Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Molecular simulation”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 937 records · Page 52

Control of Permanent Porosity in Type 3 Porous Liquids via Solvent Clustering

Porous liquids (PLs) are an exciting new class of materials for carbon capture due to their high gas adsorption capacity and ease of industrial implementation. They are composed of sorbent particles suspended in a nonadsorbed solvent, forming a liquid with permanent porosity. While PLs have a vast number of potential compositions based on the number of solvents and sorbent materials available, most of the research has been focused on the selection of the sorbent rather than the solvent. Therefore, PL design criteria on the supramolecular structures of the solvent are explored to create a fundamental understanding of how the solvent enables PL formation for rapid discovery of new PL compositions. Atomistic molecular dynamics simulation of eight solvents with a range of molecular sizes, shapes, and intramolecular bonding was performed, identifying that the shape and size of molecular clusters formed in the solvent are the driving predictor of PL formation rather than the size of the individual solvent molecule. The results demonstrate a significant departure from common approaches to PL formation based on the steric exclusion of solvent molecules from the sorbent via the size of the pore aperture. A modeling and experimental validation study further supports these findings. In conclusion, through this computational material design study, a previously unexplored mechanism in PL formation, solvent–solvent clustering, is identified as a critical factor for the accelerated discovery of liquid phase carbon capture materials.

Carbon capture↗

On the role of asymmetric molecular geometry in high-performance organic solar cells

Although asymmetric molecular design has been widely demonstrated effective for organic photovoltaics (OPVs), the correlation between asymmetric molecular geometry and their optoelectronic properties is still unclear. To access this issue, we have designed and synthesized several symmetric-asymmetric non-fullerene acceptors (NFAs) pairs with identical physical and optoelectronic properties. Interestingly, we found that the asymmetric NFAs universally exhibited increased open-circuit voltage compared to their symmetric counterparts, due to the reduced non-radiative charge recombination. From our molecular-dynamic simulations, the asymmetric NFA naturally exhibits more diverse molecular interaction patterns at the donor (D):acceptor (A) interface as compared to the symmetric ones, as well as higher D:A interfacial charge-transfer state energy. Moreover, it is observed that the asymmetric structure can effectively suppress triplet state formation. These advantages enable a best efficiency of 18.80%, which is one of the champion results among binary OPVs. Therefore, this work unambiguously demonstrates the unique advantage of asymmetric molecular geometry, unveils the underlying mechanism, and highlights the manipulation of D:A interface as an important consideration for future molecular design.

14 SOLAR ENERGY↗

Multiscale computational understanding and growth of 2D materials: a review

Abstract The successful discovery and isolation of graphene in 2004, and the subsequent synthesis of layered semiconductors and heterostructures beyond graphene have led to the exploding field of two-dimensional (2D) materials that explore their growth, new atomic-scale physics, and potential device applications. This review aims to provide an overview of theoretical, computational, and machine learning methods and tools at multiple length and time scales, and discuss how they can be utilized to assist/guide the design and synthesis of 2D materials beyond graphene. We focus on three methods at different length and time scales as follows: (i) nanoscale atomistic simulations including density functional theory (DFT) calculations and molecular dynamics simulations employing empirical and reactive interatomic potentials; (ii) mesoscale methods such as phase-field method; and (iii) macroscale continuum approaches by coupling thermal and chemical transport equations. We discuss how machine learning can be combined with computation and experiments to understand the correlations between structures and properties of 2D materials, and to guide the discovery of new 2D materials. We will also provide an outlook for the applications of computational approaches to 2D materials synthesis and growth in general.

Momeni, Kasra↗

Platinum nanoparticle compression: Combining in situ TEM and atomistic modeling

The mechanical behavior of nanoparticles governs their performance and stability in many applications. However, the small sizes of technologically relevant nanoparticles, with diameters in the range of 10 nm or less, significantly complicate experimental examination. These small nanoparticles are difficult to manipulate onto commercial test platforms and deform at loads that are below the typical noise floor of the testing instruments. Here, we synthesized small platinum nanoparticles directly onto a mechanical tester and used a modified nanomanipulator to enhance load resolution to the nanonewton scale. We demonstrated the in situ compression of an 11.5-nm platinum nanoparticle with simultaneous high-resolution measurements of load and particle morphology. Molecular dynamics simulations were performed on similarly sized particles to achieve complementary measurements of load and morphology, along with atomic resolution of dislocations. The experimental and simulation results revealed comparable values for the critical resolved shear stress for failure, 1.28 and 1.15 GPa, respectively. Altogether, this investigation demonstrated the promise of, and some initial results from, the combination of atomistic simulations and in situ experiments with an unprecedented combination of high spatial resolution and high load resolution to understand the behavior of metal nanoparticles under compression.

42 ENGINEERING↗

Critical behavior in a chiral molecular model

Understanding the condensed-phase behavior of chiral molecules is important in biology as well as in a range of technological applications, such as the manufacture of pharmaceuticals. Here, we use molecular dynamics simulations to study a chiral four-site molecular model that exhibits a second-order symmetry-breaking phase transition from a supercritical racemic liquid into subcritical D-rich and L-rich liquids. We determine the infinite-size critical temperature using the fourth-order Binder cumulant, and we show that the finite-size scaling behavior of the order parameter is compatible with the 3D Ising universality class. We also study the spontaneous D-rich to L-rich transition at a slightly subcritical temperature of T = 0.985Tc, and our findings indicate that the free energy barrier for this transformation increases with system size as N2/3, where N is the number of molecules, consistent with a surface-dominated phenomenon. The critical behavior observed herein suggests a mechanism for chirality selection in which a liquid of chiral molecules spontaneously forms a phase enriched in one of the two enantiomers as the temperature is lowered below the critical point. Furthermore, the increasing free energy barrier with system size indicates that fluctuations between the L-rich and D-rich phases are suppressed as the size of the system increases, trapping it in one of the two enantiomerically enriched phases. Such a process could provide the basis for an alternative explanation for the origin of biological homochirality. We also conjecture the possibility of observing nucleation at subcritical temperatures under the action of a suitable chiral external field.

Chemistry↗

Time reversal symmetry breaking and odd viscosity in active fluids: Green–Kubo and NEMD results

Active fluids, which are driven at the microscale by non-conservative forces, are known to exhibit novel transport phenomena due to the breaking of time reversal symmetry. Recently, Epstein and Mandadapu [arXiv:1907.10041 (2019)] obtained Green-Kubo relations for the full set of viscous coefficients governing isotropic chiral active fluids, including the so-called odd viscosity, invoking Onsager's regression hypothesis for the decay of fluctuations in active non-equilibrium steady states. In this Communication, we test these Green-Kubo relations using molecular dynamics simulations of a canonical model system consisting of actively torqued dumbbells. We find the resulting odd and shear viscosity values from the Green-Kubo relations to be in good agreement with values measured independently through non-equilibrium molecular dynamics flow simulations. This provides a test of the Green-Kubo relations and lends support to the application of the Onsager regression hypothesis in relation to viscous behaviors of active matter systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Variations in proton transfer pathways and energetics on pristine and defect-rich quartz surfaces in water: Insights into the bimodal acidities of quartz

Hypothesis. Understanding the mechanisms of proton transfer on quartz surfaces in water is critical for a range of processes in geochemical, environmental, and materials sciences. The wide range of surface acidities (>9 pKa units) found on the ubiquitous mineral quartz is caused by the structural variations of surface silanol groups. Molecular scale simulations provide essential tools for elucidating the origin of site-specific surface acidities. Simulations. Here, we used density-functional tight-binding-based molecular dynamics combined with rare-event metadynamics simulations to probe the mechanisms of deprotonation reactions from ten representative surface silanol groups found on both pristine and defect-rich quartz (1 0 1) surfaces with Si vacancies. Findings. The results show that deprotonation is a highly dynamic process where both the surface hydroxyls and bridging oxygen atoms serve as the proton acceptors, in addition to water. Deprotonation of embedded silanols through intrasurface proton transfer exhibited lower pKa values with less H-bond participation and higher energy barriers, suggesting a new mechanism to explain the bimodal acidity observed on quartz surface. Defect sites, recently shown to comprise a significant portion of the quartz (1 0 1) surface, diversify the coordination and local H-bonding environments of the surface silanols, changing both the deprotonation pathways and energetics, leading to a wider range of pKa values (2.4 to 11.5) than that observed on pristine quartz surface (10.4 and 12.1).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

When should PIC simulations be applied to atmospheric pressure plasmas? Impact of correlation heating

Abstract Molecular dynamics simulations are used to test when the particle-in-cell (PIC) method applies to atmospheric pressure plasmas. It is found that PIC applies only when the plasma density and macroparticle weight are sufficiently small because of two effects associated with correlation heating. The first is the physical effect of disorder-induced heating (DIH). This occurs if the plasma density is large enough that a species (typically ions) is strongly correlated in the sense that the Coulomb coupling parameter exceeds one. In this situation, DIH causes ions to rapidly heat following ionization. PIC is not well suited to capture DIH because doing so requires using a macroparticle weight of one and a grid that well resolves the physical interparticle spacing. These criteria render PIC intractable for macroscale domains. The second effect is a numerical error due to artificial correlation heating (ACH). ACH is like DIH in that it is caused by the Coulomb repulsion between particles, but differs in that it is a numerical effect caused by a macroparticle weight larger than one. Like DIH, it is associated with strong correlations. However, here the macroparticle coupling strength is found to scale as Γ w 2 / 3 , where Γ is the physical coupling strength and w is the macroparticle weight. So even if the physical coupling strength of a species is small, as is expected for electrons in atmospheric pressure plasmas, a sufficiently large macroparticle weight can cause the macroparticles to be strongly coupled and therefore heat due to ACH. Furthermore, it is shown that simulations in reduced dimensions exacerbate these issues.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Ab Initio Simulation of Amorphous Graphite

An amorphous graphite material has been predicted from molecular dynamics simulation using ab initio methods. Carbon materials reveal a strong proclivity to convert into a sp 2 network and then layer at temperatures near 3000 K within a density range of ca. 2.2–2.8 g/cm 3 . Each layer of amorphous graphite is a monolayer of amorphous graphene including pentagons and heptagons in addition to hexagons, and the planes are separated by about 3.1 Å. The layering transition has been studied using various structural and dynamical analyses. The transition is unique as one of partial ordering (long range order of planes and galleries, but topological disorder in the planes). The planes are quite flat, even though monolayer amorphous graphene puckers near pentagonal sites. Interplane cohesion is due partly to non-Van der Waals interactions. The structural disorder has been studied closely, especially the consequences of disorder to electronic transport. Finally, it is expected that the transition elucidated here may be salient to other layered materials.

42 ENGINEERING↗

Integrating Experiments and Simulations to Reveal Anisotropic Growth Mechanisms and Interfaces of a One-Dimensional Zeolite

Zeolites are nanoporous crystalline materials critical for diverse industrial applications, yet their growth mechanisms are poorly understood. Here, this study presents a novel integrated framework combining experimental synthesis, high-resolution imaging, coarse-grained molecular dynamics simulations, and computer vision to uncover the mechanisms of growth of SSZ-24, a 1D channel zeolite. We demonstrate how synthesis conditions, such as temperature and reactant concentration, govern crystal anisotropy and surface roughness with growth dynamics differing markedly by crystallographic orientation. Along the channels, growth involves minimal energy barriers and rapid nucleation, resulting in rough surfaces. In contrast, growth perpendicular to the channels requires cooperative molecular organization and is highly sensitive to thermodynamic and kinetic conditions, yielding smooth anisotropic surfaces under low driving forces. By simulating transmission electron microscopy (TEM) images, we bridge molecular-scale simulations with experimental observations, identifying distinct growth mechanisms along different crystal planes. This work offers molecular-level insights into zeolite crystallization, advancing the rational design of nanoporous materials. The integration of cross-disciplinary methodologies establishes a transformative framework for optimizing zeolite synthesis, with implications for broader classes of materials.

Bertolazzo, Andressa A. [Univ. of Utah, Salt Lake ↗

Ions Tune Interfacial Water Structure and Modulate Hydrophobic Interactions at Silica Surfaces

The structure and ultrafast dynamics of the electric double layer (EDL) are central to chemical reactivity and physical properties at solid/aqueous interfaces. While the Gouy–Chapman–Stern model is widely used to describe EDLs, it is solely based on the macroscopic electrostatic attraction of electrolytes for the charged surfaces. Structure and dynamics in the Stern layer are, however, more complex because of competing effects due to the localized surface charge distribution, surface–solvent–ion correlations, and the interfacial hydrogen bonding environment. Here, we report combined time-resolved vibrational sum frequency generation (TR-vSFG) spectroscopy with ab initio DFT-based molecular dynamics simulations (AIMD/DFT-MD) to get direct access to the molecular-level understanding of how ions change the structure and dynamics of the EDL. We show that innersphere adsorbed ions tune the hydrophobicity of the silica–aqueous interface by shifting the structural makeup in the Stern layer from dominant water–surface interactions to water–water interactions. This drives an initially inhomogeneous interfacial water coordination landscape observed at the neat interface toward a homogeneous, highly interconnected in-plane 2D hydrogen bonding (2D-HB) network at the ionic interface, reminiscent of the canonical, hydrophobic air–water interface. This ion-induced transformation results in a characteristic decrease of the vibrational lifetime (T 1 ) of excited interfacial O–H stretching modes from T 1 ~ 600 fs to T 1 ~ 250 fs. Hence, we propose that the T 1 determined by TR-vSFG in combination with DFT-MD simulations can be widely used for a quantitative spectroscopic probe of the ion kosmotropic/chaotropic effect at aqueous interfaces as well as of the ion-induced surface hydrophobicity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding dynamic properties of materials using neutron spectroscopy and atomistic simulation

Recent developments in first-principles lattice dynamics and classical force field based molecular dynamics are revolutionising the field of neutron spectroscopy. Herein we present a short review of these methods, their critical role in the supporting of cutting-edge experiments, and how they are improved by matching experimental data. We begin with a brief overview of how lattice dynamics calculations can be compared to inelastic neutron scattering (INS) and molecular dynamics simulations to both INS and quasi-elastic neutron scattering (QENS). We then provide a series of exemplar applications where lattice dynamics and molecular dynamics have been used in conjunction with neutron spectroscopy to bring significant understanding to topical areas of materials science namely: (i) lattice dynamics and INS for the study of hybrid organic-inorganic perovskites (ii) lattice dynamics and INS for the study of flexible porous solids and (iii) molecular dynamics and QENS for probing molecular behaviour in zeolite catalysis. In all three cases, the understanding gained through the synergy of experiment and computation would have been significantly reduced using either in isolation. Finally, we consider the current state of the art, describing outstanding challenges and suggesting future directions in this exciting and fertile area of physical science.

36 MATERIALS SCIENCE↗

Structurally Driven Environmental Degradation of Friction in MoS2 Films

Abstract We report an investigation of the friction mechanisms of MoS 2 thin films under changing environments and contact conditions using a variety of computational and experimental techniques. Molecular dynamics simulations were used to study the effects of water and molecular oxygen on friction and bonding of MoS 2 lamellae during initial sliding. Characterization via photoelectron emission microscopy (PEEM) and Kelvin probe force microscopy (KPFM) were used to determine work function changes in shear modified material within the top few nanometers of MoS 2 wear scars. The work function was shown to change with contact conditions and environment, and shown by density functional theory (DFT) calculations and literature reports to be correlated with lamellae size and thickness of the basally oriented surface layer. Results from nanoscale simulations and macroscale experiments suggest that the evolution of the friction behavior of MoS 2 is linked primarily to the formation or inhibition of a basally oriented, molecularly thin surface film with long-range order.

Curry, John F.↗

From Femtoseconds to Gigaseconds: The SolDeg Platform for the Performance Degradation Analysis of Silicon Heterojunction Solar Cells

Heterojunction Si solar cells exhibit notable performance degradation. Here, we modeled this degradation by electronic defects getting generated by thermal activation across energy barriers over time. To analyze the physics of this degradation, we developed the SolDeg platform to simulate the dynamics of electronic defect generation. First, femtosecond molecular dynamics simulations were performed to create a-Si/c-Si stacks, using the machine learning-based Gaussian approximation potential. Second, we created shocked clusters by a cluster blaster method. Third, the shocked clusters were analyzed to identify which of them supported electronic defects. Fourth, the distribution of energy barriers that control the generation of these electronic defects was determined. Fifth, an accelerated Monte Carlo method was developed to simulate the thermally activated time-dependent defect generation across the barriers. Our main conclusions are as follows. (1) The degradation of a-Si/c-Si heterojunction solar cells via defect generation is controlled by a broad distribution of energy barriers. (2) We developed the SolDeg platform to track the microscopic dynamics of defect generation across this wide barrier distribution and determined the time-dependent defect density N(t) from femtoseconds to gigaseconds, over 24 orders of magnitude in time. (3) We have shown that a stretched exponential analytical form can successfully describe the defect generation N(t) over at least 10 orders of magnitude in time. (4) We found that in relative terms, Voc degrades at a rate of 0.2%/year over the first year, slowing with advancing time. (5) We developed the time correspondence curve to calibrate and validate the accelerated testing of solar cells. We found a compellingly simple scaling relationship between accelerated and normal times t normal ∝ t accel T(accel)/T(normal) . (6) We also carried out experimental studies of defect generation in a-Si:H/c-Si stacks. We found a relatively high degradation rate at early times that slowed considerably at longer time scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Hotspot’s Better Half: Non-Equilibrium Intra-Molecular Strain in Shock Physics

Shockwave interactions with a material’s microstructure localizes energy into hotspots, which act as nucleation sites for complex processes such as phase transformations and chemical reactions. To date, hotspots have been described via their temperature fields. Nonreactive, all-atom molecular dynamics simulations of shock-induced pore collapse in a molecular crystal show that more energy is localized as potential energy (PE) than can be inferred from the temperature field and that PE localization persists beyond thermal diffusion. Furthermore, the origin of the PE hotspot is traced to large intramolecular strains, storing energy in modes readily available for chemical decomposition.

36 MATERIALS SCIENCE↗

Charged Biological Membranes Repel Large Neutral Molecules by Surface Dielectrophoresis and Counterion Pressure

Macromolecular crowding is the usual condition of cells. The implications of the crowded cellular environment for protein stability and folding, protein–protein interactions, and intracellular transport drive a growing interest in quantifying the effects of crowding. While the properties of crowded solutions have been extensively studied, less attention has been paid to the interaction of crowders with the cellular boundaries, i.e., membranes. However, membranes are key components of cells and most subcellular organelles, playing a central role in regulating protein channel and receptor functions by recruiting and binding charged and neutral solutes. While membrane interactions with charged solutes are dominated by electrostatic forces, here we show that significant charge-induced forces also exist between membranes and neutral solutes. Using neutron reflectometry measurements and molecular dynamics simulations of poly(ethylene glycol) (PEG) polymers of different molecular weights near charged and neutral membranes, we demonstrate the roles of surface dielectrophoresis and counterion pressure in repelling PEG from charged membrane surfaces. The resulting depletion zone is expected to have consequences for drug design and delivery, the activity of proteins near membrane surfaces, and the transport of small molecules along the membrane surface.

59 BASIC BIOLOGICAL SCIENCES↗

A two-dimensional type I superionic conductor

Superionic conductors (SICs) possess liquid-like ionic diffusivity in the solid state, finding wide applicability from electrolytes in energy storage to materials for thermoelectric energy conversion. Type I SICs (e.g., AgI, Ag 2 Se, etc.) are defined by a first-order transition to the superionic state and have so far been found exclusively in three-dimensional crystal structures. Here, we reveal a two-dimensional type I SIC, α-KAg 3 Se 2 by scattering techniques and complementary simulations. Quasi-elastic neutron scattering and ab initio molecular dynamics simulations confirm that the superionic Ag + ions are confined to sub-nanometre sheets, with the simulated local structure validated by experimental X-ray powder pair-distribution-function analysis. Finally, we demonstrate that the phase transition temperature can be controlled by chemical substitution of the alkali metal ions that comprise the immobile charge-balancing layers. Our work thus extends the known classes of SICs and will facilitate the design of new materials with tailored ionic conductivities and phase transitions.

36 MATERIALS SCIENCE↗

Skyrmion formation in Ni-based Janus dihalide monolayers: Interplay between magnetic frustration and Dzyaloshinskii-Moriya interaction

Here we present a comprehensive theory of the magnetic phases in monolayer nickel-based Janus dihalides (NiIBr, NiICl, NiBrCl) through a combination of first-principles calculations and atomistic simulations. Phonon band structure calculations and finite-temperature molecular dynamics simulations show that Ni-dihalide Janus monolayers are stable. The parameters of the interacting spin Hamiltonian extracted from ab initio calculations show that nickel-dihalide Janus monolayers exhibit varying degrees of magnetic frustration together with a large Dzyaloshinskii-Moriya interaction due to their inherent inversion symmetry breaking. The atomistic simulations reveal a delicate interplay between these two competing magnetic interactions in giving rise to skyrmion formation.

36 MATERIALS SCIENCE↗