examining computed [100] disorientation axis grain boundaries in Nickel

A study of 346 computed [100] disorientation axis grain boundaries provides insight into grain boundary energy structure-property relationships. The grain boundaries come from 6 coincidence site lattice misorientations at regularly spaced disorientation angles, and cover the full range of boundary plane orientations. The computed energy has clear trends in disorientation angle and boundary plane orientation. Here, the data are used to reexamine the 'special' attribute frequently applied to low Σ coincidence site lattice misorientations and low-angle boundaries and to assess the accuracy of a face-centered cubic grain boundary energy function.

36 MATERIALS SCIENCE↗

Notch insensitivity in fatigue failure of chopped carbon fiber chip-reinforced composites using experimental and computational analysis

This study focuses on the notch effect on the fatigue failure of chopped carbon fiber chip-reinforced sheet molding compound (SMC) composites by using both experimental and numerical methods. The S-N diagrams of notched specimens are first obtained experimentally, which exhibit large scatter and are shown to depend on the spatial distribution of local fiber orientations. After considering the effect of this spatial distribution by adopting a new fatigue damage parameter to normalize the results, we achieve a much better correlation in the normalized S-N diagram for all the notched specimens with different hole diameters. Next, compared with the fatigue results of smooth specimens without notches, we find that SMC composites under tension-tension fatigue loading exhibit notch-insensitivity, which renders this type of composites a better candidate in joints or similar applications. Meanwhile, the fatigue failure mechanisms of notched SMC composites are explored through a microstructure characterization procedure. On this basis, a computational micromechanics model considering the notch effect and an improved multi-scale progressive damage fatigue law, calibrated by coupon-level fatigue tests of smooth SMC composites under different loading conditions, are employed to predict the fatigue behavior of notched SMC composites. We show that detailed failure processes and fatigue life of notched SMC composites can be efficiently and adequately predicted by this computational framework.

36 MATERIALS SCIENCE↗

A Case Study on Pathogen Transport, Deposition, Evaporation and Transmission: Linking High-Fidelity Computational Fluid Dynamics Simulations to Probability of Infection

A high-fidelity, low-Mach computational fluid dynamics simulation tool that includes evaporating droplets and variable-density turbulent flow coupling is well-suited to ascertain transmission probability and supports risk mitigation methods development for airborne infectious diseases such as COVID-19. A multi-physics large-eddy simulation-based paradigm is used to explore droplet and aerosol pathogen transport from a synthetic cough emanating from a kneeling humanoid. For an outdoor configuration that mimics the recent open-space social distance strategy of San Francisco, maximum primary droplet deposition distances are shown to approach 8.1 m in a moderate wind configuration with the aerosol plume transported in excess of 15 m. In quiescent conditions, the aerosol plume extends to approximately 4 m before the emanating pulsed jet becomes neutrally buoyant. A dose–response model, which is based on previous SARS coronavirus (SARS-CoV) data, is exercised on the high-fidelity aerosol transport database to establish relative risk at eighteen virtual receptor probe locations.

59 BASIC BIOLOGICAL SCIENCES↗

Approximate Inverse Chain Preconditioner: Iteration Count Case Study for Spectral Support Solvers

As the growing availability of computational power slows, there has been an increasing reliance on algorithmic advances. However, faster algorithms alone will not necessarily bridge the gap in allowing computational scientists to study problems at the edge of scientific discovery in the next several decades. Often, it is necessary to simplify or precondition solvers to accelerate the study of large systems of linear equations commonly seen in a number of scientific fields. Preconditioning a problem to increase efficiency is often seen as the best approach; yet, preconditioners which are fast, smart, and efficient do not always exist. Following the progress of [1], we present a new preconditioner for symmetric diagonally dominant (SDD) systems of linear equations. These systems are common in certain PDEs, network science, and supervised learning among others. Based on spectral support graph theory, this new preconditioner builds off of the work of [2], computing and applying a V-cycle chain of approximate inverse matrices. This preconditioner approach is both algebraic in nature as well as hierarchically-constrained depending on the condition number of the system to be solved. Due to its generation of an Approximate Inverse Chain of matrices, we refer to this as the AIC preconditioner. We further accelerate the AIC preconditioner by utilizing precomputations to simplify setup and multiplications in the con-text of an iterative Krylov-subspace solver. While these iterative solvers can greatly reduce solution time, the number of iterations can grow large quickly in the absence of good preconditioners. Initial results for the AIC preconditioner have shown a very large reduction in iteration counts for SDD systems as compared to standard preconditioners such as Incomplete Cholesky (ICC) and Multigrid (MG). We further show significant reduction in iteration counts against the more advanced Combinatorial Multigrid (CMG) preconditioner. We have further developed no-fill sparsification techniques to ensure that the computational cost of applying the AIC preconditioner does not grow prohibitively large as the depth of the V-cycle grows for systems with larger condition numbers. Our numerical results have shown that these sparsifiers maintain the sparsity structure of our system while also displaying significant reductions in iteration counts.1 2

97 MATHEMATICS AND COMPUTING↗