SEARCH · Engineering Papers

Results for “Capacity Analysis”

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

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4

All sources NASA NTRS DOE OSTI

DOE OSTI2022

Nuclear's Role in the U.S. Electricity System: A Multi-Model Inter-Comparison Analysis

Multiple capacity expansion models (CEMs) for the U.S. power system represent the balance of options among generation, transmission, and storage assets that can satisfy electric loads, operating and planning reserves, and policy requirements. These models are typically set up to find the least-cost portfolio of assets that meet specified requirements, and model decisions can include both investments in new, and retirement of existing, resources. The scenarios explored by CEMs can help inform strategies for meeting future electricity and energy needs under a range of future conditions. However, projections can differ between models, sometimes dramatically, for a seemingly similar scenario. Differences in model coverage, structure, and input assumptions contribute to the range of model outcomes. Understanding what drives the biggest differences in model outputs improves model insights and provides context for interpreting results. This summary presents analysis that was performed through a forum of analysts who own, update, and apply CEMs, as well as nuclear experts from national laboratories, industry, and the research community. The following sections describe methods, results, and findings from an original, innovative inter-model comparison that provides insights into what drives the greatest differences in nuclear retirement and deployment projections across models and a range of technology, market, and policy conditions.

capacity expansion model↗

DOE OSTI2022

Capacity Assessment and Cost Analysis of Geologic Storage of Hydrogen: A Case Study in Intermountain-West Region USA

Hydrogen is an integral component of the current energy transition roadmap to decarbonize the economy and create an environmentally-sustainable future. However, surface storage options (e.g., tanks) do not provide the required capacity or durability to deploy a regional or nationwide hydrogen economy. In this study, we have analyzed the techno-economic feasibility of the geologic storage of hydrogen in depleted gas reservoirs, salt caverns, and saline aquifers in the Intermountain-West (I-WEST) region. We have identified the most favorable candidate sites for hydrogen storage and estimated the volumetric storage capacity. Our results show that the geologic storage of hydrogen can provide at least 72% of total energy consumption of the I-WEST region in 2020. We also calculated the capital and levelized costs of each storage option. We found that a depleted gas reservoir is the most cost-effective candidate among the three geologic storage options. Interestingly, the cushion gas type plays a significant role in the storage cost when we consider hydrogen storage in saline aquifers. The levelized costs of hydrogen storage in depleted gas reservoirs, salt caverns, and saline aquifers with large-scale storage capacity are approximately $\$$1.15, $\$$2.50, and $\$$3.27 per kg of H 2 , respectively. Here, this work provides essential guidance for the geologic hydrogen storage in the I-WEST region.

08 HYDROGEN↗

DOE OSTI2023

Summary Analysis of Different Offshore Wind Capacity Density Drivers in Proposed U.S. Projects and Impacts on Progress Towards State and Federal Deployment Targets

Understanding the density of offshore wind development - or the "capacity density" - is important for state and federal offshore wind planning efforts and to track progress towards policy goals. NREL has traditionally assumed a capacity density of 3 megawatts per square kilometer (MW/km2) when estimating the U.S. project pipeline (Musial et al. 2022), but capacity densities for existing European offshore wind farms ranged from 2-19 MW/km2 (Borrmann et al. 2018). We track the expected capacity densities of the proposed U.S. projects in the East Coast and make an analysis by state and by developer to identify what are the capacity density norms in the industry and whether the state in which the development efforts are taking place has some impact on capacity density. We also analyze the effects of the area occupied by station keeping systems on capacity density for lease areas dedicated to floating projects and provide a list of main capacity density drivers. This summary analysis sets a baseline to study how different capacity density drivers could impact the progress towards state and federal deployment targets. Given the currently delineated Renewable Energy Areas in the Outer Continental Shelf (OCS) and the basis from the summary analysis, we estimate the expected offshore wind deployment over time federally and by state and compare it to the state and federal deployment targets. The proposed analysis helps identify gaps and needs to meet state and federal targets, which provides sufficient information to propose strategic supply chain and policy planning with the objective of meeting deployment goals.

capacity density↗

DOE OSTI2024

Decomposed phase analysis for DER hosting capacity in unbalanced distribution feeders

Not Available

Mavalizadeh, Hani↗

DOE OSTI2021

Probabilistic Assessment and Uncertainty Analysis of CO2 Storage Capacity of the Morrow B Sandstone—Farnsworth Field Unit

This paper presents probabilistic methods to estimate the quantity of carbon dioxide (CO2) that can be stored in a mature oil reservoir and analyzes the uncertainties associated with the estimation. This work uses data from the Farnsworth Field Unit (FWU), Ochiltree County, Texas, which is currently undergoing a tertiary recovery process. The input parameters are determined from seismic, core, and fluid analyses. The results of the estimation of the CO2 storage capacity of the reservoir are presented with both expectation curve and log probability plot. The expectation curve provides a range of possible outcomes such as the P90, P50, and P10. The deterministic value is calculated as the statistical mean of the storage capacity. The coefficient of variation and the uncertainty index, P10/P90, is used to analyze the overall uncertainty of the estimations. A relative impact plot is developed to analyze the sensitivity of the input parameters towards the total uncertainty and compared with Monte Carlo. In comparison to the Monte Carlo method, the results are practically the same. The probabilistic technique presented in this paper can be applied in different geological settings as well as other engineering applications.

03 NATURAL GAS↗

DOE OSTI2023

Historical Pattern Analysis of Global Geothermal Power Capacity Development: Preprint

Between 1913 and 1958, Italy was the only country with an operational geothermal power plant until New Zealand installed its first plant in 1958. At present, 24 countries are involved in the geothermal power market, and they have a combined installed capacity of 16,127 GW. This study analyzes the historical patterns of geothermal power capacity in the world and in individual countries to investigate the ideal global geothermal development pattern by examining the annual cumulative capacity (ACC) and the annual capacity addition (ACA) graphs of the historical development of geothermal power capacity in 24 countries. First, the global patterns are analyzed using these graphs in five periods (1945-1957, 1958-1976, 1977-1991, 1992-2002, and 2003-2020) that are marked by a series of characteristics of ACA peaks separated by two major troughs. Then, five characteristic patterns are developed in five periods globally. These patterns correspond to the early-stage linear, the first acceleration, the first steady-state linear, the second acceleration, and the second steady-state linear developments. A positive relationship exists between global patterns and the 5-year shifted oil-price curve: two major factors influenced global development: 1) increasing oil prices and increasing awareness of global climate change, and 2) global development of geothermal power. Last, we investigate these patterns in each country. The top ten countries, which comprise 93.3% of the world's total installed capacity are separated into five groups based on the availability and characteristics of patterns globally developed in five periods. Group-1 (the United States) has an installed capacity of 3,794 MW, Group-2 (Mexico and Philippines) 963-1935 MW, Group-3 (New Zealand, Italy, Iceland, and Japan) 601-1,037 MW, and Group-4 (Indonesia, Kenya, and Turkiye) 944-2,356 MW. The remaining 14 countries (6.7%), which are called Group 5, are still in an immature stage and have installed capacities of 7-262 MW and are not involved in pattern analysis. Overall, geothermal power in the world is in its third stage of development, which had its peak development after 1977. A fourth development peak may be expected to occur after this through business-as-usual cases. The biggest barrier to the development of the global geothermal power market is the risk associated with exploration and drilling. If risk mitigation systems and funds are employed, the growth of geothermal power production projects could accelerate.

GEOTHERMAL ENERGY↗

DOE OSTI2023

Historical Pattern Analysis of Global Geothermal Power Capacity Development

GEOTHERMAL ENERGY↗

DOE OSTI2024

Direct evidence from STXM analysis of enhanced oxygen storage capacity in ceria through the addition of Cu and Mg: Correlation of HT-WGS reaction performance

Here, scanning transmission X-ray microscopy (STXM) analysis was utilized to directly present visual evidence of changes in oxygen storage capacity (OSC) when small amounts of an additive were incorporated into CeO2. Specifically, the chemical map measured by STXM analysis differentiated between Cu-rich and Ce-rich areas to derive the proportion of Ce3+. Additionally, we found that the dispersion of Cu significantly influenced the formation of OSC. The findings were applied to the high-temperature water–gas shift reaction for producing high-purity hydrogen from waste-derived syngas, establishing a correlation with catalyst performance. Consequently, the CCM75 (Ce/Mg = 75/25) catalyst demonstrated the highest Cu dispersion and OSC values (6.9 %, 800.3 μmolO/gcat), and it also showed the highest CO conversion (79 % at 450 °C) and stability (−7.7 % at 450 °C after 50 h), attributed to the significant presence of active Cu. This study confirms previously reported interactions between Cu and CeO2 and uncovers the significant roles of Cu and Mg in this catalysis system, providing new understanding of the mechanisms that facilitate OSC improvement.

Lee, Ru-Ri↗

DOE OSTI2020

Cell degradation quantification—a performance metric-based approach

A safe and reliable battery operation needs effective diagnostic tools. A quantitative failure analysis (FA) to enable cell qualification and quantify its effectiveness for reliable and safe operation of rechargeable Li batteries (RLB) is shown here. The method can identify and quantify potential failure based on the state of charge (SOC) under any operating conditions. A precise and accurate electrochemical analytic diagnosis (eCAD) of 14 rechargeable Li || NMC622 cells of the same build are used as an example. The FA by eCAD can quantitatively decipher good, bad and ugly cells in cycle aging. The cell qualification is based on thermodynamic SOC, not experimental conditions. The method provides a quantitative failure mode and effect analysis (FMEA) to reveal diverse “dead Li” formation that affects the reversibility of the Li anode and charge retention in the cell. This cell qualification method highlights the potential to improve cell quality for safe operation, with strong implications for early fault detection, FA, risk mitigation, state estimation and life prediction for reliable and safe RLB operations

25 ENERGY STORAGE↗

DOE OSTI2024

Performance Testing of an Integrated Magnetic Power Take-Off

A wave energy converter (WEC) and the power take-off (PTO) generator system can be represented by using a mass-spring-dampener model. By incorporating a negative stiffness spring within the PTO, the overall stiffness of the PTO can be lowered allowing the impedance of the PTO to be more closely matched with the WEC. By designing for impedance matching the WEC can greatly enhance its power generation capability. This project has involved the design, fabrication and testing of a new type of linear-stroke length and rotary stroke length adjustable negative stiffness magnetic springs for use within a wave energy converter (WEC). The magnetic springs were studied by using 3-D finite element analysis with the objective of creating high energy density and a long linear stroke length. After the construction and testing of both a proof-of-principle adjustable linear and rotary magnetic spring prototype the rotary (torsional) magnetic spring was selected for scaling up analysis. The selected scaled-up proof-of-principle magnetic spring had a peak torque of 850 Nm with a ±45 degree stroke length. By translating the inner rotor relative to the outer rotor, the stiffness could be adjusted to be either negative or positive stiffness. During this project a magnetic lead screw was also studied, and it was shown that by combining the magnetic lead screw with a linearly translating magnetic spring a very long rotary stroke length could be attained. However, as the magnetic lead screw increased complexity and reduced overall energy density relative to a rotary (torsional) spring, this design approach was not further pursed. Dynamometer testing of the variable stiffness magnetic springs was first completed by Portland State University and following this the magnetic spring performance was independently verified by Sandia National Laboratory (Sandia). A WEC analysis when using a variable stiffness magnetic spring was completed by using the WecOptTool. WecOptTool is an open-source WEC optimization software developed by Sandia that supports efficient power take-off (PTO) and control optimization. Wave condition data from the Oregon PacWave test-site was used in this study. The analysis showed that a WEC with a tunable stiffness value could consistently achieve about 80% of its maximum theoretical power production. The use of a tunable stiffness WEC, rather than zero-stiffness or a constant stiffness WEC was also shown to lead to a smaller maximum PTO force requirement. The variable stiffness magnetic spring was integrated into an experimental WEC developed by Sandia, called a Wave-Bot. Sandia successfully completed water-tank testing of the Wave-Bot at the Navy’s Carderock, Maryland, wave-basin test site. The wave-basin testing helped to experimentally demonstrate the operating capabilities and increased power generation capability of a WEC containing an integrated variable stiffness magnetic spring. A WEC capacity factor analysis was also completed. The capacity factor was defined as the ratio of annual average WEC generator power to the maximum (RMS) generated power. This capacity factor provided a means of identifying the ratio of potential revenue to cost. It was calculated that if a tunable variable stiffness magnetic spring has RMS constraints it could operate with a capacity factor above 30%. This is comparable to a wind turbine’s capacity factor.

16 TIDAL AND WAVE POWER↗

DOE OSTI2023

Energy Storage and Decarbonization Analysis for Energy Regulators: Technical Analysis for the Illinois Commerce Commission

Jurisdictions around the world are enacting and enforcing an increasing number of policies to fight climate change, leading to higher penetration of variable renewable energy (VRE) and energy storage systems (ESSs) in the power grid. One of the biggest challenges associated with this process is the evaluation of the appropriate amount of ESS required to mitigate the variability of the VREs and achieve decarbonization goals of a particular jurisdiction. This report presents methodologies developed and results obtained for determining the minimum amount of ESS required to adequately serve load in a system where fossil fueled generators are being replaced by VREs over the next two decades. This technical analysis is performed by Sandia National Laboratories for the DOE Office of Electricity Energy Storage Program in collaboration with the Illinois Commerce Commission (ICC). The Illinois MISO Zone 4 is used as a case study. Several boundary conditions are investigated in this analysis including capacity adequacy and energy adequacy to determine the quantity of ESS required for MISO Zone 4. Multiple scenarios are designed and evaluated to incorporate the impact of varying capacity values of VREs and on the resource adequacy of the system. Several retirement scenarios involving fossil-fueled assets are also considered. Based on the current plans of new additions and retirements of generating assets, the results of the technical analysis indicate that Illinois MISO Zone 4 will require a significant quantity of ESS to satisfy their electricity demand over the next two decades.

25 ENERGY STORAGE↗

DOE OSTI2025

Floating Photovoltaic Technical Potential: A Novel Geospatial Approach on Federally Controlled Reservoirs in the United States

Floating photovoltaic generation is a rapidly expanding sector of the solar energy industry, and understanding the quantity that can feasibly be installed is a crucial step to understand its role in future energy systems. This paper presents a novel spatially explicit methology of FPV potential for federally owned and managed reservoirs in the United States that uses site-specific attributes of reservoirs to estimate available area and potential generation capacity. The analysis finds that the proportion reservoir area that is found to be available for FPV development is similar to assumed values used in previous research on average, however there is a wide variability in this proportion on a site by site basis. Potential FPV generation capacity on these reservoirs is estimated to be in the range of 861 to 1,042 GWdc depending on input assumptions, likely representing a significant portion of future US solar generation needs. This work represents an advancement in methods used to estimate FPV potential that presents many natural extensions for further research.

floating solar↗

DOE OSTI2024

Interfacial Pressure Improves Calendar Aging of Lithium Metal Anodes

Lithium metal is a very attractive anode material because its theoretical specific capacity is approximately 10 times higher than conventional graphite anodes. Despite great promise, Li anodes suffer from capacity fade due to instabilities with the electrolyte as well as stranding of active Li. We have previously shown that applied interfacial pressure improves Li anode cycling because the pressure reduces the propensity for Li isolation and enables easier reconnection. Many researchers have also shown that calendar aging can lead to Li capacity loss and this has been attributed to either electrolyte decomposition with concurrent Li corrosion or to the formation of stranded Li. Our prior research focused on calendar aging during cycling suggests the mechanism for calendar aging is largely related to stranding of Li during rest and reconnection of the stranded Li upon further cycling, evidenced by similar average Coulombic efficiencies and Li loss in cells with and without rest. Because our calendar aging studies suggest Li stranding as a major cause of Coulombic efficiency drops and our Li cycling studies suggest this can be mitigated partially through applied interfacial pressure, we hypothesized that applied pressure would improve calendar aging by reducing stranded Li and enabling reconnection. We systematically varied applied pressure (0-1000 kPa) on Li metal anodes during cycling tests with and without intermittent calendar aging periods. Though the Coulombic efficiency decreases during aging periods, the lost capacity is recovered during subsequent cycles, as shown though average Coulombic efficiency and cumulative Li capacity loss analysis. We find that application of pressure partially mitigates calendar aging, in accordance with our hypothesis that calendar aging is caused by Li standing and can be mitigated to some degree with interfacial pressure. This is further supported by our results showing that the average Coulombic efficiency and cumulative Li capacity losses are similar over 50 cycles for cells that were continuously cycled and cells with periodic calendar aging periods. This result indicates that the losses during aging are reversible, which is consistent with Li stranding and reconnection. We show that pressure is one mitigation technique that helps reduce Li calendar aging in this study, but our finding that calendar aging is primarily governed by the stranding and reconnection of dead Li has wider implications. This research suggests that other mitigations which have been shown to prevent dead Li formation or encourage reconnection during cycling would also likely be successful for the purpose of improving calendar aging. The authors were supported by a Laboratory Directed Research and Development (LDRD) program. This work was performed, in part, at the Center for Integrated Nanotechnologies, an Office of Science User Facility operated for the U.S. Department of Energy (DOE) Office of Science. Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC (NTESS), a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration (DOE/NNSA) under contract DE-NA0003525. This written work is authored by an employee of NTESS. The employee, not NTESS, owns the right, title and interest in and to the written work and is responsible for its contents. This work was authored in part by the National Renewable Energy Laboratory, operated by Alliance for Sustainable Energy, LLC, for the U.S. Department of Energy (DOE) under Contract No. DE-AC36-08GO28308. Any subjective views or opinions that might be expressed in the written work do not necessarily represent the views of the U.S. Government.

applied pressure↗

DOE OSTI2020

Investigation on capacity loss mechanisms of lithium-ion pouch cells under mechanical indentation conditions

Capacity loss was observed in Li-ion cells after mechanical deformation approaching the onset of internal short circuit (ISCr). In this paper, a series of indentation tests were carried out on commercial Li-ion cells of three capacities (500, 1500 and 2000 mAh). Both in-situ and ex-situ methods were used to investigate the mechanisms of indentation-induced capacity loss. We note after indentation test, the cell capacity reduced by 0.5%–6% of its original value. The incremental capacity (IC) analysis results showed that IC curves generally shifted to lower voltage region, indicating the increase in cell internal resistance. In addition, the fitting results of electrochemical impedance spectroscopy (EIS) indicated that mechanical indentation can result in a reduction in ohmic resistance and the increase in polarization resistance. Scanning electron microscopy (SEM) and X-ray computed tomography (XCT) results showed crushing of graphite, mud cracking of copper current collectors and enlarged pores in separator, which is proposed to be the main reasons for the increase in polarization resistance and permanent capacity loss. The rapid capacity loss due to mechanical abuse was compared with the long-term capacity fading.

25 ENERGY STORAGE↗

DOE OSTI2025

The value of hydropower flexibility for electricity system decarbonization

Hydropower is an abundant, dispatchable, clean energy resource that will play an important role in supporting the clean energy transition. In particular, dispatchable hydropower can provide the operational flexibility that will be required in future systems with high variable renewable energy penetrations. However, the theoretical operational flexibility of hydropower can be restricted in practice by various non-power constraints. In this paper, we quantify how increasing the operational flexibility of dispatchable hydropower resources with reservoirs impacts least-cost generation portfolios and supports power system decarbonization. Specifically, we conduct a capacity expansion analysis of a two-zone system: a hydro-dominated region and a neighboring region with aggressive decarbonization targets that are represented by the United States Pacific Northwest and California respectively. We then introduce a quantifiable index for characterizing the operational flexibility of reservoir hydropower and assess how changes in this metric impact the system-optimal generation portfolio. We find that increasing hydropower flexibility leads to more investment in wind generation, less investment in natural gas generation, lower system costs, and lower system emissions. We further demonstrate a substitution effect between the grid services provided by flexible hydropower operation, increased transmission capacity on a congested line, and energy storage resources. Finally, we show that increasing the operational flexibility of hydropower increases the effective load carrying capability of both hydropower and wind resources. This research supports a more nuanced understanding of how hydropower can support electricity system decarbonization and may motivate reassessing the cost-benefit tradeoffs of non-power constraints that restrict operational flexibility.

Capacity expansion modeling↗

DOE OSTI2023

Probabilistic Multi-Hazard Performance Assessment of Concrete Structures in Nuclear Installations

Concrete structures in nuclear installations are subject to time-dependent degradation mechanisms that can deteriorate their physical and mechanical properties, potentially exacerbating the risk of structural failure under external forces such as a seismic event. Previous research has extensively investigated the seismic response of nuclear concrete structures and the associated risk, as well as their effect on structural components safety margins. However, substantial work is still necessary to incorporate concrete aging effects into such evaluations. In fact, most models in the literature assume pristine concrete conditions and do not account for the impact of aging on the structural components’ fragility curves. This work identifies relevant time-dependent degradation mechanisms and provides simplified models to predict the the evolution of key material properties based on data from the literature. Namely, this work focuses on the aging effects of corrosion, alkali–silica reaction (ASR), and irradiation on reinforced concrete within US Department of Energy (DOE) nuclear facilities and nuclear power plants (NPP) structures. Furthermore, degradation models based on literature data are presented that define the relationship between probabilistic material properties and the concrete’s age. In this work, sampled material properties served as input for a simplified finite element model (FEM) of a critical nuclear structural system, with the output of the FEM being the seismic response for a given ground motion. The results of the FEM were then used within a probabilistic performance assessment with a statistically significant number of samples. The research presented herein addresses the detrimental effects of hazards caused by natural phenomena on deteriorated concrete elements of nuclear installations. This work directly benefits the safety analysis performed on US DOE/ National Nuclear Security Administration (NNSA) nuclear facilities located in areas prone to seismic activity. The results presented herein could aid in the improvement of DOE-STD-1020, the DOE Standard that addresses seismic risk analysis and capacity evaluation in DOE facilities. DOE-STD-1020 refers to the requirements in American Society of Civil Engineers (ASCE) 4-98, now superseded by ASCE 4-16, that shall be met in performing dynamic response analyses and generating in-structure response spectra, provided that such requirements are consistent with the requirements of ASCE/Structural Engineering Institute (SEI) 43-05. Moreover, the results presented herein could also aid in the updating of section C3.1.1. of ASCE 4-16 to account for the effects of aging on the stiffness of reinforced elements and American Concrete Institute (ACI) 349.3R-18, “Report on Evaluation and Repair of Existing Nuclear Safety-Related Concrete Structures.” Ultimately, this work can assist the risk assessment of potential lifetime extension of the existing US commercial nuclear fleet (light water reactors) and the safety analysis of the emerging advanced nuclear reactors. The proposed proof-of-concept methodology employs open-source DOE computational tools and is transferable to commercial software commonly used by engineering firms.

42 ENGINEERING↗

DOE OSTI2026

Optimizing Heat Recovery with Storage: Control Validation and Sensitivity Analysis of the Time-Independent Energy Recovery Plant Using Modelica

Heat recovery in large building central plants saves energy but traditionally requires simultaneous heating and cooling. The Time-Independent Energy Recovery (TIER) plant shifts this paradigm by integrating thermal energy storage (TES) to enable heat recovery regardless of concurrent demand, offering a highly efficient, space-saving solution to achieve California’s energy goals. However, its integration of heat recovery chillers, cooling-only chillers, cooling towers, and trim air-source heat pumps (ASHPs) creates growing control and sizing complexity. To overcome this, this study employs high-fidelity Modelica dynamic simulation to validate TIER control sequences and optimize equipment sizing. We translated the written Sequences of Operation into executable Control Description Language (CDL) to test logic against sub-hourly loads. This verification workflow successfully identified and resolved critical vulnerabilities, such as thermal storage freezing and equipment short-cycling, in a virtual environment prior to physical deployment. Then, the study analyzes TIER plant performance across three simulated building types in three locations, and a real building load profile, ensuring variety in heating and cooling loads, and simultaneity factors and explores sizing rules for the TES and ASHP capacity. The analysis shows that the TIER plant operates equipment efficiently leading to a plant SCOP of around 7.5 across all scenarios, higher than a traditional ASHP plant, and a viable pathway to de-risk complex system design and control through simulation to identify optimal designs that maximize energy efficiency, minimize operational costs, and ensure robust operation in varied environmental conditions, thereby facilitating the broader adoption of such a solution for large buildings.

Zanetti, Ettore↗

DOE OSTI2021

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

Coarse-grained modeling can be used to explore general theories that are independent of specific chemical detail. In this paper, we present cg_openmm, a Python-based simulation framework for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics of cooperative secondary structures. cg_openmm facilitates the building of coarse-grained topology and random starting configurations, setup of GPU-accelerated replica exchange molecular dynamics simulations with the OpenMM software package, and features a suite of postprocessing thermodynamic and structural analysis tools. In particular, native contact analysis, heat capacity calculations, and free energy of folding calculations are used to identify and characterize cooperative folding transitions and stable secondary structures. In this work, we demonstrate the capabilities of cg_openmm on a simple 1–1 Lennard-Jones coarse-grained model, in which each residue contains 1 backbone and 1 side-chain bead. By scanning both nonbonded and bonded force-field parameter spaces at the coarse-grained level, we identify and characterize sets of parameters which result in the formation of stable helices through cooperative folding transitions. Furthermore, we show that the geometries and stabilities of these helices can be tuned by manipulating the force-field parameters.

36 MATERIALS SCIENCE↗