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At least 415 records · Page 23

Active Learning Framework

Machine learning (ML) of interatomic potentials show great promise to accelerate scientific simulation, e.g., by emulating expensive computations at a high accuracy but much reduced computational cost. Training datasets are calculated from computationally expensive ab initio quantum mechanics methods, density functional theory (DFT). Trained on this data, an ML model can be very successful in predicting energy and forces for new atomic configurations. A critical factor is the quality and diversity of the training dataset. Thus, a highly automated approach to dataset construction based on active learning framework is designed suitable for material physics. The active learning scheme begins with fully randomized atomic configurations. Then, many Molecular Dynamics (MD) trajectories are simulated using current ML potentials, where each MD trajectory is initialized to a random disordered configuration. The temperature is varied in order to diversify the sampled configuration during these simulations. The variance of predictions for eight neural networks within an ensemble is analyzed to determine whether the model is operating as expected. This helps in determining whether collecting more data would be helpful to the model by checking the ensemble variance is greater than the threshold. In this case, the MD trajectory is terminated and the final atomic configuration is placed on a queue (SQL database) for DFT calculations and added to training dataset. Periodically, ML model is retrained to the updated training model. This Active Learning loop is iterated until the cost of MD simulations becomes prohibitively expensive. The MD simulations will hopefully be sufficiently robust to support nucleation after many active learning iterations. In this sense, active learning scheme must automatically discover the important low energy and nonequilibrium physics.

Nebgen, Benjamin↗

Dislocation line tension model to improve understanding of the effects of hydrogen on the deformation of structural materials

Decarbonization efforts highlight hydrogen as an attractive alternative to fossil fuels, but its tendency to embrittle structural metals demands careful consideration when designing hydrogen infrastructure. Moreover, the mechanisms by which hydrogen degrades these materials are still being elucidated. The current work develops new computational tools to quantify the different contributions of hydrogen to the energy barrier of cross-slip, a key deformation mechanism. Novel features are implemented to a line tension model, which include the use of non-singular dislocation interactions, character-dependent dislocation energies and simulations of the constriction configurations. A new molecular dynamics technique is developed to calculate the interaction energy between the partials of a dissociated dislocation via fixing the centers of mass of the regions below and above the Shockley partials and performing time-averaged calculations. Hydrogen is found to impact the stacking fault width of dislocations in different ways depending on their characters: it decreases for dislocations with a character θ > 30°, remains unchanged for θ = 30° and increases for θ < 30°. The latter regime is a newly identified mechanism by which hydrogen inhibits cross-slip. Moreover, formation of nano-hydrides is predicted to occur around screw dislocations for high hydrogen concentrations, a phenomenon previously identified only in dislocations with an edge component. If nano-hydrides develop, their influence extending the equilibrium stacking fault width and increasing both the constriction and cross-slip energy barriers dominate over all other hydrogen contributions. The theory and tools developed will pave the way towards a comprehensive understanding of hydrogen-dislocation interactions in structural metals.

08 HYDROGEN↗

Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions

A key goal of molecular modeling is the accurate reproduction of the true quantum mechanical potential energy of arbitrary molecular ensembles with a tractable classical approximation. The challenges are that analytical expressions found in general purpose force fields struggle to faithfully represent the intermolecular quantum potential energy surface at close distances and in strong interaction regimes; that the more accurate neural network approximations do not capture crucial physics concepts, e.g., nonadditive inductive contributions and application of electric fields; and that the ultra-accurate narrowly targeted models have difficulty generalizing to the entire chemical space. We therefore designed a hybrid wide-coverage intermolecular interaction model consisting of an analytically polarizable force field combined with a short-range neural network correction for the total intermolecular interaction energy. Here, we describe the methodology and apply the model to accurately determine the properties of water, the free energy of solvation of neutral and charged molecules, and the binding free energy of ligands to proteins. The correction is subtyped for distinct chemical species to match the underlying force field, to segment and reduce the amount of quantum training data, and to increase accuracy and computational speed. For the systems considered, the hybrid ab initio parametrized Hamiltonian reproduces the two-body dimer quantum mechanics (QM) energies to within 0.03 kcal/mol and the nonadditive many-molecule contributions to within 2%. Simulations of molecular systems using this interaction model run at speeds of several nanoseconds per day.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids

Peptoids (poly-N-substituted glycines) are a class of synthetic polymers that are regioisomers of peptides (poly-C-substituted glycines), in which the point of side-chain connectivity is shifted from the backbone C to the N atom. Peptoids have found diverse applications as peptidomimetic drugs, protein mimetic polymers, surfactants, and catalysts. Computational modeling is valuable in the understanding and design of peptoid-based nanomaterials. In this work, we report the bottom-up parameterization of coarse-grained peptoid force fields based on the MARTINI peptide force field against all-atom peptoid simulation data. Our parameterization pipeline iteratively refits coarse-grained bonded interactions using iterative Boltzmann inversion and nonbonded interactions by matching the potential of mean force for chain extension. We assure good sampling of the amide bond cis/trans isomerizations in the all-atom simulation data using parallel bias metadynamics. We develop coarse-grained models for two representative peptoids—polysarcosine (poly(N-methyl glycine)) and poly(N-((4-bromophenyl)ethyl)glycine)—and show their structural and thermodynamic properties to be in excellent accord with all-atom calculations but up to 25-fold more efficient and compatible with MARTINI force fields. Here, this work establishes a new rigorously parameterized coarse-grained peptoid force field for the understanding and design of peptoid nanomaterials at length and time scales inaccessible to all-atom calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Engineering Catalysts for Selective Ester Hydrogenation

The development of efficient catalysts and processes for synthesizing functionalized (olefinic and/or chiral) primary alcohols and fluoral hemiacetals is currently needed. These are valuable building blocks for pharmaceuticals, agrochemicals, perfumes, and so forth. From an economic standpoint, bench-stable Takasago Int. Corp.’s Ru-PNP, more commonly known as Ru-MACHO, and Gusev’s Ru-SNS complexes are arguably the most appealing molecular catalysts to access primary alcohols from esters and H 2 . This work introduces economically competitive Ru-SNP(O) z complexes ( z = 0, 1), which combine key structural elements of both of these catalysts. In particular, the incorporation of SNP heteroatoms into the ligand skeleton was found to be crucial for the design of a more product-selective catalyst in the synthesis of fluoral hemiacetals under kinetically controlled conditions. Based on experimental observations and computational analysis, this paper further extends the current state-of-the-art understanding of the accelerative role of KO- t -C 4 H 9 in ester hydrogenation. Finally, it attempts to explain why a maximum turnover is seen to occur starting at ~25 mol % base, in contrast to only ~10 mol % with ketones as substrates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Roadmap on multiscale materials modeling

Modeling and simulation is transforming modern materials science, becoming an important tool for the discovery of new materials and material phenomena, for gaining insight into the processes that govern materials behavior, and, increasingly, for quantitative predictions that can be used as part of a design tool in full partnership with experimental synthesis and characterization. Modeling and simulation is the essential bridge from good science to good engineering, spanning from fundamental understanding of materials behavior to deliberate design of new materials technologies leveraging new properties and processes. This Roadmap presents a broad overview of the extensive impact computational modeling has had in materials science in the past few decades, and offers focused perspectives on where the path forward lies as this rapidly expanding field evolves to meet the challenges of the next few decades. The Roadmap offers perspectives on advances within disciplines as diverse as phase field methods to model mesoscale behavior and molecular dynamics methods to deduce the fundamental atomic-scale dynamical processes governing materials response, to the challenges involved in the interdisciplinary research that tackles complex materials problems where the governing phenomena span different scales of materials behavior requiring multiscale approaches. The shift from understanding fundamental materials behavior to development of quantitative approaches to explain and predict experimental observations requires advances in the methods and practice in simulations for reproducibility and reliability, and interacting with a computational ecosystem that integrates new theory development, innovative applications, and an increasingly integrated software and computational infrastructure that takes advantage of the increasingly powerful computational methods and computing hardware.

36 MATERIALS SCIENCE↗

Complex Structure of Molten FLiBe (2 Li F – Be F 2 ) Examined by Experimental Neutron Scattering, X-Ray Scattering, and Deep-Neural-Network Based Molecular Dynamics

The use of molten salts as coolants, fuels, and tritium breeding blankets in the next generation of fission and fusion nuclear reactors benefits from furthering the characterization of the molecular structure of molten halide salts, paving the way to predictive capability of the chemical and thermophysical properties of molten salts. Due to its neutronic, chemical, and thermochemical properties, 2 Li F - Be F 2 is a candidate molten salt for several fusion- and fission-reactor designs. We performed neutron and x-ray total-scattering measurements to determine the atomic structure of liquid 2 Li F - Be F 2 . We also performed and neural-network molecular-dynamics simulations to predict the structure obtained by neutron- and x-ray-diffraction experiments. The use of machine learning provides improvements to the efficiency in predicting the structure at a longer length scales than is achievable with simulations at significantly lower computational expense while retaining near accuracy. We found that the NNMD simulations accurately predicted the Be F 4 2 − oligomer formations seen in the experimental first-structure-factor peak. Our combination of high-resolution measurements with large-scale molecular dynamics provided an avenue to explore and experimentally verify the intermediate-range ordering beyond the first-nearest neighbor that has posed too many experimental and computational challenges in previous works. With a deeper understanding of the salt structure and ion ordering, the evolution of salt chemistry over the lifetime of a reactor can be better predicted, which is crucial to the licensing and operation of advanced fission and fusion reactors that employ molten salts. To this end, this work will serve as a reference for future studies of salt structure and macroscopic properties with and without the addition of solutes. Published by the American Physical Society 2024

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

TeraChem: A graphical processing unit-accelerated electronic structure package for large-scale ab initio molecular dynamics

TeraChem was born in 2008 with the goal of providing fast on-the-fly electronic structure calculations to facilitate ab initio molecular dynamics studies of large biochemical systems such as photoswitchable proteins and multichromophoric antenna complexes. Originally developed for videogaming applications, graphics processing units (GPUs) offered a low-cost parallel computer architecture that became more accessible for general-purpose GPU computing with the release of CUDA in 2007. The evaluation of the electron repulsion integrals (ERIs) is a major bottleneck in electronic structure codes and provides an attractive target for acceleration on GPUs. Thus, highly efficient routines for evaluation of and contractions between the ERIs and density matrices were implemented in TeraChem. Here, electronic structure methods were developed and implemented to leverage these integral contraction routines, resulting in the first quantum chemistry package designed from the ground up for GPUs. This GPU acceleration makes TeraChem capable of performing large-scale ground and excited state calculations in the gas and condensed phase. Today, TeraChem's speed forms the basis for a suite of quantum chemistry applications, including optimization and dynamics of proteins, automated and interactive chemical discovery tools, and large-scale nonadiabatic dynamics simulations.

74 ATOMIC AND MOLECULAR PHYSICS↗

Benchmarking the performance of uncertainty quantification methods for neural network-based interatomic potentials

Machine-learned interatomic potentials (ML-IAPs) continue to gain popularity as accurate, computationally efficient replacements for traditional, physics-based interatomic potentials and expensive ab initio methods. Uncertainty quantification (UQ) of ML-IAPs is a growing area of research as UQ is critical in many applications of IAPs, such as developing curated datasets, active learning-based data augmentation, self-improving models, and estimating the uncertainty of molecular dynamics simulations. In this paper, we construct and benchmark a series of different neural network potentials (NNPs) with varying network architectures to determine the performance of these models with respect to both the mean and uncertainty calibration error. Each NNP method is specifically designed to predict either epistemic or aleatoric uncertainty with particular focus on the differences in behavior between the epistemic and aleatoric uncertainty estimates. We benchmark these methods using multiple datasets common in the ML-IAP literature. The results show that the aleatoric uncertainty from single-shot model architectures is a competitive alternative to ensemble-based epistemic uncertainty predictions in regions of sufficient data-density. However, in regions where the representative data is sparse, aleatoric uncertainty models tend to overpredict and epistemic methods tend to underpredict the actual model error. We conclude that the type of UQ is crucial when discussing performance of probabilistic model results as different methods have different performance characteristics depending on the regime in which they are evaluated. Therefore, the type of UQ method should be carefully evaluated against both the data characteristics and requirements for the intended application.

97 MATHEMATICS AND COMPUTING↗

Thermal transport in defective and disordered materials

With significant recent advancements in thermal sciences—such as the development of new theoretical and experimental techniques, and the discovery of new transport mechanisms—it is helpful to revisit the fundamentals of vibrational heat conduction to formulate an updated and informed physical understanding. The increasing maturity of simulation and modeling methods sparks the desire to leverage these techniques to rapidly improve and develop technology through digital engineering and multi-scale, electro-thermal models. With that vision in mind, this review attempts to build a holistic understanding of thermal transport by focusing on the often unaddressed relationships between subfields, which can be critical for multi-scale modeling approaches. For example, we outline the relationship between mode-specific (computational) and spectral (analytical) models. We relate thermal boundary resistance models based on perturbation approaches and classic transmissivity based models. We discuss the relationship between lattice dynamics and molecular dynamics approaches along with two-channel transport frameworks that have emerged recently and that connect crystal-like and amorphous-like heat conduction. Throughout, we discuss best practices for modeling experimental data and outline how these models can guide material-level and system-level design.

42 ENGINEERING↗

Redesigned Human Metabolic Simulator

A design has been formulated for a proposed improved version of an apparatus that simulates atmospheric effects of human respiration by introducing controlled amounts of carbon dioxide, water vapor, and heat into the air. Denoted a human metabolic simulator (HMS), the apparatus is used for testing life-support equipment when human test subjects are not available. The prior version of the HMS, to be replaced, was designed to simulate the respiratory effects of as many as four persons. It exploits the catalytic combustion of methyl acetate, for which the respiratory quotient (the molar ratio of carbon dioxide produced to oxygen consumed) is very close to the human respiratory quotient of about 0.86. The design of the improved HMS provides for simulation of the respiratory effects of as many as eight persons at various levels of activity. The design would also increase safety by eliminating the use of combustion. The improved HMS (see figure) would include a computer that would exert overall control. The computer would calculate the required amounts of oxygen removal, carbon dioxide addition, water addition, and heat addition by use of empirical equations for metabolic profiles of respiration and heat. A blower would circulate air between the HMS and a chamber containing a life-support system to be tested. With the help of feedback from a mass flowmeter, the blower speed would be adjusted to regulate the rate of flow according to the number of persons to be simulated and to a temperature-regulation requirement (the air temperature would indirectly depend on the rate of flow, among other parameters). Oxygen would be removed from the circulating air by means of a commercially available molecular sieve configured as an oxygen concentrator. Oxygen, argon, and trace amounts of nitrogen would pass through a bed in the molecular sieve while carbon dioxide, the majority of nitrogen, and other trace gases would be trapped by the bed and subsequently returned to the chamber. If, as recommended, the oxygen concentrator were of a rotating twelve-bed design, then variations in the product stream could be made very small. Carbon dioxide would be added directly to the circulating air by simple injection from a supply tank. The rate of injection would be maintained at the required rate by use of a mass flowmeter/controller. In the same way, nitrogen would be added to make up for the small amount of nitrogen lost through the oxygen concentrator. Water vapor would be added to the circulating air by heating the corresponding required flow of water to steam in a heat exchanger. More heat, required to complete the simulation of the thermal effect of respiration, would be added through another heat exchanger. Heat would be supplied to both heat exchangers via a hot-oil loop.

Duffield, Bruce↗

CO 2 in Ionene–Ionic Liquid Composite Membranes

Abstract Ionene – ionic liquid (IL) composites are promising materials for CO 2 separation, yet a molecular‐level understanding of their structure and its impact on CO 2 speciation, solubility, rotation, and diffusivity remains unclear. Herein, using multimodal nuclear magnetic resonance (NMR), time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS), atomic force microscopy (AFM), and molecular dynamics (MD) simulations, we reveal that the composites contain IL‐rich domains extending across hundreds of nanometres within the ionene matrix, and these bicontinuous domains span the entire membrane depth. CO 2 also absorbs into the ionene matrix, with the distribution between two CO 2 species varying with temperature and time. The rotational correlation times of these two species are on the timescale of 0.1 and 1 ns, respectively. As IL content increases, the ionic domains expand, resulting in higher CO 2 solubility due to enhanced molecular dynamics and increased free volume in both ionene backbones and IL‐rich regions. Although CO 2 diffusion in the membranes is an order of magnitude slower than in bulk IL, the activation energy for CO 2 diffusion remains comparable. Ionene‐IL composites represent a promising platform for designing CO 2 separation membranes, offering enhanced CO 2 diffusion and selectivity through IL‐rich domains, and increased CO 2 solubility and mechanical integrity from the ionene matrix.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thermal modeling of nickel-hydrogen battery cells operating under transient orbital conditions

An analytical study of the thermal operating characteristics of nickel-hydrogen battery cells is presented. Combined finite-element and finite-difference techniques are employed to arrive at a computationally efficient composite thermal model representing a series-cell arrangement operating in conjunction with a radiately coupled baseplate and coldplate thermal bus. An aggressive, low-mass design approach indicates that thermal considerations can and should direct the design of the thermal bus arrangement. Special consideration is given to the potential for mixed conductive and convective processes across the hydrogen gap. Results of a compressible flow model are presented and indicate the transfer process is suitably represented by molecular conduction. A high-fidelity thermal model of the cell stack (and related components) indicates the presence of axial and radial temperature gradients. A detailed model of the thermal bus reveals the thermal interaction of individual cells and is imperative for assessing the intercell temperature gradients.

Schrage, Dean S.↗

Standard Isotherm Fit Information for Dry CO2 on Sorbents for 4-Bed Molecular Sieve

Onboard the ISS, one of the systems tasked with removal of metabolic carbon dioxide (CO2) is a 4-bed molecular sieve (4BMS) system. In order to enable a 4-person mission to succeed, systems for removal of metabolic CO2 must reliably operate for several years while minimizing power, mass, and volume requirements. This minimization can be achieved through system redesign and/or changes to the separation material(s). A material screening process has identified the most reliable sorbent materials for the next 4BMS. Sorbent characterization will provide the information necessary to guide system design by providing inputs for computer simulations.

Cmarik, G. E.↗

Probing the Local Site Disorder and Distortion in Pyrochlore High-Entropy Oxides

High-entropy oxides (HEOs) have attracted great interest in diverse fields because of their inherent opportunities to tailor and combine materials functionalities. The control of local order/disorder in the class is by extension a grand challenge toward realizing their vast potential. In this paper, we report the first examples of pyrochlore HEOs with five M-site cations, for Nd 2 M 2 O 7 , in which the local structure has been investigated by neutron diffraction and pair distribution function (PDF) analysis. The average structure of the pyrochlores is found to be orthorhombic Imma, in agreement with radius-ratio rules governing the structural archetype. The computed PDFs from density functional theory relaxed special quasirandom structure models are compared with real space PDFs in this work to evaluate M-site order/disorder. Reverse Monte Carlo combined with ab initio molecular dynamics and Metropolis Monte Carlo simulations demonstrates that Nd 2 (Ta 0.2 Sc 0.2 Sn 0.2 Hf 0.2 Zr 0.2 ) 2 O 7 is synthesized with its M-site local to nanoscale order highly randomized/disordered, while Nd 2 (Ti 0.2 Nb 0.2 Sn 0.2 Hf 0.2 Zr 0.2 ) 2 O 7+x exhibits a strong distortion of the TiO 6 octahedron and small degree of Ti chemical short-range order (SRO) on the subnanometer scale. Calculations suggest that this may be intrinsic, energetically favored SRO rather than due to sample processing. These results offer an important demonstration that the engineered variation of participating ions in HEOs, even among those with very similar radii, provides richly diverse opportunities to control local order/disorder motifs—and therefore materials properties for future designs. This work also hints at the exquisite level of detail that may be needed in computational and experimental data analysis to guide structure–property tuning in the emerging HEO materials class.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Building Toward the Future in Chemical and Materials Simulation with Accessible and Intelligently Designed Web Applications

Over the last few decades, significant progress has been made in the development and use of electronic structure and other molecular simulation methods. As these methods become more mature and are able to simulate larger and more complex chemical simulations, the need for improvement in scientific visualization, molecular builders, simplified input to simulation methods, and the development of new approaches and languages to describe simulations, along with workflows to carry them out, becomes more apparent. In this chapter, we describe our recent efforts in developing a prototype open-source computational tool called Arrows that combines NWChem, SQL and NoSQL databases, email, web APIs, and web applications in a way that make molecular and materials modeling accessible to all scientists and engineers. At the same time, because of its simplified input, it provides a framework for expert users to carry out large numbers of calculations and run complex workflows.

A density-functional theory study of the Al/AlOx/Al tunnel junction

The aluminum oxide tunnel junction is a key component of the majority of superconducting quantum devices. For high-quality, reproducible, and scalably manufacturable qubits, the ability to fabricate Josephson junctions (JJs) with a targeted critical current and high uniformity is essential. In this study, we use first-principles modeling to assess fundamental aspects of the atomic structure of both amorphous and crystalline aluminum oxide tunnel junctions and relate the structure to predicted performance metrics. We use modified ab initio molecular dynamics to develop realistic models of the tunnel junction, from which interface roughness and local thickness fluctuations are analyzed in an unbiased manner by training a neural network to identify the boundary between metal and oxide. We show that the effective thickness of the insulating part of the junction can be different from the apparent physical thickness. We calculate the rate of Cooper pair tunneling for the atomically resolved electrostatic potential using direct numerical solution in 3D, which shows a channeling effect that impacts the junction critical current. The predicted critical current is a useful JJ design parameter that can be accessed from the ab initio calculations without fitting parameters. To assess the limits of uniformity and fabrication choices (e.g., oxidation vs epitaxy), we compare the amorphous junctions to crystalline models, which show order of magnitude more efficient tunneling compared to the amorphous case, underlining the connection between atomistic structure and Cooper pair tunneling efficiency. Further, this work provides a foundation for ab initio materials design and evaluation to help accelerate future development of improved tunnel junctions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Free-Energy Calculations. A Mathematical Perspective

Ion channels are pore-forming assemblies of transmembrane proteins that mediate and regulate ion transport through cell walls. They are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses. They are also essential to cardiac processes, muscle contraction and epithelial transport. Ion channels from lower organisms can act as toxins or antimicrobial agents, and in a number of cases are involved in infectious diseases. Because of their important and diverse biological functions they are frequent targets of drug action. Also, simple natural or synthetic channels find numerous applications in biotechnology. For these reasons, studies of ion channels are at the forefront of biophysics, structural biology and cellular biology. In the last decade, the increased availability of X-ray structures has greatly advanced our understanding of ion channels. However, their mechanism of action remains elusive. This is because, in order to assist controlled ion transport, ion channels are dynamic by nature, but X-ray crystallography captures the channel in a single, sometimes non-native state. To explain how ion channels work, X-ray structures have to be supplemented with dynamic information. In principle, molecular dynamics (MD) simulations can aid in providing this information, as this is precisely what MD has been designed to do. However, MD simulations suffer from their own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. To assess the reliability of MD simulations it is only natural to turn to the main function of channels - conducting ions - and compare calculated ionic conductance with electrophysiological data, mainly single channel recordings, obtained under similar conditions. If this comparison is satisfactory it would greatly increase our confidence that both the structures and our computational methodologies are sufficiently accurate. Channel conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

free energy↗