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At least 397 records · Page 22

Quantitative comparison of adaptive sampling methods for protein dynamics

Adaptive sampling methods, often used in combination with Markov state models, are becoming increasingly popular for speeding up rare events in simulation such as molecular dynamics (MD) without biasing the system dynamics. Several adaptive sampling strategies have been proposed, but it is not clear which methods perform better for different physical systems. Here, we present a systematic evaluation of selected adaptive sampling strategies on a wide selection of fast folding proteins. The adaptive sampling strategies were emulated using models constructed on already existing MD trajectories. We provide theoretical limits for the sampling speed-up and compare the performance of different strategies with and without using some a priori knowledge of the system. The results show that for different goals, different adaptive sampling strategies are optimal. In order to sample slow dynamical processes such as protein folding without a priori knowledge of the system, a strategy based on the identification of a set of metastable regions is consistently the most efficient, while a strategy based on the identification of microstates performs better if the goal is to explore newer regions of the conformational space. Interestingly, the maximum speed-up achievable for the adaptive sampling of slow processes increases for proteins with longer folding times, encouraging the application of these methods for the characterization of slower processes, beyond the fast-folding proteins considered here.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Full-torus impurity transport simulation for optimizing plasma discharge operation using a multi-species impurity powder dropper in the large helical device

The transport of impurities supplied by a multi-species impurity powder dropper (IPD) in the large helical device (LHD) is investigated using a three-dimensional peripheral plasma fluid code (EMC3-EIRENE) coupled with a dust transport simulation code (DUSTT). The trajectories of impurity powder particles (Boron, Carbon, Iron, and Tungsten) dropped from the IPD and the impurity transport in the peripheral plasma are studied in a full-torus geometry. The simulation reveals an appropriate size of the impurity powder particles and an optimum operational range of the dust drop rates for investigating the impurity transport without inducing radiation collapse. The simulation also predicts a favourable plasma discharge condition for wall conditioning (boronization) using the IPD in order to deposit boron to high plasma flux and neutral particle density areas in the divertor region in the inboard side of the torus.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An efficient cost reduction procedure for bounded-control LQR problems

A novel approach has been developed for approximating the solution to the constrained LQR problem, based on updating the final state and costate of a related regular problem, and on slightly shifting the switching times (the instants when the control meets the constraints). The main result is the expression of a suboptimal control in feedback form using the solution of some compatible Riccati equation. The gradient method is applied to reduce the cost via explicit algebraic formula for its partial derivatives with respect to the hidden final state/costate of the related regular problem and to the switching times. The numerical method is termed efficient because it does not involve integrations of states or cost trajectories, and reduces to its minimum the dimension of the unknown parameters at the final condition. All the relevant objects are calculated from a few auxiliary matrices, which are computed only once. The scheme is here applied to two case studies whose optimal solutions are known. The first example is a two-dimensional model of the ‘cheapest stop of a train’ problem. The second one refers to the temperature control of a metallic strip leaving a multi-stand rolling mill, a problem with a high-dimensional state.

97 MATHEMATICS AND COMPUTING↗

Multi-resolution, Multi-scale Modeling for Scalable Macroalgae Production

Macroalgae harvested along coastlines and in the open ocean has traditionally been used as food for human consumption, animal feed, and fertilizer. The U.S. ARPA-E MARINER Program estimates that the nation has suitable conditions and geography to produce at least 500 million dry metric tons of macroalgae per year, yielding approximately 2.7 quadrillion BTUs of energy in the form of liquid fuel, which is roughly 10% of the nation’s annual transportation energy demand. Adverse environmental effects of nutrient overload and ocean acidification may also be reduced by large-scale macroalgae cultivation in many coastal ocean regions. However, the successful deployment of large-scale marine macroalgae farms for fuel production depends on ambient hydrodynamic conditions and nutrient availability, as well as their interactions with macroalgae farm structures. Pacific Northwest National Laboratory led an ARPA-E MARINER project to develop a set of numerical modeling tools capable of simulating ocean hydrodynamic and biogeochemical processes, macroalgae trajectories for free-floating systems, macroalgae growth and biomass yields, and hydrodynamic load on macroalgae canopies and farm structures using a multi-resolution and multi-scale approach. This set of modeling tools provides a suite of information essential for system design, optimal project siting, risk analysis, and management of macroalgae production systems in the ocean. Better clarity can also help macroalgae system developers reduce deployment costs, operational risk, and potential impacts on the local marine environment.

59 BASIC BIOLOGICAL SCIENCES↗

Scaling of silicon nanoparticle growth in low temperature flowing plasmas

Low temperature plasmas are an emerging method to synthesize high quality nanoparticles (NPs). An established and successful technique to produce NPs is using a capacitively coupled plasma (CCP) in cylindrical geometry. Although a robust synthesis technique, optimizing or specifying NP properties using CCPs, is challenging. In this paper, results from a computational investigation for the growth of silicon NPs in flowing inductively coupled plasmas (ICPs) using Ar/SiH 4 gas mixtures of up to a few Torr are discussed. ICPs produce more locally constrained and quiescent plasma potentials. These positive plasma potentials produce an electrostatic trap for negatively charged NPs, which can significantly extend the residence time of NPs in the plasma, which in turn provides a controllable period for particle growth. The computational platforms used in this study consist of a two-dimensional plasma hydrodynamics model, a three-dimensional nanoparticle growth and trajectory tracking model, and a molecular dynamics simulation for deriving reactive sticking coefficients of silane radicals on Si NPs. Trends for the nanoparticle growth as a function of SiH 4 inlet fraction, gas residence time, energy deposition per particle, pressure, and reactor diameter are discussed. The general path for particle synthesis is the trapping of small NPs in the positive electrostatic potential, followed by entrainment in the gas flow upon reaching a critical particle size. Optimizing or controlling NP synthesis then depends on the spatial distribution of plasma potential, the density of growth species, and the relative time that particles spend in the electrostatic trap and flowing through higher densities of growth species upon leaving the trap.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Zgoubi Users' Guide

The computer code zgoubi calculates trajectories of charged particles in magnetic and electric fields. At the origin specially adapted to the definition and adjustment of beam lines and magnetic spectrometers, it has so evolved that it allows the study of systems including complex sequences of optical elements such as dipoles, quadrupoles, arbitrary multipoles, FFAG magnets and other magnetic or electric devices, and is able as well to handle periodic structures. Compared to other codes, it presents several peculiarities, as follows - a non-exhaustive list : • a numerical method for integrating the Lorentz equation, based on Taylor series, which optimizes computing time and provides high accuracy and strong symplecticity, • spin tracking, using the same numerical method as for the Lorentz equation, • account of stochastic photon emission, and its effects on particle dynamics, • calculation of the synchrotron radiation electric field and spectra in arbitrary magnetic fields, from the ray-tracing outcomes, • the possibility of using a mesh, which allows ray-tracing from simulated or measured (1-D, 2-D or 3-D) electric and magnetic field maps, • a number Monte Carlo procedures : unlimited number of trajectories, in-flight decay, stochastic radiation, etc., • built-in fitting procedures allowing arbitrary variables and a large variety of constraints, easily expandable, • multi-turn tracking in circular accelerators including features proper to machine parameter calculation and survey, • simulation of time-varying power supplies, and • simulation of arbitrary radio-frequency programs. The initial version of zgoubi was dedicated to ray-tracing in magnetic elements, beam lines, spectrometers. It was perfected for the purpose of studying, and operating, the four spectrometers SPES I, II, III, IV at the Laboratoire National SATURNE (CEA-Saclay, France), and, later, SPEG at GANIL (Caen, France). Developments regarding spin tracking and ray-tracing in combined electric and magnetic fields were implemented, in the late 1980s and early 1990s respectively. In the mid-1990s, the computation of synchrotron radiation electromagnetic impulse and spectra was introduced, for the purpose of synchrotron radiation diagnostic R&D at LEP, and further applied to the design of the SR diagnostics installations at LHC in the early 2000s. In the mean time, several new optical elements were added, such as electro-magnetic and other electrostatic lenses. Used since several years for special studies in periodic machines (e.g., SATURNE at Saclay, COSY at Julich, LEP and LHC at CERN), zgoubi has also undergone extensive developments regarding storage ring related features. Many developments have been accomplished since the early 2000s in the frame of a number of project design and beam dynamics studies, as the neutrino factory, lepton and hadron colliders, spin studies at AGS and RHIC, etc. As a consequence the list of optical elements and the compendium of numerical methods, so-called “Glossary of Keywords” list, pp. 7 and 169, has stretched with new simulation and computing procedures, ranging from fitting (FIT2 procedure ; additional constraints) to overlapping magnetic field capabilities (DIPOLES, FFAG), spin manipulation (SPINR), optical elements (BEAMBEAM), radiation damping tools (SRLOSS) and many others (FAISTORE, MAP2D-E, OPTICS, PICKUPS, TWISS, etc.). The graphic interface to zgoubi (zpop, Part D) has undergone extensive developments, making it a convenient companion tool to the use of zgoubi.

43 PARTICLE ACCELERATORS↗

Influence of magnetic field strength on potential well in the ionization stage of a double stage Hall thruster

Similar to a single stage Hall thruster, the magnetic field, which controls electron trajectory and electric field distribution, is the most important factor determining the performance of a double stage Hall thruster. Especially, a potential well, which is helpful to reduce the ion loss on the thruster walls, is shaped in the ionization stage due to the existence of an annular magnetic field topology there. In this paper, the influence of magnetic field strength in the ionization stage on the potential well is researched with both experiments and particle-in-cell simulations. It is found that the depth of potential well increases with the magnetic field strength as a result of enhanced magnetic confinement and lowered electron conductivity. Consequently, the plasma density as well as the ion current entering the acceleration stage increases. However, an excessive magnetic field strength leads to an excess of ion loss on the walls of the acceleration stage. Therefore, there is an appropriate magnetic field strength in the ionization stage that results in a proper potential well and consequently an optimal performance of a double stage Hall thruster.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Giant magnetoresistance modulated by magnetic field in graphene p-n junction

We investigate the tunneling transport across a graphene p-n junction under the influence of a perpendicular magnetic field (B field). We observe a sideway deflection of the transmission profile, which can be quantitatively explained by invoking the classical Lorentz force. By considering the trajectory of the Dirac fermions along their cyclotron orbits, we analytically derive the incident angles for transmission across the graphene junction under a B field, as well as the critical magnetic field for full suppression of tunneling across the junction. These analytical predictions are consistent with the numerical results obtained via the non-equilibrium Green's function method. A stronger B-field conductance modulation is obtained for a p-n as opposed to an n-n or p-p type graphene junction. The magnetic field also induces a forbidden region of almost zero transmission for electron energy close to the Dirac point, which can be utilized to achieve a giant magnetoresistance effect. Based on our analysis, we devise an optimal magneto-electrical transport modulation, which can potentially realize a giant magnetoresistance effect in graphene p-n junction systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Coordination Sphere of Lanthanide Aqua Ions Resolved with Ab Initio Molecular Dynamics and X-ray Absorption Spectroscopy

To resolve the fleeting structures of lanthanide Ln 3+ aqua ions in solution, we (i) performed the first ab initio molecular dynamics (AIMD) simulations of the entire series of Ln 3+ aqua ions in explicit water solvent using pseudopotentials and basis sets recently optimized for lanthanides and (ii) measured the symmetry of the hydrating waters about Ln 3+ ions (Nd 3+ , Dy 3+ , Er 3+ , Lu 3+ ) for the first time with extended X-ray absorption fine structure (EXAFS). EXAFS spectra were measured experimentally and generated from AIMD trajectories to directly compare simulation, which concurrently considers the electronic structure and the atomic dynamics in solution, with experiment. In this study, we performed a comprehensive evaluation of EXAFS multiple-scattering analysis (up to 6.5 Å) to measure Ln–O distances and angular correlations (i.e., symmetry) and elucidate the molecular geometry of the first hydration shell. This evaluation, in combination with symmetry-dependent L 3 - and L 1 -edge spectral analysis, shows that the AIMD simulations remarkably reproduces the experimental EXAFS data. The error in the predicted Ln–O distances is less than 0.07 Å for the later lanthanides, while we observed excellent agreement with predicted distances within experimental uncertainty for the early lanthanides. Our analysis revealed a dynamic, symmetrically disordered first coordination shell, which does not conform to a single molecular geometry for most lanthanides. This work sheds critical light on the highly elusive coordination geometry of the Ln 3+ aqua ions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SU-G-JeP1-12: Head-To-Head Performance Characterization of Two Multileaf Collimator Tracking Algorithms for Radiotherapy

Purpose: Multi-leaf collimator (MLC) tracking is being clinically pioneered to continuously compensate for thoracic and abdominal motion during radiotherapy. The purpose of this work is to characterize the performance of two MLC tracking algorithms for cancer radiotherapy, based on a direct optimization and a piecewise leaf fitting approach respectively. Methods: To test the algorithms, both physical and in silico experiments were performed. Previously published high and low modulation VMAT plans for lung and prostate cancer cases were used along with eight patient-measured organ-specific trajectories. For both MLC tracking algorithm, the plans were run with their corresponding patient trajectories. The physical experiments were performed on a Trilogy Varian linac and a programmable phantom (HexaMotion platform). For each MLC tracking algorithm, plan and patient trajectory, the tracking accuracy was quantified as the difference in aperture area between ideal and fitted MLC. To compare algorithms, the average cumulative tracking error area for each experiment was calculated. The two-sample Kolmogorov-Smirnov (KS) test was used to evaluate the cumulative tracking errors between algorithms. Results: Comparison of tracking errors for the physical and in silico experiments showed minor differences between the two algorithms. The KS D-statistics for the physical experiments were below 0.05 denoting no significant differences between the two distributions pattern and the average error area (direct optimization/piecewise leaf-fitting) were comparable (66.64 cm2/65.65 cm2). For the in silico experiments, the KS D-statistics were below 0.05 and the average errors area were also equivalent (49.38 cm2/48.98 cm2). Conclusion: The comparison between the two leaf fittings algorithms demonstrated no significant differences in tracking errors, neither in a clinically realistic environment nor in silico. The similarities in the two independent algorithms give confidence in the use of either algorithm for clinical implementation.

60 APPLIED LIFE SCIENCES↗

Programmable-trajectory ultrafast flying focus pulses

“Flying focus” techniques produce laser pulses with dynamic focal points that travel distances much greater than a Rayleigh length. The implementation of these techniques in laser-based applications requires the design of optical configurations that can both extend the focal range and structure the radial group delay. This article describes a method for designing optical configurations that produce ultrashort flying focus pulses with programmable-trajectory focal points. The method is illustrated by several examples that employ an axiparabola for extending the focal range and either a reflective echelon or a deformable mirror-spatial light modulator pair for structuring the radial group delay. The latter configuration enables rapid exploration and optimization of flying foci, which could be ideal for experiments.

47 OTHER INSTRUMENTATION↗

A Hamiltonian Surface-Shaping Approach for Control System Analysis and the Design of Nonlinear Wave Energy Converters

The dynamic model of Wave Energy Converters (WECs) may have nonlinearities due to several reasons such as a nonuniform buoy shape and/or nonlinear power takeoff units. This paper introduces the Hamiltonian Surface-Shaping (HSS) approach as a tool for the analysis and design of nonlinear control of WECs. The Hamiltonian represents the stored energy in the system and can be constructed as a function of the WEC’s system states, its position, and velocity. The Hamiltonian surface is defined by the energy storage, while the system trajectories are constrained to this surface and determined by the power flows of the applied non-conservative forces. The HSS approach presented in this paper can be used as a tool for the design of nonlinear control systems that are guaranteed to be stable. The optimality of the obtained solutions is not addressed in this paper. The case studies displayed here cover regular and irregular waves and demonstrate that a nonlinear control system can result in a multiple fold increase in the harvested energy.

16 TIDAL AND WAVE POWER↗

Correlated Trajectory Uncertainty for Adaptive Sequential Decision Making

One of the great challenges with decision making tasks on real world systems is the fact that data is sparse and acquiring additional data is expensive. In these cases, it is often crucial to make a model of the environment to assist in making decisions. At the same time, limited data means that learned models are erroneous, making it just as important to equip the model with good predictive uncertainties. In the context of learning sequential decision making policies, these uncertainties can prove useful for informing which data to collect for the greatest improvement in policy performance \citep{mehta2021experimental, mehta2022exploration} or informing the policy about unsure regions of state and action space to avoid during test time \citep{yu2020mopo}. Additionally, assuming that realistic samples of the environment can be drawn, an adaptable policy can be trained that attempts to make optimal decisions for any given possible instance of the environment \citep{ghosh2022offline, chen2021offline}. In this work, we examine the so-called ``probabilistic neural network'' (PNN) model that is ubiquitous in model-based reinforcement learning (MBRL) works. We argue that while PNN models may have good marginal uncertainties, they form a distribution of non-smooth transition functions. Not only are these samples unrealistic and may hamper adaptability, but we also assert that this leads to poor uncertainty estimates when predicting multiple step trajectory estimates. To address this issue, we propose a simple sampling method that can be implemented on top of pre-existing models.We evaluate our sampling technique on a number of environments, including a realistic nuclear fusion task, and find that, not only do smooth transition function samples produce more calibrated uncertainties, but they also lead to better downstream performance for an adaptive policy.

Offline Reinforcement Learning↗

Enhancement of electron energy during vacuum laser acceleration in an inhomogeneous magnetic field

In this paper, the effect of a stationary inhomogeneous magnetic field on the electron acceleration by a high intensity Gaussian laser pulse is investigated. A focused TEM (0,0) laser mode with linear polarization in the transverse x-direction that propagates along the z-axis is considered. The magnetic field is assumed to be stationary in time, but varies longitudinally in space. A linear spatial profile for the magnetic field is adopted. In other words, the axial magnetic field increases linearly in the z-direction up to an optimum point z{sub m} and then becomes constant with magnitude equal to that at z{sub m}. Three-dimensional single-particle simulations are performed to find the energy and trajectory of the electron. The electron rotates around and stays near the z-axis. It is shown that with a proper choice of the magnetic field parameters, the electron will be trapped at the focus of the laser pulse. Because of the cyclotron resonance, the electron receives enough energy from the laser fields to be accelerated to relativistic energies. Using numerical simulations, the criteria for optimum regime of the acceleration mechanism is found. With the optimized parameters, an electron initially at rest located at the origin achieves final energy of γ=802. The dynamics of a distribution of off-axis electrons are also investigated in which shows that high energy electrons with small energy and spatial spread can be obtained.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Interpretation of autoencoder-learned collective variables using Morse–Smale complex and sublevelset persistent homology: An application on molecular trajectories

Dimensionality reduction often serves as the first step toward a minimalist understanding of physical systems as well as the accelerated simulations of them. In particular, neural network-based nonlinear dimensionality reduction methods, such as autoencoders, have shown promising outcomes in uncovering collective variables (CVs). However, the physical meaning of these CVs remains largely elusive. In this work, we constructed a framework that (1) determines the optimal number of CVs needed to capture the essential molecular motions using an ensemble of hierarchical autoencoders and (2) provides topology-based interpretations to the autoencoder-learned CVs with Morse–Smale complex and sublevelset persistent homology. Furthermore, this approach was exemplified using a series of n-alkanes and can be regarded as a general, explainable nonlinear dimensionality reduction method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Improving qubit readout with hidden Markov models

We demonstrate the application of pattern recognition algorithms via hidden Markov models (HMM) for qubit readout. This scheme provides a state-path trajectory approach capable of detecting qubit-state transitions and makes for a robust classification scheme with higher starting-state assignment fidelity than when compared to a multivariate Gaussian or a support vector machine scheme. Therefore, the method also eliminates the qubit-dependent readout time optimization requirement in current schemes. Using a HMM state discriminator we estimate fidelities reaching the ideal limit. Unsupervised learning gives access to transition matrix, priors, and IQ distributions, providing a toolbox for studying qubit-state dynamics during strong projective readout.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Toward fusion plasma scenario planning for NSTX-U using machine-learning-accelerated models

One of the most promising devices for realizing power production through nuclear fusion is the tokamak. To maximize performance, it is preferable that tokamak reactors achieve advanced operating scenarios characterized by good plasma confinement, improved magnetohydrodynamic (MHD) stability, and a largely non-inductively driven plasma current. Such scenarios could enable steady-state reactor operation with high \emph{fusion gain} --- the ratio of produced fusion power to the external power provided through the plasma boundary. Precise and robust control of the evolution of the plasma boundary shape as well as the spatial distribution of the plasma current, density, temperature, and rotation will be essential to achieving and maintaining such scenarios. The complexity of the evolution of tokamak plasmas, arising due to nonlinearities and coupling between various parameters, motivates the use of model-based control algorithms that can account for the system dynamics. In this work, a learning-based accelerated model trained on data from the National Spherical Torus Experiment Upgrade (NSTX-U) is employed to develop planning and control strategies for regulating the density and temperature profile evolution around desired trajectories. The proposed model combines empirical scaling laws developed across multiple devices with neural networks trained on empirical data from NSTX-U and a database of first-principles-based computationally intensive simulations. The reduced execution time of the accelerated model will enable practical application of optimization algorithms and reinforcement learning approaches for scenario planning and control development. An initial demonstration of applying optimization approaches to the learning-based model is presented, including a strategy for mitigating the effect of leaving the finite validity range of the accelerated model. The approach shows promise for actuator planning between experiments and in real-time.

machine learning↗

Optimizing infrasound observations for sample return capsule re-entry: Insights from OSIRIS-REx and Hayabusa2

The atmospheric entry of meteoroids presents a rare and unpredictable phenomenon, posing challenges for systematic observation and detailed characterization. Such events are nonetheless critical for advancing understanding of acoustic wave propagation, atmospheric structure, and entry dynamics. In contrast, sample return capsules (SRCs) from space missions follow well constrained re-entry trajectories, enabling planned observations of shock wave generation and propagation under controlled conditions. This study compares two SRC atmospheric entries, Hayabusa2 in 2020 and OSIRIS-REx in 2023, to assess how different infrasound array configurations influence shock wave detection and trajectory validation. Hayabusa2’s re-entry was monitored using a distributed network of 28 portable infrasound sensors across seven arrays in Woomera, Australia, permitting three-dimensional reconstruction of the trajectory and analysis of wave characteristics. For OSIRIS-REx, a compact four-sensor array deployed near Eureka Airport provided trajectory confirmation through arrival-time differences and back-azimuth estimates. Spectral and waveform analyses revealed differences in signal properties associated with variations in entry angle and velocity. The results illustrate both the strengths and the limitations of the deployed array configurations. The dense and distributed arrays during Hayabusa2’s re-entry enabled detailed trajectory reconstruction, whereas the compact array at Eureka primarily provided confirmation of signal coherence and back-azimuth consistency. These case studies highlight that even relatively small arrays, if located close to the predicted ground track, can still capture useful information on arrival direction and timing. Such insights provide practical guidance for planning future observational campaigns of SRC returns and other controlled atmospheric entries, and may also inform approaches to opportunistic observations of meteoroid events and other atmospheric acoustic phenomena.

celestial mechanics: orbit determination↗