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At least 1,423 records · Page 79
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Large–Scale Syntheses of 2D Materials: Flash Joule Heating and Other Methods

In the past 17 years, the larger-scale production of graphene and graphene family materials has proven difficult and costly, thus slowing wider-scale commercial applications. Here, the quality of the graphene that is prepared on larger scales has often been poor, demonstrating a need for improved quality controls. Here, current industrial graphene synthetic and analytical methods, as well as recent academic advancements in larger-scale or sustainable synthesis of graphene, defined here as weights more than 200 mg or films larger than 200 cm 2 , are compiled and reviewed. There is a specific emphasis on recent research in the use of flash Joule heating as a rapid, efficient, and scalable method to produce graphene and other 2D nanomaterials. Reactor design, synthetic strategies, safety considerations, feedstock selection, Raman spectroscopy, and future outlooks for flash Joule heating syntheses are presented. To conclude, the remaining challenges and opportunities in the larger-scale synthesis of graphene and a perspective on the broader use of flash Joule heating for larger-scale 2D materials synthesis are discussed.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2015

On the use of Darcy's law and invasion-percolation approaches for modeling large-scale geologic carbon sequestration

Most large-scale flow and transport simulations for geologic carbon sequestration (GCS) applications are carried out using simulators that solve flow equations arising from Darcy's law. Recently, the computational advantages of invasion-percolation (IP) modeling approaches have been presented. We show that both the Darcy's-law- and the gravity-capillary balance solved by IP approaches can be derived from the same multiphase continuum momentum equation. More specifically, Darcy's law arises from assuming creeping flow with no viscous momentum transfer to stationary solid grains, while it is assumed in the IP approach that gravity and capillarity are the dominant driving forces in a quasi-static two-phase (or more) system. There is a long history of use of Darcy's law for large-scale GCS simulation. However, simulations based on Darcy's law commonly include significant numerical dispersion as users employ large grid blocks to keep run times practical. In contrast, the computational simplicity of IP approaches allows large-scale models to honor fine-scale hydrostratigraphic details of the storage formation which makes these IP models suitable for analyzing the impact of small-scale heterogeneities on flow. However, the lack of time-dependence in the IP models is a significant disadvantage, while the ability of Darcy's law to simulate a range of flows from single-phase- and pressure-gradient-driven flows to buoyant multiphase gravity-capillary flow is a significant advantage. We believe on balance that Darcy's law simulations should be the preferred approach to large-scale GCS simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Validation of Spawn Checks and Saltwater Age Assignments Based on Scales from Known Repeat-Spawning Steelhead

Abstract It is critical to resolve the effects of regeneration, false annuli, and resorption on interpretation of scale patterns. We used scales collected from known repeat-spawning steelhead Oncorhynchus mykiss from the Snake River to (1) determine the accuracy of spawn check identification and (2) investigate errors in assignment of saltwater ages before and after spawn checks. Scale readers (n = 4) accurately identified over 96% of known repeat spawners (n = 107) and did not identify spawn checks in known first-time spawners (n = 197). Scale resorption associated with the spawn check caused an obscured or lost saltwater annulus in 66% of samples, most frequently in fish that spent 2 years versus 1 year in saltwater. Presence or absence of an annulus after the spawn check was accurately assigned in 86% of samples (n = 100). The potential for scale resorption to affect interpretation of the life history of iteroparous anadromous salmonids is significant. We supply two examples of how circulus counts can provide guidance to scale readers, but this analysis should be customized to the growth characteristics of each stock of interest.

Copeland, Timothy↗
DOE OSTI2016

Manufacturing demonstration of microbially mediated zinc sulfide nanoparticles in pilot-plant scale reactors

The thermophilic anaerobic metal-reducing bacterium Thermoanaerobacter sp. X513 efficiently produces zinc sulfide (ZnS) nanoparticles (NPs) in laboratory-scale ( ≤24-L) reactors. To determine whether this process can be up-scaled and adapted for pilot-plant production while maintaining NP yield and quality, a series of meso-scale experiments were performed using 100-l and 900-l reactors. Pasteurization and N 2 -sparging replaced autoclaving and boiling for deoxygenating media in the transition from small-scale to pilot-plant reactors. Consecutive 100-L batches using new or recycled media produced ZnS NPs with highly reproducible ~2 nm average crystallite size (ACS) and yields of ~0.5g L -1 , similar to small-scale batches. The 900-L pilot plant reactor produced ~ 320 g ZnS without process optimization or replacement of used medium; this quantity would be sufficient to form a ZnS thin film with ~120 nm thickness over 0.5 m width 13 km length. At all scales, the bacteria produced significant amounts of acetic, lactic and formic acids, which could be neutralized by the controlled addition of sodium hydroxide without the use of an organic pH buffer, eliminating 98% of the buffer chemical costs. In conclusion, the final NP products were characterized using XRD, ICP-OES, FTIR, DLS, and C/N analyses, which confirmed the growth medium without organic buffer enhanced the ZnS NP properties by reducing carbon and nitrogen surface coatings and supporting better dispersivity with similar ACS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Scale-Adaptive Simulation of Transient Two-Phase Flow in Continuous-Casting Mold

Scale-adaptive simulation (SAS) of the transient gas–liquid two-phase flow in a laboratory-scale continuous-casting mold is presented. The main objective is to investigate the applicability of the scale-adaptive unsteady Reynolds-averaged Navier–Stokes turbulent model (URANS SAS) for predicting the transient multiscale turbulent structures in a two-phase flow. Good quantitative agreements with the experimental data and the large eddy simulation (LES) results are obtained both for the time-averaged velocity field and for the transient turbulent characteristics. The introduction of the von Karman length-scale into the turbulence-scale equation allows the SAS model to dynamically adjust to the resolved turbulent structures. The LES-like pulsating behavior of the air gas and the large-scale liquid eddy magnitudes in the unsteady regions of flow field are captured by the SAS model. The classical − 5/3 law of power spectrum density (PSD) of the axial velocity is kept properly for the single-phase turbulent flow. For two-phase flow, the decay of PSD is too steep at the high-frequency region; the predicted PSD obtained with SAS is damped stronger than that estimated by LES. The SAS model offers an attractive alternative to the existing LES approach or to the other hybrid RANS/LES models for strongly unsteady flows.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Landscape composition and configuration have scale-dependent effects on agricultural pest suppression

Increasing landscape heterogeneity (composition and configuration) can enhance natural enemy populations and support pest suppression in agricultural landscapes. Using a network-based data mining approach, we examined independent gradients of landscape composition and configuration at six spatial scales that were associated with pest suppression services measured at 32 sites in Michigan and Wisconsin, USA. We compared the relative effects of landscape composition and configuration across scales with those of local crop type (corn or grassland). We found that multiple gradients of configurational heterogeneity were independent of composition and strongly associated with pest suppression, with different configuration metrics being predictive of pest suppression depending on the spatial scales and regions considered. Landscapes that were more configurationally heterogeneous at smaller spatial scales consistently supported higher pest suppression. In Michigan, pest suppression increased in landscapes with high edge contrast between annual crops and surrounding habitats and high edge density of grassland within 250-500 m radii. In Wisconsin, pest suppression increased with large core area of grassland and high field density within a 250 m radius. The main compositional effect we found was a positive relationship between grassland cover and pest suppression occurring at larger spatial scales (1000-1500 m) and occurring in Wisconsin but not in Michigan. Our findings demonstrate that effects of landscape composition and configuration on pest suppression differ across spatial scales and vary regionally. The network-based data mining techniques used here could be useful for disentangling intercorrelated landscape metrics in a variety of other contexts in landscape ecology.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Standard Model in conformal geometry: Local vs gauged scale invariance

Here, we discuss comparatively local versus gauged Weyl symmetry beyond Standard Model (SM) and Einstein gravity and their geometric interpretation. The SM and Einstein gravity admit a natural embedding in Weyl integrable geometry which is a special limit of Weyl conformal (non-metric) geometry. The theory has a local Weyl scale symmetry but no associated gauge boson. Unlike previous models with such symmetry, this embedding is truly minimal i.e. with no additional fields beyond SM and underlying geometry. This theory is compared to a similar minimal embedding of SM and Einstein gravity in Weyl conformal geometry (SMW) which has a full gauged scale invariance, with an associated Weyl gauge boson. At large field values, both theories give realistic, Starobinsky–Higgs like inflation. The broken phase of the current model is the decoupling limit of the massive Weyl gauge boson of the broken phase of SMW, while the local scale symmetry of the current model is part of the larger gauged scale symmetry of SMW. Hence, the current theory has a gauge embedding in SMW. Unlike in the SMW, we note that in models with local scale symmetry the associated current is trivial, which is a concern for the physical meaning of this symmetry. Therefore, the SMW is a more fundamental UV completion of SM in a full gauge theory of scale invariance that generates Einstein gravity in the (spontaneously) broken phase, as an effective theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

PS3: The Pheno-Synthesis software suite for integration and analysis of multi-scale, multi-platform phenological data

Phenology is the study of recurring plant and animal life-cycle stages which can be observed across spatial and temporal scales that span orders of magnitude (e.g., organisms to landscapes). The variety of scales at which phenological processes operate is reflected in the range of methods for collecting phenologically relevant data, and the programs focused on these collections. Consideration of the scale at which phenological observations are made, and the platform used for observation, is critical for the interpretation of phenological data and the application of these data to both research questions and land management objectives. However, there is currently little capacity to facilitate access, integration and analysis of cross-scale, multi-platform phenological data. This paper reports on a new suite of software and analysis tools – the “Pheno-Synthesis Software Suite,” or PS3 – to facilitate integration and analysis of phenological and ancillary data, enabling investigation and interpretation of phenological processes at scales ranging from organisms to landscapes and from days to decades. We use PS3 to investigate phenological processes in a semi-aride, mixed shrub-grass ecosystem, and find that the apparent importance of seasonal precipitation to vegetation activity (i.e., “greenness”) is affected by the scale and platform of observation. We end by describing potential applications of PS3 to phenological modeling and forecasting, understanding patterns and drivers of phenological activity in real-world ecosystems, and supporting agricultural and natural resource management and decision-making.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

How well do terrestrial biosphere models simulate coarse-scale runoff in the contiguous United States?

Significant changes in the water cycle are expected under current global environmental change. Robust assessment of present-day water cycle dynamics at continental to global scales is confounded by shortcomings in the observed record. Modeled assessments also yield conflicting results which are linked to differences in model structure and simulation protocol. Here we compare simulated gridded (1 spatial resolution) runoff from six terrestrial biosphere models (TBMs), seven reanalysis products, and one gridded surface station product in the contiguous United States (CONUS) from 2001 to 2005. We evaluate the consistency of these 14 estimates with stream gauge data, both as depleted flow and corrected for net withdrawals (2005 only), at the CONUS and water resource region scale, as well as examining similarity across TBMs and reanalysis products at the grid cell scale. Mean runoff across all simulated products and regions varies widely (range: 71 to 356 mm yr(-1)) relative to observed continental-scale runoff (209 or 280 mm yr(-1) when corrected for net withdrawals). Across all 14 products 8 exhibit Nash-Sutcliffe efficiency values in excess of 0.8 and three are within 10% of the observed value. Region-level mismatch exhibits a weak pattern of overestimation in western and underestimation in eastern regions although two products are systematically biased across all regions and largely scales with water use. Although gridded composite TBM and reanalysis runoff show some regional similarities, individual product values are highly variable. At the coarse scales used here we find that progress in better constraining simulated runoff requires standardized forcing data and the explicit incorporation of human effects (e.g., water withdrawals by source, fire, and land use change). (C) 2015 Elsevier B.V. All rights reserved.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

A sub-pore model for multi-scale reaction–diffusion problems in porous media

Applications of reaction–diffusion systems in porous media pose a challenging problem for computational modeling approaches due to their multi-physics and multi-scale nature. The length scales usually span 3–4 orders of magnitude while physical phenomena involved include heat and mass transfer processes, and surface reactions. In this paper, a novel methodology that accounts for all the length scales and physical phenomena involved in a single framework is described. A length scale based dual approach is proposed – the larger pore channels (macro-pores) are resolved using conventional numerical techniques and a novel ‘sub-pore’ model is used to account for the unresolved pore channels (sub-pores) and the important physics therein. The porous network in the sub-pore system is composed of a fractal-like hierarchical system of straight cylindrical pores. Simplified governing equations for mass and energy transport are solved within the sub-pore system along with a reaction kinetics model to account for surface adsorption. An implicit coupling strategy is used to couple the macro-pore and the sub-pore systems so as to ensure conservation. The developed methodology is then applied to a few test cases and it is established that the proposed framework is necessary for problems where the adsorption time scale is much smaller than (diffusion-limited) or comparable to the diffusion time scale. Furthermore, it is also demonstrated that the framework can be potentially used to model the network of porous channels in its entirety thus significantly reducing computational costs.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Coarse-graining and hybrid methods for efficient simulation of stochastic multi-scale models of tumour growth

The development of hybrid methodologies is of current interest in both multi-scale modelling and stochastic reaction–diffusion systems regarding their applications to biology. We formulate a hybrid method for stochastic multi-scale models of cells populations that extends the remit of existing hybrid methods for reaction–diffusion systems. Such method is developed for a stochastic multi-scale model of tumour growth, i.e. population-dynamical models which account for the effects of intrinsic noise affecting both the number of cells and the intracellular dynamics. In order to formulate this method, we develop a coarse-grained approximation for both the full stochastic model and its mean-field limit. Such approximation involves averaging out the age-structure (which accounts for the multi-scale nature of the model) by assuming that the age distribution of the population settles onto equilibrium very fast. We then couple the coarse-grained mean-field model to the full stochastic multi-scale model. By doing so, within the mean-field region, we are neglecting noise in both cell numbers (population) and their birth rates (structure). This implies that, in addition to the issues that arise in stochastic-reaction diffusion systems, we need to account for the age-structure of the population when attempting to couple both descriptions. We exploit our coarse-graining model so that, within the mean-field region, the age-distribution is in equilibrium and we know its explicit form. This allows us to couple both domains consistently, as upon transference of cells from the mean-field to the stochastic region, we sample the equilibrium age distribution. Furthermore, our method allows us to investigate the effects of intracellular noise, i.e. fluctuations of the birth rate, on collective properties such as travelling wave velocity. We show that the combination of population and birth-rate noise gives rise to large fluctuations of the birth rate in the region at the leading edge of front, which cannot be accounted for by the coarse-grained model. Such fluctuations have non-trivial effects on the wave velocity. Beyond the development of a new hybrid method, we thus conclude that birth-rate fluctuations are central to a quantitatively accurate description of invasive phenomena such as tumour growth. - Highlights: • A hybrid method for stochastic multi-scale models of cells populations that extends existing hybrid methods for reaction–diffusion system. • Our analysis unveils non-trivial macroscopic effects triggered by noise at the level of structuring variables. • Our hybrid method hugely speeds up age-structured SSA simulations while preserving stochastic effects.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Scale bridging damage model for quasi-brittle metals informed with crack evolution statistics

Computationally efficient methods for bridging length scales, from highly resolved micro/meso-scale models that can explicitly model crack growth, to macro-scale continuum models that are more suitable for modeling large parts, have been of interest to researchers for decades. In this work, an improved brittle damage model is presented for the simulation of dynamic fracture in continuum scale quasi-brittle metal components. Crack evolution statistics, including the number, length, and orientation of individual cracks, are extracted from high-fidelity, finite discrete element method (FDEM) simulations and used to generate effective material moduli that reflect the material’s damaged state over time. This strategy allows for the retention of small-scale physical behaviors such as crack growth and coalescence in continuum scale hydrodynamic simulations. However, the high-fidelity simulations required to generate the crack statistics are computationally expensive. Thus, steps were taken to produce a flexible constitutive model to reduce the number of costly high-fidelity simulations needed to produce accurate results. A new stress based degradation criterion is introduced for the degradation of individual material zones. This allows for the development of a heterogeneous damage distribution within the bulk material. Then a flow stress model is added to the hydrodynamic simulation to account for plasticity in quasi-brittle materials. As a result, the effective moduli model can be applied to a larger range of materials. The effective moduli constitutive model is used to simulate beryllium flyer plate experiments. The results from the continuum scale simulations using statistics from a single high-fidelity simulation are found to be in excellent agreement with numerical and experimental velocity interferometer data. The same set of crack statistics are used to extrapolate the results of a higher rate flyer plate case using the effective moduli model. In conclusion, the extension of this model to higher rate cases shows promise for further reducing the number of costly high-fidelity simulations needed to generate crack statistics.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Local electrical degradations of solid-state electrolyte by nm-scale operando imaging of ionic and electronic transports

We report on degradation mechanisms of solid-state electrolyte (SSE) based on insights from nm-scale ionic conduction and electronic leakage for solid-state batteries. The significantly different local degradations revealed by nm-scale ionic and electronic transport imaging demonstrate the need for this nm-scale investigation. State-of-the-art lithium-ion conductive glass ceramic (Li 2 O–Al 2 O 3 –SiO 2 –P 2 O5–TiO2-GeO2) SSE shows at least two types of degradations spatially separated within the SSE, namely: (1) ionic conduction blocking and slight electronic leaking and (2) highly electronic shunting. Degradation was significantly suppressed by application of a Li-containing polyacrylonitrile thin coating on both sides of the ceramic SSE. With this coating, the ionic conduction was not reduced by the extensive cycling; instead, it improved slightly, although accompanied by a slight increase in electronic leaking. Our nm-scale transport imaging was achieved using an atomic force microscopy (AFM)-based half-cell setup and a logarithmic-scale amplifier with current sensitivity down to the fA (10-15 A) range. This half-cell setup consisting of an AFM-probe/SSE/Li structure can distinguish the ionic from the electronic current by flipping the bias-voltage polarity. This nm-scale operando imaging opens up novel characterization of ionic and electronic transport in the field of solid-state batteries.

42 ENGINEERING↗
DOE OSTI2018

Asymptotic scaling laws and semi-similarity solutions for a finite-source spherical blast wave

A spherical blast wave generated by a sudden release of a sphere of compressed gas is an important model problem to understand blast phenomena such as volcanic eruptions and explosive detonations. The resulting explosion flow physics, such as the instability at the gas contact discontinuity and the interaction between the shock wave and the gas contact, are dictated by the initial pressure and sound-speed ratios between the compressed gas and the ambience. Since the initial pressure and sound-speed ratios vary over a wide range in practical applications, it is of interest to investigate the scaling laws and similarity solutions for the spherical symmetric explosion flow. In the present study, numerical simulation of a spherical blast wave is performed. A long-term length scale that incorporates the initial charge radius and the initial pressure ratio is introduced. The trajectories of the main shock normalized by the long-term length scale for a wide range of parameters collapse after a short transition time, indicating an asymptotic similarity solution exists for the far field in the long term. With the assistance of this similarity solution, the full evolution of the main shock can be obtained semi-analytically. For near-field features, i.e. the gas contact and the secondary shock wave, only semi-similarity solutions are observed, which depend on the initial sound-speed ratio but not the initial pressure ratio. The gas contact and the secondary shock share the same scaling relations. Asymptotic analysis is performed to obtain the short-term dynamics of the gas contact, including the gas contact acceleration and the Atwood number, which are the key parameters determining the Rayleigh–Taylor instability development at the gas contact. The asymptotic contact radius as $t\rightarrow \infty$ is also obtained, which is found to be well represented by the long-term length scale and thus only depends on the initial pressure ratio. A simple model of an oscillating bubble is employed to explain the scaling relation of the asymptotic gas contact radius.

Mechanics↗
DOE OSTI2018

Similarity of wake meandering for different wind turbine designs for different scales

The wake meandering characteristics of four different wind turbine designs with diameters ranging from a few centimetres (wind tunnel scale) to a hundred metres (utility scale) are investigated using large-eddy simulation with the turbine blades and nacelle parametrised using a new actuator surface model. Different velocity fields and meandering behaviours are observed at near-wake locations. At far-wake locations, on the other hand, the mean velocity deficit profiles begin to collapse when scaled by the centreline velocity deficit based on the incoming wind speed at turbine hub height, suggesting far-wake similarity across scales. The turbine-added turbulence kinetic energy profiles are shown to also nearly collapse with each other in the far wake when normalised using a velocity scale defined by the thrust on the turbine rotor. Moreover, we show that at far-wake locations, the simulated flow fields for all four turbine designs exhibit similar wake meandering characteristics in terms of (1) a Strouhal number independent of rotor designs of different sizes and (2) the distributions of wake meandering wavelengths and amplitudes when normalised by the rotor diameter and a length scale defined by the turbine thrust respectively.

Mechanics↗
DOE OSTI2022

A scale-wise analysis of intermittent momentum transport in dense canopy flows

We investigate the intermittent dynamics of momentum transport and its underlying time scales in the near-wall region of the neutrally stratified atmospheric boundary layer in the presence of a vegetation canopy. This is achieved through an empirical analysis of the persistence time scales (periods between successive zero-crossings) of momentum flux events, and their connection to the ejection–sweep cycle. Using high-frequency measurements from the GoAmazon campaign, spanning multiple heights within and above a dense canopy, the analysis suggests that, when the persistence time scales ( $t_p$ ) of momentum flux events from four different quadrants are separately normalized by $\varGamma _{w}$ (integral time scale of the vertical velocity), their distributions $P(t_p/\varGamma _{w})$ remain height-invariant. This result points to a persistent memory imposed by canopy-induced coherent structures, and to their role as an efficient momentum-transporting mechanism between the canopy airspace and the region immediately above. Moreover, $P(t_p/\varGamma _{w})$ exhibits a power-law scaling at times $t_{p}<\varGamma _{w}$ , with an exponential tail appearing for $t_{p} \geq \varGamma _{w}$ . By separating the flux events based on $t_p$ , we discover that around 80 % of the momentum is transported through the long-lived events ( $t_{p} \geq \varGamma _{w}$ ) at heights immediately above the canopy, while the short-lived ones ( $t_{p} < \varGamma _{w}$ ) only contribute marginally ( $\approx 20\,\%$ ). To explain the role of instantaneous flux amplitudes in momentum transport, we compare the measurements with newly developed surrogate data and establish that the range of time scales involved with amplitude variations in the fluxes tends to increase as one transitions from within to above the canopy.

Mechanics↗
DOE OSTI2015

Investigating the reversibility of structural modifications of Li x Ni y Mn z Co 1-y-z O₂ cathode materials during initial charge/discharge, at multiple length scales

In this work, we investigate the structural modifications occurring at the bulk, subsurface, and surface scales of Li x Ni y Mn z Co 1-y-z O₂ (NMC; y, z = 0.8, 0.1 and 0.4, 0.3, respectively) cathode materials during the initial charge/discharge. Various analytical tools, such as X-ray diffraction, selected-area electron diffraction, electron energy-loss spectroscopy, and high-resolution electron microscopy, are used to examine the structural properties of the NMC cathode materials at the three different scales. Cut-off voltages of 4.3 and 4.8 V are applied during the electrochemical tests as the normal and extreme conditions, respectively. The high-Ni-content NMC cathode materials exhibit unusual behaviors, which is deviate from the general redox reactions during the charge or discharge. The transition metal (TM) ions in the high-Ni-content NMC cathode materials, which are mostly Ni ions, are reduced at 4.8 V, even though TMs are usually oxidized to maintain charge neutrality upon the removal of Li. It was found that any changes in the crystallographic and electronic structures are mostly reversible down to the sub-surface scale, despite the unexpected reduction of Ni ions. However, after the discharge, traces of the phase transitions remain at the edges of the NMC cathode materials at the scale of a few nanometers (i.e., surface scale). This study demonstrates that the structural modifications in NMC cathode materials are induced by charge as well as discharge at multiple length scales. These changes are nearly reversible after the first cycle, except at the edges of the samples, which should be avoided because these highly localized changes can initiate battery degradation.

25 ENERGY STORAGE↗
DOE OSTI2021

Assembly and Analysis of Cell-Scale Membrane Envelopes

The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms-a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗