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Using neutron scattering dynamics measurements to validate molecular dynamic simulations, it is found that the rates of solvent exchange are not likely to limit the rates of calcite crystal growth and dissolution.
Electron diffraction of a crystal is fundamentally a function of the potential of that crystal. The intensity of electron diffraction patterns is, as a result, sensitive to the charge density of atoms and bonding inside crystals. Experimentally, the traditional method to probe this information is quantitative Convergent Beam Electron Diffraction (CBED). Quantitative CBED or QCEBD is a method which uses dynamic diffraction theory to quantify CBED intensities and to extract information about crystal structure and bonding. The sensitivity of dynamical scattering is leveraged to measure crystal symmetry and crystal structure factors. At its limit, electron structure factors are measured at high accuracy allowing access to chemical bonding information, which corroborate theoretical calculations through multipole model refinements of the experimental charge density. The primary limit to QCBED is the requirement of a non-overlapping convergent beam. This subsequently limits QCBED to crystals with small unit cells which are stable under the focused probe.
We report the rate at which helium ( 4 He ) and deuterium (d) fuse together to produce lithium-6 ( 6 Li) and a γ ray, 4 $\mathrm{H}$e($d, γ$) 6 $\mathrm{L}$i, is a critical puzzle piece in resolving the discrepancy between big bang predictions and astronomical observations for the primordial abundance of 6 Li . The accurate determination of this radiative capture rate requires the quantitative and predictive description of the fusion probability across the big bang energy window (30 keV ≲ E ≲ 400 keV), where measurements are hindered by low counting rates. We present first-principle (or, ab initio) predictions of the 4 $\mathrm{H}$e($d, γ$) 6 $\mathrm{L}$i astrophysical S factor using validated nucleon-nucleon and three-nucleon interactions derived within the framework of chiral effective field theory. By employing the ab initio no-core shell model with continuum to describe 4 He-d scattering dynamics and bound 6 Li product on an equal footing, we accurately and consistently determine the contributions of the main electromagnetic transitions driving the radiative capture process. Our results reveal an enhancement of the capture probability below 100 keV owing to previously neglected magnetic dipole (M1) transitions and reduce by an average factor of 7 the uncertainty of the thermonuclear capture rate between 0.002 and 2 GK.
Interactions between molecules in the synovial fluid and the cartilage surface may play a vital role in the formation of adsorbed films that contribute to the low friction of cartilage boundary lubrication. Osteoarthritis (OA) is the most common degenerative joint disease. Previous studies have shown that in OA-diseased joints, hyaluronan (HA) not only breaks down resulting in a much lower molecular weight (MW), but also its concentration is reduced ten times. Here, we have investigated the structural changes of lipid-HA complexes as a function of HA concentration and MW to simulate the physiologically relevant conditions that exist in healthy and diseased joints. Small angle neutron scattering and dynamic light scattering were used to determine the structure of HA-lipid vesicles in bulk solution, while a combination of atomic force microscopy and quartz crystal microbalance was applied to study their assembly on a gold surface. We infer a significant influence of both MW and HA concentrations on the structure of HA-lipid complexes in bulk and assembled on a gold surface. Our results suggest that low MW HA cannot form an amorphous layer on the gold surface, which is expected to negatively impact the mechanical integrity and longevity of the boundary layer and could contribute to the increased wear of the cartilage that has been reported in joints diseased with OA.
Bimetallic nanoparticles (BNPs) consist of two different types of metals or alloys that are bonded together. Unique properties such as optical, electronic, thermal, and catalytic effects differ for each type of BNP. Important BNPs range from Au-Pd, Ag- Pt, Au-Pt, and Ag-Ni. Pd bimetallic nanoparticles are of interest due to their many applications such as catalysis and sensing. Bimetallic catalysts have increase reaction rates and have improved catalyst stability through the geometry and ligand distribution. Pd nanoparticles are considered to be a strong catalyst due to their high activity at low temperatures and high tolerance to moisture. The catalytic properties of bimetallic nanoparticles depend on the structural properties such as size and shape. Core-shell, hollow structure, and multi-shell alloy are three possible structures nanoparticles can form as bimetallic catalysts. BNPs can be synthesized through different methods to control the size, shape, and structure. To obtain different morphologies, a variety of methods can be performed. Different methods can range from the usage of the glancing angle deposition (GLAD) to the galvanic replacement reaction, but the methods all depend on the properties of the metals. The galvanic displacement reaction was the method used to obtain Pd-based nanoparticles. This reaction is best know for obtaining hollow shaped NPs. To determine what redox process was preformed, the activity series of metals was used. From the activity series of metals, silver (Ag) was selected to preform Pd-based nanoparticles. Objectives: Synthesize Ag nanoparticles and Ag-Pd nanoparticles to understand the morphology. Characterize the synthesized nanoparticles using scanning electron microscopy (SEM), phase analysis light scattering (PALS), dynamic light scattering (DLS), energy dispersive X-ray spectroscopy (EDS), and UV-Vis spectroscopy. Results: In the UV-Vis spectrum, the Ag-Pd bimetallic NP's plasmon band decreased as the volume of palladium increased. The surface charge increases as the concentration of palladium increases. The Pd{sup 2+} ions interact with the sodium citrate surface, and decrease the negative charge. Conclusion: Ag-Pd nanoparticles were successfully created and stabilized with sodium citrate. The addition of Pd decreased the prominent plasmon band of the Ag nanoparticles. The SEM analysis showed that Ag nanoparticles had a well-defined structure, while the Ag-Pd nanoparticles showed hollow and rough structure. The EDX analysis confirmed the presence of silver and palladium. This material can be used in many industrial and research fields such as organic synthesis, fuel cells, and environmental sensing and remediation.
Here, a time-resolved x-ray scattering (TRXS) investigation of the photodissociation dynamics of gas-phase 2-iodothiophene molecules following 252 nm excitation is presented. Structural evolution of the molecule and dynamical information on the resulting photofragments were captured using femtosecond x-ray free-electron laser pulses. Two dissociation pathways were identified, arising via excitation to ππ* and (n/π)σ* states, respectively, yielding distinct interfragment recoil velocities of ∼6.4 Åps −1 and 17.0 Åps −1 . A comparison of asymptotic scattering data with simulated patterns indicates that the thiophene ring remains closed following dissociation at this wavelength. Modeling the experimental data yields a branching ratio of ∼3:1 in favor of the high velocity channel. These findings demonstrate the capability of TRXS to disentangle concurrent ultrafast reaction pathways and provide detailed structural insight into energy redistribution during photoinduced bond fission in complex molecular systems.
The unfolding dynamics of ubiquitin were studied using a combination of x-ray solution scattering (XSS) and molecular dynamics (MD) simulations. The kinetic analysis of the XSS ubiquitin signals showed that the protein unfolds through a two-state process, independent of the presence of destabilizing salts. In order to characterize the ensemble of unfolded states in atomic detail, the experimental XSS results were used as a constraint in the MD simulations through the incorporation of x-ray scattering derived potential to drive the folded ubiquitin structure toward sampling unfolded states consistent with the XSS signals. We detail how biased MD simulations provide insight into unfolded states that are otherwise difficult to resolve and underscore how experimental XSS data can be combined with MD to efficiently sample structures away from the native state. Our results indicate that ubiquitin samples unfolded in states with a high degree of loss in secondary structure yet without a collapse to a molten globule or fully solvated extended chain. Finally, we propose how using biased-MD can significantly decrease the computational time and resources required to sample experimentally relevant nonequilibrium states.
We recently introduced in [9] a boundary-to-bound dictionary between gravitational scattering data and observables for bound states of non-spinning bodies. In this paper, we elaborate further on this holographic map. We start by deriving the following — remarkably simple — formula relating the periastron advance to the scattering angle: $ΔΦ(J,ε)=χ(J,ε)+χ(-J,ε)$, via analytic continuation in angular momentum and binding energy. Using explicit expressions from [9], we confirm its validity to all orders in the Post-Minkowskian (PM) expansion. Furthermore, we reconstruct the radial action for the bound state directly from the knowledge of the scattering angle. The radial action enables us to write compact expressions for dynamical invariants in terms of the deflection angle to all PM orders, which can also be written as a function of the PM-expanded amplitude. As an example, we reproduce our result in [9] for the periastron advance, and compute the radial and azimuthal frequencies and redshift variable to two-loops. Agreement is found in the overlap between PM and Post-Newtonian (PN) schemes. Last but not least, we initiate the study of our dictionary including spin. We demonstrate that the same relation between deflection angle and periastron advance applies for aligned-spin contributions, with J the (canonical) total angular momentum. Explicit checks are performed to display perfect agreement using state-of-the-art PN results in the literature. Using the map between test- and two-body dynamics, we also compute the periastron advance up to quadratic order in spin, to one-loop and to all orders in velocity. We conclude with a discussion on the generalized ‘impetus formula’ for spinning bodies and black holes as ‘elementary particles’. Our findings here and in [9] imply that the deflection angle already encodes vast amount of physical information for bound orbits, encouraging independent derivations using numerical and/or self-force methodologies.
The protein folding process often proceeds through partially folded transient states. Therefore, a structural understanding of these disordered states is crucial for developing mechanistic models of the folding process. Characterization of unfolded states remains challenging due to their disordered nature, and incorporating multiple methods is necessary. Combining the time-resolved x-ray solution scattering (TRXSS) signal with molecular dynamics (MD), we are able to characterize transient partially folded states of bovine α-lactalbumin, a model system widely used for investigation of molten globule states, during its unfolding triggered by a temperature jump. We track the unfolding process between 20 μs and 70 ms and demonstrate that it passes through three distinct kinetic states. The scattering signals associated with these transient species are then analyzed with TRXSS constrained MD simulations to produce protein structures that are compatible with the input signals. Without utilizing any experimentally extracted kinetic information, the constrained MD simulation successfully drove the protein to an intermediate molten globule state; signals for two later disordered states are refined to terminal unfolded states. From our examination of the structural characteristics of these disordered states, we discuss the implications disordered states have on the folding process, especially on the folding pathway. Finally, we discuss the potential applications and limitations of this method.
Abstract Inelastic neutron scattering (INS) provides a weighted density of phonon modes. Currently, INS spectra can only be interpreted for perfectly crystalline materials because of high computational cost for electronic simulations. INS has the potential to provide detailed morphological information if sufficiently large volumes and appropriate structural variety are simulated. Here, we propose a method that allows direct comparison between INS data with molecular dynamics simulations, a simulation method that is frequently used to simulate semicrystalline/amorphous materials. We illustrate the technique by analyzing spectra of a well-studied conjugated polymer, poly(3-hexylthiophene-2,5-diyl) (P3HT) and conclude that our technique provides improved volume and structural variety, but that the classical force field requires improvement before the morphology can be accurately interpreted.
Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.
Determining the structure of nanoconfined fluids is essential for predicting the fate of these fluids in subsurface geologic formations with nanoporous features and for engineering novel nanoporous materials for storing compressed gases. In this study, we probe the structure of nanoconfined methane at pressures in the range of 15–100 bar using in situ small-angle neutron scattering (SANS) measurements and molecular dynamics (MD) simulations. The structure of methane is probed in MCM-41 and SBA-15 with cylindrical pores and diameters of 3.3 and 6.8 nm, respectively. In situ SANS measurements and MD simulations showed that the confined methane molecules are organized in a core–shell structure, with the shell arising from the adsorption of methane molecules on the silica surface. The shell thicknesses of the adsorbed deuterated methane (CD4) molecules in MCM-41 obtained by SANS measurements are 1.4 ± 0.5, 2.1 ± 0.1, 3.2 ± 0.8, 4.0 ± 0.3, and 6.0 ± 0.7 Å at equilibrated pressures of 15.6, 35.6, 55.5, 73.3, and 95.7 bar, respectively. The shell thicknesses of the adsorbed CD4 layer in SBA-15 pores are 2.7 ± 0.5, 4.3 ± 0.7, 6.6 ± 0.7, 10.2 ± 0.3, and 14.6 ± 0.8 Å at equilibrated pressures of 15.5, 32.7, 52.4, 70, and 99.5 bar, respectively. These experimental results are in close agreement with the results predicted from MD simulations. Adsorption of methane molecules on the silica surfaces is primarily driven by van der Waals interactions between the methane molecules and the hydroxyl groups on the silica surface, while electrostatic interactions play a minor role. In conclusion, the experimental and simulation approaches described in this study provide fundamental insights into the organization of confined gases using methane as a specific example in the context of compressed fluid storage in natural and engineered materials for adaptive energy use.
We characterize a concentrated 7.3 m CaCl 2 solution, combining neutron diffraction with chloride isotopic substitution (Cl-NDIS) in null water and molecular dynamics (MD) simulations. We elucidate the solution structure, thermodynamic properties, and extent of ion pairing previously suggested as concentration-dependent and often not observed at lower concentrations. Our Cl-NDIS measurements designate the solvent-shared ion pairing as dominant and the contact ion pairing (CIP) as insignificant even under conditions close to the solubility limit. The MD models parameterized against neutron diffraction with calcium isotopic substitution (Ca-NDIS) overestimate CIP despite successfully reproducing most of the Cl-NDIS signal. This drawback originates from the fact that Ca 2+ –Cl - interactions were primarily “hidden” in the Ca-NDIS signal due to overlapping with Ca 2+ –O w and Ca 2+ –H w contributions to the total scattering. Contrary, MD models with moderate CIP and possessing generally good performance at high concentrations fail to reproduce the NDIS measurements accurately. Therefore, the electronic polarization, introduced in most of the recent MD models via scaling ionic charges, resolves some but not all parameterization drawbacks. We conclude that despite improving the quality of MD models “on average,” the question “which model is the best” has not been answered but replaced by the question “which model is better for a given research.” An overall “good” model can still be inappropriate or, in some instances, “bad” and, unfortunately, produce erroneous results. Additionally, the accurate interpretation of several NDIS datasets, complemented by MD simulations, can prevent such mistakes and help identify the strengths, weaknesses, and convenient applications for corresponding computational models.
Calcium silicate hydrate (C-S-H) is a disordered, nanocrystalline material that acts as a primary binding phase in Portland cement. Thin films of water are present on the surfaces and in nanopores of C-S-H, impacting many of its chemical and mechanical properties, such as ion transport, creep, or thermal behavior. Despite decades of research, a full understanding of the structural details of adsorbed, confined, and bulk water in C-S-H remains elusive. In this work, we applied a multitechnique study involving molecular dynamics (MD) simulations validated by neutron diffraction with isotopic substitution (NDIS) and X-ray scattering methods to investigate the structure of water in C-S-H and C-A-S-H (an Al-bearing, low-CO 2 C-S-H substitute). Direct comparison of NDIS data with the MD results reveals that the structure of confined and interfacial water differs significantly from the bulk water and exhibits a larger degree of mesoscale ordering for more hydrated C-S-H structures. As a result, this observation suggests an important role of water as a stabilizer of the atomistic-level structure of C-S-H.
Compatibility between polymers with different glass transition temperatures controls the thermomechanical properties of blends. This work explores the segmental dynamics of poly(methyl acrylate) (PMA) chains when they are blended with polymers of different rigidities and miscibility. Inspired by the intriguing dynamic asymmetry of chains within the interfacial layer of nanoparticles, this study aims to understand dynamic heterogeneity in dynamically asymmetric blends of PMA/poly(methyl methacrylate) (PMMA), PMA/polystyrene (PS), and PMA/poly(ethylene oxide) (PEO) using the differential scanning calorimetry (DSC) and quasi-elastic neutron scattering (QENS) measurements below and above the glass transition temperature of PMMA or PS. Further, results revealed that the segmental jump distance of PMA increased on blending due to volume enhancement. The reduced effective diffusivity of PMA in PMMA is attributed to PMMA's enhanced flexibility (lower characteristic ratio, C ∞ ) and superior interaction (lower ) when compared with the PS environment. The results demonstrate that the chain rigidity and miscibility affect the free volume, interchain cooperativity, and segmental dynamics in dynamically asymmetric blends.
In the past few decades, prediction of macromolecular structures beyond the native conformation has been aided by the development of molecular dynamics (MD) protocols aimed at exploration of the energetic landscape of proteins. Yet, the computed structures do not always agree with experimental observables, calling for further development of the MD strategies to bring the computations and experiments closer together. Here, we report a scalable, efficient MD simulation approach that incorporates an x-ray solution scattering signal as a driving force for the conformational search of stable structural configurations outside of the native basin. We further demonstrate the importance of inclusion of the hydration layer effect for a precise description of the processes involving large changes in the solvent exposed area, such as unfolding. Utilization of the graphics processing unit allows for an efficient all-atom calculation of scattering patterns on-the-fly, even for large biomolecules, resulting in a speed-up of the calculation of the associated driving force. The utility of the methodology is demonstrated on two model protein systems, the structural transition of lysine-, arginine-, ornithine-binding protein and the folding of deca-alanine. We discuss how the present approach will aid in the interpretation of dynamical scattering experiments on protein folding and association.
Inelastic neutron scattering (INS) is a widely used technique to study atomic and molecular vibrations. With the increasing complexity of materials and thus the INS spectra, being able to simulate the spectra from various atomistic models becomes an essential step and also a major bottleneck for INS data analysis. The conventional approach using density functional theory and lattice dynamics often falls short when the materials of interest are complex (e.g., defective, disordered, heterogeneous, amorphous, large-scale), for which molecular dynamics driven by an interatomic force field is a more common approach. In this paper, we demonstrate a method to directly convert molecular dynamics trajectories into simulated INS spectra, including not only fundamental but also higher order excitations. In this work, the results are compared with data collected on various representative samples from different neutron spectrometers. This development will open great opportunities by providing the key tool to perform in-depth analysis of INS data and to validate and optimize computer models.
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