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At least 1,693 records · Page 94
All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2017

GPU accelerated Discrete Element Method (DEM) molecular dynamics for conservative, faceted particle simulations

Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging to model in these systems because they require detailed dynamical information at the individual particle level. Within the granular materials community the Discrete Element Method has been used extensively to model systems of anisotropic particles under gravity, with friction. We provide an implementation of this method intended for simulation of hard, faceted nanoparticles, with a conservative Weeks–Chandler–Andersen (WCA) interparticle potential, coupled to a thermodynamic ensemble. This method is a natural extension of classical molecular dynamics and enables rigorous thermodynamic calculations for faceted particles.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Curated Collection of More than 20,000 Experimentally Reported One-Dimensional Metal–Organic Frameworks

Herein, a collection of more than 20,000 experimentally derived crystal structures for metal–organic frameworks (MOFs) that do not have two- or three-dimensional covalently bonded networks has been developed from the materials available at the Cambridge Crystallographic Data Centre. Of these 20,000 1D MOFs, more than 12,000 structures have been verified to be solvent-free and in exact agreement with the stoichiometry of the synthesized materials. More than 10% of the complete data set comprise materials including two or more distinct metals. The band gaps of more than 12,000 1D MOFs have been computed at the density functional theory-generalized gradient approximation level, finding more than 2000 materials that have a zero band gap. Molecular simulations of CH4 adsorption in a small number of 1D MOFs indicated that adsorbate-induced deformation plays a significant role in determining adsorption isotherms in these materials. As a result, methods that have been used previously for high-throughput predictions of molecular adsorption in 3D MOFs are not suitable for 1D MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Atomistic simulations for investigation of substrate effects on lipid in-source fragmentation in secondary ion mass spectrometry

In beam-based ionization methods, the substrate plays an important role on the desorption mechanism of molecules from surfaces. Both the specific orientation that a molecule adopts at a surface and the strength of the molecule-surface interaction can greatly influence desorption processes, which in turn will affect the ion yield and the degree of in-source fragmentation of a molecule. In the beam-based method of secondary ion mass spectrometry (SIMS), in-source fragmentation can be significant and molecule specific due to the hard ionization method of using a primary ion beam for molecule desorption. To investigate the role of the substrate on orientation and in-source fragmentation, we have used atomistic simulations—molecular dynamics in combination with density functional theory calculations—to explore the desorption of a sphingolipid (palmitoylsphingomyelin) from a model surface (gold). We then compare SIMS data from this model system to our modeling findings. Using this approach, we found that the combined adsorption and binding energy of certain bonds associated with the headgroup fragments (C3H8N+, C5H12N+, C5H14NO+, and C5H15PNO4+) was a good predictor for fragment intensities (as indicated by relative ion yields). This is the first example where atomistic simulations have been applied in beam-based ionization of lipids, and it presents a new approach to study biointerfacial lipid ordering effects on SIMS imaging.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Modeling adsorption properties of structurally deformed metal–organic frameworks using structure–property map

Structural deformation and collapse in metal-organic frameworks (MOFs) can lead to loss of long-range order, making it a challenge to model these amorphous materials using conventional computational methods. In this work, we show that a structure–property map consisting of simulated data for crystalline MOFs can be used to indirectly obtain adsorption properties of structurally deformed MOFs. The structure–property map (with dimensions such as Henry coefficient, heat of adsorption, and pore volume) was constructed using a large data set of over 12000 crystalline MOFs from molecular simulations. By mapping the experimental data points of deformed SNU-200, MOF-5, and Ni-MOF-74 onto this structure–property map, we show that the experimentally deformed MOFs share similar adsorption properties with their nearest neighbor crystalline structures. Furthermore, once the nearest neighbor crystalline MOFs for a deformed MOF are selected from a structure–property map at a specific condition, then the adsorption properties of these MOFs can be successfully transformed onto the degraded MOFs, leading to a new way to obtain properties of materials whose structural information is lost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9

The microsomal, membrane-bound, human cytochrome P450 (CYP) 2C9 is a liver-specific monooxygenase essential for drug metabolism. CYPs require electron transfer from the membrane-bound CYP reductase (CPR) for catalysis. The structural details and functional relevance of the CYP-membrane interaction are not understood. From multiple coarse grained molecular simulations started with arbitrary configurations of protein-membrane complexes, we found two predominant orientations of CYP2C9 in the membrane, both consistent with experiments and conserved in atomic-resolution simulations. The dynamics of membrane-bound and soluble CYP2C9 revealed correlations between opening and closing of different tunnels from the enzyme’s buried active site. The membrane facilitated the opening of a tunnel leading into it by stabilizing the open state of an internal aromatic gate. Other tunnels opened selectively in the simulations of product-bound CYP2C9. We propose that the membrane promotes binding of liposoluble substrates by stabilizing protein conformations with an open access tunnel and provide evidence for selective substrate access and product release routes in mammalian CYPs. The models derived here are suitable for extension to incorporate other CYPs for oligomerization studies or the CYP reductase for studies of the electron transfer mechanism, whereas the modeling procedure is generally applicable to study proteins anchored in the bilayer by a single transmembrane helix.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Importance of counteranions on the hydration structure of the curium ion

Using density functional theory based ab initio molecular dynamics and metadynamics we show that counter ions can trigger noticeable changes in the hydration shell structure of the curium ion. The free energies of curium-water coordination and the solvent hydrogen bond (HB) lifetimes in the absence and presence the counter anions predict that chloride and bromide counter anions strengthen the first shell and consequently the 8-fold coordination state is dominant by at least 98%. In contrast, the perchlorate counter anions are found to weaken the coordination shell and the HB network, with the 9-fold and 8-fold states existing in an 8:1 ratio, which is in good agreement with reported 9:1 ratio seen in time resolved fluorescence spectroscopy experiments. To our knowledge this is the first time molecular simulations have shown that counter anions can directly affect the first hydration shell structure of a cation.

Curium ion, hydration, hydrogen bonding, perchlora↗
DOE OSTI2015

A flexible metal–organic framework: Guest molecules controlled dynamic gas adsorption

A flexible metal–organic framework (MOF) of [Zn 3 (btca) 2 (OH) 2 ]·(guest) n (H 2 btca = 1,2,3-benzotriazole-5-carboxylic acid) that exhibits guest molecule-controlled dynamic gas adsorption is reported in which carbon dioxide molecules rather than N 2 , He, and Ar induce a structural transition with a corresponding appearance of additional steps in the isotherms. Physical insights into the dynamic adsorption behaviors of flexible compound 1 were detected by gas adsorption at different temperatures and different pressures and confirmed by Fourier transform infrared spectroscopy and molecular simulations. Interestingly, by taking advantage of the flexible nature inherent to the framework, this MOF material enables highly selective adsorption of CO 2 /N 2 , CO 2 /Ar, and CO 2 /He of 36.3, 32.6, and 35.9, respectively, at 298 K. Furthermore, this class of flexible MOFs has potential applications for controlled release, molecular sensing, noble gas separation, smart membranes, and nanotechnological devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Nonvariational ADAPT algorithm for quantum simulations

We explore a nonvariational quantum state preparation approach combined with the ADAPT operator selection strategy in the application of preparing the ground state of a desired target Hamiltonian. In this algorithm, energy gradient measurements determine both the operators and the gate parameters in the quantum circuit construction. We compare this nonvariational algorithm with ADAPT-VQE and with feedback-based quantum algorithms in terms of the rate of energy reduction, the circuit depth, and the measurement cost in molecular simulation. We find that, despite using deeper circuits, this new algorithm reaches chemical accuracy at a similar measurement cost to ADAPT-VQE. Since it does not rely on a classical optimization subroutine, it may provide robustness against circuit parameter errors due to imperfect control or gate synthesis.

Tang'S, Ho Lun [Virginia Polytechnic Inst. and Sta↗
DOE OSTI2019

A Multifunctional Cosolvent Pair Reveals Molecular Principles of Biomass Deconstruction

The complex structure of plant cell walls resists chemical or biological degradation, challenging the breakdown of lignocellulosic biomass into renewable chemical precursors that could form the basis of future production of green chemicals and transportation fuels. In this report, experimental and computational results reveal that the effect of the tetrahydrofuran (THF)–water cosolvents on the structure of lignin and on its interactions with cellulose in the cell wall drives multiple synergistic mechanisms leading to the efficient breakdown and fractionation of biomass into valuable chemical precursors. Molecular simulations reflect that THF–water is an excellent “theta” solvent, such that lignin dissociates from itself and from cellulose and expands to form a random coil. The expansion of the lignin molecules exposes interunit linkages, rendering them more susceptible to depolymerization by acid-catalyzed cleavage of aryl-ether bonds. Nanoscale infrared sensors confirm cosolvent-mediated molecular rearrangement of lignin in the cell wall of micrometer-thick hardwood slices and track the disappearance of lignin. At bulk scale, adding dilute acid to the cosolvent mixture liberates the majority of the hemicellulose and lignin from biomass, allowing unfettered access of cellulolytic enzymes to the remaining cellulose-rich material, allowing them to sustain high rates of hydrolysis to glucose without enzyme deactivation. Through this multiscale analysis, synergistic mechanisms for biomass deconstruction are confirmed, portending a paradigm shift toward first-principles design and evaluation of other cosolvent methods to realize low cost fuels and bioproducts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Fluorescence Imaging of Single-Molecule Retention Trajectories in Reversed-Phase Chromatographic Particles

Due to its high specific surface area and chemical stability, porous silica is used as a support structure in numerous applications, including heterogeneous catalysis, biomolecule immobilization, sensors, and liquid chromatography. Reversed-phase liquid chromatography (RPLC), which uses porous silica support particles, has become an indispensable separations tool in quality control, pharmaceutics, and environmental analysis requiring identification of compounds in mixtures. For complex samples, the need for higher resolution separations requires an understanding of the time scale of processes responsible for analyte retention in the stationary phase. In the present work, single-molecule fluorescence imaging is used to observe transport of individual molecules within RPLC porous silica particles. This technique allows direct measurement of intraparticle molecular residence times, intraparticle diffusion rates, and the spatial distribution of molecules within the particle. On the basis of the localization uncertainty and characteristic measured diffusion rates, statistical criteria were developed to resolve the frame-to-frame behavior of molecules into moving and stuck events. The measured diffusion coefficient of moving molecules was used in a Monte Carlo simulation of a random-walk model within the cylindrical geometry of the particle diameter and microscope depth-of-field. Furthermore, the simulated molecular transport is in good agreement with the experimental data, indicating transport of moving molecules in the porous particle is described by a random-walk. Histograms of stuck-molecule event times, locations, and their contributions to intraparticle residence times were also characterized.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Structural rearrangement and dispersion of functionalized graphene sheets in aqueous solutions

Surfactants are widely used for dispersing graphene and functionalized graphene sheets (FGS) in colloidal suspensions, but there have been few studies of the structure of the dispersed graphene-surfactant complexes in suspension and of their time evolution. Here, we combine experimental study of efficiencies of ionic surfactants/polymers in suspending FGS in water with characterization using atomic force microscopy, small angle neutron scattering, and molecular simulations to probe the detailed structures of FGSs. A systematic study of FGS dispersions using ionic surfactants with varying chain lengths revealed that the effective charge density of surfactant layer defines the concentration of dispersed FGS while the strength of interfacial binding defines the stability of graphene dispersion over long time aging. Ionic surfactants with strong interfacial binding and large molecular weight increase the dispersing power by over an order of magnitude.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Systematic and simulation-free coarse graining of homopolymer melts: A structure-based study

We propose a systematic and simulation-free strategy for coarse graining of homopolymer melts, where each chain of N{sub m} monomers is uniformly divided into N segments, with the spatial position of each segment corresponding to the center-of-mass of its monomers. We use integral-equation theories suitable for the study of equilibrium properties of polymers, instead of many-chain molecular simulations, to obtain the structural and thermodynamic properties of both original and coarse-grained (CG) systems, and quantitatively examine how the effective pair potentials between CG segments and the thermodynamic properties of CG systems vary with N. Our systematic and simulation-free strategy is much faster than those using many-chain simulations, thus effectively solving the transferability problem in coarse graining, and provides the quantitative basis for choosing the appropriate N-values. It also avoids the problems caused by finite-size effects and statistical uncertainties in many-chain simulations. Taking the simple hard-core Gaussian thread model [K. S. Schweizer and J. G. Curro, Chem. Phys. 149, 105 (1990)] as the original system, we demonstrate our strategy applied to structure-based coarse graining, which is quite general and versatile, and compare in detail the various integral-equation theories and closures for coarse graining. Our numerical results show that the effective CG potentials for various N and closures can be collapsed approximately onto the same curve, and that structure-based coarse graining cannot give thermodynamic consistency between original and CG systems at any N < N{sub m}.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Technical Note: Development of a 3D printed subresolution sandwich phantom for validation of brain SPECT analysis

Purpose: To make an adaptable, head shaped radionuclide phantom to simulate molecular imaging of the brain using clinical acquisition and reconstruction protocols. This will allow the characterization and correction of scanner characteristics, and improve the accuracy of clinical image analysis, including the application of databases of normal subjects. Methods: A fused deposition modeling 3D printer was used to create a head shaped phantom made up of transaxial slabs, derived from a simulated MRI dataset. The attenuation of the printed polylactide (PLA), measured by means of the Hounsfield unit on CT scanning, was set to match that of the brain by adjusting the proportion of plastic filament and air (fill ratio). Transmission measurements were made to verify the attenuation of the printed slabs. The radionuclide distribution within the phantom was created by adding {sup 99m}Tc pertechnetate to the ink cartridge of a paper printer and printing images of gray and white matter anatomy, segmented from the same MRI data. The complete subresolution sandwich phantom was assembled from alternate 3D printed slabs and radioactive paper sheets, and then imaged on a dual headed gamma camera to simulate an HMPAO SPECT scan. Results: Reconstructions of phantom scans successfully used automated ellipse fitting to apply attenuation correction. This removed the variability inherent in manual application of attenuation correction and registration inherent in existing cylindrical phantom designs. The resulting images were assessed visually and by count profiles and found to be similar to those from an existing elliptical PMMA phantom. Conclusions: The authors have demonstrated the ability to create physically realistic HMPAO SPECT simulations using a novel head-shaped 3D printed subresolution sandwich method phantom. The phantom can be used to validate all neurological SPECT imaging applications. A simple modification of the phantom design to use thinner slabs would make it suitable for use in PET.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Learning local equivariant representations for large-scale atomistic dynamics

Abstract A simultaneously accurate and computationally efficient parametrization of the potential energy surface of molecules and materials is a long-standing goal in the natural sciences. While atom-centered message passing neural networks (MPNNs) have shown remarkable accuracy, their information propagation has limited the accessible length-scales. Local methods, conversely, scale to large simulations but have suffered from inferior accuracy. This work introduces Allegro, a strictly local equivariant deep neural network interatomic potential architecture that simultaneously exhibits excellent accuracy and scalability. Allegro represents a many-body potential using iterated tensor products of learned equivariant representations without atom-centered message passing. Allegro obtains improvements over state-of-the-art methods on QM9 and revMD17. A single tensor product layer outperforms existing deep MPNNs and transformers on QM9. Furthermore, Allegro displays remarkable generalization to out-of-distribution data. Molecular simulations using Allegro recover structural and kinetic properties of an amorphous electrolyte in excellent agreement with ab-initio simulations. Finally, we demonstrate parallelization with a simulation of 100 million atoms.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Exploring the impacts of conformer selection methods on ion mobility collision cross section predictions

The prediction of structure dependent molecular properties, such as collision cross sections as measured using ion mobility spectrometry, are crucially dependent on the selection of the correct population of molecular conformers. Here, we report an in-depth evaluation of multiple conformation selection techniques, including simple averaging, Boltzmann weighting, lowest energy selection, low energy threshold reductions, and similarity reduction. Generating 50,000 conformers each for 18 molecules, we used the In Silico Chemical Library Engine (ISiCLE) to calculate the collision cross sections for the entire dataset. First, we employed Monte Carlo simulations to understand the variability between conformer structures as generated using simulated annealing. Then we employed Monte Carlo simulations to the aforementioned conformer selection techniques applied on the simulated molecular property—the ion mobility collision cross section. Based on our analyses, we found Boltzmann weighting to be a good tradeoff between precision and theoretical accuracy. Combining multiple techniques revealed that energy thresholds and root-mean-squared deviation-based similarity reductions can save considerable computational expense while maintaining property prediction accuracy. Molecular dynamic conformer generation tools like AMBER can continue to generate new lowest energy conformers even after tens of thousands of generations, decreasing precision between runs. This reduced precision can be ameliorated and theoretical accuracy increased by running density functional theory geometry optimization on carefully selected conformers.

Nielson, Felicity F.↗
DOE OSTI2016

Highly stable and self-repairing membrane-mimetic 2D nanomaterials assembled from lipid-like peptoids

Two-dimensional (2D) materials with molecular-scale thickness have attracted increasing interest for separation, electronic, catalytic, optical, energy and biomedical applications. Although extensive research on 2D materials, such as graphene and graphene oxide, has been performed in recent years, progress is limited on self-assembly of 2D materials from sequence-specific macromolecules, especially from synthetic sequences that could exhibit lipid-like self-assembly of bilayer sheets and mimic membrane proteins for functions. The creation of such new class of materials could enable development of highly stable biomimetic membranes that exhibit cell-membrane-like molecular transport with exceptional selectively and high transport rates. Here we demonstrate self-assembly of lipid-like 12-mer peptoids into extremely stable, crystalline, flexible and free-standing 2D membrane materials. As with cell membranes, upon exposure to external stimuli, these materials exhibit changes in thickness, varying from 3.5 nm to 5.6 nm. We find that self-assembly occurs through a facile crystallization process, in which inter-peptoid hydrogen bonds and enhanced hydrophobic interactions drive the formation of a highly-ordered structure. Molecular simulation confirms this is the energetically favored structure. Displaying functional groups at arbitrary locations of membrane-forming peptoids produces membranes with similar structures. This research further shows that single-layer membranes can be coated onto substrate surfaces. Moreover, membranes with mechanically-induced defects can self-repair. Given that peptoids are sequence-specific and exhibit protein-like molecular recognition with enhanced stability, we anticipate our membranes to be a robust platform tailored to specific applications.

36 MATERIALS SCIENCE↗