SEARCH · Engineering Papers

Results for “Unfolding”

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 235 records · Page 13

All sources NASA NTRS DOE OSTI

DOE OSTI2020

Operando Revealing Dynamic Reconstruction of NiCo Carbonate Hydroxide for High-Rate Energy Storage

Transition metal carbonate hydroxide (CH) has been widely explored as a promising battery-type electrode for high-rate energy storage. However, its genuine active sites under realistic operating conditions remains elusive. In this work, by virtue of the cutting-edge operando X-ray absorption spectroscopy, we unfold the dynamic evolution of the local electronic and geometric structures for the CH electrode upon cycling. Our results reveal that the irreversible redox of Co cations at the early stage of cyclic voltammetry (CV) cycling induces a phase transition in the NiCo CH nanowires forming oxygen vacancies-enriched NiCo layered double hydroxide (LDH) nanosheets with superior high-rate energy storage ability. Theoretical modeling demonstrates that the unsaturated 5-coordinated Co sites exhibit optimal redox reaction energy barrier and immensely promote the performance. These findings not only elucidate the electrochemical susceptibility of the Co-based carbonate hydroxide under operando conditions, but also highlight an electrochemical coordination-engineering strategy for the rational design of high-performance electrode.

25 ENERGY STORAGE↗

DOE OSTI2020

Quantitative and three-dimensional assessment of holdup material

Nuclear material deposited in equipment, transfer lines, and ventilation systems of a processing facility is usually referred to as holdup. Operators need to know the location and amount of holdup in their facility for radiation safety and material accountability. In this work, we propose to use an array of detectors co-axial to the inspected pipe to measure the holdup material. This method is implementable into an automated system capable of crawling on surfaces and pipes of various curvatures, which would enable faster, easier, and more accurate holdup safeguards measurements. We first demonstrated that the current holdup assay procedure could lead to a non-negligible bias in the estimate of special nuclear material mass, due to the simplified assumption of deposited geometry introduced by the Generalized Geometry Holdup (GGH) model. The new approach consists of imaging the inner holdup material by characterizing the detector array’s response and unfolding it from the measured light output. Our experimental proof of principle consists of three NaI(Tl) detectors surrounding an aluminum pipe containing two cesium-137 ( 137 Cs) sources. We derived the source distribution inside the pipe by first calculating the detector response matrix using a method adaptive to the surface geometry of the object containing the measured holdup material. Creating a matrix of the detector array’s measured counts, we then proceed to solve an inverse problem, resulting in an accurately located source position and activity distribution within the response matrix’s spatial resolution. Furthermore, we then developed a simulated model of the envisioned experimental setup, which accurately described both the activity and position of the source in 2D. Finally, we extended our model onto a discretized three-dimensional model of the system, encompassing 36 detectors. The model was simulated to measure the source distribution and activity of multiple sources in pipes of varied geometries, which could then be conveniently translated to a real-time holdup measurement protocol. For the 3D simulation of four different source geometries, the model accurately localized the source position in 3D, while the activity retained a maximum relative error of ±5.32%.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2021

Influence of functional groups on low-temperature combustion chemistry of biofuels

Ongoing progress in synthetic biology, metabolic engineering, and catalysis continues to produce a diverse array of advanced biofuels with complex molecular structure and functional groups. In order to integrate biofuels into existing combustion systems, and to optimize the design of next-generation combustion systems, understanding connections between molecular structure and ignition at low-temperature conditions (< 1000 K) remains a priority that is addressed in part using chemical kinetics modeling. The development of predictive models relies on detailed information, derived from experimental and theoretical studies, on molecular structure and chemical reactivity, both of which influence the balance of chain reactions that occur during combustion – propagation, termination, and branching. In broad context, three main categories of reactions affect ignition behavior: (i) initiation reactions that generate a distribution of organic radicals, ; (ii) competing unimolecular decomposition of and bimolecular reaction of with O2; (iii) decomposition mechanisms of peroxy radical adducts (RO), including isomerization via RO ⇌ OOH. Furthermore, all three categories are influenced by functional groups in different ways, which causes a shift in the balance of chain reactions that unfold over complex temperature- and pressure-dependent mechanisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Measurement of the charge asymmetry in top-quark pair production in association with a photon with the ATLAS experiment

A measurement of the charge asymmetry in top-quark pair ($t\bar{t}$) production in association with a photon is presented. The measurement is performed in the single-lepton $t\bar{t}$ decay channel using proton–proton collision data collected with the ATLAS detector at the Large Hadron Collider at CERN at a centre-of-mass-energy of 13 TeV during the years 2015–2018, corresponding to an integrated luminosity of 139 fb –1 . The charge asymmetry is obtained from the distribution of the difference of the absolute rapidities of the top quark and antiquark using a profile likelihood unfolding approach. It is measured to be A C =–0.003 ± 0.029 in agreement with the Standard Model expectation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Multiplicity dependence of charged-particle production in pp, p–Pb, Xe–Xe and Pb–Pb collisions at the LHC

Multiplicity (N ch ) distributions and transverse momentum (p T ) spectra of inclusive primary charged particles in the kinematic range of |η| < 0.8 and 0.15 GeV/c < p T < 10 GeV/c are reported for pp, p–Pb, Xe–Xe and Pb–Pb collisions at centre-of-mass energies per nucleon pair ranging from $\sqrt{s_{NN}}$ = 2.76 TeV up to 13 TeV. A sequential two-dimensional unfolding procedure is used to extract the correlation between the transverse momentum of primary charged particles and the charged-particle multiplicity of the corresponding collision. This correlation sharply characterises important features of the final state of a collision and, therefore, can be used as a stringent test of theoretical models. The multiplicity distributions as well as the mean and standard deviation derived from the p T spectra are compared to state-of-the-art model predictions. Providing these fundamental observables of bulk particle production consistently across a wide range of collision energies and system sizes can serve as an important input for tuning Monte Carlo event generators.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Girth and groomed radius of jets recoiling against isolated photons in lead-lead and proton-proton collisions at $\sqrt{s_{NN}} = 5.02$ TeV

This Letter presents the first measurements of the groomed jet radius R g and the jet girth g in events with an isolated photon recoiling against a jet in lead-lead (PbPb) and proton-proton (pp) collisions at the LHC at a nucleon-nucleon center-of-mass energy of 5.02 TeV. The observables R g and g provide a quantitative measure of how narrow or broad a jet is. The analysis uses PbPb and pp data samples with integrated luminosities of 1.7 nb -1 and 301 pb -1 , respectively, collected with the CMS experiment in 2018 and 2017. Events are required to have a photon with transverse momentum $p^{γ}_{T} > 100$ GeV and at least one jet back-to-back in azimuth with respect to the photon and with transverse momentum $p^{jet}_{T}$ such that $p^{jet}_{T}/p^{γ}_{T} > 0.4$ . The measured R g and g distributions are unfolded to the particle level, which facilitates the comparison between the PbPb and pp results and with theoretical predictions. It is found that jets with $p^{jet}_{T}/p^{γ}_{T} > 0.8$ , i.e., those that closely balance the photon $p^{γ}_{T}$ , are narrower in PbPb than in pp collisions. Relaxing the selection to include jets with $p^{jet}_{T}/p^{γ}_{T} > 0.4$ reduces the narrowing of the angular structure of jets in PbPb relative to the pp reference. This shows that selection bias effects associated with jet energy loss play an important role in the interpretation of jet substructure measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Measurements of Lund subjet multiplicities in 13 TeV proton-proton collisions with the ATLAS detector

This Letter presents a differential cross-section measurement of Lund subjet multiplicities, suitable for testing current and future parton shower Monte Carlo algorithms. This measurement is made in dijet events in 140 fb -1 of $\sqrt{s}$ =13 TeV proton–proton collision data collected with the ATLAS detector at CERN's Large Hadron Collider. The data are unfolded to account for acceptance and detector-related effects, and are then compared with several Monte Carlo models and to recent resummed analytical calculations. The experimental precision achieved in the measurement allows tests of higher-order effects in QCD predictions. Most predictions fail to accurately describe the measured data, particularly at large values of jet transverse momentum accessible at the Large Hadron Collider, indicating the measurement's utility as an input to future parton shower developments and other studies probing fundamental properties of QCD and the production of hadronic final states up to the TeV-scale.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Measurement of the Drell–Yan forward-backward asymmetry and of the effective leptonic weak mixing angle in proton-proton collisions at $\sqrt{s}$ 13 TeV

The forward-backward asymmetry in Drell-Yan production and the effective leptonic electroweak mixing angle are measured in proton-proton collisions at $\sqrt{s}$ = 13 TeV, collected by the CMS experiment and corresponding to an integrated luminosity of 138 fb$^{-1}$. The measurement uses both dimuon and dielectron events, and is performed as a function of the dilepton mass and rapidity. The unfolded angular coefficient $A_4$ is also extracted, as a function of the dilepton mass and rapidity. Using the CT18Z set of parton distribution functions, we obtain $\sin^{2}\theta^\ell_\text{eff}$ = 0.23152 $\pm$ 0.00031, where the uncertainty includes the experimental and theoretical contributions. The measured value agrees with the standard model fit result to global experimental data. This is the most precise $\sin^{2}\theta^\ell_\text{eff}$ measurement at a hadron collider, with a precision comparable to the results obtained at LEP and SLD.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Point cloud-based diffusion models for the Electron-Ion Collider

At high-energy collider experiments, generative models can be used for a wide range of tasks, including fast detector simulations, unfolding, searches of physics beyond the Standard Model, and inference tasks. In particular, it has been demonstrated that score-based diffusion models can generate high-fidelity and accurate samples of jets or collider events. This work expands on previous generative models in three distinct ways. First, our model is trained to generate entire collider events, including all particle species with complete kinematic information. We quantify how well the model learns event-wide constraints such as the conservation of momentum and discrete quantum numbers. We focus on the events at the future Electron-Ion Collider, but we expect that our results can be extended to proton-proton and heavy-ion collisions. Second, previous generative models often relied on image-based techniques. The sparsity of the data can negatively affect the fidelity and sampling time of the model. We address these issues using point clouds and a novel architecture combining edge creation with transformer modules called Point Edge Transformers. Third, we adapt the foundation model OmniLearn, to generate full collider events. This approach may indicate a transition toward adapting and fine-tuning foundation models for downstream tasks instead of training new models from scratch.

Araz, Jack Y. [Stony Brook Univ., NY (United State↗

DOE OSTI2022

Wavefront preserving X-ray optics for Synchrotron and Free Electron Laser photon beam transport systems

We report in the last two decades, after the first light from the new Free Electron Lasers, either in the UV (FLASH and FERMI@Elettra) or X-ray (LCLS and SACLA), more and more new diffraction limited sources have been either constructed or planned. Third generation storage rings are upgraded to provide a more collimated, brighter, and coherent light for the next generation experimental techniques. X-ray optics are the bridge between the light sources and the experimental stations. They are the key to the success of advanced experiments but also the potential bottleneck preventing the exploitation of the full characteristics of the source. The beam degradation originated by any mirror defect (either from mirror polishing or from contamination) is amplified with a coherent source. Delivering diffraction-limited spots, including the option for variable spot sizes in and out of focus, requires the control of the surface of the optics at the 1 nm rms level, if not better. At LCLS, only very recently an almost perfectly uniform beam out of focus has been obtained in the hard X-rays. It has been obtained after two 1-m long mirrors with 0.5 nm rms shape precision (after installation). Those mirrors were not readily available just a decade ago. But, thanks to the pioneering work performed at the Osaka University, those optics are now commercially available with arbitrary tangential profiles. This new generation of mirrors permits achieving unprecedented results. However, they do not remove all road blocks to a perfect photon transport system. Instead, they highlighted the critical importance of mirror mounting, handling of the thermal deformation, and the need of advanced diagnostics to properly exploit all the new potentiality of these optics. Besides the need of “perfect” mirrors, other aspects of the beamline design and elements may impact the quality of the beam in the experimental station, from the lack of blaze gratings to the need of advanced simulation tools, just to cite two. In this article, after a brief historical excursus, we will present the current state of the art of mirrors, gratings, crystals, lenses, diagnostics, and simulation tools. The main problems yet to solve and a look ahead at what would be achievable in the next decade will give the reader an idea on the search for an almost ideal photon transport system and how the path toward experiments, not conceivable today, will unfold.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

How irradiation promotes intergranular stress corrosion crack initiation

Irradiation assisted stress corrosion cracking (IASCC) is a form of intergranular stress corrosion cracking that occurs in irradiated austenitic alloys. It requires an irradiated microstructure along with high temperature water and stress. The process is ubiquitous in that it occurs in a wide range of austenitic alloys and water chemistries, but only when the alloy is irradiated. Despite evidence of this degradation mode that dates back to the 1960s, the mechanism by which it occurs has remained elusive. Here, using high resolution electron backscattering detection to analyze local stress-strain states, high resolution transmission electron microscopy to identify grain boundary phases at crack tips, and decoupling the roles of stress and grain boundary oxidation, we are able to unfold the complexities of the phenomenon to reveal the mechanism by which IASCC occurs. The significance of the findings impacts the mechanical integrity of core components of both current and advanced nuclear reactor designs worldwide.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Amorphous nonstoichiometric oxides with tunable room-temperature ferromagnetism and electrical transport

Material functionalities strongly depend on the stoichiometry, crystal structure, and homogeneity. Here we demonstrate an approach of amorphous nonstoichiometric inhomogeneous oxides to realize tunable ferromagnetism and electrical transport at room temperature. In order to verify the origin of the ferromagnetism, we employed a series of structural, chemical, and electronic state characterizations. Combined with electron microscopy and transport measurements, synchrotron-based grazing incident wide angle X-ray scattering, soft X-ray absorption and circular dichroism clearly reveal that the room-temperature ferromagnetism originates from the In 0.23 Co 0.77 O 1-v amorphous phase with a large tunable range of oxygen vacancies. The room-temperature ferromagnetism is tunable from a high saturation magnetization of 500 emu cm -3 to below 25 emu cm -3 , with the evolving electrical resistivity from 5 × 10 3 μΩ cm to above 2.5 × 10 5 μΩ cm. Inhomogeneous nano-crystallization emerges with decreasing oxygen vacancies, driving the system towards non-ferromagnetism and insulating regime. Our work unfolds the novel functionalities of amorphous nonstoichiometric inhomogeneous oxides, which opens up new opportunities for developing spintronic materials with superior magnetic and transport properties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Efimov-like states and quantum funneling effects on synthetic hyperbolic surfaces

Engineering lattice models with tailored inter-site tunnelings and onsite energies could synthesize essentially arbitrary Riemannian surfaces with highly tunable local curvatures. Here, we point out that discrete synthetic Poincaré half-planes and Poincaré disks, which are created by lattices in flat planes, support infinitely degenerate eigenstates for any nonzero eigenenergies. Such Efimov-like states exhibit a discrete scaling symmetry and imply an unprecedented apparatus for studying quantum anomaly using hyperbolic surfaces. Furthermore, all eigenstates are exponentially localized in the hyperbolic coordinates, signifying the first example of quantum funneling effects in Hermitian systems. As such, any initial wave packet travels towards the edge of the Poincaré half-plane or its equivalent on the Poincaré disk, delivering an efficient scheme to harvest light and atoms in two dimensions. Furthermore, our findings unfold the intriguing properties of hyperbolic spaces and suggest that Efimov states may be regarded as a projection from a curved space with an extra dimension.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Isoform-specific functions of synaptopodin-2 variants in cytoskeleton stabilization and autophagy regulation in muscle under mechanical stress

Highlights: • Muscle cells express different synaptopodin-2 isoforms with individual functions. • Reduced SYNPO2 expression results in enhanced vulnerability of myofibrils. • SYNPO2e recruites BAG3 to mechanically stressed myofibrillar areas. • SYNPO2 is an organizer and regulator of BAG3-containing proteostasis systems. • BAG3 forms functionally distinct protein complexes with different SYNPO2 isoforms. Protein homeostasis (proteostasis) in multicellular organisms depends on the maintenance of force-bearing and force-generating cellular structures. Within myofibrillar Z-discs of striated muscle, isoforms of synaptopodin-2 (SYNPO2/myopodin) act as adapter proteins that are engaged in proteostasis of the actin-crosslinking protein filamin C (FLNc) under mechanical stress. SYNPO2 directly binds F-actin, FLNc and α-actinin and thus contributes to the architectural features of the actin cytoskeleton. By its association with autophagy mediating proteins, i.e. BAG3 and VPS18, SYNPO2 is also engaged in protein quality control and helps to target mechanical unfolded and damaged FLNc for degradation. Here we show that deficiency of all SYNPO2-isoforms in myotubes leads to decreased myofibrillar stability and deregulated autophagy under mechanical stress. In addition, isoform-specific proteostasis functions were revealed. The PDZ-domain containing variant SYNPO2b and the shorter, PDZ-less isoform SYNPO2e both localize to Z-discs. Yet, SYNPO2e is less stably associated with the Z-disc than SYNPO2b, and is dynamically transferred into FLNc-containing myofibrillar lesions under mechanical stress. SYNPO2e also recruits BAG3 into these lesions via interaction with the WW domain of BAG3. Our data provide evidence for a role of myofibrillar lesions as a transient quality control compartment essential to prevent and repair contraction-induced myofibril damage in muscle and indicate an important coordinating activity for SYNPO2 therein.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

N -Arylimide Molecular Balances: A Comprehensive Platform for Studying Aromatic Interactions in Solution

Noncovalent interactions of aromatic surfaces play a key role in many biological processes and in determining the properties and utility of synthetic materials, sensors, and catalysts. However, the study of aromatic interactions has been challenging because these interactions are usually very weak and their trends are modulated by many factors such as structural, electronic, steric, and solvent effects. Recently, N-arylimide molecular balances have emerged as highly versatile and effective platforms for studying aromatic interactions in solution. These molecular balances can accurately measure weak noncovalent interactions in solution via their influence on the folded–unfolded conformational equilibrium. The structure (i.e., size, shape, π-conjugation, and substitution) and nature (i.e., element, charge, and polarity) of the π-surfaces and interacting groups can be readily varied, enabling the study of a wide range of aromatic interactions. These include aromatic stacking, heterocyclic aromatic stacking, and alkyl–π, chalcogen–π, silver–π, halogen–π, substituent–π, and solvent–π interactions. The ability to measure a diverse array of aromatic interactions within a single model system provides a unique perspective and insights as the interaction energies, stability trends, and solvent effects for different types of interactions can be directly compared. Some broad conclusions that have emerged from this comprehensive analysis include: (1) The strongest aromatic interactions involve groups with positive charges such as pyridinium and metal ions which interact with the electrostatically negative π-face of the aromatic surface via cation–π or metal–π interactions. Attractive electrostatic interactions can also form between aromatic surfaces and groups with partial positive charges. (2) Electrostatic interactions involving aromatic surfaces can be switched from repulsive to attractive using electron-withdrawing substituents or heterocycles. These electrostatic trends appear to span many types of aromatic interactions involving a polar group interacting with a π-surface such as halogen–π, chalcogen–π, and carbonyl–π. (3) Nonpolar groups form weak but measurable stabilizing interactions with aromatic surfaces in organic solvents due to favorable dispersion and/or solvophobic effects. Furthermore, a good predictor of the interaction strength is provided by the change in solvent-accessible surface area. (4) Solvent effects modulate the aromatic interactions in the forms of solvophobic effects and competitive solvation, which can be modeled using solvent cohesion density and specific solvent–solute interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin

Serum albumin is the most abundant protein in blood plasma, and it is involved in multiple biological processes. Serum albumin has recently been adapted for improving biomaterial integration with bone tissue, and studies have shown the importance of this protein in bone repair and regeneration. However, the mechanism of action is not yet clear. In stark contrast, other studies have demonstrated that albumin blocks cell adhesion to surfaces, which is seen as a limitation to its bone healing role. These apparent contradictions suggest that the conformation of albumin facilitates its bioactivity, leading to enhanced bone repair. Serum albumin is known to play a major role in maintaining the calcium ion concentration in blood plasma. Due to the prevalence of calcium at bone repair and regeneration sites, it has been hypothesized that calcium binding to serum albumin triggers a conformational change, leading to bioactivity. In the current study, molecular modeling approaches including molecular docking, atomic molecular dynamics (MD) simulation, and coarse-grained MD simulation were used to test this hypothesis by investigating the conformational changes induced in bovine serum albumin by interaction with calcium ions. The computational results were qualitatively validated with experimental Fourier-transform infrared spectroscopy analysis. We find that free calcium ions in solution transiently bind with the three major loops in albumin, triggering a conformational change where N-terminal and C-terminal domains separate from each other in a partial unfolding process. The separation distance between these domains was found to correlate with the calcium ion concentration. The experimental data support the simulation results showing that albumin has enhanced conformational heterogeneity upon exposure to intermediate levels of calcium, without any significant secondary structure changes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

A Deep Learning-Driven Sampling Technique to Explore the Phase Space of an RNA Stem-Loop

The folding and unfolding of RNA stem-loops are critical biological processes; however, their computational studies are often hampered by the ruggedness of their folding landscape, necessitating long simulation times at the atomistic scale. Here, we adapted DeepDriveMD (DDMD), an advanced deep learning-driven sampling technique originally developed for protein folding, to address the challenges of RNA stem-loop folding. Although tempering- and order parameter-based techniques are commonly used for similar rare-event problems, the computational costs or the need for a priori knowledge about the system often present a challenge in their effective use. DDMD overcomes these challenges by adaptively learning from an ensemble of running MD simulations using generic contact maps as the raw input. DeepDriveMD enables on-the-fly learning of a low-dimensional latent representation and guides the simulation toward the undersampled regions while optimizing the resources to explore the relevant parts of the phase space. We showed that DDMD estimates the free energy landscape of the RNA stem-loop reasonably well at room temperature. Our simulation framework runs at a constant temperature without external biasing potential, hence preserving the information on transition rates, with a computational cost much lower than that of the simulations performed with external biasing potentials. Here, we also introduced a reweighting strategy for obtaining unbiased free energy surfaces and presented a qualitative analysis of the latent space. This analysis showed that the latent space captures the relevant slow degrees of freedom for the RNA folding problem of interest. Finally, throughout the manuscript, we outlined how different parameters are selected and optimized to adapt DDMD for this system. We believe this compendium of decision-making processes will help new users adapt this technique for the rare-event sampling problems of their interest.

Gupta, Ayush↗

DOE OSTI2024

Adjusting the Energy Profile for CH–O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations

The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but RNA simulation methods and force fields are less mature. It remains challenging to generate stable RNA simulations, even for small systems where well-defined, thermostable structures have been established by experiments. Further many different aspects of RNA energetics have been adjusted in force fields, seeking improvements that are transferable across a variety of RNA structural motifs. In this work, the role of weak CH···O interactions is explored, which are ubiquitous in RNA structure but have received less attention in RNA force field development. By comparing data extracted from high-resolution RNA crystal structures to energy profiles from quantum mechanics and force field calculations, it is shown that CH···O interactions are overly repulsive in the widely used Amber RNA force fields. A simple, targeted adjustment of CH···O repulsion that leaves the remainder of the force field unchanged was developed. Then, the standard and modified force fields were tested using molecular dynamics (MD) simulations with explicit water and salt, amassing over 300 μs of data for multiple RNA systems containing important features such as the presence of loops, base stacking interactions as well as canonical and noncanonical base pairing. In this work and others, standard force fields lead to reproducible unfolding of the NMR-based structures. Including a targeted CH···O adjustment in an otherwise identical protocol dramatically improves the outcome, leading to stable simulations for all RNA systems tested.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗