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At least 1,459 records · Page 81

Computational Workflow for Accelerated Molecular Design Using Quantum Chemical Simulations and Deep Learning Models

Efficient methods for searching the chemical space of molecular compounds are needed to automate and accelerate the design of new functional molecules such as pharmaceuticals. Given the high cost in both resources and time for experimental efforts, computational approaches play a key role in guiding the selection of promising molecules for further investigation. Here, we construct a workflow to accelerate design by combining approximate quantum chemical methods [i.e. density-functional tight-binding (DFTB)], a graph convolutional neural network (GCNN) surrogate model for chemical property prediction, and a masked language model (MLM) for molecule generation. Property data from the DFTB calculations are used to train the surrogate model; the surrogate model is used to score candidates generated by the MLM. The surrogate reduces computation time by orders of magnitude compared to the DFTB calculations, enabling an increased search of chemical space. Furthermore, the MLM generates a diverse set of chemical modifications based on pre-training from a large compound library. We utilize the workflow to search for near-infrared photoactive molecules by minimizing the predicted HOMO-LUMO gap as the target property. Our results show that the workflow can generate optimized molecules outside of the original training set, which suggests that iterations of the workflow could be useful for searching vast chemical spaces in a wide range of design problems.

Blanchard, Andrew↗

EXPERIMENTAL AND COMPUTATIONAL STUDY OF DIRECT CONTACT MEMBRANE DISTILLATION

Experimental and computational studies of direct contact membrane distillation (DCMD) are conducted. The permeate flux is measured in a module containing a flat sheet membrane. Polytetrafluoroethylene (PTFE) hydrophobic membrane (Membrane Solutions, FPB045A16) with a nominal pore size of 0.45 μm, the thickness of 179~239 μm, the porosity of 80% is used in the experiments. The feed solution is a binary mixture of water and NaCl. The inlet feed temperature is fixed at 70°C, and the feed Reynolds number is varied between 500 and 2000. Two inlet feed concentrations, 0 and 35g/L, are considered. The permeate flow rate was kept constant at Re of 1300 and temperature of 20°C. Three-dimensional steady-state computational fluid dynamics (CFD) simulations are performed using the laminar model. The Navier’s Stokes, energy, and mass transport equations in each channel coupled with flux boundary conditions imposed at the membrane surface are solved. The predicted module-averaged flux is compared to measured data for all operating conditions. Measured and predicted flux agrees well; validating both experiments and model, Temperature polarization in the feed and permeate channel and concentration polarization in the feed channel are characterized by validated CFD simulations.

Oztekin, Alparslan↗

Exploration of superconducting multi-mode cavity architectures for quantum computing

Superconducting radio-frequency (SRF) cavities coupled to transmon circuits have proven to be a promising platform for building high-coherence quantum information processors. An essential aspect of this realization involves designing high quality factor three-dimensional superconducting cavities to extend the lifetime of quantum systems. To increase the computational capability of this architecture, we are exploring a multimode approach. This paper presents the design optimization process of a multi-cell SRF cavity to perform quantum computation based on an existing design developed in the scope of particle accelerator technology. We perform parametric electromagnetic simulations to evaluate and optimize the design. In particular, we focus on the analysis of the interaction between a nonlinear superconducting circuit known as the transmon and the cavity. This parametric design optimization is structured to serve as a blueprint for future studies on similar systems.

Reineri, Alessandro↗

Execution of computation graphs

A computation graph is accessed. In the computation graph, operations to be performed are represented as interior nodes, inputs to the operations are represented as leaf nodes, and a result of the operations is represented as a root. Selected sets of the operations are combined to form respective kernels of operations. Code is generated execute the kernels of operations. The code is executed to determine the result.

Ravishankar, Mahesh↗

Computer system with moving target defenses against vulnerability attacks

A computer system includes an ensemble moving target defense architecture that protects the computer system against attack using one or more composable protection layers that change each churn cycle, thereby requiring an attacker to acquire information needed for an attack (e.g., code and pointers) and successfully deploy the attack, before the layers have changed state. Each layer may deploy a respective attack information asset protection providing multiple respective attack protections each churn cycle, wherein the respective attack information asset protections may differ.

Austin, Todd↗

Fundamental Superconductivity of Nb films for Quantum Computing Application

Niobium is a widely accepted material for quantum computing device as well as superconducting radio frequency (SRF) technology. Superconducting niobium is a marginal type II superconductor which has a very narrow gap (~20-30 mT) of the mixed state at 2K, even showing the intermediate state (IMS) at the early stage of magnetic vortex penetration. Tremendous progress has been made in understanding the impact of the Nb surface and bulk superconductivities on SRF resonator performance. However, the effect of thin superconducting Nb films for quantum computing applications requires further examination. In this study, we explore the fundamental superconducting properties of various thin Nb films and compare them with respect to the energy relaxation time, T1, measured from superconducting qubit fabricated with these films. The Nb films are fabricated both with or without a surface protective layer that prevents the formation of lossy Nb2O5. Electromagnetic properties are characterized by means of bulk magnetization, electromagnetic transport, and dynamics of surface superconductivity. In addition, analytical electron microscopy is implemented to further connect the superconducting properties to microstructure.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Accelerated pattern matching method on a quantum computing system

A method of determining a pattern in a sequence of bits using a quantum computing system includes setting a first register of a quantum processor in a superposition of a plurality of string index states, encoding a bit string in a second register of the quantum processor, encoding a bit pattern in a third register of the quantum processor, circularly shifting qubits of the second register conditioned on the first register, amplifying an amplitude of a state combined with the first register in which the circularly shifted qubits of the second register matches qubits of the third register, measuring an amplitude of the first register and determining a string index state of the plurality of string index states associated with the amplified state, and outputting, by use of a classical computer, a string index associated with the first register in the measured state.

NIROULA, Pradeep↗

COMPUTATIONAL MODELING OF IGNITION AND PREMIXED FLAME PROPAGATION INITIATED BY A PRE-CHAMBER TURBULENT JET

Addressing the pressing need for reduced carbon emissions, Turbulent Jet Ignition (TJI) emerges as a promising technology for ultra-lean combustion, offering enhanced thermal efficiencies and minimized cyclic variability in spark-ignited engines. To facilitate rapid testing and integration of this technology, a robust computational modeling framework is crucial. This study delves into the predictive capabilities of computational models for main-chamber ignition and premixed flame propagation using a single-cycle TJI rig measured by Biswas et al. (Applied Thermal Engineering, vol 106, 2016). Employing an open-source compressible flow simulation solver with Large Eddy Simulation (LES) for turbulence modeling, the investigation integrates the conventional Laminar Finite Rate Chemistry (LFRC) model alongside the transported Probability Density Method (PDF) for turbulence-chemistry interaction. A fully-consistent Eulerian Monte-Carlo Fields (EMCF) method is utilized to approximate the transported PDF, while Interaction by Exchange with Mean is employed to close micro-mixing terms in stochastic differential equations. A reduced chemical reaction mechanism with 21 species and 84 reactions (DRM-19) is used for solving chemical kinetics, and a double Gaussian energy deposition model is used to approximate the spark ignition in the pre-chamber. An unstructured O-grid mesh with 0.3 million cells in the prechamber and 1 million cells in the main chamber is employed. Results are divided into two phases: pre-chamber initialization and full TJI simulations. Validation of the predicted pre-chamber flame propagation and the lean ignition in the main-chamber is carried out by using available experimental data. Under quiescent conditions, both the LFRC and transported PDF methods largely underestimate the flame speed and subsequent pressure growth in the pre-chamber. A linear momentum forcing technique is applied to investigate the impact of initial turbulence in the pre-chamber, demonstrating a notable influence on flame propagation. Fine-tuning of the forcing coefficient reproduces the sudden pressure growth observed in the experiment. The experimentally validated pre-chamber simulation serves as the initial condition for the full TJI simulations. It is found that the LFRC model fails to predict lean-ignition in the main-chamber, resulting in a misfiring event. Incorporation of turbulence-chemistry interaction using the transported PDF method substantially improves the prediction of the ignition event in the main-chamber, achieving fair qualitative agreement and quantitative validation of combustion parameters within ±10% of the reported experimental data. The rich simulation results consisting of a full set of statistical description of the thermo-chemical states enable us to gain deep insights into the ignition mechanisms in the main chamber, which is limited when done experimentally. A novel dual ignition phenomenon is revealed in the TJI rig for the first time. Initially, a primary ignition kernel is formed at a downstream location which eventually detaches from the main jet. As the jet momentum decreases, a secondary ignition event follows, this time at a more upstream location which eventually combines with the primary ignition kernel to form a single connected flame front. Investigation of these ignition sequences in chemical composition space reveal distinct differences between the two. The primary ignition event in the main-chamber is followed by a large concentration of active radicals from the pre-chamber jet, accelerating the chain-branching steps, characterizing what has been referred to as flame ignition. In contrast, the secondary ignition occurs in the absence of active radicals in the pre-chamber jet, hence characterized as jet ignition. Further analysis of the effect of pre-chamber jet characteristics on lean ignition in the main-chamber is conducted by setting up cases with different initial pressure ratios (por) between the two chambers, a non-dimensional parameter, ranging from 1.2 to 3.2. As the initial pressure ratio increases, jet momentum increases, with dual ignition observed in cases above por= 2.2. Case with por= 3.2 lead to misfiring. The effect of ignition sequence on global combustion characteristics of TJI is analyzed. Dual ignition events lead to non-monotonicity in combustion characteristics such as global reaction progress variable, flame penetration, and global heat release rate. In dual ignition events, although the rate of fuel consumption and global heat release rate is initially lower, the secondary ignition leads to a sudden increase in flame surface area, resulting in a sudden jump and promoting the overall performance of the TJI system.

42 ENGINEERING↗

Quantum computation of mass gap in an asymptotically free theory

In relativistic field theories, the mass spectrum is given by the difference between the energy of the vacuum and the excited states. Near the continuum limit, the cancellation between these two values leads to loss of precision. We propose a method to extract the mass gap directly using quantum computers and apply it to a particular version of the nonlinear $σ$-model with the correct continuum limit and perform calculations in quantum hardware (at strong coupling) and simulation in classical computers (at weak coupling).

Bedaque, Paulo F. [Maryland U.] (ORCID:00000001521↗

Numerical Method Improvements in Griffin for Pebble Bed Reactors with a Focus on the Computation of Burnup

Griffin, a MOOSE (Multiphysics Object-Oriented Simulation Environment) based application targeting transient multiphysics modeling of advanced reactors, has been used recently to model both high-temperature gas-cooled and fluoride-salt-cooled pebble bed reactors (PBRs). Griffin uses deterministic methods for solving neutron transport and an Eulerian approach to model pebble movement. An Eulerian approach is also used to directly compute burnup instead of using a pass approach like other tools such as VSOP or PANGU. This work discusses verification efforts and numerical method improvements related specifically to the Eulerian modeling approach implemented for directly computing pebble burnup.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

A novel A-ϕ formulation for efficient electromagnetic computations

In numerical simulation of electromagnetic prob- lems, potential-based formulations have advantages over field- based formulations because of their immunity to the low- frequency breakdown catastrophe. Recently, an all-frequency stable formulation has been proposed to solve electromagnetic problems in a wide frequency band. This formulation employs magnetic vector and electric scalar potentials, as well as an auxiliary potential to enforce an inhomogeneous Coulomb gauge. However, such a three-potential formulation has encountered convergence issues at low frequencies. To avoid the convergence issue and improve computational efficiency, a novel formulation with only two potentials and an implicit Coulomb gauge is proposed in this paper. A numerical example is presented to show its solution accuracy and computational efficiency.

Mekonnen, Minyechil↗

Computing the Critical Temperature of the Affine-Transformed $D=3$ Ising Model Using Masked Autoregressive Flow

The simple Ising model provides a rich environment to build and study lattice field theories. As part of an ongoing project to construct a conformal field theory (CFT) on an arbitrarily curved manifold, in this work we develop methods to measure the critical temperature $β_c$ of the affine-transformed Ising model on the face-centered cubic (FCC) lattice. The main challenge in this endeavor is finding a computationally efficient and accurate method of interpolating and extrapolating Monte Carlo observables with respect to coupling coefficients and temperature. Herein, we compare two such methods. A traditional statistical approach uses the multiple histogram (MH) method, while a newer machine learning approach uses a masked autoregressive flow (MAF) to estimate the underlying probability density function of a set of observables. While the MH method is specifically designed to interpolate and extrapolate Monte Carlo observables, we find that MAF is a viable alternative for measuring $β_c$ with a computational cost that scales more favorably. Furthermore, we comment on additional advantages of MAF relevant to our work, such as extrapolating in system volume.

Svenson, Kai [Texas U.]↗

Mochi: Composing Data Services for High-Performance Computing Environments

Technology enhancements and the growing breadth of application workflows running on high-performance computing (HPC) platforms drive the development of new data services that provide high performance on these new platforms, provide capable and productive interfaces and abstractions for a variety of applications, and are readily adapted when new technologies are deployed. The Mochi framework enables composition of specialized distributed data services from a collection of connectable modules and subservices. Rather than forcing all applications to use a one-size-fits-all data staging and I/O software configuration, Mochi allows each application to use a data service specialized to its needs and access patterns. This paper introduces the Mochi framework and methodology. The Mochi core components and microservices are described. Examples of the application of the Mochi methodology to the development of four specialized services are detailed. Finally, a performance evaluation of a Mochi core component, a Mochi microservice, and a composed service providing an object model is performed. The paper concludes by positioning Mochi relative to related work in the HPC space and indicating directions for future work.

97 MATHEMATICS AND COMPUTING↗

Alternative mixed integer linear programming optimization for joint job scheduling and data allocation in grid computing

This paper presents a novel approach to the joint optimization of job scheduling and data allocation in grid computing environments. We formulate this joint optimization problem as a mixed integer quadratically constrained program. To tackle the nonlinearity in the constraint, we alternatively fix a subset of decision variables and optimize the remaining ones via Mixed Integer Linear Programming (MILP). We solve the MILP problem at each iteration via an off-the-shelf MILP solver. Our experimental results show that our method significantly outperforms existing heuristic methods, employing either independent optimization or joint optimization strategies. We have also verified the generalization ability of our method over grid environments with various sizes and its high robustness to the algorithm setting.

97 MATHEMATICS AND COMPUTING↗

3D microstructure design of lithium-ion battery electrodes assisted by X-ray nano-computed tomography and modelling

Driving range and fast charge capability of electric vehicles are heavily dependent on the 3D microstructure of lithium-ion batteries (LiBs) and substantial fundamental research is required to optimise electrode design for specific operating conditions. Here we have developed a full microstructure-resolved 3D model using a novel X-ray nano-computed tomography (CT) dual-scan superimposition technique that captures features of the carbon-binder domain. This elucidates how LiB performance is markedly affected by microstructural heterogeneities, particularly under high rate conditions. The elongated shape and wide size distribution of the active particles not only affect the lithium-ion transport but also lead to a heterogeneous current distribution and non-uniform lithiation between particles and along the through-thickness direction. Building on these insights, we propose and compare potential graded-microstructure designs for next-generation battery electrodes. To guide manufacturing of electrode architectures, in-situ X-ray CT is shown to reliably reveal the porosity and tortuosity changes with incremental calendering steps.

33 ADVANCED PROPULSION SYSTEMS↗

Measuring the capabilities of quantum computers

Quantum computers can now run interesting programs, but each processor’s capability—the set of programs that it can run successfully—is limited by hardware errors. These errors can be complicated, making it difficult to accurately predict a processor’s capability. Benchmarks can be used to measure capability directly, but current benchmarks have limited flexibility and scale poorly to many-qubit processors. We show how to construct scalable, efficiently verifiable benchmarks based on any program by using a technique that we call circuit mirroring. With it, we construct two flexible, scalable volumetric benchmarks based on randomized and periodically ordered programs. We use these benchmarks to map out the capabilities of twelve publicly available processors, and to measure the impact of program structure on each one. We find that standard error metrics are poor predictors of whether a program will run successfully on today’s hardware, and that current processors vary widely in their sensitivity to program structure.

97 MATHEMATICS AND COMPUTING↗

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. Overall, this protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.

59 BASIC BIOLOGICAL SCIENCES↗

Ergodicity, lack thereof, and the performance of reservoir computing with memristive networks

Abstract Networks composed of nanoscale memristive components, such as nanowire and nanoparticle networks, have recently received considerable attention because of their potential use as neuromorphic devices. In this study, we explore ergodicity in memristive networks, showing that the performance on machine leaning tasks improves when these networks are tuned to operate at the edge between two global stability points. We find this lack of ergodicity is associated with the emergence of memory in the system. We measure the level of ergodicity using the Thirumalai-Mountain metric, and we show that in the absence of ergodicity, two different memristive network systems show improved performance when utilized as reservoir computers (RC). We highlight that it is also important to let the system synchronize to the input signal in order for the performance of the RC to exhibit improvements over the baseline.

97 MATHEMATICS AND COMPUTING↗