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DOE OSTI2016

SU-G-TeP1-02: Analytical Stopping Power and Range Parameterization for Therapeutic Energy Intervals

Purpose: To develop a simple, analytic parameterization of stopping power and range, which covers a wide energy interval and is applicable to many species of projectile ions and target materials, with less than 15% disagreement in linear stopping power and 1 mm in range. Methods: The new parameterization was required to be analytically integrable from stopping power to range, and continuous across the range interval of 1 µm to 50 cm. The model parameters were determined from stopping power and range data for hydrogen, carbon, iron, and uranium ions incident on water, carbon, aluminum, lead and copper. Stopping power and range data was taken from SRIM. A stochastic minimization algorithm was used to find model parameters, with 10 data points per energy decade. Additionally, fitting was performed with 2 and 26 data points per energy decade to test the model’s robustness to sparse Results: 6 free parameters were sufficient to cover the therapeutic energy range for each projectile ion species (e.g. 1 keV – 300 MeV for protons). The model agrees with stopping power and range data well, with less than 9% relative stopping power difference and 0.5 mm difference in range. As few as, 4 bins per decade were required to achieve comparable fitting results to the full data set. Conclusion: This study successfully demonstrated that a simple analytic function can be used to fit the entire energy interval of therapeutic ion beams of hydrogen and heavier elements. Advantages of this model were the small number (6) of free parameters, and that the model calculates both stopping power and range. Applications of this model include GPU-based dose calculation algorithms and Monte Carlo simulations, where available memory is limited. This work was supported in part by a research agreement between United States Naval Academy and Louisiana State University: Contract No N00189-13-P-0786. In addition, this work was accepted for presentation at the American Nuclear Society Annual Meeting 2016.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2016

Hybrid framework for the simulation of stochastic chemical kinetics

Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie Stochastic Simulation Algorithm (SSA) [25]. While easy to implement and exact, the computational cost of using the Gillespie SSA to simulate such systems can become prohibitive as the frequency of reaction events increases. This has motivated numerous coarse-grained schemes, where the “fast” reactions are approximated either using Langevin dynamics or deterministically. While such approaches provide a good approximation when all reactants are abundant, the approximation breaks down when one or more species exist only in small concentrations and the fluctuations arising from the discrete nature of the reactions become significant. This is particularly problematic when using such methods to compute statistics of extinction times for chemical species, as well as simulating non-equilibrium systems such as cell-cycle models in which a single species can cycle between abundance and scarcity. In this paper, a hybrid jump-diffusion model for simulating well-mixed stochastic kinetics is derived. It acts as a bridge between the Gillespie SSA and the chemical Langevin equation. For low reactant reactions the underlying behaviour is purely discrete, while purely diffusive when the concentrations of all species are large, with the two different behaviours coexisting in the intermediate region. A bound on the weak error in the classical large volume scaling limit is obtained, and three different numerical discretisations of the jump-diffusion model are described. The benefits of such a formalism are illustrated using computational examples.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2019

Advising Big Data Transfer Over Dedicated Connections Based on Profiling Optimization

Big data transfer in next-generation scientific applications is currently commonly carried out over dedicated channels in high-performance networks (HPNs), where transport protocols play a critical role in maximizing application-level throughput. Optimizing the performance of these protocols is challenging: i) transport protocols perform differently in various network environments, and the protocol choice is not straightforward; ii) even for a given protocol in a given environment, different parameter settings of the protocol may lead to significantly different performance and oftentimes the default setting does not yield the best performance. However, it is prohibitively time-consuming to conduct exhaustive transport profiling due to the large parameter space. In this paper, we propose a PRofiling Optimization Based DAta Transfer Advisor (ProbData) to help end users determine the most effective transport method with the most appropriate parameter settings to achieve satisfactory performance for big data transfer over dedicated connections in HPNs. ProbData employs a fast profiling scheme based on the Simultaneous Perturbation Stochastic Approximation algorithm, namely, FastProf, to accelerate the exploration of the optimal operational zones of various transport methods to improve profiling efficiency. We first present a theoretical background of the optimized profiling approach in ProbData and then detail its design and implementation. The advising procedure and performance benefits of FastProf and ProbData are illustrated and evaluated by both extensive emulations based on real-life performance measurements and experiments over various physical connections in existing production HPNs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Adaptive tau-leaping methods for microscopic-lattice kinetic Monte Carlo simulations

Traditional Kinetic Monte Carlo (KMC) approaches, rooted in Gillespie’s stochastic simulation algorithm, become computationally demanding in systems with a large range of timescales. The goal of this work is to propose and study new adaptive lattice-KMC time integration strategies for spatially non-uniform systems. To that end, two novel adaptive tau-leaping methods and their corresponding time integration strategies are developed based on the idea of the “n-fold” direct KMC method. These strategies allow for the simultaneous execution of multiple reactions, advancing time by adaptively selected coarse increments. We present numerical experiments comparing the proposed methods with existing approaches in a catalytic surface kinetics application involving ammonia decomposition.

Bimolecular reactions↗

DOE OSTI2019

Stochastic self-tuning hybrid algorithm for reaction-diffusion systems

Many biochemical phenomena involve reactants with vastly different concentrations, some of which are amenable to continuum-level descriptions, while the others are not. We present a hybrid self-tuning algorithm to model such systems. The method combines microscopic (Brownian) dynamics for diffusion with mesoscopic (Gillespie-type) methods for reactions and remains efficient in a wide range of regimes and scenarios with large variations of concentrations. Furthermore, its accuracy, robustness, and versatility are balanced by redefining propensities and optimizing the mesh size and time step. We use a bimolecular reaction to demonstrate the potential of our method in a broad spectrum of scenarios: from almost completely reaction-dominated systems to cases where reactions rarely occur or take place very slowly. The simulation results show that the number of particles present in the system does not degrade the performance of our method. This makes it an accurate and computationally efficient tool to model complex multireaction systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

A Monte Carlo Rectangle Packing Algorithm for Identifying Likely Spatial Distributions of Final Closure Cap Subsidence in the E-Area Low-Level Waste Facility

A Monte Carlo rectangle packing algorithm, summarized in Figure ES-1, has been developed to provide insights into the likely spatial distribution of subsided areas or holes in the final closure cap for the E-Area Low-Level Waste Facility (ELLWF) resulting from the placement of non-crushable waste containers within slit and engineered trench disposal units. Using historical records provided by Solid Waste Management as an indicator of future waste streams, a probability distribution of unique waste containers was constructed, and Monte Carlo sampling was used to sequentially select waste containers for placement in a rectangular region bounded by the disposal unit footprint. Within this Monte Carlo approach, the probability of any container type being selected is weighted by the fractional abundance relative to all other container types. For each Monte Carlo realization, the frequency of non-crushable waste containers appearing at each location on a spatially discretized mesh is updated. After many realizations, the location(s) with the highest frequencies of non-crushable waste containers are regarded as the most likely locations to experience subsidence (i.e., for a hole to form). Utilizing this approach has enabled the down-selection of a computationally intractable set of subsidence hole combinations to be explored in three-dimensional finite element groundwater flow and contaminant transport models. Such an approach can be applied to a number of different packaging problems.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2017

Analysis of Monte Carlo accelerated iterative methods for sparse linear systems: Analysis of Monte Carlo accelerated iterative methods for sparse linear systems

Here, we consider hybrid deterministic-stochastic iterative algorithms for the solution of large, sparse linear systems. Starting from a convergent splitting of the coefficient matrix, we analyze various types of Monte Carlo acceleration schemes applied to the original preconditioned Richardson (stationary) iteration. We expect that these methods will have considerable potential for resiliency to faults when implemented on massively parallel machines. We also establish sufficient conditions for the convergence of the hybrid schemes, and we investigate different types of preconditioners including sparse approximate inverses. Numerical experiments on linear systems arising from the discretization of partial differential equations are presented.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Parameter optimization for transitions between memory states in small arrays of Josephson junctions

Coupled arrays of Josephson junctions possess multiple stable zero voltage states. Such states can store information and consequently can be utilized for cryogenic memory applications. Basic memory operations can be implemented by sending a pulse to one of the junctions and studying transitions between the states. In order to be suitable for memory operations, such transitions between the states have to be fast and energy efficient. Here in this article we employed simulated annealing, a stochastic optimization algorithm, to study parameter optimization of array parameters which minimizes times and energies of transitions between specifically chosen states that can be utilized for memory operations (Read, Write, and Reset). Simulation results show that such transitions occur with access times on the order of 10–100 ps and access energies on the order of 10 -19 –5×10 -18 J. Numerical simulations are validated with approximate analytical results.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides, important for metal extraction chemistry, are parametrized using ParFit.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

A light weight regularization for wave function parameter gradients in quantum Monte Carlo

The parameter derivative of the expectation value of the energy, ∂E/∂p, is a key ingredient in variational Monte Carlo (VMC) wave function optimization methods. In some cases, a naïve estimate of this derivative suffers from an infinite variance, which inhibits the efficiency of optimization methods that rely on a stable estimate of the derivative. In this work, we derive a simple regularization of the naïve estimator, which is trivial to implement in existing VMC codes, has finite variance, and a negligible bias, which can be extrapolated to zero bias with no extra cost. We use this estimator to construct an unbiased, finite variance estimation of ∂E/∂p for a multi-Slater–Jastrow trial wave function on the LiH molecule and in the optimization of a multi-Slater–Jastrow trial wave function on the CuO molecule. This regularized estimator is a simple and efficient estimator of ∂E/∂p for VMC optimization techniques.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Nonequilibrium design strategies for functional colloidal assemblies

Here, we use a nonequilibrium variational principle to optimize the steady-state, shear-induced interconversion of self-assembled nanoclusters of DNA-coated colloids. Employing this principle within a stochastic optimization algorithm allows us to identify design strategies for functional materials. We find that far-from-equilibrium shear flow can significantly enhance the flux between specific colloidal states by decoupling trade-offs between stability and reactivity required by systems in equilibrium. For isolated nanoclusters, we find nonequilibrium strategies for amplifying transition rates by coupling a given reaction coordinate to the background shear flow. We also find that shear flow can be made to selectively break detailed balance and maximize probability currents by coupling orientational degrees of freedom to conformational transitions. For a microphase consisting of many nanoclusters, we study the flux of colloids hopping between clusters. We find that a shear flow can amplify the flux without a proportional compromise on the microphase structure. This approach provides a general means of uncovering design principles for nanoscale, autonomous, functional materials driven far from equilibrium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Validating sequential Monte Carlo for gravitational-wave inference

Nested sampling (NS) is the preferred stochastic sampling algorithm for gravitational-wave inference for compact binary coalescences. It can handle the complex nature of the gravitational-wave likelihood surface and provides an estimate of the Bayesian model evidence. However, there is another class of algorithms that meets the same requirements, but has not been used for gravitational-wave analyses: sequential Monte Carlo (SMC), an extension of importance sampling that maps samples from an initial density to a target density via a series of intermediate densities. In this work, we validate a type of SMC algorithm, called persistent sampling (PS), for gravitational-wave inference. We consider a range of different scenarios including binary black holes and binary neutron stars and real and simulated data and show that PS produces results that are consistent with NS whilst being, on average, 2 times more efficient and 2.74 times faster. This demonstrates that PS is a viable alternative to NS that should be considered for future gravitational-wave analyses.

black hole mergers↗

DOE OSTI2023

Solving the nuclear pairing model with neural network quantum states

In this work, we present a variational Monte Carlo method that solves the nuclear many-body problem in the occupation number formalism exploiting an artificial neural network representation of the groundstate wave function. A memory-efficient version of the stochastic reconfiguration algorithm is developed to train the network by minimizing the expectation value of the Hamiltonian. We benchmark this approach against widely used nuclear many-body methods by solving a model used to describe pairing in nuclei for different types of interaction and different values of the interaction strength. Despite its polynomial computational cost, our method outperforms coupled-cluster and provides energies that are in excellent agreement with the numerically-exact full configuration interaction values.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2018

Simulation-Based Parameter Optimization Framework for Large-Scale Hybrid Smart Grid Communications Systems Design

The design of reliable, dynamic, fault-tolerant hybrid smart grid communication networks is a challenge to achieve for autonomous power grids. Hybrid networks use different communications technologies for different area networks. A simulation-based parameter optimization framework is proposed to tune parameters of hybrid communication technologies to achieve the optimal network performance. It consists of three main components: a parallel executor used to speedup a list of simulations; a sampler running simulations using the parallel executor at each generation; and a hybrid stochastic optimization algorithm for tuning configurable parameters of hybrid designs and applications. The proposed hybrid metaheuristic optimization algorithm combines an evolutionary algorithm with a gradient method to quickly achieve an approximately global optimum solution. Three optimization test functions are employed to train the adjustable parameters of the hybrid algorithm. Results show the proposed parameter optimization framework can help the designer choose the right hybrid architecture with an optimal parameter set for a large-scale broadband PLC-WiMAX hybrid smart grid communication network.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2025

Distributed Stochastic Optimization of a Neural Representation Network for Time-Space Tomography Reconstruction

4D time-space reconstruction of dynamic events or deforming objects using X-ray computed tomography (CT) is an important inverse problem in non-destructive evaluation. Conventional back-projection based reconstruction methods assume that the object remains static for the duration of several tens or hundreds of X-ray projection measurement images (reconstruction of consecutive limited-angle CT scans). However, this is an unrealistic assumption for many in-situ experiments that causes spurious artifacts and inaccurate morphological reconstructions of the object. To solve this problem, we propose to perform a 4D time-space reconstruction using a distributed implicit neural representation (DINR) network that is trained using a novel distributed stochastic training algorithm. Our DINR network learns to reconstruct the object at its output by iterative optimization of its network parameters such that the measured projection images best match the output of the CT forward measurement model. Here, we use a forward measurement model that is a function of the DINR outputs at a sparsely sampled set of continuous valued 4D object coordinates. Unlike previous neural representation architectures that forward and back propagate through dense voxel grids that sample the object's entire time-space coordinates, we only propagate through the DINR at a small subset of object coordinates in each iteration resulting in an order-of-magnitude reduction in memory and compute for training. DINR leverages distributed computation across several compute nodes and GPUs to produce high-fidelity 4D time-space reconstructions. We use both simulated parallel-beam and experimental cone-beam X-ray CT datasets to demonstrate the superior performance of our approach.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Optimization of rotational arc station parameter optimized radiation therapy

Purpose: To develop a fast optimization method for station parameter optimized radiation therapy (SPORT) and show that SPORT is capable of matching VMAT in both plan quality and delivery efficiency by using three clinical cases of different disease sites. Methods: The angular space from 0° to 360° was divided into 180 station points (SPs). A candidate aperture was assigned to each of the SPs based on the calculation results using a column generation algorithm. The weights of the apertures were then obtained by optimizing the objective function using a state-of-the-art GPU based proximal operator graph solver. To avoid being trapped in a local minimum in beamlet-based aperture selection using the gradient descent algorithm, a stochastic gradient descent was employed here. Apertures with zero or low weight were thrown out. To find out whether there was room to further improve the plan by adding more apertures or SPs, the authors repeated the above procedure with consideration of the existing dose distribution from the last iteration. At the end of the second iteration, the weights of all the apertures were reoptimized, including those of the first iteration. The above procedure was repeated until the plan could not be improved any further. The optimization technique was assessed by using three clinical cases (prostate, head and neck, and brain) with the results compared to that obtained using conventional VMAT in terms of dosimetric properties, treatment time, and total MU. Results: Marked dosimetric quality improvement was demonstrated in the SPORT plans for all three studied cases. For the prostate case, the volume of the 50% prescription dose was decreased by 22% for the rectum and 6% for the bladder. For the head and neck case, SPORT improved the mean dose for the left and right parotids by 15% each. The maximum dose was lowered from 72.7 to 71.7 Gy for the mandible, and from 30.7 to 27.3 Gy for the spinal cord. The mean dose for the pharynx and larynx was reduced by 8% and 6%, respectively. For the brain case, the doses to the eyes, chiasm, and inner ears were all improved. SPORT shortened the treatment time by ∼1 min for the prostate case, ∼0.5 min for brain case, and ∼0.2 min for the head and neck case. Conclusions: The dosimetric quality and delivery efficiency presented here indicate that SPORT is an intriguing alternative treatment modality. With the widespread adoption of digital linac, SPORT should lead to improved patient care in the future.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Whole cell simulator

A whole cell model (WCM) is a comprehensive multi-scale computational model representing all the known biochemical processes in a cell. It relies on a variety of intracellular pathway models and omics data. This computational framework enables seamless integration of diverse simulation methods used in WCM such as stochastic simulation algorithm (SSA), ordinary differential equations (ODE), flux balance analysis (FBA), and logic-based approaches. These methods run simultaneously, not only for whole pathways but also for subsets of reactions. Furthermore, we aim to enable dynamic switching between the methods when beneficial. Is

GEORGAKOUDIS, GIORGIS↗

DOE OSTI2019

Application of a new hybrid particle swarm optimization-mixed kernels function-based support vector machine model for reservoir porosity prediction: A case study in Jacksonburg-Stringtown oil field, West Virginia, USA

Porosity is a fundamental property that characterizes the storage capability of fluid and gas-bearing formations in a reservoir. An accurate porosity value can be measured from core samples in the laboratory; however, core analysis is expensive and time consuming. Well-log data can be used to calculate porosity, but the availability of log suites is often limited in mature fields. Therefore, robust porosity prediction requires integration of core-measured porosity with available well-log suites to control for changes in lithology and fluid content. A support vector machine (SVM) model with mixed kernel function (MKF) is used to construct the relationship between limited conventional well-log suites and sparse core data. Porosity is the desired output, and two conventional well-log responses (gamma ray [GR] and bulk density) and three well-log-derived parameters (the slope of GR, the slope of density, and [Formula: see text]) are input parameters. A global stochastic searching algorithm, particle swarm optimization (PSO), is applied to improve the efficiency of locating the appropriate values of five control parameters in MKF-SVM model. The results of SVM with different traditional kernel functions were compared, and the MKF-SVM model provided an improvement over the traditional SVM model. To confirm the advantage of the hybrid PSO-MKF-SVM model, the results from three models: (1) radial basis function (RBF)-based least-squares SVM, (2) multilayer perceptron artificial neural network (ANN), and (3) RBF ANN, are compared with the result of the hybrid PSO-MKF-SVM model. The results indicate that the hybrid PSO-MKF-SVM model improves porosity prediction with the highest correlation coefficient ([Formula: see text] of 0.9560), the highest coefficient of determination ([Formula: see text] of 0.9140), the lowest root-mean-square error (1.6505), average absolute error value (1.4050), and maximum absolute error (2.717).

Geochemistry & Geophysics↗