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DOE OSTI2024

Effect of layer bending on montmorillonite hydration and structure from molecular simulation

Conceptual models of smectite hydration include planar (flat) clay layers that undergo stepwise expansion as successive monolayers of water molecules fill the interlayer regions. However, X-ray diffraction (XRD) studies indicate the presence of interstratified hydration states, suggesting non-uniform interlayer hydration in smectites. Additionally, recent theoretical studies have shown that clay layers can adopt bent configurations over nanometer-scale lateral dimensions with minimal effect on mechanical properties. Therefore, in this study we used molecular simulations to evaluate structural properties and water adsorption isotherms for montmorillonite models composed of bent clay layers in mixed hydration states. Results are compared with models consisting of planar clay layers with interstratified hydration states (e.g. 1W–2W). The small degree of bending in these models (up to 1.5 Å of vertical displacement over a 1.3 nm lateral dimension) had little or no effect on bond lengths and angle distributions within the clay layers. Except for models that included dry states, porosities and simulated water adsorption isotherms were nearly identical for bent or flat clay layers with the same averaged layer spacing. Similar agreement was seen with Na- and Ca-exchanged clays. In conclusion, while the small bent models did not retain their configurations during unconstrained molecular dynamics simulation with flexible clay layers, we show that bent structures are stable at much larger length scales by simulating a 41.6×7.1 nm 2 system that included dehydrated and hydrated regions in the same interlayer.

58 GEOSCIENCES↗

DOE OSTI2025

Stockmayer fluid simulations for viscosity and glass transition temperature of ionic liquids

We develop a Stockmayer fluid model for molecular dynamics simulations of ionic liquids that captures molecular polarization, ionic conductivity, viscosity, and glass transition temperature, using ethylammonium nitrate (EAN) as an example. The ions in EAN are treated as spheres interacting via the Lennard-Jones potential with an embedded point charge and a permanent dipole moment. We show that our simulation results for EAN are consistent with experimental data and then explore the effects of the molecular parameters on the viscosity of ionic liquids. Our results indicate that viscosity monotonically increases with ionic charge and dipole moment but non-monotonically changes with ionic diameter (or molar volume). This non-monotonic trend arises from the competition among the electrostatic interactions, molecular packing, and size asymmetry between the cation and anion. In conclusion, our model also shows that long-lived ion pairs result in higher viscosities.

Coarse-grained simulations↗

DOE OSTI2020

Interfacial solvation and slow transport of hydrated excess protons in non-ionic reverse micelles

This work employs molecular dynamics simulations to investigate the solvation and transport properties of hydrated excess protons (with a hydronium-like core structure) in non-ionic Igepal CO-520 reverse micelles of various sizes in a non-polar solvent. Multiscale Reactive Molecular Dynamics (MS-RMD) simulations were used to describe vehicular and hopping diffusion during the proton transport process. As detailed herein, an excess proton shows a marked tendency to localize in the interfacial region of micellar water pools. Slow proton transport was observed which becomes faster with increasing micellar size. Further analysis reveals that the slow diffusion of an excess proton is a combined result of slow water diffusion and the low proton hopping rate. This study also confirms that a low proton hopping rate in reverse micelles stems from the interfacial solvation of hydrated excess protons and the immobilization of interfacial water. The low water density in the interfacial region makes it difficult to form a complete hydrogen bond network near the hydrated excess proton, and therefore locks in the orientation of hydrated proton cations. The immobilization of the interfacial water also slows the relaxation of the overall hydrogen bond network.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

First-Principles Grand-Canonical Simulations of Water Adsorption in Proton-Exchanged Zeolites

Water appears by design or as impurities in many important reactive systems. For those catalyzed by porous solid acids, such as widely used zeolites, experimentally quantifying the amount or elucidating the structure of adsorbed water clusters at reaction conditions is challenging, while computational studies (e.g., first-principles molecular dynamics simulations) often need to assume the loading to examine solvation effects. Furthermore, we perform first-principles grand-canonical simulations to predict water adsorption to H-ZSM-5 zeolites under specified experimental conditions. Presampling with inexpensive force fields and a pool-based parallelization algorithm are used to improve simulation efficiency, while molecular dynamics is used to sample configurations involving hydronium species. We observe that H + exchange dramatically increases the hydrophilicity of zeolite MFI and an appreciable amount of water is present at very low relative humidities. At all conditions examined, the zeolitic protons are found to dissociate readily from the surface basic sites and become mobile by participating in the hydrogen-bonded chains of adsorbed water molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Discrete stochastic model of point defect-dislocation interaction for simulating dislocation climb

Dislocation climb is an important high temperature process in metals plasticity, responsible for the phenomena such as creep, swelling, or hardening. Climb is defined by the ability of dislocations to leave their original glide plane by interacting with point defects. As such, dislocation climb is controlled by point defect diffusion/absorption/emission, all of which involve thermal activation. The existing thermodynamically consistent models for climb are generally formulated in a continuum framework, through the definition of effective defect fluxes and climb propensities in response to thermodynamic driving forces. However, the point-wise discrete nature of vacancies (and/or self-interstitials) confers a highly discrete nature to the climb dynamics, which is also strongly affected by elastic forces. The combination of discreteness, thermal activation, and elasticity makes this process too challenging for direct atomistic methods such as molecular dynamics. Here we develop a kinetic Monte Carlo model that captures vacancy generation and transport kinetics acting in conjuction with the evolving elastic fields provided by discrete dislocation dynamics simulations. The two models are coupled via the applied stresses and stress gradients generated by dislocation structures at vacancy locations. Our simulations reveal two surprising results. First that climb is dominated by vacancy emission even when the background vacancy concentration is much higher than the equilibrium one. And, second, that climb velocities might be much faster than otherwise believed when one uses the classical theories of climb. These effects are due to the locality of vacancy-dislocation processes, which are not captured in classical treatments that assume smooth vacancy fluxes and homogeneous concentrations. We apply the method to study elementary climb processes in body-centered cubic iron and furnish climb mobility functions to be used in parametric dislocation dynamics and/or crystal plasticity simulations. Here, we apply the technique to study non-conservative plastic bypass of spherical precipitates by edge dislocations and point out the differences between our discrete approach and existing continuum formulations.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Charge regulation effects on colloidal mixture nanoparticles

Changes in pH within a system containing dissociable sites affect the protonation and deprotonation of these groups, thereby influencing their physical properties. In response, the system modifies their surface charge, affecting electrostatic interactions, aggregation, stability, and structural behavior. Although the pH can be tuned in experiments, it is difficult to model this phenomenon using simulations or theoretical approaches. Here, we perform hybrid Monte Carlo-molecular dynamics simulations to model charge regulation effects in an equimolar colloidal charged system. We compare charge regulation effects with those of a system in which the charges of colloidal nanoparticles are not dissociable. The comparison between the two cases modifies the phase diagram, and it changes the volume fraction where a percolation network of nanoparticles is found. Charge regulation is found to destroy network formation, as the charge in the nanoparticles is modified because of the cooperativity dependency of the degree of charge dissociation sites among the nanoparticles favoring cluster formation. Furthermore, our work suggests that the ionic and/or electronic conductivity in functionalized nanoparticles can be modified by changing pH values. It also guides the experimental design of oppositely charged nanoparticles as inks for 3D printing processes.

Classical statistical mechanics↗

DOE OSTI2024

A model for trapping and re-solution regarding intra-granular bubbles in UO 2 , linked to atomic-scale simulations

In the literature, a clear definition of the irradiation re-solution frequency of gas from bubbles in the UO 2 fuel is absent. Moreover, for intra-granular bubbles, a detailed calculation of the cumulated displaced gas quantities in function of the distance from the radius of the bubble after a re-solution event has never been published. The assessment of these two elements is very useful if we want to increase the adherence of fission gas release codes to our present knowledge of the behavior of fission gases. Hence, we suggest to link the definition of the re-solution frequency to atomic-scale simulations. Furthermore, we present the cumulated displaced gas quantities obtained from Molecular Dynamics calculations, from which we have derived a re-solution profile that can be exploited to better consider the irradiation re-solution phenomenon inside Fission Gas Release codes. On top of that, we have built a new trapping/re-solution model for intra-granular bubbles linked to Molecular Dynamics simulations that can be easily incorporated into Fission Gas Release codes. In conclusion, we also check that the model is properly built through the comparison of the new model against a reference.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Sequence Modulates Polypeptoid Hydration Water Structure and Dynamics

We use molecular dynamics simulations to investigate the effect of polypeptoid sequence on the structure and dynamics of its hydration waters. Polypeptoids provide an excellent platform to study small-molecule hydration in disordered polymers, as they can be precisely synthesized with a variety of sidechain chemistries. We examine water behavior near a set of peptoid oligomers in which the number and placement of nonpolar versus polar sidechains are systematically varied. To do this, we leverage a new computational workflow enabling accurate sampling of polypeptoid conformations. We find that the hydration waters are less dense, are more tetrahedral, and have slower dynamics compared to bulk water. The magnitude of these shifts increases with the number of nonpolar groups. Here, we also find that shifts in the water structure and dynamics are strongly correlated, suggesting that experimental insight into the dynamics of hydration water obtained by Overhauser dynamic nuclear polarization (ODNP) also contains information about water structural properties. We then demonstrate the ability of ODNP to probe site-specific dynamics of hydration water near these model peptoid systems.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Dynamic soil columns simulate Arctic redox biogeochemistry and carbon release during changes in water saturation

Thawing Arctic permafrost can induce hydrologic change and alter redox conditions, shifting the balance of soil organic matter (SOM) decomposition. There remains uncertainty about how soil saturation and redox transitions impact dissolved and gas phase carbon fluxes, and efforts to link hydrobiogeochemical processes to ecosystem-scale models are limited. This study evaluates SOM decomposition of Arctic tundra soils using column experiments, water chemistry measurements, microbial community analysis, and a PFLOTRAN reactive transport model. Soil columns from a thermokarst channel (TC) and an upland tundra (UC) were exposed to cycles of saturation and drainage, which controlled carbon emissions. During saturation, an outflow of dissolved organic carbon from the UC soil correlated with elevated reduced iron and decreased pH; during drainage, UC carbon dioxide fluxes were 70% higher than TC fluxes. Intermittent methane release was observed for TC, consistent with higher methanogen abundance. Slower drainage in the TC soil correlated with more subtle biogeochemical changes. PFLOTRAN simulations captured experimental trends in soil carbon fluxes, oxygen concentrations, and water contents. The model was then used to evaluate additional soil water drainage rates. This study emphasizes the importance of considering hydrologic change when evaluating and simulating SOM decomposition in dynamic Arctic tundra environments.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Structure and dynamical properties of two-dimensional dusty plasmas on one-dimensional periodic substrates

In the presence of the substrate, various structural and dynamical properties of two-dimensional dusty plasma (2DDP) were investigated using Langevin dynamical simulations. This paper reviews a series of results of the structural and dynamical properties of 2DDP modified by one-dimensional periodic substrates (1DPSs) as follows. First, when the depth of the 1DPS increases gradually, it is found that the static structural order of 2DDP along each potential well of the 1DPS increases first, and then decreases gradually. When the width of the 1DPS increases gradually, the particle arrangement in each potential well of the 1DPS changes from one straight row gradually to two rows, including the stable zigzag structure. Second, when there are two rows in each potential well of the 1DPS, the phonon spectra are split into two branches, corresponding to the breathing and sloshing modes, respectively. In addition, due to the pure repulsion between dust particles, from the obtained phonon spectra, the sloshing wave propagates backward at small wave numbers. Third, the calculated mean-square displacement (MSD) shown that, at the intermediate timescale between the initial ballistic and final diffusive motions, the particle motion tends to be more subdiffusive while the depth of the 1DPS increases. While the width of the 1DPS increases gradually, the long-time diffusive motion first increases, then decreases, and finally increases again, exhibiting the oscillation-like diffusion, due to the stable zigzag structure. Finally, when an external direct-current driving force is applied on all particles of 2DDP, three different depinning phases are discovered, which are the pinned, disordered plastic flow, and moving ordered states, respectively, as the driving force increases from zero. In addition, the continuous/discontinuous property of the phase transition between these different depinning states is investigated, showing that the transition property is modulated by the depth of the applied 1DPS

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Effect of water models on structure and dynamics of lignin in solution

Lignin, a major biomass component, can be an excellent source for different monomers in the polymer industry. However, the complex and heterogeneous structure of lignin poses a significant challenge for designing energy-efficient processes for depolymerization. As many proposed depolymerization processes are solvothermal, it is essential to understand the structure and dynamics of lignin in solution, in particular aqueous solution. Here, we utilize molecular dynamics simulations to understand the effect of water models on the structure and dynamics of different model lignin oligomers (softwood and hardwood) as a function of temperature. We have examined three different water models: TIP3P, TIP4P/Ew, and flexible SPC/Fw. We find that the diffusion constant of lignin oligomers in an aqueous solution differs significantly depending on the water model used. The diffusion constant of lignin in the TIP3P water model is almost twice as large as that in SPC/Fw and TIP4P/Ew. The softwood and hardwood oligomers adopt an extended structure in TIP3P water compared to SPC/Fw and TIP4P/Ew. Given the different levels of sensitivity of transport and structural properties of aqueous lignin on water models, it is important to take these into account when discussing results from a specific water model.

09 BIOMASS FUELS↗

DOE OSTI2026

Solvent effects on triplet yields in BODIPY-based photosensitizers

Here, we employ molecular dynamics simulations and quantum rate theories to elucidate the complex condensed-phase dynamics underpinning triplet-state formation in organic photosensitizers. Using models informed by first-principles calculations complete with a molecular representation of solvents of different polarities, we elucidate the interplay of the internal and environmental interactions underlying triplet yield. We find that triplet yields depend sensitively on the dielectric stabilization of the charge transfer intermediate that facilitates a transition into the triplet manifold. Our results illustrate the importance of molecularly detailed models in understanding the excited-state internal charge-transfer dynamics of photochemically relevant organic molecules.

Coello Escalante, Leonardo [University of Californ↗

DOE OSTI2020

Model-Free Dynamic Voltage Control of a Synchronous Generator-Based Microgrid

The main goal of this paper is to present a new dynamic voltage stability mechanism, based on model-free control (MFC), for effective control and coordination of synchronous generator (SG)-based reactive power resources in a microgrid setting. MFC has shown successful operation in various domains, and this paper presents its first use in the voltage stability of a power system. It is utilized as an online controller to achieve the dynamic voltage stability of a microgrid system under different disturbances and fault conditions. A 21-bus microgrid system fed by SG-based distributed energy resources (DERs) is considered as a use case study. The overall dynamic voltage stability of the microgrid system is investigated using time-domain dynamic simulations during emergency, hazard, and disaster events. Simulation results show that there are significant improvements and enhancements on the dynamic load bus voltage profiles of the microgrid system by the effective model-free control and coordination of the reactive power reserves of the SG-based DERs.

Hatipoglu, Kenan↗

DOE OSTI2020

Model-Free Dynamic Voltage Control of Distributed Energy Resource (DER)-Based Microgrids

In this paper, we present a new control technique for sustaining dynamic voltage stability by effective reactive power control and coordination of distributed energy resources (DERs) in microgrids. The proposed control technique is based on model-free control (MFC), which has shown successful operation and improved performance in different domains and applications. This paper presents its first use in the voltage stability of a microgrid setting employing multiple synchronous generator (SG)-based and power electronic (PE)-based DERs. MFC is a computationally efficient, data-driven control technique that does not require modelling of the different components and disturbances in the power system. It is utilized as an online controller to achieve the dynamic voltage stability of a microgrid system under different disturbances and fault conditions. A 21-bus microgrid system fed by multiple DERs is considered as a case study and the overall dynamic voltage stability is investigated using time-domain dynamic simulations. Numerical results show that the proposed MFC provides improvements on the dynamic load bus voltage profiles and requires less computational time as compared to the traditional enhanced microgrid voltage stabilizer (EMGVS) scheme. Due to its simplicity and low computational requirement, MFC can be easily implemented in resource-constrained computing devices such as smart inverters.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Mobile barrier mechanisms for Na + -coupled symport in an MFS sugar transporter

While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of major facilitator superfamily transporters. With a conformation-selective nanobody, we determined a low-sugar affinity inward-facing Na + -bound cryoEM structure. The available outward-facing sugar-bound structures showed that the N- and C-terminal residues of the inner barrier contribute to the sugar selectivity. The inward-open conformation shows that the sugar selectivity pocket is also broken when the inner barrier is broken. Isothermal titration calorimetry measurements revealed that this inward-facing conformation trapped by this nanobody exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is supported by molecular dynamics simulations. Furthermore, the hydron/deuterium exchange mass spectrometry analyses allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study

A rationally designed gold-functionalized surface capable of capturing a target protein is presented using the biotin–streptavidin pair as a proof-of-concept. We carried out multiscale simulations to shed light on the binding mechanism of streptavidin on four differently biotinylated surfaces. Brownian Dynamics simulations were used to reveal the preferred initial orientation of streptavidin over the surfaces, whereas classical molecular dynamics was used to refine the binding poses and to investigate the fundamental forces involved in binding, and the binding kinetics. We assessed the binding events and the stability of the streptavidin attachment through a quartz crystal microbalance with dissipation monitoring (QCM-D). The sensing element comprises of biotinylated polyethylene glycol chains grafted on the sensor’s gold surface via thiol-Au chemistry. Finally, we compared the results from experiments and simulations. We found that the confined biotin moieties can specifically capture streptavidin from the liquid phase and provide guidelines on how to exploit the microscopic parameters obtained from simulations to guide the design of further biosensors with enhanced sensitivity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

On Practical Aspects of Variational Consistency in Contact Dynamics

Usage of contact mechanics methodologies is a pervasive modeling requirement in dynamic simulations. While for some trivial problems, solutions taken from analytical geometry are available, use of a finite element framework is common to achieve formulation generality. This work explores two dynamic contact formulations: one based on the traditional node-to-segment (NTS) approach, and a variationally consistent segment-to-segment (STS) mortar formulation. The NTS formulation employed here enforces the constraints kinematically (i.e., the interpenetration is enforced to the solver tolerance), whereas the mortar approach uses Lagrange multipliers to enforce the contact constraints. Both approaches are implemented in the open-source finite element framework Multiphysics Object-Oriented Simulation Environment (MOOSE). The results highlight two relevant contact-interface-related dynamic phenomena in finite element simulations. First, stabilization of contact constraints is discussed, taking into account the evolution of the total energy in a benchmark problem. Second, the influence of finite element discretization on both of the aforementioned contact formulations is analyzed by exercising a large-deformation example with continuous relative sliding. Variationally consistent contact approaches such as the mortar formulation lead to improved energy preservation and avoid spurious excitation of the system's frequencies. This is especially relevant in settings where inertia and vibrations are of importance.

42 ENGINEERING↗

DOE OSTI2026

Free Energy and Flexibility Analysis of Autoinhibited Human BRAF

The RAF serine/threonine protein kinases function as direct effectors of RAS in the intracellular transmission of extracellular growth signals, and they are key targets for drug discovery, given the high incidence of oncogenic mutations in RAF and other components of this signaling pathway. In its inactive state, RAF is held in an autoinhibited conformation in the cytosol through a combination of intramolecular interactions and binding to a regulatory 14−3−3 protein dimer. Activation of RAF is initiated by its interaction with membrane-localized GTP-bound RAS, which induces conformational changes that release RAF from its autoinhibited state. However, the molecular mechanisms governing RAF activation remain incomplete, largely due to the challenges in experimentally capturing the intermediate conformational states in this process. To address this gap, we developed a comprehensive all-atom model of BRAF based on existing cryo-EM structures. Using this model, we performed extensive molecular dynamics simulations to evaluate the stability and free energy landscape of autoinhibited BRAF in solution. Our analysis reveals conformational flexibility within the autoinhibited complex, suggesting that this dynamic behavior may play a role in facilitating BRAF activation upon engagement with the membrane-bound RAS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗