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At least 1,225 records · Page 68

Efficient Treatment of Large Active Spaces through Multi-GPU Parallel Implementation of Direct Configuration Interaction

In this study, we have extended our graphical processing unit (GPU)-accelerated direct configuration interaction program to multiple devices, reducing iteration times for configuration spaces of 165 million determinants to only 3 s using NVIDIA P100 GPUs. Similar improvements in the one- and two-particle reduced density matrix formation allow for fast analytical energy gradients and electronic properties. Our parallel algorithm enables the calculation of arbitrarily large configuration spaces (limited only by available system memory), with iteration times of 13 min for an active space of 18 electrons in 18 orbitals (2.4 billion determinants) using six consumer grade NVIDIA 1080Ti GPUs. These advances enable routine molecular dynamics simulations, geometry optimizations, and absorption spectrum calculations for molecules with large configuration spaces, a task that has heretofore required massive computational effort. In this work, we demonstrate the utility of our program by generating the absorption spectrum for diphenyl acetylene at the floating occupation molecular orbital complete active space configuration interaction level of theory. Lastly, several active spaces were investigated to assess the dependence of spectral features on orbital space dimension.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Critical fluctuations in liquid–liquid extraction organic phases controlled by extractant and diluent molecular structure

Extractant aggregation in liquid–liquid extraction organic phases impacts extraction energetics and is related to the deleterious efficiency-limiting liquid–liquid phase transition known as third phase formation. Using small angle X-ray scattering, we find that structural heterogeneities across a wide range of compositions in binary mixtures of malonamide extractants and alkane diluents are well described by Ornstein–Zernike scattering. This suggests that structure in these simplified organic phases originates from the critical point associated with the liquid–liquid phase transition. To confirm this, we measure the temperature dependence of the organic phase structure, finding critical exponents consistent with the 3D Ising model. Molecular dynamics simulations were also consistent with this mechanism for extractant aggregation. Due to the absence of water or any other polar solutes required to form reverse-micellar-like nanostructures, these fluctuations are inherent to the binary extractant/diluent mixture. Further, we also show how the molecular structure of the extractant and diluent modulate these critical concentration fluctuations by shifting the critical temperature: critical fluctuations are suppressed by increasing extractant alkyl tail lengths or decreasing diluent alkyl chain lengths. This is consistent with how extractant and diluent molecular structure are known to impact metal and acid loading capacity in many-component LLE organic phases, suggesting phase behavior of practical systems may be effectively studied in simplified organic phases. Overall, the explicit connection between molecular structure, aggregation and phase behavior demonstrated here will enable the design of more efficient separations processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polar liquids at charged interfaces: A dipolar shell theory

The structure of polar liquids and electrolytic solutions, such as water and aqueous electrolytes, at interfaces underlies numerous phenomena in physics, chemistry, biology, and engineering. In this work, we develop a continuum theory that captures the essential features of dielectric screening by polar liquids at charged interfaces, including decaying spatial oscillations in charge and mass, starting from the molecular properties of the solvent. The theory predicts an anisotropic dielectric tensor of interfacial polar liquids previously studied in molecular dynamics simulations. We explore the effect of the interfacial polar liquid properties on the capacitance of the electrode/electrolyte interface and on hydration forces between two plane-parallel polarized surfaces. In the linear response approximation, we obtain simple formulas for the characteristic decay lengths of molecular and ionic profiles at the interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Disentangling the effects of non-adiabatic interactions upon ion self-diffusion within warm dense hydrogen

Warm dense matter is a material state in the region of parameter space connecting condensed matter to classical plasma physics. In this intermediate regime, we investigate the significance of non-adiabatic electron-ion interactions upon ion dynamics. To disentangle non-adiabatic from adiabatic electron-ion interactions, we compare the ion self-diffusion coefficient from the non-adiabatic electron force field computational model with an adiabatic, classical molecular dynamics simulation. A classical pair potential developed through a force-matching algorithm ensures the only difference between the models is due to the electronic inertia. Here, we implement this new method to characterize non-adiabatic effects on the self-diffusion of warm dense hydrogen over a wide range of temperatures and densities. Ultimately we show that the impact of non-adiabatic effects is negligible for equilibrium ion dynamics in warm dense hydrogen.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Neural network representation of electronic structure from ab initio molecular dynamics

Despite their rich information content, electronic structure data amassed at high volumes in ab initio molecular dynamics simulations are generally under-utilized. Here we introduce a transferable high-fidelity neural network representation of such data in the form of tight-binding Hamiltonians for crystalline materials. This predictive representation of ab initio electronic structure, combined with machine-learning boosted molecular dynamics, enables efficient and accurate electronic evolution and sampling. When it is applied to a one-dimension charge-density wave material, carbyne, we are able to compute the spectral function and optical conductivity in the canonical ensemble. The spectral functions evaluated during soliton-antisoliton pair annihilation process reveal significant renormalization of low-energy edge modes due to retarded electron-lattice coupling beyond the Born–Oppenheimer limit. The availability of an efficient and reusable surrogate model for the electronic structure dynamical system will enable calculating many interesting physical properties, paving the way to previously inaccessible or challenging avenues in materials modeling.

74 ATOMIC AND MOLECULAR PHYSICS↗

Elucidating the Mechanism of Helium Evaporation from Liquid Water

Here, we investigate the evaporation of trace amounts of helium solvated in liquid water using molecular dynamics simulations and theory. Consistent with experimental observations, we find a super-Maxwellian distribution of kinetic energies of evaporated helium. This excess of kinetic energy over typical thermal expectations is explained by an effective continuum theory of evaporation based on a Fokker–Planck equation, parametrized molecularly by a potential of mean force and position-dependent friction. Using this description, we find that helium evaporation is strongly influenced by the friction near the interface, which is anomalously small near the Gibbs dividing surface due to the ability of the liquid–vapor interface to deform around the gas particle. Our reduced description provides a mechanistic interpretation of trace gas evaporation as the motion of an underdamped particle in a potential subject to a viscous environment that varies rapidly across the air–water interface. From it we predict the temperature dependence of the excess kinetic energy of evaporation, which is yet to be measured.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly

The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed “fatal,” and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context.

59 BASIC BIOLOGICAL SCIENCES↗

Ab Initio Bulk Free Energy Surface of Proper Ferroelectrics

We report a systematic and accurate approach for deriving the bulk free energy surface (FES), a function of temperature, polarization, and strain, from the first-principles density functional theory (DFT) of proper ferroelectrics. The core of our approach is the metadynamics algorithm that extracts the polarization dependence of the FES from all-atom molecular dynamics simulations without an a priori ansatz. The rest of the FES is derived from the metadynamics trajectories that span the relevant phase space. We demonstrate our approach in the case of lead titanate. The errors across the phase transition, due to DFT numerics, all-atom molecular dynamics, and free energy evaluation by enhanced sampling, can be systematically controlled and are of the order of 1 meV/atom. The accuracy of the resulting ab initio FES is only limited by the adopted functional approximation of DFT.

Xie, Pinchen [Lawrence Berkeley National Laborator↗

The effect of protein mutations on drug binding suggests ensuing personalised drug selection

The advent of personalised medicine promises a deeper understanding of mechanisms and therefore therapies. However, the connection between genomic sequences and clinical treatments is often unclear. We studied 50 breast cancer patients belonging to a population-cohort in the state of Qatar. From Sanger sequencing, we identified several new deleterious mutations in the estrogen receptor 1 gene (ESR1). The effect of these mutations on drug treatment in the protein target encoded by ESR1, namely the estrogen receptor, was achieved via rapid and accurate protein–ligand binding affinity interaction studies which were performed for the selected drugs and the natural ligand estrogen. Four nonsynonymous mutations in the ligand-binding domain were subjected to molecular dynamics simulation using absolute and relative binding free energy methods, leading to the ranking of the efficacy of six selected drugs for patients with the mutations. Our study shows that a personalised clinical decision system can be created by integrating an individual patient’s genomic data at the molecular level within a computational pipeline which ranks the efficacy of binding of particular drugs to variant proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Biphasic solvents for post-combustion CO 2 capture from natural gas flue Gas

Fossil fuel fired power plants are generally expected to remain one of the most significant global sources of electricity for decades to come. Consequently, carbon management technologies are needed to reduce or eliminate ongoing emissions from these sources. Amongst the many techniques for carbon capture, aqueous amine-based absorbents (monoethanolamine, MEA, in particular) are, presently, considered the leading technology for post-combustion CO 2 point-source capture. These technologies are nevertheless limited by their high capital and regeneration energy costs. Biphasic solvents have been identified as an attractive alternative to traditional MEA based absorbents due to their potential energy savings. Thus far, however, the research on biphasic solvents has largely focused on their performance in coal flue gas while more dilute natural gas flue gas applications have received relatively little attention. Here, this work examines the performances of two novel biphasic solvent blends, diethylenetriamine (DETA) and triethylenetetramine (TETA), in CO 2 capture from a natural gas flue gas simulant. Across several regeneration tests, both solvents achieved considerable energy savings over the benchmark MEA solution. Specifically, the energy consumption per mol CO 2 recovered for the DETA-based and TETA-based solvents was 46 % and 35 % less than that of the benchmark MEA solution, respectively. Molecular dynamics simulations were also performed to gain a deeper understanding of the phase separation phenomena that occur as a consequence of CO 2 absorption. These simulations indicated that phase change was driven by the strong interaction between the absorption products and water, while the degree of separation depended on the CO 2 loading.

Biphasic solvents↗

Nonlinear Shear Rheology of Entangled Polymer Rings

Steady-state shear viscosity η($\bar{γ}$) of unconcatenated ring polymer melts as a function of the shear rate $\bar{γ}$ is studied by a combination of experiments, simulations, and theory. Experiments using polystyrenes with Z ≈ 5 and Z ≈ 11 entanglements indicate weaker shear thinning for rings compared to linear polymers exhibiting power law scaling of shear viscosity η ~ $\bar{γ}$ –0.56 ± 0.02 , independent of chain length, for Weissenberg numbers up to about 10 2 . Nonequilibrium molecular dynamics simulations using the bead-spring model reveal a similar behavior with η ~ $\bar{γ}$ -0.57 ± 0.08 for 4 ≤ Z ≤ 57. Viscosity decreases with chain length for high $\bar{γ}$. In our experiments, we see the onset of this regime, and in simulations, which we extended to Wi ~ 10 4 , the nonuniversality is fully developed. In addition to a naive scaling theory yielding for the universal regime η ~ $\bar{γ}$ –0.57 , we developed a novel shear slit model explaining many details of observed conformations and dynamics as well as the chain length-dependent behavior of viscosity at large $\bar{γ}$. The signature feature of the model is the presence of two distinct length scales: the size of tension blobs and much larger thickness of a shear slit in which rings are self-consistently confined in the velocity gradient direction and which is dictated by the size of a chain section with relaxation time 1/$\bar{γ}$. These two length scales control the two normal stress differences. In this model, the chain length-dependent onset of nonuniversal behavior is set by tension blobs becoming as small as about one Kuhn segment. This model explains the approximate applicability of the Cox–Merz rule for ring polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomistic Materials Modeling of High-Pressure Hydrogen Interactions in Ethylene Propylene Diene Monomer (EPDM) Rubber

Elastomeric rubbers serve a vital role as sealing materials in the hydrogen storage and transport infrastructure. With applications including O-rings and hose-liners, these components are exposed to pressurized hydrogen at a range of temperatures, cycling rates, and pressure extremes. Cyclic (de)pressurization is known to degrade these materials through the process of cavitation. This readily visible failure mode occurs as a fracture or rupture of the material and is due to the oversaturated gas localizing to form gas bubbles. Computational modeling in the Hydrogen Materials Compatibility Program (H-Mat), co-led by Sandia National Laboratories and Pacific Northwest National Laboratory, employs multi-scale simulation efforts to build a predictive understanding of hydrogen-induced damage in materials. Modeling efforts within the project aim to provide insight into how to formulate materials that are less sensitive to high-pressure hydrogen-induced failure. In this document, we summarize results from atomistic molecular dynamics simulations, which make predictive assessments of the effects of compositional variations in the commonly used elastomer, ethylene propylene diene monomer (EPDM).

08 HYDROGEN↗

Scanning the RBD-ACE2 molecular interactions in Omicron variant

The emergence of new SARS-CoV-2 variants poses a threat to the human population where it is difficult to assess the severity of a particular variant of the virus. Spike protein and specifically its receptor binding domain (RBD) which makes direct interaction with the ACE2 receptor of the human has shown prominent amino acid substitutions in most of the Variants of Concern. Here, in this work, by using all-atom molecular dynamics simulations we compare the interaction of Wild-type RBD/ACE2 receptor complex with that of the latest Omicron variant of the virus. We observed a very interesting diversification of the charge, dynamics and energetics of the protein complex formed upon mutations. These results would help us in understanding the molecular basis of binding of the Omicron variant with that of SARS-CoV-2 Wild-type.

60 APPLIED LIFE SCIENCES↗

Toward a First-Principles Framework for Predicting Collective Properties of Electrolytes

Conspectus Given the universal importance of electrolyte solutions, it is natural to expect that we have a nearly complete understanding of the fundamental properties of these solutions (e.g., the chemical potential) and that we can therefore explain, predict, and control the phenomena occurring in them. In fact, reality falls short of these expectations. But, recent advances in the simulation and modeling of electrolyte solutions indicate that it should soon be possible to make progress toward these goals. In this Account, we will discuss the use of first-principles interaction potentials based in quantum mechanics (QM) to enhance our understanding of electrolyte solutions. Specifically, we will focus on the use of quantum density functional theory (DFT) combined with molecular dynamics simulation (DFT-MD) as the foundation for our approach. The overarching concept is to understand and accurately reproduce the balance between local or short-ranged (SR) structural details and long-range (LR) correlations, allowing the prediction of the thermodynamics of both single ions in solution as well as the collective interactions characterized by activity/osmotic coefficients. In doing so, relevant collective motions and driving forces characterized by chemical potentials can be determined. Here, in this Account, we will make the case that understanding electrolyte solutions requires a faithful QM representation of the SR nature of the ion–ion, ion–water, and water–water interactions. However, the number of molecules that is required for collective behavior makes the direct application of high-level QM methods that contain the best SR physics untenable, making methods that balance accuracy and efficiency a practical goal. Alternatives such as continuum solvent models (CSMs) and empirically based classical molecular dynamics have been extensively employed to resolve this problem but without yet overcoming the fundamental issue of SR accuracy. We will demonstrate that accurately describing the SR interaction is imperative for predicting both intrinsic properties, namely, at infinite dilution, and collective properties of electrolyte solutions. DFT has played an important role in our understanding of condensed phase systems, e.g., bulk liquid water, the air–water interface, ions in bulk, and at the air–water interface. This approach holds huge promise to provide benchmark calculations of electrolyte solution properties that will allow for the development and improvement of more efficient methods, as well as an enhanced understanding of fundamental phenomena. However, the standard protocol using the generalized gradient approximation with van der Waals (vdW) correction requires improvement in order to achieve a high level of quantitative accuracy. Simply simulating with higher level DFT functionals may not be the best route considering the significant computational cost. Alternative methods of incorporating information from higher levels of QM should be explored; e.g., using force matching techniques on small clusters, where high level benchmark calculations are possible, to develop ideal correction terms to the DFT functional is a promising possibility. We argue that DFT with statistical mechanics is becoming an increasingly useful framework enabling the prediction of collective electrolyte properties.

Duignan, Timothy T.↗

Unraveling disadhesion mechanism of epoxy/CSH interface under aggressive conditions

Almost all FRP-reinforced concrete exposed to the marine environment are susceptible to durability deficiencies due to failure of the FRP/epoxy/concrete interface, especially the vulnerable epoxy/concrete interface, which is frequently attacked by water and ions. Herein, molecular dynamics simulations of epoxy/CSH interface under different environmental exposures are utilized to specifically elucidate the degradation principles of water and ions on the bonding properties and mechanical responses of the epoxy/concrete interface. The environmental sequences associated with the interfacial bonding degradation are arranged as Na{sub 2}SO{sub 4} + NaCl>NaCl>Na{sub 2}SO{sub 4} > Water>Dry. Remarkably, water molecules weaken the interaction between the epoxy and CSH by robbing interfacial H- and Ca-O bonds, thereby reducing the energy barrier to interfacial peel and shear failure. The weakening effects are exacerbated by the presence of aggressive ions, as Na{sup +} ions attracted to the CSH surface accumulate more water molecules in the interfacial region by forming hydrated ions clusters, which ultimately accelerates the epoxy/CSH interfacial degradation.

36 MATERIALS SCIENCE↗

Non-equilibrium simulations of hydraulic permeation: Role of mechanical boundary conditions in dense membranes

Understanding the mechanisms of water transport in reverse osmosis membranes is critical for improving membrane performance and guiding material design. While classical models describe transport as either solution-diffusion (SD)—involving concentration-driven diffusion through a homogeneous medium—or pore-flow (PF)—involving pressure-driven convection through percolated water channels—their applicability to crosslinked polyamide membranes remains debated. Here, using non-equilibrium molecular dynamics simulations, we investigate the impact of mechanical support conditions on pressure-driven water transport in polyamide membranes across varying crosslink densities and pressure differentials (1000–5000 bar). Two support conditions are considered: graphene-restrained, representing experimentally relevant supported membranes, and freeze-restrained, mimicking a self-supported structure. In graphene-restrained systems, water concentration gradients and constant pressure profiles emerge, consistent with SD theory and incompatible with PF assumptions due to the absence of percolated pores and sub-nanometer voids. In contrast, freeze-restrained systems display uniform water concentration and linearly decreasing pressure at 1000 bar, and exhibit compressibility-induced water gradients and partial percolation at 5000 bar, resembling PF-like behavior. However, the underlying assumptions of PF theory—continuous solvent pathways and pressure transmission through water-filled pores—are not met under most conditions. Our results demonstrate that accurate modeling of reverse osmosis membranes must incorporate realistic mechanical boundary conditions to distinguish between transport mechanisms. For dense polyamide membranes supported by porous substrates, graphene-restrained simulations best reflect experimental setups and support the SD model as the dominant mechanism of water permeation.

molecular dynamics↗

Ion density waves driving the formation of filamentary dust structures

The PlasmaKristall-4 (PK-4) experiment on the International Space Station allows for the study of the 3-dimensional interaction between plasma and dust particles. Previous simulations of the PK-4 environment have discovered fast moving ionization waves in the dc discharge. These ionization waves vary the plasma parameters by up to an order of magnitude, which may affect the mechanisms responsible for the self-organization of chains seen in the PK-4 experiment. Here, we adapt a molecular dynamics simulation to employ temporally varying plasma conditions in order to investigate the effect on the dust charging and electrostatic potential. In order to describe the differences between the average of the plasma conditions and the time-varying plasma condition, we present a model to reproduce the interaction that takes into account the negative potential from the dust grain and the positive potential from the ion wake.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Molecular Design Principles for Photosystem I-Based Biohybrid Solar Fuel Catalysts

Direct solar-to-chemical conversion offers a compelling route to clean, dispatchable energy. Photosystem I (PSI), an evolutionarily optimized light-driven oxidoreductase, can be repurposed for solar-fuel production by coupling its photochemistry to catalytic interfaces. However, the molecular determinants that govern productive electron transfer to abiotic catalysts remain poorly understood. Here, we present molecular structures of active PSI-Pt nanoparticle (PtNP) biohybrids that reveal how protein architecture controls catalyst access, binding geometry, and photocatalytic efficiency. Removal of stromal subunits exposes the electron transfer chain and enables PtNP binding proximal to the F X cluster, demonstrating that steric occlusion limits access to native acceptor regions in PSI. In contrast, in trimeric PSI, PtNPs bind at multiple sites per monomer, but only a subset are positioned within electron transfer distance of terminal cofactors, resulting in a heterogeneous population of productive and nonproductive configurations. Structural analyses and molecular dynamics simulations define the interface topology, electrostatics, and cofactor-to-nanoparticle distances that govern catalyst binding and electron transfer. These results establish that catalytic inefficiency arises not only from intrinsic electron transfer constraints but also from the distribution of binding geometries imposed by the protein scaffold. Together, these findings provide a molecular framework linking protein structure to biohybrid function and define design principles for engineering PSI-based solar fuel systems and protein-nanomaterial interfaces for light-driven catalysis.

biohybrid↗