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At least 577 records · Page 32

BioCARS: Synchrotron facility for probing structural dynamics of biological macromolecules

A major goal in biomedical science is to move beyond static images of proteins and other biological macromolecules to the internal dynamics underlying their function. This level of study is necessary to understand how these molecules work and to engineer new functions and modulators of function. Stemming from a visionary commitment to this problem by Keith Moffat decades ago, a community of structural biologists has now enabled a set of x-ray scattering technologies for observing intramolecular dynamics in biological macromolecules at atomic resolution and over the broad range of timescales over which motions are functionally relevant. Many of these techniques are provided by BioCARS, a cutting-edge synchrotron radiation facility built under Moffat leadership and located at the Advanced Photon Source at Argonne National Laboratory. BioCARS enables experimental studies of molecular dynamics with time resolutions spanning from 100 ps to seconds and provides both time-resolved x-ray crystallography and small- and wide-angle x-ray scattering. Structural changes can be initiated by several methods—UV/Vis pumping with tunable picosecond and nanosecond laser pulses, substrate diffusion, and global perturbations, such as electric field and temperature jumps. Studies of dynamics typically involve subtle perturbations to molecular structures, requiring specialized computational techniques for data processing and interpretation. In this review, we present the challenges in experimental macromolecular dynamics and describe the current state of experimental capabilities at this facility. As Moffat imagined years ago, BioCARS is now positioned to catalyze the scientific community to make fundamental advances in understanding proteins and other complex biological macromolecules.

59 BASIC BIOLOGICAL SCIENCES↗

Experimental investigation of abnormal transverse flow enhancement of α particles in heavy-ion collisions

The mass dependence of the transverse flow for Z = 1–5 fragments from the collisions of 40 Ar + 27 Al, 40 Ar + 48 Ti, and 40 Ar + 58 Ni at 47 MeV/nucleon is investigated experimentally in this article. The transverse flow values are determined using the in-plane components of the fragment transverse momenta, where three conventional methods, i.e., the kinetic flow tensor method, the transverse momentum analysis method, and the azimuthal correlation method, are applied to reconstruct the reaction plane in an event-by-event basis. It is demonstrated from the comparison of the present experimental mass dependent flow measurements and the model simulations using an improved antisymmetrized molecular dynamics model that the experimentally observed abnormal α transverse flow enhancement is closely related to the reaction plane reconstruction procedure in the flow extraction. We further investigate the physical existence of the abnormal α flow behavior using a two-particle azimuthal correlation method, which allows us to provide the relative flow magnitude information with an identification of fragment charge number without the knowledge of the reaction plane differing from the three conventional methods. It is found that the relative flow magnitudes deduced from the two-particle azimuthal correlation functions with an identification of Z, with the correction for the recoil effect imposed by the momentum conservation, show a monotonically increasing trend as a function of fragment charge number, with no exception of the α flow enhancement. These results, in addition to those from the improved antisymmetrized molecular dynamics model simulations, definitely provide experimental evidences for the inexistence of the abnormal α flow behavior in the heavy-ion collisions at the present incident energy region in nature.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Nonideal mixing effects in warm dense matter studied with first-principles computer simulations

Here, we study nonideal mixing effects in the regime of warm dense matter (WDM) by computing the shock Hugoniot curves of BN, MgO, and MgSiO 3 . First, we derive these curves from the equations of state (EOS) of the fully interacting systems, which were obtained using a combination of path integral Monte Carlo calculations at high temperature and density functional molecular dynamics simulations at lower temperatures. We then use the ideal mixing approximation at constant pressure and temperature to rederive these Hugoniot curves from the EOS tables of the individual elements. We find that the linear mixing approximation works remarkably well at temperatures above ~2 × 10 5 K, where the shock compression ratio exceeds ~3.2. The shape of the Hugoniot curve of each compound is well reproduced. Regions of increased shock compression, which emerge because of the ionization of L and K shell electrons, are well represented, and the maximum compression ratio of the Hugoniot curves is reproduced with high precision. Some deviations are seen near the onset of the L shell ionization regime, where ionization equilibrium in the fully interacting system cannot be well reproduced by the ideal mixing approximation. This approximation also breaks down at lower temperatures, where chemical bonds play an increasingly important role. However, the results imply that the equilibrium properties of binary and ternary mixtures in the regime of WDM can be derived from the EOS tables of the individual elements. This significantly simplifies the characterization of binary and ternary mixtures in the WDM and plasma phases, which otherwise requires large numbers of more computationally expensive first-principles computer simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploration of a Novel Technique for Waste Heat Recovery Through Molecular Dynamics: Influence of Wettability and Electric Field on Water and Water-Based Nanofluids

Most of the energy produced globally comes by way of a heat engine. The Carnot principle places a limit as to how thermodynamically efficient a heat engine can be. There is no heat engine that can be 100% thermodynamically efficient and as such a substantial proportion of all heat supplied to a heat engine is lost as waste heat. Waste heat therefore is a large energy source ready to be properly utilized. Herein, a novel approach for converting waste heat to electricity is discussed. It involves the use of the liquid to vapor phase change of a material dielectric (water) or electrolyte (nanofluid) in the embodiment of a capacitor for direct thermal to electrostatic energy conversion. While this method of waste heat recovery could potentially be added to the ever expanding portfolio of energy conversion techniques, a number of aspects must be addressed before it can be brought into practice. Water was seen as an ideal dielectric phase change material given its high relative permittivity ratio when in the liquid form as compared to its vapor form. However, given its short voltage holdoff time the phase change of water would need to occur rapidly. This brings up concerns of explosive boiling. Herein, molecular dynamics analysis into the explosive boiling behavior of thin water films gave more insight into how the interaction between the surface and liquid affected explosive boiling onset time. A Lennard-Jones potential with one interaction site and a Morse potential with three interaction sites between water and solid substrate were used. It was found generally that a stronger interaction between water film and substrate led to faster explosive boiling onset times but an increase in the number of interaction sites delayed explosive boiling, even at the same wettability (contact angle). Understanding changes in the density and enthalpy of vaporization of a liquid dielectric such as water in the presence of an electric field is of importance due to the electrostatic nature of the waste heat conversion method under consideration. Specifically, if both density and enthalpy of vaporization are increased, the thermodynamic efficiency of the waste heat conversion method under consideration is decreased. Electric field effects are explored herein via molecular dynamics using two water models, the TIP4P-Ew and SWM4-NDP. The SWM4-NDP model is polarizable while the TIP4P-Ew model is not, which allows for a determination of the importance of model polarizability (i.e. variation in water model dipole moment) on these two properties of water when subjected to an electric field. Herein it was found that both water models respond similarly in terms of density and vaporization enthalpy variance upon the introduction of an electric field. Comparison was also made to the pressure induced by the electric field (electrostriction pressure) by way of a density comparison and it was found that the predicted electrostriction pressure overestimates the pressure experienced by water. Water by itself has a high enthalpy of vaporization, which limits the efficiency of the newly proposed conversion method. Research both experimental and through simulation has shown that the vaporization enthalpy of nanofluids can be engineered via nanoparticle size and material selection. An avenue less explored is manipulating the enthalpy of vaporization by altering the interaction strength between the nanoparticles and the base fluid. In practice this could be achieved through the addition of coatings to the nanoparticles to alter their wettability to the base fluid. This was explored by using a Lennard-Jones potential and Morse potential to model the interaction between base fluid (water) and the nanoparticle. For nanoparticles 2nm in diameter and at weight percentages up to 6%, the change in vaporization enthalpy due to alterations of the interaction strength between nanoparticle and base fluid was not significant (less than a 1% difference) when compared to the effect of altering the weight percentage of nanoparticles in the nanofluid or introducing an electric field. However, the effect of wettability may still become important at other nanoparticle concentrations and sizes. In all, the studies presented here further the understanding of phase change and thermodynamic properties of water and water based nanofluids under an electrostatic field which will help inform the development of a novel approach to waste heat conversion. The reduction of waste heat will improve energy sustainability outlooks.

30 DIRECT ENERGY CONVERSION↗

Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing

Characterizing structural ensembles of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins is essential for studying structure–function relationships. Due to the different neutron scattering lengths of hydrogen and deuterium, selective labeling and contrast matching in small-angle neutron scattering (SANS) becomes an effective tool to study dynamic structures of disordered systems. However, experimental timescales typically capture measurements averaged over multiple conformations, leaving complex SANS data for disentanglement. We hereby demonstrate an integrated method to elucidate the structural ensemble of a complex formed by two IDRs. We use data from both full contrast and contrast matching with residue-specific deuterium labeling SANS experiments, microsecond all-atom molecular dynamics (MD) simulations with four molecular mechanics force fields, and an autoencoder-based deep learning (DL) algorithm. From our combined approach, we show that selective deuteration provides additional information that helps characterize structural ensembles. We find that among the four force fields, a99SB-disp and CHARMM36m show the strongest agreement with SANS and NMR experiments. In addition, our DL algorithm not only complements conventional structural analysis methods but also successfully differentiates NMR and MD structures which are indistinguishable on the free energy surface. Finally, we present an ensemble that describes experimental SANS and NMR data better than MD ensembles generated by one single force field and reveal three clusters of distinct conformations. Our results demonstrate a new integrated approach for characterizing structural ensembles of IDPs.

59 BASIC BIOLOGICAL SCIENCES↗

An ab initio exciton model for singlet fission

Here we present an ab initio exciton model that extends the Frenkel exciton model and includes valence, charge-transfer, and multiexcitonic excited states. It serves as a general, parameter-free, yet computationally efficient and scalable approach for simulation of singlet fission processes in multichromophoric systems. A comparison with multiconfigurational methods confirms that our exciton model predicts consistent energies and couplings for the pentacene dimer and captures the correct physics. Calculations of larger pentacene clusters demonstrate the computational scalability of the exciton model and suggest that the mixing between local and charge-transfer excitations narrows the gap between singlet and multiexcitonic states. Local vibrations of pentacene molecules are found to facilitate singlet–multiexcitonic state-crossing and hence are important for understanding singlet fission. The exciton model developed in this work also sets the stage for further implementation of the nuclear gradients and nonadiabatic couplings needed for first principles nonadiabatic quantum molecular dynamics simulations of singlet fission.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polymorphic structure of $\langle a \rangle$-type screw dislocation cores in $\alpha$-Ti

The dislocation core structure has a significant role in determining the dominant slip plane and the magnitude of the Peierls stress for a dislocation. An important challenge when studying dislocation cores is to determine the stable and metastable core morphologies, and then relate these structures to the dynamics of the dislocations. ere this study introduces a method for identifying core structures that are metastable at zero temperature. Application of this method to $\langle$a$\rangle$-type screw dislocations in α-Ti (as described using an empirical potential) reveals a multitude of (meta)stable nonplanar cores. Molecular dynamics studies show how the competing metastable core structures determine the properties of the dislocations at temperature and under a range of non-Schmid stresses.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Regimes of evaporation and mixing behaviors of nanodroplets at transcritical conditions

The objective of this paper is to examine the fundamental mechanisms responsible for the transition between subcritical evaporation and supercritical dense-fluid-mixing in the absence of convection effects, specifically focusing on the liquid–vapor interfacial dynamics. To isolate the dynamics of this transition process, we characterize the different physical behaviors exhibited by an -dodecane nanoscale droplet placed in different nitrogen ambient conditions across the fuel’s critical point. We employ a continuum-based interface-resolving diffuse-interface method to explore the underlying phase-exchange mechanisms that bring about such distinct dynamics. Following the comparison against molecular dynamics simulations and experiments of evaporating droplets and experimental data for vapor–liquid equilibria, a parametric study at various ambient conditions and droplet sizing is performed to identify four regimes of evaporation/mixing behaviors: sub- and supercritical droplet evaporation, and sub- and supercritical dense-fluid-mixing. It is shown that the distinction in the phase-exchange mechanisms in these four regimes are brought about by the different thermodynamic phases the droplet center can exhibit during the evaporation/mixing process: subcritical liquid, supercritical liquid-like, subcritical gaseous, and supercritical gas-like, respectively. It is shown that the subcritical dense-fluid-mixing behavior is a direct result of nanoconfinement of the liquid–vapor interfacial structure and thus is not present for large droplet sizes. Finally, the present study also shows that the supercritical phase-exchange dynamics can follow two different pathways: supercritical droplet-like evaporation and supercritical dense-fluid-mixing. Furthermore, promoting the early transition to supercritical dense-fluid-mixing can significantly expedite the phase-exchange process through the disintegration of the liquid-like droplet core.

42 ENGINEERING↗

Ab initio molecular dynamics on quantum computers

Ab initio molecular dynamics (AIMD) is a valuable technique for studying molecules and materials at finite temperatures where the nuclei evolve on potential energy surfaces obtained from accurate electronic structure calculations. In this work, we present an approach to running AIMD simulations on noisy intermediate-scale quantum (NISQ)-era quantum computers. The electronic energies are calculated on a quantum computer using the variational quantum eigensolver (VQE) method. Algorithms for computation of analytical gradients entirely on a quantum computer require quantum fault-tolerant hardware, which is beyond NISQ-era. Therefore, we compute the energy gradients numerically using finite differences, the Hellmann-Feynman theorem, and a correlated sampling technique. This method only requires additional classical calculations of electron integrals for each degree of freedom without any additional computations on a quantum computer beyond the initial VQE run. As a proof of concept, AIMD simulations are demonstrated for the H-2 molecule on IBM quantum devices. In addition, we demonstrate the validity of the method for larger molecules using full configuration interaction wave functions. As quantum hardware and noise mitigation techniques continue to improve, the method can be utilized for studying larger molecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomic resolution coherent x-ray imaging with physics-based phase retrieval

Coherent x-ray imaging and scattering from accelerator based sources such as synchrotrons continue to impact biology, medicine, technology, and materials science. Many synchrotrons around the world are currently undergoing major upgrades to increase their available coherent x-ray flux by approximately two orders of magnitude. The improvement of synchrotrons may enable imaging of materials in operando at the atomic scale which may revolutionize battery and catalysis technologies. Current algorithms used for phase retrieval in coherent x-ray imaging are based on the projection onto sets method. These traditional iterative phase retrieval methods will become more computationally expensive as they push towards atomic resolution and may struggle to converge. Additionally, these methods do not incorporate physical information that may additionally constrain the solution. In this work, we present an algorithm which incorporates molecular dynamics into Bragg coherent diffraction imaging (BCDI). This algorithm, which we call PRAMMol (Phase Retrieval with Atomic Modeling and Molecular Dynamics) combines statistical techniques with molecular dynamics to solve the phase retrieval problem. We present several examples where our algorithm is applied to simulated coherent diffraction from 3D crystals and show convergence to the correct solution at the atomic scale.

47 OTHER INSTRUMENTATION↗

Multiscale Molecular Dynamics Simulations: Accelerating Conformational Sampling of Biomolecular Systems by Iterating All-Atom and Coarse-Grained Simulations

We developed the atomistic-coarse-grained multiscale MD simulation method in the OpenMM simulation package by iterating between the all-atom (AA) and coarse-grained (CG) MD simulations to enhance the sampling of biomolecular conformations. As the free energy surfaces are flattened during CG MD simulations, we can accelerate the transitions between different low-energy conformations. The AA-CG-AA cycles are repeated, facilitating the accelerated sampling of biomolecular conformations at a CG level, while the finer atomistic interactions are refined with AA simulators.

Do, Hung Nguyen↗

Breaking the mold: Overcoming the time constraints of molecular dynamics on general-purpose hardware

The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of accuracy, atom count (spatial scale), and duration (temporal scale). Since the mid-2000s, computer platforms have, however, failed to provide strong scaling for MD, as scale-out central processing unit (CPU) and graphics processing unit (GPU) platforms that provide substantial increases to spatial scale do not lead to proportional increases in temporal scale. Important scientific problems therefore remained inaccessible to direct simulation, prompting the development of increasingly sophisticated algorithms that present significant complexity, accuracy, and efficiency challenges. While bespoke MD-only hardware solutions have provided a path to longer timescales for specific physical systems, their impact on the broader community has been mitigated by their limited adaptability to new methods and potentials. In this work, we show that a novel computing architecture, the Cerebras wafer scale engine, completely alters the scaling path by delivering unprecedentedly high simulation rates up to 1.144 M steps/s for 200 000 atoms whose interactions are described by an embedded atom method potential. This enables direct simulations of the evolution of materials using general-purpose programmable hardware over millisecond timescales, dramatically increasing the space of direct MD simulations that can be carried out. In this paper, we provide an overview of advances in MD over the last 60 years and present our recent result in the context of historical MD performance trends.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sulfonyl PIM–1: A diverse separation membrane with dilation resistance

A sulfone modified variant (soPIM–1) of the first polymer of intrinsic microporosity has been studied through molecular simulations to analyze its applicability for adsorption–based separations of diverse nonpolar, quadrupolar, and dipolar adsorbate species. Single component gas phase adsorption isotherms of each adsorbate are provided. Here, the adsorptive properties of soPIM–1 are reported from the application of two methods: (a) traditional grand canonical Monte Carlo (GCMC) simulations and (b) a combination of Monte Carlo and molecular dynamics (GCMC/MD) techniques, which accounts for sorption–induced polymer dynamics. The calculated isosteric heats of adsorption are compared to those from the parent PIM–1 structure and reveals increased CO2 affinity with relatively no change in hydrocarbon affinity. Moreover, to quantify soPIM–1's resistance to dilation the evolution of the microporous structure across the adsorption isotherm loading pressures has been evaluated. Relatedly, nonequilibrium MD simulations have been utilized to determine that soPIM–1 is approximately twice as stiff as PIM–1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transport and Energetics of Carbon Dioxide in Ionic Liquids at Aqueous Interfaces

A major hurdle in utilizing carbon dioxide (CO 2 ) lies in separating it from industrial flue gas mixtures and finding suitable storage methods that enable its application in various industries. To address this issue, we utilized a combination of molecular dynamics simulations and experiments to investigate the behavior of CO 2 in common room-temperature ionic liquids (RTIL) when in contact with aqueous interfaces. Here, our investigation of RTILs, [EMIM][TFSI] and [OMIM][TFSI], and their interaction with a pure water layer mimics the environment of a previously developed ultrathin enzymatic liquid membrane for CO 2 separation. We analyzed diffusion constants and viscosity, which reveals that CO 2 molecules exhibit faster mobility within the selected ILs compared to what would be predicted solely based on the viscosity of the liquids using the standard Einstein–Stokes relation. Moreover, we calculated the free energy of translocation for various species across the aqueous–IL interface, including CO 2 and HCO 3 – . Free energy profiles demonstrate that CO 2 exhibits a more favorable partitioning behavior in the RTILs compared to that in pure water, while a significant barrier hinders the movement of HCO 3 – from the aqueous layer. Experimental measurement of the CO 2 transport in the RTILs corroborates the model. These findings strongly suggest that hydrophobic RTILs could serve as a promising option for selectively transporting CO 2 from aqueous media and concentrating it as a preliminary step toward storage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Colloidal Nafion Particles: Are Cylinders Ubiquitous?

Colloidal Nafion morphology plays a critical role in determining the performance of fuel cells and electrolyzers. While small-angle neutron scattering (SANS) studies previously described Nafion in liquid media as dispersed cylinders, the analysis remains nonunique with multiple possible morphological descriptions of the data. Here, using SANS and all-atomistic molecular dynamics, we confirm that Nafion morphology in liquid media differs substantially depending on dispersing agent and dispersion method. H + Nafion dispersed in N-methyl pyrrolidone forms swollen cluster particles with physically cross-linked ionic groups. Scattering profiles from dispersed Nafion membrane have a large structure factor feature not observed for redispersed Nafion D-521. H + Nafion dispersed in water has a highly elongated cylindrical morphology (radius = 10 ± 1.5 Å, height = 358 ± 4.7 Å) with fully dissociated and solvated sulfonic acid groups on the particle wall. In conclusion, these results highlight an important discrepancy between the methods of preparing Nafion dispersions and the use of simplified analysis techniques to describe Nafion morphology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multicolor polymeric carbon dots: synthesis, separation and polyamide-supported molecular fluorescence

Multicolor carbon dots (CDs) have been developed recently and demonstrate great potential in bio-imaging, sensing, and LEDs. However, the fluorescence mechanism of their tunable colors is still under debate, and efficient separation methods are still challenging. Herein, we synthesized multicolor polymeric CDs through solvothermal treatment of citric acid and urea in formamide. Automated reversed-phase column separation was used to achieve fractions with distinct colors, including blue, cyan, green, yellow, orange and red. This work explores the physicochemical properties and fluorescence origins of the red, green, and blue fractions in depth with combined experimental and computational methods. Three dominant fluorescence mechanism hypotheses were evaluated by comparing time-dependent density functional theory and molecular dynamics calculation results to measured characteristics. We find that blue fluorescence likely comes from embedded small molecules trapped in carbonaceous cages, while pyrene analogs are the most likely origin for emission at other wavelengths, especially in the red. Also important, upon interaction with live cells, different CD color fractions are trafficked to different sub-cellular locations. Super-resolution imaging shows that the blue CDs were found in a variety of organelles, such as mitochondria and lysosomes, while the red CDs were primarily localized in lysosomes. These findings significantly advance our understanding of the photoluminescence mechanism of multicolor CDs and help to guide future design and applications of these promising nanomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

pnnl/mol_dgnn

Molecular dynamics simulations often rely on parameterized atomistic potentials, which can be inaccurate compared to ab initio simulation methods. However, dynamic ab initio simulations come with high computational cost. Deep learning techniques offer a method to obtain both high accuracy and low cost predictions of dynamics. Our method gives a prediction of the structural dynamics of a molecule accounting for the prior dynamics, giving high-accuracy predictions at low computational cost

Ashby, Michael↗

Realistic Ion Dynamics through Charge Renormalization in Nonaqueous Electrolytes

While many practically important electrolytes contain lithium ions, interactions of these ions are particularly difficult to probe experimentally because of their small X-ray and neutron scattering cross sections and large neutron absorption cross sections. Molecular dynamics (MD) is a powerful tool for understanding the properties of nonaqueous electrolyte solutions from the atomic level, but the accuracy of this computational method crucially depends on the physics built into the classical force field. In this study, we demonstrate that several force fields for lithium bistriflimide (LiTFSI) in acetonitrile yield a solution structure that is consistent with the neutron scattering experiments, yet these models produce dramatically different ion dynamics in solution. Such glaring discrepancies indicate that inadequate representation of long-range interactions leads to excessive ionic association and ion-pair clustering. We show that reasonable agreement with the experimental observations can be achieved by renormalization of the ion charges using a “titration” method suggested herewith. This simple modification produces realistic concentration dependencies for ionic diffusion and conductivity in <2 M solutions, without loss in quality for simulation of the structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗