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At least 181 records · Page 10

Embedded training of neural-network subgrid-scale turbulence models

We report that the weights of a deep neural-network model are optimized in conjunction with the governing flow equations to provide a model for subgrid-scale stresses in a temporally developing plane turbulent jet at Reynolds number Re 0 = 6000 . The objective function for training is first based on the instantaneous filtered velocity fields from a corresponding direct numerical simulation, and the training is by a stochastic gradient descent method, which uses the adjoint Navier-Stokes equations to provide the end-to-end sensitivities of the model weights to the velocity fields. In-sample and out-of-sample testing on multiple dual-jet configurations show that its required mesh density in each coordinate direction for prediction of mean flow, Reynolds stresses, and spectra is half that needed by the dynamic Smagorinsky model for comparable accuracy. The same neural-network model trained directly to match filtered subgrid-scale stresses, without the constraint of being embedded within the flow equations during the training, fails to provide a qualitatively correct prediction. The coupled formulation is generalized to train based only on mean-flow and Reynolds stresses, which are more readily available in experiments. The mean-flow training provides a robust model, which is important, though a somewhat less accurate prediction for the same coarse meshes, as might be anticipated due to the reduced information available for training in this case. The anticipated advantage of the formulation is that the inclusion of resolved physics in the training increases its capacity to extrapolate. This is assessed for the case of passive scalar transport, for which it outperforms established models due to improved mixing predictions.

42 ENGINEERING↗

Stochastic Constrained Extended System Dynamics for Solving Charge Equilibration Models

In this work, we present a new stochastic extended Lagrangian molecular dynamics solution to charge equilibration that eliminates self-consistent field (SCF) calculations, thus eliminating the computational bottleneck in solving the charge distribution with standard SCF solvers. By formulating both charges and chemical potential as latent variables and introducing a holonomic constraint that satisfies charge conservation, the SC-XLMD method accurately reproduces thermodynamic, dynamic, and structural properties within the framework of ReaxFF for a bulk water system and highly reactive RDX molecules simulated at high temperature. The SC-XLMD method shows excellent computational performance and is available in the publicly available LAMMPS package.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Uncertainty quantification for Multiphase-CFD simulations of bubbly flows: a machine learning-based Bayesian approach supported by high-resolution experiments

In this paper, we developed a machine learning-based Bayesian approach to inversely quantify and reduce the uncertainties of multiphase computational fluid dynamics (MCFD) simulations for bubbly flows. The proposed approach is supported by high-resolution two-phase flow measurements, including those by double-sensor conductivity probes, high-speed imaging, and particle image velocimetry. Local distributions of key physical quantities of interest (QoIs), including the void fraction and phasic velocities, are obtained to support the Bayesian inference. In the process, the epistemic uncertainties of the closure relations are inversely quantified while the aleatory uncertainties from stochastic fluctuations of the system are evaluated based on experimental uncertainty analysis. The combined uncertainties are then propagated through the MCFD solver to obtain uncertainties of the QoIs, based on which probability-boxes are constructed for validation. The proposed approach relies on three machine learning methods: feedforward neural networks and principal component analysis for surrogate modeling, and Gaussian processes for model form uncertainty modeling. The whole process is implemented within the framework of an open-source deep learning library PyTorch with graphics processing unit (GPU) acceleration, thus ensuring the efficiency of the computation. The results demonstrate that with the support of high-resolution data, the uncertainties of MCFD simulations can be significantly reduced. The proposed approach has the potential for other applications that involve numerical models with empirical parameters.

42 ENGINEERING↗

Investigating the effects of electron bounce-cyclotron resonance on plasma dynamics in capacitive discharges operated in the presence of a weak transverse magnetic field

Recently, Patil et al. [Phys. Rev. Res. 4, 013059 (2022)] have reported the existence of an enhanced operating regime when a low-pressure (5 mTorr) capacitively coupled discharge (CCP) is driven by a very high radio frequency (60 MHz) source in the presence of a weak external magnetic field applied parallel to its electrodes. Their particle-in-cell simulations show that a significantly higher bulk plasma density and ion flux can be achieved at the electrode when the electron cyclotron frequency equals half of the applied radio frequency for a given fixed voltage. In the present work, we take a detailed look at this phenomenon and further delineate the effect of this “electron bounce-cyclotron resonance (EBCR)” on the electron and ion dynamics of the system. We find that the ionization collision rate and stochastic heating are maximum under resonance condition. The electron energy distribution function also indicates that the population of tail-end electrons is highest for the case where EBCR is maximum. Formation of electric field transients in the bulk plasma region is also seen at lower values of applied magnetic field. Finally, we demonstrate that the EBCR-induced effect is a low-pressure phenomenon and weakens as the neutral gas pressure increases. The potential utility of this effect to advance the operational performance of CCP devices for industrial purposes is discussed in this report.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Decadal Spiciness Variability in the Subtropical-Tropical Pacific in the CESM2 Large Ensemble

Tropical Pacific decadal variations impact weather and climate around the world and are also connected to variations in the global warming trend. The mechanisms driving these long-term modulations, particularly the role of subsurface ocean dynamics, are still debated. Here, we investigate the dynamics of spiciness (density-compensated temperature and salinity) anomalies in the tropical and subtropical Pacific, which are hypothesized as a possible driving mechanism of decadal climate variability. Based on the analysis of 100 realizations from the Community Earth System Model Version 2 Large Ensemble (CESM2-LE), we demonstrate a coupling between the subtropics and the equatorial Pacific by propagating spiciness anomalies at decadal time scales. The CESM2-LE simulates spiciness variability along a subduction path from the subtropics to the equator with frequency spectra that show the highest power at low frequencies and a power decay proportional to a −4 slope for frequencies greater than 0.01 cycles per months, corresponding to periods smaller than ∼8.5 years. Signals that originate in the Southern Hemisphere (SH) dominate and arrive with a larger magnitude at the equator compared to spiciness anomalies from the Northern Hemisphere (NH). Spiciness anomalies from the SH have shorter propagation times and are strengthened along their pathway as stochastic wind stress curl forcing generates anomalous baroclinic ocean pressure gradients. These pressure gradients generate spiciness anomalies via anomalous advection across climatological spiciness gradients in the SH. We conclude that the observed spiciness variance at decadal time scales is consistent with a forcing by stochastic wind variations that are low-pass filtered by ocean dynamics.

54 ENVIRONMENTAL SCIENCES↗

Quantum Vibronic Effects on the Electronic Properties of Molecular Crystals

We present a study of molecular crystals, focused on the effect of nuclear quantum motion and anharmonicity on their electronic properties. We consider a system composed of relatively rigid molecules, a diamondoid crystal, and one composed of floppier molecules, NAI-DMAC, a thermally activated delayed fluorescence compound. We compute fundamental electronic gaps at the density functional theory (DFT) level of theory, with the Perdew–Burke–Erzenhof (PBE) and strongly constrained and approximately normed (SCAN) functionals, by coupling first-principles molecular dynamics with a nuclear quantum thermostat. We find a sizable zero-point renormalization (ZPR) of the band gaps, which is much larger in the case of diamondoids (0.6 eV) than for NAI-DMAC (0.22 eV). We show that the frozen phonon (FP) approximation, which neglects intermolecular anharmonic effects, leads to a large error (~50%) in the calculation of the band gap ZPR. Instead, when using a stochastic method, we obtain results in good agreement with those of our quantum simulations for the diamondoid crystal. However, the agreement is worse for NAI-DMAC where intramolecular anharmonicities contribute to the ZPR. Our results highlight the importance of accurately including nuclear and anharmonic quantum effects to predict the electronic properties of molecular crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantifying Turbine-Level Risk to Golden Eagles Using a High-Fidelity Updraft Model and a Stochastic Behavioral Model

To minimize the effects of wind farms on Golden Eagle (Aquila chrysaetos) populations while enabling sustainable development of renewable energy resources, it is important to understand how eagles interact with atmospheric flows, terrain features, and anthropogenic structures. Models that predict migratory flight paths provide one tool that helps us grasp how the location of wind farms may influence interactions and impacts on migrating Golden Eagles. The current state-of-the-art in predicting migratory flight paths uses a deterministic fluid-flow analogy to predict eagle trajectory using only an orographic updraft potential computed from topographical features. This model does not take into account variables, such as thermal updrafts and time varying atmospheric conditions that are known to influence migratory behavior. In this work, we improve on the model with the objective of developing tools that advance our understanding of how atmospheric flows and terrain features affect migratory eagle behavior and their interactions with wind farms. Specifically, we 1) incorporate both orographic and thermal updraft information in simulating eagle flight paths; 2) incorporate stochasticity into eagle travel patterns to better capture the influence of exogenous factors on, and the inherent stochasticity of eagle behavior; 3) consider spatio-temporal atmospheric data at wind-farm-scale when computing updraft potential; and 4) account for how atmospheric conditions and the direction of migration change seasonally and how these changes affect eagle migratory flight behavior. We tested the model using a 50km by 50km region with 50 m resolution in the western United States. We simulated 900 independent, probabilistic eagle tracks during southerly and northerly migration, assuming eagles solely rely on orographic updrafts. The preliminary results indicate that the inclusion of finer resolution atmospheric data allows for the inclusion of realistic conditions that an eagle experiences. The stochasticity in eagle tracks provides a platform to include uncertainty in eagle decision making and help produce robust eagle presence maps. We will deploy updraft and downdraft velocities computed using a high-fidelity, wind farm scale, computational fluid dynamics solver under development at National Renewable Energy Laboratory. This work is a first step in the development of a predictive and generalizable eagle behavior model at the wind farm scale that does not rely on empirical data collection. Although the current model is intended for migratory eagles, we will extend and refine this model to inform the development of additional behavioral modes, including resident eagle behavior. This modeling approach improves our ability to understand eagle use of the landscape at a fine scale, and it is our hope that this work will ultimately help advance strategies that minimize the impact of wind development on Golden Eagle populations.

49 EE - Wind and Water Power Program - Wind (EE-4W↗

On analysis and stochastic modeling of the particle kinetic energy equation in particle-laden isotropic turbulent flows

In this study, we analyze three-dimensional particle-laden, isotropic turbulence to develop an understanding of inertial particle dynamics from a kinetic energy perspective. Data trends implying inhomogeneous sampling of the flow by particles are identified and used to support a proposed particle behavior: particles appear to accumulate in regions of low flow kinetic energy over time because they lose kinetic energy and slow down in such regions, ultimately causing them to spend more time there. To elucidate this behavior, we derive a particle kinetic energy equation from the particle momentum equation, which incorporates inertial effects through the Schiller–Naumann drag correlation. Upon extracting fundamental physics from this equation, hypotheses regarding the role of the Stokes number in the temporal change of particle kinetic energy and the previously proposed particle behavior are evaluated using simulation data considering three Stokes numbers. Finally, a Fokker–Planck equation is used to derive the steady-state probability density function of the particle kinetic energy. The model fits the simulation data well and provides a tool for further investigation into understanding preferential concentration, as well as a reduced order model for predicting particle kinetic energy in turbulent flows.

42 ENGINEERING↗

Fluctuation–dissipation relation for a quantum Brownian oscillator in a parametrically squeezed thermal field

In this paper we study the nonequilibrium evolution of a quantum Brownian oscillator, modeling the internal degree of freedom of a harmonic atom or an Unruh–DeWitt detector, coupled to a nonequilibrium and nonstationary quantum field bath and inquire whether a fluctuation–dissipation relation (FDR) can exist after/if it approaches equilibration. This is a nontrivial issue because a squeezed field bath cannot reach equilibration and yet, as this work shows, the system oscillator indeed can, which is a necessary condition for FDRs. We discuss three different settings: (A) The bath field essentially remains in a squeezed thermal state throughout, whose squeeze parameter is a mode- and time-independent constant. This situation is often encountered in quantum optics and quantum thermodynamics. (B) The bath field is initially in a thermal state, but is subjected to a parametric process leading to mode- and time-dependent squeezing. This scenario is encountered in cosmology and dynamical Casimir effects. The squeezing in the bath in both types of processes will affect the oscillator’s nonequilibrium evolution. We show that at late times it approaches equilibration and this stationarity condition warrants the existence of a FDR. The trait of squeezing is marked by the oscillator’s effective equilibrium temperature, and the proportionality factor in the FDR is only related to the stationary component of the noise kernel of the bath field. Setting (C) is more subtle: A finite system–bath coupling strength can set the oscillator in a squeezed state even though the bath field is stationary and does not engage in any parametric process. The squeezing of the system in this case is in general time-dependent but becomes constant when the internal dynamics is fully relaxed. We begin with comments on the broad range of physical processes involving squeezed thermal baths and end with some remarks on the significance of FDRs in capturing the essence of quantum backreaction in nonequilibrium and stochastic systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Improving noisy free-energy measurements by adding more noise

Estimating free-energy differences using nonequilibrium work relations, such as the Jarzynski equality, is hindered by poor convergence when work fluctuations are large. For systems governed by overdamped Langevin dynamics, we propose the counterintuitive approach of adding noise in order to increase the precision of such calculations. Here, by introducing additional stochastic fluctuations to the system and rescaling its potential energy accordingly, we leave the thermodynamics of the system unchanged while increasing its relaxation rate. For a given time-dependent protocol this modification reduces the dissipated reduced work, leading to more accurate free-energy estimates. The method is designed to be used in experiment, and we illustrate its operation using computer simulations applied to two model systems. However, the regime of applicability of this strategy is likely limited, because it requires control of the system's potential energy in a way that is feasible in only a few experimental settings.

Whitelam, Stephen [Lawrence Berkeley National Labo↗

How good are learning-based control v.s. model-based control for load shifting? Investigations on a single zone building energy system

Both model predictive control (MPC) and deep reinforcement learning control (DRL) have been presented as a way to approximate the true optimality of a dynamic programming problem, and these two have shown significant operational cost saving potentials for building energy systems. Furthermore, there is still a lack of in-depth quantitative studies on their approximation levels to the true optimality, especially in the building energy domain. To fill in the gap, this paper provides a numerical framework that enables the evaluation of the optimality levels of different controllers for building energy systems. This framework is then used to comprehensively compare the optimal control performance of both MPC and DRL controllers with given computation budgets for a single zone fan coil unit system. Note the optimality is estimated based on a user-specific selection of trade-off weights among energy costs, thermal comfort and control slew rates. Compared with the best optimality we can find through expensive optimization simulations, the best DRL agent can maximally approximate the optimality by 96.54%, which outperforms the best MPC whose optimality level is 90.11%. However, due to the stochasticity, the DRL agent is only expected to approximate the optimality by 90.42%, which is almost equivalent to the best MPC. Except for Proximal Policy Optimization (PPO), all DRL agents can have a better approximation to the optimality than the best MPC, and are expected to have better approximation than the MPC with a prediction horizon of 32 steps (15 min per step). In terms of reducing energy cost and thermal discomfort, MPC can outperform the rule-based control (RBC) by 18.47%–25.44%. DRL can be expected to outperform RBC by 18.95%–25.65% ,and the best DRL control policy can outperform RBC by 20.29%–29.72%. Although the comparison of the optimality level is performed in a perfect setting, e.g., MPC assumes perfect models, and DRL assumes a perfect offline training process and online deployment process, this can shed insight on their capabilities of approximating to the original dynamic programming problem.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Neutrino-driven Winds in Three-dimensional Core-collapse Supernova Simulations

Abstract In this paper, we analyze the neutrino-driven winds that emerge in 12 unprecedentedly long-duration 3D core-collapse supernova simulations done using the code F ornax . The 12 models cover progenitors with zero-age main-sequence mass between 9 and 60 solar masses. In all our models, we see transonic outflows that are at least 2 times as fast as the surrounding ejecta and that originate generically from a proto−neutron star surface atmosphere that is turbulent and rotating. We find that winds are common features of 3D simulations, even if there is anisotropic early infall. We find that the basic dynamical properties of 3D winds behave qualitatively similarly to those inferred in the past using simpler 1D models, but that the shape of the emergent wind can be deformed, very aspherical, and channeled by its environment. The thermal properties of winds for less massive progenitors very approximately recapitulate the 1D stationary solutions, while for more massive progenitors they deviate significantly owing to aspherical accretion. The Y e temporal evolution in winds is stochastic, and there can be some neutron-rich phases. Though no strong r -process is seen in any model, a weak r -process can be produced, and isotopes up to 90 Zr are synthesized in some models. Finally, we find that there is at most a few percent of a solar mass in the integrated wind component, while the energy carried by the wind itself can be as much as 10%–20% of the total explosion energy.

79 ASTRONOMY AND ASTROPHYSICS↗

An Efficient Three-Dimensional CFD-Based Numerical Wave Tank for a Wave Energy Converter in Extreme Irregular Waves

A numerical wave tank approach for computational fluid dynamics (CFD) modelling of an extreme irregular seastate is presented. The technique couples a potential flow solution with a CFD solver for more efficient numerical predictions. This method has recently become attractive both for the research community and the industry working with offshore structures. The model is used to determine the response of a submerged pressure differential wave energy converter (WEC) in a fully nonlinear irregular wave condition using the high-fidelity CFD code, STAR-CCM+. Potential flow based numerical models are commonly used to predict motions and performance of wave energy converters. Wave kinematics can deviate from potential flow predictions for extreme wave conditions; the excitation loads on an absorber can also be increasingly influenced by viscous effects, not predicted by potential flow engineering level models. In these extreme conditions, a Reynolds-averaged Navier-Stokes CFD model can better predict motions and loads for a WEC. Long time series with varying random seed numbers can be used to identify singular extreme wave events from a stochastic irregular sea state. This approach simulates a more realistic wave series for a given sea state than a regular wave or a focused wave. However, it is computationally infeasible to run these long time series for three-dimensional (3D) CFD simulations. In this work, two-dimensional (2D) CFD simulations with a long domain allow the full development of an extreme nonlinear wave condition. The results are used to identify extreme events from a 50-year storm condition for the PacWave site off the coast of Oregon. A relatively short time window including this extreme event is then mapped to a 3D simulation using a user defined wave methodology. Convergence studies for domain length, wave forcing lengths, and time before the extreme event were conducted.

CFD↗

Strong-field QED limitations on TeV-class plasma wakefield accelerators

We demonstrate that quantum and classical radiation effects can become non-negligible for TeV-class beams propagating through plasma channels typical of staged plasma accelerators. Although the quantum nonlinearity parameter χ e remains small under currently envisioned experimental conditions, the cumulative influence of radiation over long acceleration distances can lead to significant modifications to the beam’s energy spread, emittance, and polarization. Our analytic models, validated by particle-in-cell simulations, highlight that for standard Gaussian beams, the orbit-induced energy spread dominates over quantum stochastic effects but can be mitigated by tailoring the beam profile, for example, through ring-shaped transverse distributions. In regimes where the radiation reaction approaches the accelerating force, the emittance may be cooled, forming distinctive ring-shaped phase-space structures. Finally, we analyze the influence of the radiation effect on spin transport inside the wakefield. These findings underscore the importance of considering both classical and quantum radiation dynamics in the design and optimization of future high-intensity plasma accelerators.

accelerator↗

Semi-Analytical Hierarchical Bayesian Inference of Nonlinear Model Structure in Stochastic Dynamics: Applied to Compartmental Models of Infectious Diseases

A Bayesian computational framework for parsimonious inference in stochastic nonlinear dynamical systems is presented. This framework enables the concurrent estimation of system states, time-varying parameters, time-invariant parameters, and the optimal sparsity structure of the model parameters. Because differential equation-based models are often simplified mechanistic or phenomenological representations, robust inference from noisy measurement data requires explicit treatment of model error and uncertainty. Model error and time-varying parameters can be represented as random processes, enabling inference while making minimal assumptions about the underlying sources of discrepancy and variability. Adopting stochastic differential equation representations affords the model significant flexibility, but can also render it susceptible to overfitting during statistical inversion, where the inferred model may track noise rather than the underlying signal. To alleviate the effects of overfitting and to enable the discovery of the optimal sparse representation of the time-invariant parameters, a Bayesian sparse learning algorithm is embedded within the framework. This sparse learning framework adopts an approximate hierarchical Bayesian setting defined by a series of semi-analytical expressions. The model structure inference framework is validated using a stochastic compartmental model for tracking and forecasting active cases of an infectious disease. Compartmental models describe population-level infectious disease dynamics through interactions among population fractions grouped by disease state. Mathematically, such models consist of a system of coupled ordinary differential equations. This example adopts an expressive compartmental model that includes multiple possible interactions between disease states, motivated by early uncertainty surrounding COVID-19 reinfection dynamics and their implications for long-term epidemic forecasting. The sparse learning exercise permits the inference of a priori unknown epidemiological dynamics from simulated public health data, discovering the nested compartmental model that optimizes the trade-off between average data-fit and model complexity. It is shown that inducing sparsity among the model parameters eliminates redundant interactions between compartments, equivalently revealing the optimal coupling structure between differential equations.

97 MATHEMATICS AND COMPUTING↗

EGR Dilution and Fuel Property Effects on High-Efficiency Spark-Ignition Flames

Modern spark ignition internal combustion engines rely on fast combustion rates and high dilution to achieve high brake thermal efficiencies. To accomplish this, new engine designs have moved towards increased tumble ratios and stroke-to-bore ratios. Increased tumble ratios correlate positively with increases in turbulent kinetic energy and improved fuel and residual gas mixing, all of which favor faster and more efficient combustion. Longer stroke-to-bore ratios allow higher geometric compression ratios and use of late intake valve closing to control peak compression pressures and temperatures. The addition of dilution to improve efficiency is limited by the resulting increase in combustion instabilities manifested by cycle-to-cycle variability. A number of effects - preferential diffusion, turbulence-combustion interactions, stochastic flow patterns, laminar-turbulent flame kernel transitions, and relative length and velocity scales between flame and turbulence - are believed to be responsible for the increase in cycle-to-cycle variations, where their contributions are likely interlinked. Several studies have shown the influence of stochastic flow characteristics on the nature of combustion instabilities, such as velocity patterns on flame kernel formation and cycle-to-cycle variations in residual gas. However, few have focused on the specific effects of fuel properties. The objective of this work is to contrast the effects of dilution on propane stoichiometric combustion against gasoline. Dilution tolerance experiments were conducted in a purpose-built high stroke-to-bore ratio single cylinder engine with both gasoline and LPG. Three-dimensional full cycle computational fluid dynamics (CFD) simulations employing a level-set combustion approach and Reynolds averaged Navier-Stokes (RANS) turbulence modeling was used to qualitatively assess the changes in length and velocity scales for turbulence and the flame. The experimental results showed that LPG can tolerate higher exhaust gas recirculation (EGR) dilution under a variety of conditions. Analysis of CFD simulations showed that propane flames are likely less sensitive to influences from the flow field due to less thickening of the flame and higher effective flame speeds.

33 ADVANCED PROPULSION SYSTEMS↗

XFEL SASE pulses can enhance time-dependent observables

Abstract X-ray free electron lasers (XFELs) have emerged as powerful sources of short and intense x-ray pulses. We propose a simple and robust procedure which takes advantage of the inherent stochasticity of self-amplified stimulated emission (SASE) pulses to enhance the time-resolution and signal strength of the recorded data. Notably, the proposed method is able to enhance the average signal without knowledge of the signal strength of individual shots. Simple metrics for the probe pulses are introduced, such as an effective pulse duration applicable to SASE pulses characterised in the time domain using e.g. an X-band transverse cavity. The approach is evaluated using simulated and real pulse data in the context of ultrafast electron dynamics in a molecule. Utilising H 2 as a model system, we demonstrate the efficacy of the method theoretically, successfully enhancing the predicted nonresonant ultrafast x-ray scattering signal associated with electron dynamics. The method presented is broadly applicable and offers a general strategy for enhancing time-dependent observables at XFELs.

data analysis↗

Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework

The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. In this work, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (~98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ~1.5 million atoms is discussed in the context of MuMMI.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗