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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.

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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Correlated conformational dynamics of the human GluN1-GluN2A type N-methyl-D-aspartate (NMDA) receptor

N-Methyl-D-aspartate receptors (NMDARs) are glutamate-gated ion channels found in the nerve cell membranes. As a result of overexcitation of NMDARs, neuronal death occurs and may lead to diseases such as epilepsy, stroke, Alzheimer’s disease, and Parkinson’s disease. In this study, human GluN1- GluN2A type NMDAR structure is modeled based on the X-ray structure of the Xenopus laevis template and missing loops are added by ab-initio loop modeling. The final structure is chosen according to two different model assessment scores. To be able to observe the structural changes upon ligand binding, glycine and glutamate molecules are docked into the corresponding binding sites of the receptor. Subsequently, molecular dynamics simulations of 1.3 μs are performed for both apo and ligand-bound structures. Structural parameters, which have been considered to show functionally important changes in previous NMDAR studies, are monitored as conformational rulers to understand the dynamics of the conformational changes. Moreover, principal component analysis (PCA) is performed for the equilibrated part of the simulations. Additionally, from these analyses, the differences in between apo and ligand-bound simulations can be summarized as the following: The girdle right at the beginning of the pore loop, which connects M2 and M3 helices of the ion channel, partially opens. Ligands act like an adhesive for the ligand-binding domain (LBD) by keeping the bi-lobed structure together and consequently this is reflected to the overall dynamics of the protein as an increased correlation of the LBD with especially the amino-terminal domain (ATD) of the protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Prediction and Experimental Verification of Electrolyte Solvation Structure from an OMol25-Trained Interatomic Potential

A molecular-level understanding of electrolyte solvation structure and ion–ion correlations is critical to developing next-generation battery chemistries. Atomistic simulation capabilities with sufficient accuracy, speed, and transferability to deliver reliable structural insights while avoiding arduous system-specific reparameterization are thus highly desirable. Machine learning interatomic potentials (MLIPs) trained on large, chemically diverse data sets are revolutionizing computational chemistry, enabling molecular dynamics simulations of battery electrolytes with near-DFT accuracy over 10,000× faster than DFT. While previous MLIP training data sets with suitable elemental coverage for electrolytes have been based on inorganic materials, the Open Molecules 2025 (OMol25) data set provides large-scale molecular DFT MLIP training data with broad elemental coverage and specifically samples tens of millions of electrolyte configurations. Here, we integrate computational modeling with experimental validation to systematically assess the ability of large-scale MLIPs pretrained on materials data or on OMol25 to accurately resolve nanoscale structural organization and ion-solvation characteristics in Na-ion battery electrolytes across diverse physicochemical conditions and compositional regimes. We find that the OMol25-trained Universal Model of Atoms (UMA-OMol) predicts experimentally measured densities and X-ray structure factors in substantially better agreement compared to state-of-the-art models trained only on inorganic materials data. Using UMA-OMol, we further analyze systematic trends in solvation structure as a function of cation identity, anion chemistry, salt concentration, and solvent topology. We observe that increasing system temperature amplifies the heterogeneity within the solvation environment, perturbing cation–solvent interactions and promoting the formation of contact ion pairs (CIPs). Moreover, subtle variations in the solvent topology of glyme-based electrolytes cause pronounced changes in ion correlations and solvation structure. The experimental agreement and microscopic insights shown here position OMol25-trained MLIPs as a practical route to predictive, high-throughput electrolyte simulations beyond the limits of classical force fields and direct DFT molecular dynamics, serving as a powerful tool for accelerating the design of next-generation Na-ion battery electrolytes and beyond.

MLIPs↗
DOE OSTI2020

Concentration and velocity profiles in a polymeric lithium-ion battery electrolyte

Predictive knowledge of ion transport in electrolytes which bridges microscopic and macroscopic length scales is imperative to design new ion conductors and to simulate device performance. Here, we employed a novel approach combining operando X-ray photon correlation spectroscopy, X-ray absorption microscopy, continuum modelling, and molecular dynamics simulations to probe the ion transport in a baseline polymeric lithium-ion battery electrolyte. In a Li/PEO–LiTFSI/Li symmetric cell under polarization, we determined and rationalized microscopic properties including local electrolyte velocities and ion correlations and connected this insight to measured and simulated macroscopic ion concentration gradients. By relating our results across length scales, we suggest a fairly concentration-independent transference number of about 0.2. Our study shows the broad applicability of operando X-ray photon correlation spectroscopy to the understanding of dynamic phenomena.

25 ENERGY STORAGE↗
DOE OSTI2022

Atomistic Simulations of the Elastic Compression of Platinum Nanoparticles

Abstract The elastic behavior of nanoparticles depends strongly on particle shape, size, and crystallographic orientation. Many prior investigations have characterized the elastic modulus of nanoscale particles using experiments or simulations; however their reported values vary widely depending on the methods for measurement and calculation. To understand these discrepancies, we used classical molecular dynamics simulation to model the compression of platinum nanoparticles with two different polyhedral shapes and a range of sizes from 4 to 20 nm, loaded in two different crystal orientations. Multiple standard methods were used to calculate the elastic modulus from stress-vs-strain data for each nanoparticle. The magnitudes and particle-size dependence of the resulting moduli varied with calculation method and, even for larger nanoparticles where bulk-like behavior may be expected, the effective elastic modulus depended strongly on shape and orientation. Analysis of per-atom stress distributions indicated that the shape- and orientation-dependence arise due to stress triaxiality and inhomogeneity across the particle. When the effective elastic modulus was recalculated using a representative volume element in the center of a large nanoparticle, the elastic modulus had the expected value for each orientation and was shape independent. It is only for single-digit nanoparticles that meaningful differences emerged, where even the very center of the particle had a lower modulus due to the effect of the surface. These findings provide better understanding of the elastic properties of nanoparticles and disentangle geometric contributions (such as stress triaxiality and spatial inhomogeneity) from true changes in elastic properties of the nanoscale material.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Hydrogen effects on the deformation and slip localization in a single crystal austenitic stainless steel

Hydrogen is known to embrittle austenitic stainless steels, which are widely used in high-pressure hydrogen storage and delivery systems, but the mechanisms that lead to such material degradation are still being elucidated. The current work investigates the deformation behavior of single crystal austenitic stainless steel 316L through combined uniaxial tensile testing, characterization and atomistic simulations. Thermally precharged hydrogen is shown to increase the critical resolved shear stress (CRSS) without previously reported deviations from Schmid’s law. Molecular dynamics simulations further expose the statistical nature of the hydrogen and vacancy contributions to the CRSS in the presence of alloying. Slip distribution quantification over large in-plane distances (> 1 mm), achieved via atomic force microscopy (AFM), highlights the role of hydrogen increasing the degree of slip localization in both single and multiple slip configurations. The most active slip bands accumulate significantly more deformation in hydrogen precharged specimens, with potential implications for damage nucleation. For $\langle$110$\rangle$ tensile loading, slip localization further enhances the activity of secondary slip, increases the density of geometrically necessary dislocations and leads to a distinct lattice rotation behavior compared to hydrogen-free specimens, as evidenced by electron backscatter diffraction (EBSD) maps. Finally, the results of this study provide a more comprehensive picture of the deformation aspect of hydrogen embrittlement in austenitic stainless steels.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Probing the atomic dynamics of ultrafast melting with femtosecond electron diffraction

Melting is an every-day phase transition that is determined by thermodynamic parameters like temperature and pressure. In contrast, ultra-fast melting is governed by the microscopic response to a rapid energy input and, thus, can reveal the strength and dynamics of atomic bonds as well as the energy flow rate to the lattice. Accurately describing these processes remains challenging and requires detailed insights into transient states encountered. Here, we present data from femtosecond electron diffraction measurements that capture the structural evolution of copper during the ultrafast solid-to-liquid phase transformations. At absorbed energy densities 2-4 times the melting threshold, melting begins at the surface slightly below the nominal melting point followed by rapid homogeneous melting throughout the volume. Molecular dynamics simulations reproduce these observations and reveal a weak electron-lattice energy transfer rate for the given experimental conditions. Both simulations and experiments show no indications of rapid lattice collapse when its temperature surpasses proposed limits of superheating, providing evidence that the inherent dynamics limits the speed of disordering in ultrafast melting of metals.

FOS: Physical sciences↗
DOE OSTI2021

Modeling nanoparticle charge distribution in the afterglow of non-thermal plasmas and comparison with measurements

Particle charging in the afterglows of non-thermal plasmas typically take place in a non-neutral space charge environment. We model the same by incorporating particle-ion collision rate constant models, developed in prior work by analyzing particle-ion trajectories calculated using Langevin Dynamics simulations, into species transport equations for ions, electrons and charged particles in the afterglow. A scaling analysis of particle charging and additional Langevin Dynamics calculations of the particle-ion collision rate constant are presented to extend the range of applicability to ion electrostatic to thermal energy ratios of 300 and diffusive Knudsen number (that scales inversely with gas pressure) up to 2000. The developed collision rate constant models are first validated by comparing predictions of particle charge against measured values in a stationary, non-thermal DC plasma from past PK-4 campaigns published in Phys. Rev. Lett. 93(8): 085001 and Phys. Rev. E 72(1): 016406). The comparisons reveal excellent agreement within ±35% for particles of radius 0.6,1.0,1.3 μm in the gas pressure range of ~20-150 Pa. The experiments to probe particle charge distributions by Sharma et al. (J. Physics D: Appl. Phys. 53(24): 245204) are modeled using the validated particle-ion collision rate constant models and the calculated charge fractions are compared with measurements. The comparisons reveal that the ion/electron concentration and gas temperature in the afterglow critically influence the particle charge and the predictions are generally in qualitative agreement with the measurements. Along with critical assessment of the modeling assumptions, several recommendations are presented for future experimental design to probe charging in afterglows.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Simulations of short-term exposure to NO 2 and PM 2.5 to inform capture efficiency standards

The California building code requires all new or renovated residential dwelling units to have kitchen exhaust ventilation to manage air pollutants and moisture generated during cooking. Current performance requirements are specified as a minimum airflow and maximum sound level. This report presents an analysis to support consideration of adding a capture efficiency requirement to the code. The analysis uses a physics-based simulation model to calculate air pollutant concentrations in homes that result from cooking and the inflow of outdoor air, mediated by loss and removal process including deposition, dwelling unit ventilation, and the use of a range hood with varying levels of capture efficiency. Calculated pollutant concentrations are compared to relevant, health-based guidelines. The analysis considers the highest 1-hour concentration of nitrogen dioxide (NO 2 ), which is a product of natural gas combustion and the highest 24-hour concentrations of fine particulate matter (PM 2.5 ) which is emitted in substantial quantities from frying, broiling and grilling among other cooking activities. For NO 2 , the analysis considers cooking of a dinner for 3-4 persons consisting of pasta, meat sauce, a par-boiled vegetable, and baked garlic bread. For PM 2.5 , the analysis considers a day in which breakfast emitted particles at the 80th percentile and lunch and dinner entailed particle emissions at the 50th percentile of cooking emission events reported in the literature. Model simulations were performed to determine the level of range hood capture efficiency that will allow these cooking scenarios to occur in the vast majority (>99%) of new homes being built in California while maintaining pollutant concentrations below the health-based guidelines, if the range hood is used throughout cooking. All homes were assumed to have dwelling unit ventilation at the rate required in the building code. Simulation model input parameters were specified using a Monte Carlo approach to represent a range of housing characteristics, outdoor conditions, and indoor pollutant dynamics. Simulation results suggest that requiring a minimum capture efficiency of at least 70% is needed to avoid unacceptably high NO 2 (1-h average concentration of 100 ppb or higher) and at least 60% to avoid unacceptably high PM 2.5 (24-h average of 25 μg/m³ or higher). These results were driven by multi-family homes, which have a smaller volume of air to dilute any pollutants not captured and removed at the cooking area, resulting in higher concentrations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex

The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.

3DRISM↗
DOE OSTI2025

GR-Athena++: General-relativistic Magnetohydrodynamics Simulations of Neutron Star Spacetimes

We present the extension of GR-Athena++ to general-relativistic magnetohydrodynamics (GRMHD) for applications to neutron star spacetimes. The new solver couples the constrained transport implementation of Athena++ to the Z4c formulation of the Einstein equations to simulate dynamical spacetimes with GRMHD using oct-tree adaptive mesh refinement. We consider benchmark problems for isolated and binary neutron star spacetimes demonstrating stable and convergent results at relatively low resolutions and without grid symmetries imposed. The code correctly captures magnetic field instabilities in nonrotating stars with total relative violation of the divergence-free constraint of 10 –16 . It handles evolutions with a microphysical equation of state and black hole formation in the gravitational collapse of a rapidly rotating star. For binaries, we demonstrate correctness of the evolution under the gravitational radiation reaction and show convergence of gravitational waveforms. We showcase the use of adaptive mesh refinement to resolve the Kelvin–Helmholtz instability at the collisional interface in a merger of magnetised binary neutron stars. GR-Athena++ shows strong scaling efficiencies above 80% in excess of 10 5 CPU cores and excellent weak scaling is shown up to ~5 × 10 5 CPU cores in a realistic production setup. GR-Athena++ allows for the robust simulation of GRMHD flows in strong and dynamical gravity with exa-scale computers.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

What do far-infrared spectra of solitary water in “water-in-solvent” systems reveal about water’s solvation and dynamics?

Classical molecular dynamics simulations of water in ionic and dipolar solvents were used to interpret the far-infrared (FIR) rotation/libration spectra of “solitary water” in terms of water’s rotational dynamics and interactions with solvents. Seven solvents represented by nonpolarizable all-atom force fields and a series of idealized variable-charge solvents were used to span the range of solvent polarities (hydrogen bonding) studied experimentally. Simulated spectra capture the solvent dependence observed, as well as the relationship between the frequencies of water libration (νL) and OH stretching bands (νOH). In more strongly interacting solvents, simulated νL are ∼20% higher than those of experiment. In all solvents, the simulated spectra are composites of rotational motions about the two axes perpendicular to water’s dipole moment, and the different frequencies of these two motions are responsible for the breadth of the libration band and the bimodal shape observed in halide ionic liquids. Simulations overestimate the separation of these two components in most solvents. The character of water rotational motions changes markedly with solvent polarity, from quasi-free rotation in nonpolar and weakly polar solvents to highly constrained libration in strongly hydrogen bonding environments. The changeover to librational motions dominating the spectrum occurs between solvents such as benzene (νL ∼ 250 cm−1) and acetonitrile (νL ∼ 400 cm−1). For solvents in the latter category, the mean frequency of the experimental FIR band provides a direct measure of mean-squared torques and, therefore, force constants associated with interactions constraining water’s librational motion.

Chemistry↗
DOE OSTI2020

Patchy particle model of hydrated amorphous silica

Glasses corroded in static aqueous conditions typically reach a slow, residual rate of dissolution as a result of the complex interplay between multiple processes. While intrinsically suited to address this problem, Monte Carlo (MC) models developed to date have relied on lattices to describe the amorphous structure of glass and are thus unable to reproduce the residual rate of glass corrosion. A recently developed MC approach based on amorphous structures derived from molecular dynamics simulations offers a solution [Kerisit and Du J. Non-Cryst. Solids 522 (2019) 119601], but it requires a simple model that can rapidly relax the glass-water interface upon each dissolution/condensation event to retain the ability of MC simulations to reach large spatial and temporal scales. To this end, a patchy particle model of hydrated amorphous silica was developed and evaluated against atomistic simulations in this work. Models of water and amorphous silica were first developed separately, and cross terms were then defined to enable simulations of hydrated amorphous silica structures with varying water content. While the nature of its interaction potential prevents the patchy particle model from reproducing simultaneously the structure and dynamics of the systems of interest with a single set of parameters, it described well the connectivity of hydrated amorphous silica structures and the local coordination geometry of individual species. Therefore, this model opens the door to MC simulations of the residual rate of glass corrosion and offers an alternative to atomistic models to investigate the evolution of silica gels over large spatial and temporal scales.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Mesoscopic two-point collective dynamics of glass-forming liquids

The collective density–density and hydrostatic pressure–pressure correlations of glass-forming liquids are spatiotemporally mapped out using molecular dynamics simulations. It is shown that the sharp rise of structural relaxation time below the Arrhenius temperature coincides with the emergence of slow, nonhydrodynamic collective dynamics on mesoscopic scales. The observed long-range, nonhydrodynamic mode is independent of wave numbers and closely coupled to the local structural dynamics. Below the Arrhenius temperature, it dominates the slow collective dynamics on length scales immediately beyond the first structural peak in contrast to the well-known behavior at high temperatures. Furthermore, these results highlight a key connection between the qualitative change in mesoscopic two-point collective dynamics and the dynamic crossover phenomenon.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Unusual dynamics of tetrahedral liquids caused by the competition between dynamic heterogeneity and structural heterogeneity

Tetrahedral liquids exhibit intriguing thermodynamic and transport properties because of the various ways tetrahedra can be packed and connected. Recently, an unusual temperature dependence of the stretching exponent β in a model tetrahedral liquid ZnCl 2 from T m + 85 K to T m + 35 K has been reported using neutron-spin echo spectroscopy. This discovery stands in sharp contrast to other glass-forming liquids. In this study, we conducted neural network force field driven molecular dynamic simulations of ZnCl 2 . We found a non-monotonic temperature dependence of β from liquid to supercooled liquid temperatures. Further structural decomposition and dynamic analysis suggest that this unusual dynamic behavior is a result of the competition between the decrease in the diversity of tetrahedra motifs (structural heterogeneity) and the increase in glassy dynamic heterogeneity. Furthermore, this result may contribute to new understandings of the structural relaxation of other network liquids.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Self-Assembly of Anisotropic Particles on Curved Surfaces

The surface curvature of membranes, interfaces, and substrates plays a crucial role in shaping the self-assembly of particles adsorbed on these surfaces. However, little is known about the interplay between particle anisotropy and surface curvature and how they couple to alter the free energy landscape of particle assemblies. Using molecular dynamics simulations, we investigate the effect of prescribed curvatures on a quasi-2D assembly of anisotropic patchy particles. By varying curvature and surface coverage, we uncover a rich geometric phase diagram, with curvature inducing ordered structures entirely absent on planar surfaces. Large spatial domains of ordered structures can contain hidden microdomains of orientational textures imprinted by the surface on the assembly. The dynamical landscape is also reshaped by surface curvature, with a glass-like state emerging at modest densities and high curvature. Changes to the symmetry of the surface curvature are found to result in distinct structures, including phases with mesoscale ordering. In conclusion, our findings show that the coupling between surface curvature and particle geometry opens an unexplored space of morphologies and structures that can be exploited for material design.

Fluids↗
DOE OSTI2021

Simulations of the IR and Raman spectra of water confined in amorphous silica slit pores

Water in nano-scale confining environments is a key element in many biological, material, and geological systems. The structure and dynamics of the liquid can be dramatically modified under these conditions. Probing these changes can be challenging, but vibrational spectroscopy has emerged as a powerful tool for investigating their behavior. A critical, evolving component of this approach is a detailed understanding of the connection between spectroscopic features and molecular-level details. In this paper, this issue is addressed by using molecular dynamics simulations to simulate the linear infrared (IR) and Raman spectra for isotopically dilute HOD in D 2 O confined in hydroxylated amorphous silica slit pores. The effect of slit-pore width and hydroxyl density on the silica surface on the vibrational spectra is also investigated. The primary effect of confinement is a blueshift in the frequency of OH groups donating a hydrogen bond to the silica surface. This appears as a slight shift in the total (measurable) spectra but is clearly seen in the distance-based IR and Raman spectra. Analysis indicates that these changes upon confinement are associated with the weaker hydrogen-bond accepting properties of silica oxygens compared to water molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Anomalous phase separation in a correlated electron system: Machine-learning–enabled large-scale kinetic Monte Carlo simulations

Significance Phase separation is crucial to the functionalities of many correlated electron materials with notable examples including colossal magnetoresistance in manganites and high- T c superconductivity in cuprates. However, the nonequilibrium phase-separation dynamics in such systems are poorly understood theoretically, partly because the required multiscale modeling is computationally very demanding. With the aid of machine-learning methods, we have achieved large-scale dynamical simulations in a representative correlated electron system. We observe an unusual relaxation process that is beyond the framework of classical phase-ordering theories. We also uncover a correlation-induced freezing behavior, which could be a generic feature of phase separation in correlated electron systems.

Zhang, Sheng↗
DOE OSTI2023

Multiscale simulations reveal TDP-43 molecular-level interactions driving condensation

The RNA-binding protein TDP-43 is associated with mRNA processing and transport from the nucleus to the cytoplasm. TDP-43 localizes in the nucleus as well as accumulating in cytoplasmic condensates such as stress granules. Aggregation and formation of amyloid-like fibrils of cytoplasmic TDP-43 are hallmarks of numerous neurodegenerative diseases, most strikingly present in >90% of amyotrophic lateral sclerosis (ALS) patients. If excessive accumulation of cytoplasmic TDP-43 causes, or is caused by, neurodegeneration is presently not known. In this work, we use molecular dynamics simulations at multiple resolutions to explore TDP-43 self- and cross-interaction dynamics. A full-length molecular model of TDP-43, all 414 amino acids, was constructed from select structures of the protein functional domains (N-terminal domain, and two RNA recognition motifs, RRM1 and RRM2) and modeling of disordered connecting loops and the low complexity glycine-rich C-terminus domain. All-atom CHARMM36m simulations of single TDP-43 proteins served as guides to construct a coarse-grained Martini 3 model of TDP-43. The Martini model and a coarser implicit solvent Cα model, optimized for disordered proteins, were subsequently used to probe TDP-43 interactions; self-interactions from single-chain full-length TDP-43 simulations, cross-interactions from simulations with two proteins and simulations with assemblies of dozens to hundreds of proteins. Our findings illustrate the utility of different modeling scales for accessing TDP-43 molecular-level interactions and suggest that TDP-43 has numerous interaction preferences or patterns, exhibiting an overall strong, but dynamic, association and driving the formation of biomolecular condensates.

59 BASIC BIOLOGICAL SCIENCES↗