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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Adaptive variational ground state preparation for spin-1 models on qubit-based architectures

Here, we apply the adaptive variational quantum imaginary time evolution (AVQITE) method to prepare ground states of one-dimensional spin S = 1 models. We compare different spin-to-qubit encodings (standard binary, Gray, unary, and multiplet) with regard to the performance and quantum resource cost of the algorithm. Using state-vector simulations, we study two well-known spin-1 models: the Blume-Capel model of transverse-field Ising spins with single-ion anisotropy, and the XXZ model with single-ion anisotropy. We consider system sizes of up to 20 qubits, which corresponds to spin-1 chains up to length 10. We determine the dependence of the number of CNOT gates in the AVQITE state preparation circuit on the encoding, the initial state, and the choice of operator pool in the adaptive method. Independent of the choice of encoding, we find that the CNOT gate count scales cubically with the number of spins for the Blume-Capel model and quartically for the anisotropic XXZ model. However, the multiplet and Gray encodings present smaller prefactors in the scaling relations. These results provide useful insights for the implementation of AVQITE on quantum hardware.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Open data set of live cyanobacterial cells imaged using an X-ray laser

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Calorimeter with Bayesian unfolding of spectra of high-flux broadband x rays

We report the development of a multipurpose differential x-ray calorimeter with a broad energy bandwidth. The absorber architecture is combined with a Bayesian unfolding algorithm to unfold high energy x-ray spectra generated in high-intensity laser–matter interactions. Particularly, we show how to extract absolute energy spectra and how our unfolding algorithm can reconstruct features not included in the initial guess. The performance of the calorimeter is evaluated via Monte Carlo generated data. The method accuracy to reconstruct electron temperatures from bremsstrahlung is shown to be 5% for electron temperatures from 1 to 50 MeV. We study bremsstrahlung generated in solid target interaction showing an electron temperature of 0.56 ± 0.04 MeV for a 700 μm Ti titanium target and 0.53 ± 0.03 MeV for a 50 μm target. We investigate bremsstrahlung from a target irradiated by laser-wakefield accelerated electrons showing an endpoint energy of 551 ± 5 MeV, inverse Compton generated x rays with a peak energy of 1.1 MeV, and calibrated radioactive sources. The total energy range covered by all these sources ranges from 10 keV to 551 MeV.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

Optimal experimental design for prediction based on push-forward probability measures

Incorporating experimental data is essential for increasing the credibility of simulation-aided decision making and design. This paper presents a method which uses a computational model to guide the optimal acquisition of experimental data to produce data-informed predictions of quantities of interest (QoI). Many strategies for optimal experimental design (OED) select data that maximize some utility that measures the reduction in uncertainty of uncertain model parameters, for example the expected information gain between prior and posterior distributions of these parameters. In this paper, we seek to maximize the expected information gained from the pushforward of an initial (prior) density to the push-forward of the updated (posterior) density through the parameter-to-prediction map. The formulation presented is based upon the solution of a specific class of stochastic inverse problems which seeks a probability density that is consistent with the model and the data in the sense that the push-forward of this density through the parameter-to-observable map matches a target density on the observable data. While this stochastic inverse problem forms the mathematical basis for our approach, we develop a one-step algorithm, focused on push-forward probability measures, that leverages inference-for-prediction to bypass constructing the solution to the stochastic inverse problem. A number of numerical results are presented to demonstrate the utility of this optimal experimental design for prediction and facilitate comparison of our approach with traditional OED.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Nonlinear sparse Bayesian learning for physics-based models

This paper addresses the issue of overfitting while calibrating unknown parameters of over-parameterized physics-based models with noisy and incomplete observations. Here, a semi-analytical Bayesian framework of nonlinear sparse Bayesian learning (NSBL) is proposed to identify sparsity among model parameters during Bayesian inversion. NSBL offers significant advantages over machine learning algorithm of sparse Bayesian learning (SBL) for physics-based models, such as 1) the likelihood function or the posterior parameter distribution is not required to be Gaussian, and 2) prior parameter knowledge is incorporated into sparse learning (i.e. not all parameters are treated as questionable). NSBL employs the concept of automatic relevance determination (ARD) to facilitate sparsity among questionable parameters through parameterized prior distributions. The analytical tractability of NSBL is enabled by employing Gaussian ARD priors and by building a Gaussian mixture-model approximation of the posterior parameter distribution that excludes the contribution of ARD priors. Subsequently, type-II maximum likelihood is executed using Newton's method whereby the evidence and its gradient and Hessian information are computed in a semi-analytical fashion. We show numerically and analytically that SBL is a special case of NSBL for linear regression models. Subsequently, a linear regression example involving multimodality in both parameter posterior pdf and model evidence is considered to demonstrate the performance of NSBL in cases where SBL is inapplicable. Next, NSBL is applied to identify sparsity among the damping coefficients of a mass-spring-damper model of a shear building frame. These numerical studies demonstrate the robustness and efficiency of NSBL in alleviating overfitting during Bayesian inversion of nonlinear physics-based models.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Small arms suppression project (LLNL final report)

US Special Operations Command (USSOCOM) was seeking a technological leap in small firearms weapon suppressor technology, because anticipated enemy capabilities are requiring the operators to have smaller detection cross sections to ensure the safe execution of missions. Suppressors have been developed almost exclusively through trial-and-error methods since the time of the original design by Hiram Maxim over one hundred years ago. Consequently USSOCOM deemed it prudent to perform a physicsbased study of weapon suppression to understand performance limits and possibly identify breakthrough technologies. Lawrence Livermore National Laboratory’s (LLNL’s) high performance production level computational tool called ALE3D (Arbitrary Lagrangian-Eulerian 3D and 2D) has unique physics models and numerical algorithms for modeling suppressor dynamics. The flexible and extendable code framework supports fully integrated hydrodynamics, heat transfer, solid and fluid dynamics, and chemistry that can be applied to simulating propellant-driven motion of a bullet down a gun barrel, the transfer of heat from the burning propellant to the barrel and suppressor, the chemistry of muzzle flash, and the shock/acoustic/optical signatures in the near-field. LLNL’s originally anticipated role was to augment ALE3D for this task, by developing the software and analysis methodologies specific to the simulation of blast and muzzle flash phenomena. It was believed that insights provided by our ALE3D simulations in tandem with a coordinated experimental component by our other team members from Oak Ridge National Laboratory (ORNL) and the U. S. Army Armament, Research, Development and Engineering Center (ARDEC), would have excellent prospects of yielding useful suppressor design improvements that could be transitioned to industry and utilized by US Special Operations Command. The three year effort has come to fruition with the development of revolutionary suppressor designs that far outperform any previous or current design by anyone outside this multi-lab team.

42 ENGINEERING↗
DOE OSTI2020

Detection prospects for the second-order weak decays of 124 Xe in multi-tonne xenon time projection chambers

We investigate the detection prospects for two-neutrino and neutrinoless second-order weak decays of 124 Xe – double-electron capture (0/2νECEC), electron capture with positron emission (0/2νECβ + ) and double-positron emission (0/2νβ + β + ) – in multi-tonne xenon time projection chambers. We simulate the decays in a liquid xenon medium and develop a reconstruction algorithm which uses the multi-particle coincidence in these decays to separate signal from background. This is used to compute the expected detection efficiencies as a function of position resolution and energy threshold for planned experiments. In addition, we consider an exhaustive list of possible background sources and find that they are either negligible in rate or can be greatly reduced using our topological reconstruction criteria. In particular, we draw two conclusions: First, with a theoretical half-life of $T^{2νECβ^+}_{1/2}$= (1.7 ± 0.6) ∙10 23 year, the 2νECβ + decay of 124 Xe will likely be detected in upcoming Dark Matter experiments (e.g. XENONnT or LZ), and their major background will be γ-rays from detector construction materials. Second, searches for the 0νECβ + decay mode will likely be background-free, and new parameter space may be within reach. To this end we investigate two different scenarios of existing experimental constraints on the effective neutrino mass. The necessary 500 kg-year exposure of 124 Xe could be achieved by the baseline design of the DARWIN observatory, or by extracting and using the 124 Xe from the tailings of the nEXO experiment. We demonstrate how a combination of 124 Xe results with those from 0νβ - β - searches in 136 Xe could help to identify the neutrinoless decay mechanism.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Multi-angle quantum approximate optimization algorithm

The quantum approximate optimization algorithm (QAOA) generates an approximate solution to combinatorial optimization problems using a variational ansatz circuit defined by parameterized layers of quantum evolution. In theory, the approximation improves with increasing ansatz depth but gate noise and circuit complexity undermine performance in practice. Here, we investigate a multi-angle ansatz for QAOA that reduces circuit depth and improves the approximation ratio by increasing the number of classical parameters. Even though the number of parameters increases, our results indicate that good parameters can be found in polynomial time for a test dataset we consider. This new ansatz gives a 33% increase in the approximation ratio for an infinite family of MaxCut instances over QAOA. The optimal performance is lower bounded by the conventional ansatz, and we present empirical results for graphs on eight vertices that one layer of the multi-angle anstaz is comparable to three layers of the traditional ansatz on MaxCut problems. Similarly, multi-angle QAOA yields a higher approximation ratio than QAOA at the same depth on a collection of MaxCut instances on fifty and one-hundred vertex graphs. Many of the optimized parameters are found to be zero, so their associated gates can be removed from the circuit, further decreasing the circuit depth. These results indicate that multi-angle QAOA requires shallower circuits to solve problems than QAOA, making it more viable for near-term intermediate-scale quantum devices.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

An added-mass partition algorithm for fluid–structure interactions of compressible fluids and nonlinear solids

We describe an added-mass partitioned (AMP) algorithm for solving fluid–structure interaction (FSI) problems involving inviscid compressible fluids interacting with nonlinear solids that undergo large rotations and displacements. The computational approach is a mixed Eulerian–Lagrangian scheme that makes use of deforming composite grids (DCG) to treat large changes in the geometry in an accurate, flexible, and robust manner. The current work extends the AMP algorithm developed in Banks et al. [1] for linearly elasticity to the case of nonlinear solids. To ensure stability for the case of light solids, the new AMP algorithm embeds an approximate solution of a nonlinear fluid–solid Riemann (FSR) problem into the interface treatment. The solution to the FSR problem is derived and shown to be of a similar form to that derived for linear solids: the state on the interface being fundamentally an impedance-weighted average of the fluid and solid states. Numerical simulations demonstrate that the AMP algorithm is stable even for light solids when added-mass effects are large. The accuracy and stability of the AMP scheme is verified by comparison to an exact solution using the method of analytical solutions and to a semi-analytical solution that is obtained for a rotating solid disk immersed in a fluid. The scheme is applied to the simulation of a planar shock impacting a light elliptical-shaped solid, and comparisons are made between solutions of the FSI problem for a neo-Hookean solid, a linearly elastic solid, and a rigid solid. The ability of the approach to handle large deformations is demonstrated for a problem of a high-speed flow past a light, thin, and flexible solid beam.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Theory of Trotter Error with Commutator Scaling

The Lie-Trotter formula, together with its higher-order generalizations, provides a simple approach to decomposing the exponential of a sum of operators. Despite significant effort, the error scaling of such product formulas remains poorly understood. We develop a theory of Trotter error that overcomes the limitations of truncating the Baker-Campbell-Hausdorff expansion. Our analysis directly exploits the commutativity of operator summands, producing tighter error bounds for both real- and imaginary-time evolutions. Whereas previous work achieves similar goals for systems with geometric locality or Lie-algebraic structure, our approach holds in general. We give a host of improved algorithms for digital quantum simulation and quantum Monte Carlo methods, nearly matching or even outperforming the best previous results. Our applications include: (i) a simulation of second-quantized plane-wave electronic structure, nearly matching the interaction-picture algorithm of Low and Wiebe; (ii) a simulation of $k$-local Hamiltonians almost with induced one-norm scaling, faster than the qubitization algorithm of Low and Chuang; (iii) a simulation of rapidly decaying power-law interactions, outperforming the Lieb-Robinson-based approach of Tran et al.; (iv) a hybrid simulation of clustered Hamiltonians, dramatically improving the result of Peng, Harrow, Ozols, and Wu; and (v) quantum Monte Carlo simulations of the transverse field Ising model and quantum ferromagnets, tightening previous analyses of Bravyi and Gosset. We obtain further speedups using the fact that product formulas can preserve the locality of the simulated system. Specifically, we show that local observables can be simulated with complexity independent of the system size for power-law interacting systems, which implies a Lieb-Robinson bound nearly matching a recent result of Tran et al. Our analysis reproduces known tight bounds for first- and second-order formulas. We further investigate the tightness of our bounds for higher-order formulas. For quantum simulation of a one-dimensional Heisenberg model with an even-odd ordering of terms, our result overestimates the complexity by only a factor of $5$. Our bound is also close to tight for power-law interactions and other orderings of terms. This suggests that our theory can accurately characterize Trotter error in terms of both the asymptotic scaling and the constant prefactor.

quantum computing, numerical analysis↗
DOE OSTI2017

Late-time growth rate, mixing, and anisotropy in the multimode narrowband Richtmyer–Meshkov instability: The θ-group collaboration

Turbulent Richtmyer–Meshkov instability (RMI) is investigated through a series of high resolution three-dimensional simulations of two initial conditions with eight independent codes. The simulations are initialised with a narrowband perturbation such that instability growth is due to non-linear coupling/backscatter from the energetic modes, thus generating the lowest expected growth rate from a pure RMI. By independently assessing the results from each algorithm and computing ensemble averages of multiple algorithms, the results allow a quantification of key flow properties as well as the uncertainty due to differing numerical approaches. A new analytical model predicting the initial layer growth for a multimode narrowband perturbation is presented, along with two models for the linear and non-linear regimes combined. Overall, the growth rate exponent is determined as θ=0.292±0.009, in good agreement with prior studies; however, the exponent is decaying slowly in time. Also, θ is shown to be relatively insensitive to the choice of mixing layer width measurements. The asymptotic integral molecular mixing measures Θ=0.792±0.014, Ξ=0.800±0.014, and Ψ=0.782±0.013 are lower than some experimental measurements but within the range of prior numerical studies. The flow field is shown to be persistently anisotropic for all algorithms, at the latest time having between 49% and 66% higher kinetic energy in the shock parallel direction compared to perpendicular and does not show any return to isotropy. The plane averaged volume fraction profiles at different time instants collapse reasonably well when scaled by the integral width, implying that the layer can be described by a single length scale and thus a single θ. In conclusion, quantitative data given for both ensemble averages and individual algorithms provide useful benchmark results for future research.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

End-to-End Workflow for Machine-Learning-Based Qubit Readout With QICK and hls4ml

In this article, we present an end-to-end workflow for superconducting qubit readout that embeds codesigned neural networks into the quantum instrumentation control kit (QICK). Capitalizing on the custom firmware and software of the QICK platform, which is built on Xilinx radiofrequency system-on-chip field-programmable gate arrays (FPGAs), we aim to leverage machine learning (ML) to address critical challenges in qubit readout accuracy and scalability. The workflow utilizes the hls4ml package and employs quantization-aware training to translate ML models into hardware-efficient FPGA implementations via user-friendly Python application programming interfaces. We experimentally demonstrate the design, optimization, and integration of an ML algorithm for single transmon qubit readout, achieving 96% single-shot fidelity with a latency of 32.25 ns and less than 16% FPGA lookup table resource utilization. Our results offer the community an accessible workflow to advance ML-driven readout and adaptive control in quantum information processing applications.

42 ENGINEERING↗
DOE OSTI2018

Generalized Multiscale Inversion for Heterogeneous Problems

In this work, we propose a generalized multiscale inversion algorithm for heterogeneous problems that aims at solving an inverse problem on a computational coarse grid. Previous inversion techniques for multiscale problems seek a coarse-grid medium properties, e.g., permeability and conductivity, and by doing so, they assume that there exists a homogenized representation of the underlying fine-scale permeability field on a coarse grid. Generally such assumptions do not hold for highly heterogeneous fields, e.g., fracture media or channelized fields, where the width of channels are very small compared to the scale of coarse grids. In these cases, grid refinement can lead to many degrees of freedom, and thus numerically unattractive to apply. The proposed algorithm is based on the Generalized Multiscale Finite Element Method (GMsFEM), which uses local spectral problems to identify non-localized features, i.e., channels (high-conductivity inclusions that connect the boundaries of the coarse-grid block). The inclusion of these features in the coarse space enables one to achieve a good accuracy. The approach is valid under the assumption that the solution can be well represented in a reduced-dimensional space spanned by multiscale basis functions. In practice, these basis functions are non-observable as we do not identify the fine-scale features of the permeability field. Our inversion algorithm finds the discretization parameters of the resulting system on the coarse grid. By doing so, we identify the appropriate coarse-grid parameters representing the permeability field instead of fine-grid permeability field. We illustrate the potential of the approach by numerical results for fractured media.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Anderson acceleration and application to the three-temperature energy equations

The Anderson acceleration method is an algorithm for accelerating the convergence of fixed-point iterations, including the Picard method. Anderson acceleration was first proposed in 1965 and, for some years, has been used successfully to accelerate the convergence of self-consistent field iterations in electronic-structure computations. Recently, the method has attracted growing attention in other application areas and among numerical analysts. Compared with a Newton-like method, an advantage of Anderson acceleration is that there is no need to form the Jacobian matrix. Thus the method is easy to implement. In this paper, an Anderson-accelerated Picard method is employed to solve the three-temperature energy equations, which are a type of strong nonlinear radiation-diffusion equations. Two strategies are used to improve the robustness of the Anderson acceleration method. One strategy is to adjust the iterates when necessary to satisfy the physical constraint. Another strategy is to monitor and, if necessary, reduce the matrix condition number of the least-squares problem in the Anderson-acceleration implementation so that numerical stability can be guaranteed. Numerical results show that the Anderson-accelerated Picard method can solve the three-temperature energy equations efficiently. Compared with the Picard method without acceleration, Anderson acceleration can reduce the number of iterations by at least half. A comparison between a Jacobian-free Newton–Krylov method, the Picard method, and the Anderson-accelerated Picard method is conducted in this paper.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

We report the development and deployment of a coarse-graining method that is well suited for computer simulations of aggregation and phase separation of protein sequences with block-copolymeric architectures. Our algorithm, named CAMELOT for Coarse-grained simulations Aided by MachinE Learning Optimization and Training, leverages information from converged all atom simulations that is used to determine a suitable resolution and parameterize the coarse-grained model. To parameterize a system-specific coarse-grained model, we use a combination of Boltzmann inversion, non-linear regression, and a Gaussian process Bayesian optimization approach. The accuracy of the coarse-grained model is demonstrated through direct comparisons to results from all atom simulations. We demonstrate the utility of our coarse-graining approach using the block-copolymeric sequence from the exon 1 encoded sequence of the huntingtin protein. This sequence comprises of 17 residues from the N-terminal end of huntingtin (N17) followed by a polyglutamine (polyQ) tract. Simulations based on the CAMELOT approach are used to show that the adsorption and unfolding of the wild type N17 and its sequence variants on the surface of polyQ tracts engender a patchy colloid like architecture that promotes the formation of linear aggregates. These results provide a plausible explanation for experimental observations, which show that N17 accelerates the formation of linear aggregates in block-copolymeric N17-polyQ sequences. The CAMELOT approach is versatile and is generalizable for simulating the aggregation and phase behavior of a range of block-copolymeric protein sequences.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Machine Learning Force Field Parameters from Ab Initio Data

Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. Our results were further improved by introducing an offset factor during the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local “shape” of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Multipartite Entanglement in Rabi-Driven Superconducting Qubits

The exploration of highly connected networks of qubits is invaluable for implementing various quantum algorithms and simulations, as it allows for entangling qubits with reduced circuit depth. Here, we demonstrate a multiqubit sideband tone-assisted Rabi-driven gate. Our scheme is inspired by the ion-qubit Mølmer-Sørensen gate and is mediated by a shared photonic mode and Rabi-driven superconducting qubits, which relaxes restrictions on qubit frequencies during fabrication and supports scalability. We achieve a two-qubit gate with a maximum state fidelity of 95% in 310 ns, a three-qubit gate with a state fidelity of 90.5% in 217 ns, and a four-qubit gate with a state fidelity of 66% in 200 ns. Furthermore, we develop a model of the gate that shows that the four-qubit gate is limited by shared resonator losses and the spread of qubit-resonator couplings, which must be addressed to reach high-fidelity operations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Scalable molecular dynamics on CPU and GPU architectures with NAMD

NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

high-performance computing↗