Nonequilibrium Simulations Research Articles

Forming mechanism of equilibrium and non-equilibrium metallurgical phases in dissimilar aluminum/steel (Al\u2013Fe) joints

Forming metallurgical phases has a critical impact on the performance of dissimilar materials joints. Here, we shed light on the forming mechanism of equilibrium and non-equilibrium intermetallic compounds (IMCs) in dissimilar aluminum/steel joints with respect to processing history (e.g., the pressure and temperature profiles) and chemical composition, where the knowledge of free energy and atomic diffusion in the Al–Fe system was taken from first-principles phonon calculations and data available in the literature. We found that the metastable and ductile (judged by the presently predicted elastic constants) Al6Fe is a pressure (P) favored IMC observed in processes involving high pressures. The MoSi2-type Al2Fe is brittle and a strong P-favored IMC observed at high pressures. The stable, brittle η-Al5Fe2 is the most observed IMC (followed by θ-Al13Fe4) in almost all processes, such as fusion/solid-state welding and additive manufacturing (AM), since η-Al5Fe2 is temperature-favored, possessing high thermodynamic driving force of formation and the fastest atomic diffusivity among all Al–Fe IMCs. Notably, the ductile AlFe3, the less ductile AlFe, and most of the other IMCs can be formed during AM, making AM a superior process to achieve desired IMCs in dissimilar materials. In addition, the unknown configurations of Al2Fe and Al5Fe2 were also examined by machine learning based datamining together with first-principles verifications and structure predictions. All the IMCs that are not P-favored can be identified using the conventional equilibrium phase diagram and the Scheil-Gulliver non-equilibrium simulations.

Molecular Simulation of External Electric Fields on the Crystal State: A Perspective

Unpacking the mechanistic insights into how externally applied electric fields affect the physicochemical properties of crystals represents a challenge of great importance for a plethora of natural phenomena, in addition to a broad array of industrial operations and technologies. As such, the key goals in such field effect studies centre around how thermodynamic and kinetic relaxation processes in crystals are affected, including charge carrier conduction and energy transfer processes, and this is a very recent area of fundamental scrutiny. Indeed, in recent years, there has been a steadily mounting number of reports of field-manipulated crystal-state phenomena. Taking as the background a range of natural phenomena, phenomenological theory, state-of-the-art experiments and technological observations, the present review examines the role of nonequilibrium molecular simulation in its scrutiny of intra-crystal phenomena from an atomistic viewpoint, in addition to providing a framework for a predictive molecular design philosophy by which to refine field crystal understanding.

Reweighted Jarzynski Sampling: Acceleration of Rare Events and Free Energy Calculation with a Bias Potential Learned from Nonequilibrium Work.

We introduce a simple enhanced sampling approach for the calculation of free energy differences and barriers along a one-dimensional reaction coordinate. First, a small number of short nonequilibrium simulations are carried out along the reaction coordinate, and the Jarzynski equality is used to learn an approximate free energy surface from the nonequilibrium work distribution. This free energy estimate is represented in a compact form as an artificial neural network and used as an external bias potential to accelerate rare events in a subsequent molecular dynamics simulation. The final free energy estimate is then obtained by reweighting the equilibrium probability distribution of the reaction coordinate sampled under the influence of the external bias. We apply our reweighted Jarzynski sampling recipe to four processes of varying scales and complexities─spanning chemical reaction in the gas phase, pair association in solution, and droplet nucleation in supersaturated vapor. In all cases, we find reweighted Jarzynski sampling to be a very efficient strategy, resulting in rapid convergence of the free energy to high precision.

Phonon transport across GaN/AlN interface: Interfacial phonon modes and phonon local non-equilibrium analysis

Interfacial thermal conductance (ITC) is of critical importance for GaN-based device performance. GaN/AlN is a key component in GaN-based devices. Therefore, systematically investigating the interfacial thermal transport between GaN and AlN is of great significance for the thermal management of GaN-based devices. The temperature dependence of ITC across GaN/AlN interfaces are investigated using nonequilibrium molecular dynamics (NEMD) and Monte Carlo simulations based on first-principles calculations. Interestingly, the calculated ITC is much larger than that of GaN/metal, GaN/Si and GaN/SiC. Structural similarity and interfacial phonon modes are used to reveal the underlying mechanism. Moreover, the modal temperature and wave-resolved spectral heat flux are calculated to understand the interfacial thermal nonequilibrium and the dominant thermal transport channel, respectively. This study explores the modal-level and frequency-level mechanisms for interfacial thermal transport between GaN and AlN, which provides effective understanding in thermal management of GaN-based devices.

Three-Dimensional Pore-Scale Simulation of Flow and Thermal Non-Equilibrium for Premixed Gas Combustion in a Random Packed Bed Burner

Pore-scale studies of premixed gas combustion in a packed bed is conducted to study the flow and thermal non-equilibrium phenomenon in packed bed. The 3D random packed bed is generated using the EDEM software and solid surface radiation is computed using Discrete Ordinates (DO) model. The simulations are carried out using a commercial software package based on the finite volume method. It is shown that the local variation of species mass fraction, reaction rate et al. in pores near the flame front is significant, the radiation heat flux is transferred layer-by-layer. Cold flow simulation without reaction reveals that flow non-equilibrium is one of the essential characteristics of packing bed and increase in flow velocity leads to intensify non-equilibrium phenomenon. The distributions for content of axial velocity and gas temperature are wave-like shape in the burner and vary with time.

Dissipative morphological characteristics of photo-responsive block copolymers driven by time-oscillatory irradiations: An in silico study

Dissipative or dynamic self-assembly has become one of the most important topics in the past twenty years. Under continuous energy input, the building blocks may form various dissipative structures in steady states, which will be destroyed when the energy input is stopped. Among the common forms of energy input, light is widely used for its high efficiency and adjustability. However, there is lack of study on the dissipative self-assembly of photo-responsive block copolymers under time-dependent light irradiations (especially in time-oscillatory light irradiations) as well as its design strategies. We performed non-equilibrium dissipative particle dynamics simulations of azobenzene-contained semiflexible block copolymers in melt and investigated important controlling factors that influence dissipative structures, including the volume ratio of blocks, the interaction between blocks, the oscillation period and the volume fraction of photo-responsive polymers in the system. We found that, when the oscillation period is much smaller than the diffusional timescale of block copolymer, dissipative steady structures will be formed. With the increase of oscillation period, oscillatory dissipative structures with periodic structural variation were formed based on dissipative steady structures. As oscillation period increased further, there would be no regular structure. Furthermore, the dissipative steady structures could be finely tuned by adjusting the volume fraction of photo-responsive chains in block copolymer melt. Our study provides a guidance for the design of azobenzene-contained block copolymers that can form dissipative structures in time-oscillatory irradiations and helps to predict the self-assembled morphologies.

CORE-MD II: A fast, adaptive, and accurate enhanced sampling method.

In this paper, we present a fast and adaptive correlation guided enhanced sampling method (CORE-MD II). The CORE-MD II technique relies, in part, on partitioning of the entire pathway into short trajectories that we refer to as instances. The sampling within each instance is accelerated by adaptive path-dependent metadynamics simulations. The second part of this approach involves kinetic Monte Carlo (kMC) sampling between the different states that have been accessed during each instance. Through the combination of the partition of the total simulation into short non-equilibrium simulations and the kMC sampling, the CORE-MD II method is capable of sampling protein folding without any a priori definitions of reaction pathways and additional parameters. In the validation simulations, we applied the CORE-MD II on the dialanine peptide and the folding of two peptides: TrpCage and TrpZip2. In a comparison with long time equilibrium Molecular Dynamics (MD), 1 µs replica exchange MD (REMD), and CORE-MD I simulations, we find that the level of convergence of the CORE-MD II method is improved by a factor of 8.8, while the CORE-MD II method reaches acceleration factors of ∼120. In the CORE-MD II simulation of TrpZip2, we observe the formation of the native state in contrast to the REMD and the CORE-MD I simulations. The method is broadly applicable for MD simulations and is not restricted to simulations of protein folding or even biomolecules but also applicable to simulations of protein aggregation, protein signaling, or even materials science simulations.

Evaluation of Computational Models for Electron Transpiration Cooling

Recent developments in the world of hypersonic flight have brought increased attention to the thermal response of materials exposed to high-enthalpy gases. One promising concept is electron transpiration cooling (ETC) that provides the prospect of a passive heat removal mechanism, rivaling and possibly outperforming that of radiative cooling. In this work, non-equilibrium CFD simulations are performed to evaluate the possible roles of this cooling mode under high-enthalpy conditions obtainable in plasma torch ground-test facilities capable of long flow times. The work focuses on the test case of argon gas being heated to achieve enthalpies equivalent to post-shock conditions experienced by a vehicle flying through the atmosphere at hypersonic speed. Simulations are performed at a range of conditions and are used to calibrate direct comparisons between torch operating conditions and resulting flow properties. These comparisons highlight important modeling considerations for simulating long-duration, hot chamber tests. Simulation results correspond well with the experimental measurements of gas temperature, material surface temperature as well as measured current generated in the test article. Theoretical methods taking into consideration space charge limitations are presented and applied to provide design suggestions to boost the ETC effect in future experiments.

Revealing the role of hydrogen bonding in polyurea with multiscale simulations

ABSTRACT Typically, polyurea is a polymer forming microphase-separated structures. Various coarse-grained (CG) simulation models have been developed to study the microphase structure and viscoelastic properties of polyurea. However, since the hydrogen atoms were modelled implicitly in the existing CG models, the anisotropic hydrogen bonding between urea groups in the hard domain might not be treated properly. Here, we introduce a hybrid all-atom/coarse-grained (AA/CG) model for polyurea, the CGU model, in which atomistic resolution are preserved for the urea groups. This model is proven to reproduce the results of the AA model, despite 24 times faster to run. By comparing the traditional CG model and the CGU model, we found that hydrogen bonding leads to a head-to-tail arrangement of the urea groups and a significant slowdown of the hard segment dynamics. Non-equilibrium simulations of stress relaxation process indicate that hydrogen bonding causes a broad relaxation time spectrum, which is consistent with experiment results.

Dynamical Water Ingress and Dissolution at the Amorphous-Crystalline Cellulose Interface.

The use of cellulose has considerable promise in a wide range of industrial applications but is hampered by degradation in mechanical properties due to ambient moisture uptake. Existing models of equilibrium moisture content can predict the impact of these effects, but at present, the dynamical, atomic-scale picture of water ingress into cellulose is lacking. The present work reports nonequilibrium molecular simulations of the interface between cellulose and water aimed at capturing the initial stages of two simultaneous dynamical processes, water ingress into cellulose and cellulose dissolution into water. These simulations demonstrate that the process depends on the temperature and chain length in the amorphous region, where high temperatures can induce more mass exchange and short chains can easily detach from amorphous cellulose. A cooperative mechanism that involves both chemical and physical aspects, namely, hydrogen bonding and chain intertwining, respectively, is proposed to interpret the incipient dual ingress/dissolution process. Outcomes of this work will provide a foundation for cellulose functionalization strategies to impede moisture uptake and preserve the mechanical properties of nanocellulose in applications.

Non-equilibrium molecular dynamics study of human aquaporin-2 in the static external electric fields

In this paper, non-equilibrium MD simulations (NEMD) of human aquaporin-2 (AQP2) in the presence of an external static electric field have been performed along + z and − z directions of the pore axis. The impacts of the electric field direction on the gating mechanism corresponding to the selectivity filter (SF) region of AQP2 have been studied. Besides, the effects of applied external electric field on the PMF profile of water molecules translocation, water permeability, and molecules dipole orientation are investigated. Our results showed that when the external electric field is implemented along the + z direction of the channels, the selectivity filter region is kept in the wide conformation for the majority of the time. Therefore, a remarkable increase in the overall water permeability can be seen compared to the case without any external electric field. This is in contrast to the effects of − z-directed electric field on the conformations of the selectivity filter, which induces mostly narrow conformations in this constriction region. A substantial higher energy barrier emerged in the middle of the AQP2’s pores under the effect of –z-directed electric field in comparison with the zero and + z-directed electric field strengths, which is mainly ascribed to the deviation from bipolar dipole orientation within the AQP2’s pores. Communicated by Ramaswamy H. Sarma

Extrinsic Complex Structure Developed through Novel Simulation Methodology: Key Putative Atomic-Level Interactions Identified

The ternary extrinsic complex of the coagulation pathway (Tissue Factor (TF): Factor VIIa (FVIIa): Factor X (FX)) is critically important to the regulation of blood clotting. Activation of FX in this membrane-bound complex is vital to both the major pathways which produce the explosive burst of thrombin required for clot formation to proceed. Despite high interest in this complex as a potential drug target for hemophilia and thrombosis, little has been determined experimentally concerning its structure due to the lipid-dependent nature of its formation. As the complex will only form on the surface of a membrane with a specific composition of anionic phospholipids, experimental structure determination through NMR or X-ray crystallography is prohibitively difficult.We will present the first atomic-level resolution structure of the ternary complex to include membrane interactions, developed using a novel methodology which combines protein-protein docking and extensive non-equilibrium molecular dynamics simulations. Over 560,000 protein-only structures predicting interactions between key domains of the extrinsic complex were first developed using the DOT2 protein docking program. Top docked structures were selected based on agreement with experimental information, and used to identify residues of FX and TF:FVIIa likely to interact. Protein-protein contact information from docking was then used to developed biased non-equilibrium simulations in which the complex was induced to form along a particular pathway. Using five non-equilibrium simulations of 200 ns, binding between membrane-bound structures of FX and TF:FVIIa was slowly induced. The highly mobile membrane mimetic (HMMM) model, an advanced membrane model which replaces slow-moving lipid tails with detergent molecules, was used to allow increased sampling of protein-lipid interacts during this deliberate complex formation. Each of the five resulting complexes was simulated for an additional 200 ns without biases, and putative key protein-protein and protein-lipid interactions involved in complex formation were identified. Residues on the membrane-binding domain of FX where found in the simulations to bind residues of TF previously identified experimentally as critical for complex formation. This structure provides not only the best available information on protein binding for the extrinsic complex but the only atomic-level information on the protein-lipid interactions which are crucial for its formation. DisclosuresNo relevant conflicts of interest to declare.

GKS and UGKS for High-Speed Flows

The gas-kinetic scheme (GKS) and the unified gas-kinetic scheme (UGKS) are numerical methods based on the gas-kinetic theory, which have been widely used in the numerical simulations of high-speed and non-equilibrium flows. Both methods employ a multiscale flux function constructed from the integral solutions of kinetic equations to describe the local evolution process of particles’ free transport and collision. The accumulating effect of particles’ collision during transport process within a time step is used in the construction of the schemes, and the intrinsic simulating flow physics in the schemes depends on the ratio of the particle collision time and the time step, i.e., the so-called cell’s Knudsen number. With the initial distribution function reconstructed from the Chapman–Enskog expansion, the GKS can recover the Navier–Stokes solutions in the continuum regime at a small Knudsen number, and gain multi-dimensional properties by taking into account both normal and tangential flow variations in the flux function. By employing a discrete velocity distribution function, the UGKS can capture highly non-equilibrium physics, and is capable of simulating continuum and rarefied flow in all Knudsen number regimes. For high-speed non-equilibrium flow simulation, the real gas effects should be considered, and the computational efficiency and robustness of the schemes are the great challenges. Therefore, many efforts have been made to improve the validity and reliability of the GKS and UGKS in both the physical modeling and numerical techniques. In this paper, we give a review of the development of the GKS and UGKS in the past decades, such as physical modeling of a diatomic gas with molecular rotation and vibration at high temperature, plasma physics, computational techniques including implicit and multigrid acceleration, memory reduction methods, and wave–particle adaptation.

Heat conduction in a three-dimensional momentum-conserving fluid.

Size dependence of energy transport and the effects of reduced dimensionality on transport coefficients are of key importance for understanding nonequilibrium properties of matter on the nanoscale. Here, we perform nonequilibrium and equilibrium simulations of heat conduction in a three-dimensional (3D) fluid with the multiparticle collision dynamics, interacting with two thermal walls. We find that the bulk 3D momentum-conserving fluid has a finite nondiverging thermal conductivity. However, for large aspect ratios of the simulation box, a crossover from 3D to one-dimensional (1D) abnormal behavior of the thermal conductivity occurs. In this case, we demonstrate a transition from normal to abnormal transport by a suitable decomposition of the energy current. These results not only provide a direct verification of Fourier's law, but also further confirm the validity of existing theories for 3D fluids. Moreover, they indicate that abnormal heat transport persists also for almost 1D fluids over a large range of sizes.

Oscillatory shear-induced bcc-fcc martensitic transformation in a colloidal suspension with long-range repulsive interactions.

We perform non-equilibrium Brownian dynamics simulations to investigate the out-of-equilibrium phase behavior of a suspension of charged colloids under external oscillatory shear. We independently vary the frequency f and the maximum strain amplitude γmax of the oscillations and map out an out-of-equilibrium phase diagram in the f-γmax plane. Similar to what has been observed in earlier studies on colloidal hard spheres, we find the formation of a twinned face-centered-cubic phase in a specific range of γmax, which displays a martensitic transition to a body-centered-cubic crystal within half of the oscillation cycle. We provide a comprehensive analysis of these structures and show how the system transforms from one to the other. We also report evidence of a sliding layer phase and a string phase.

Estimating the Directional Flexibility of Proteins from Equilibrium Thermal Fluctuations.

The directional flexibility of proteins is an equilibrium molecular property which is accessible to both experiment and computation. Single molecule force spectroscopy (SMFS) experiments report effective directional spring constants to describe the collective anisotropic response of a protein structure to mechanical pulling forces applied along selected axes. On the other hand, computational methods have thus far employed either indirect force based nonequilibrium simulations or coarse-grained elastic network models (ENM) to predict protein directional spring constants. Here, we examine the ability of equilibrium atomistic Molecular Dynamics (MD) simulations to estimate the directional flexibility and mechanical anisotropy of proteins. MD-derived effective directional spring constants are found to correlate well with SMFS spring constants (ρ2 = 0.97-0.99; Adj R2 = 0.92-0.99) and unfolding forces (ρ2 = 0.85-0.97; Adj R2 = 0.63-0.91) for five different globular proteins. Specifically, the computed spring constants reproduce the mechanical anisotropy reported by SMFS along five different directions of green fluorescence protein (GFP) and six directions of the immunoglobulin-binding B1 domain of streptococcal protein G (GB1). Further, protein dynamics as captured in MD can be translated into spring constants which can distinguish the N-C directional flexibility of ubiquitin (Ub) from two structurally homologous small ubiquitin-like modifier (SUMO1 and SUMO2) isoforms. We apply our computational framework to study the mechanical anisotropy of Ub along the seven lysine-C-term directions which are functionally relevant. We show that Ub possesses two distinct flexibility scales along these directions which roughly differ by an order of magnitude. Further, our studies reveal that the mechanical anisotropy of Ub is modified in contrasting ways by the binding of two partner proteins (UBCH5A and UEV) which attach and recognize these biomolecular tag proteins. On the basis of equilibrium MD benchmarks for flexibility along 2485 bond vectors in Ub, we propose and validate a new covariance-propagation scheme to extract spring constants from ENM normal modes. We also critically examine the ability of ENM to predict directional flexibility of proteins and suggest modifications to improve these intuitive and scalable descriptions.

Shock interactions in inviscid air and hbox {CO}_2\u2013hbox {N}_2 flows in thermochemical non-equilibrium

The present study aims at providing insights into shock wave interference patterns in gas flows when a mixture different than air is considered. High-energy non-equilibrium flows of air and hbox {CO}_2–hbox {N}_2 over a double-wedge geometry are studied numerically. The impact of freestream temperature on the non-equilibrium shock interaction patterns is investigated by simulating two different sets of freestream conditions. To this purpose, the SU2 solver has been extended to account for the conservation of chemical species as well as multiple energies and coupled to the Mutation++ library (Multicomponent Thermodynamic And Transport properties for IONized gases in C++) that provides all the necessary thermochemical properties of the mixture and chemical species. An analysis of the shock interference patterns is presented with respect to the existing taxonomy of interactions. A comparison between calorically perfect ideal gas and non-equilibrium simulations confirms that non-equilibrium effects greatly influence the shock interaction patterns. When thermochemical relaxation is considered, a type VI interaction is obtained for the hbox {CO}_2-dominated flow, for both freestream temperatures of 300 K and 1000 K; for air, a type V six-shock interaction and a type VI interaction are obtained, respectively. We conclude that the increase in freestream temperature has a large impact on the shock interaction pattern of the air flow, whereas for the hbox {CO}_2–hbox {N}_2 flow the pattern does not change.

Allosteric communication in class A β-lactamases occurs via cooperative coupling of loop dynamics.

Understanding allostery in enzymes and tools to identify it offer promising alternative strategies to inhibitor development. Through a combination of equilibrium and nonequilibrium molecular dynamics simulations, we identify allosteric effects and communication pathways in two prototypical class A β-lactamases, TEM-1 and KPC-2, which are important determinants of antibiotic resistance. The nonequilibrium simulations reveal pathways of communication operating over distances of 30 Å or more. Propagation of the signal occurs through cooperative coupling of loop dynamics. Notably, 50% or more of clinically relevant amino acid substitutions map onto the identified signal transduction pathways. This suggests that clinically important variation may affect, or be driven by, differences in allosteric behavior, providing a mechanism by which amino acid substitutions may affect the relationship between spectrum of activity, catalytic turnover, and potential allosteric behavior in this clinically important enzyme family. Simulations of the type presented here will help in identifying and analyzing such differences.

Molecular Simulation of Crystallisation in External Electric Fields: A Review

Elucidating the underlying mechanisms of molecular solidification in both homo- and hetero-geneous systems is of paramount importance for a large swathe of natural phenomena (whether on Earth or throughout the Universe), as well as a whole litany of industrial processes. One lesser-studied aspect of these disorder-order transitions is the effect of external applied fields, shifting both thermodynamic driving forces and underlying kinetics, and, indeed, fundamental mechanisms themselves. Perhaps this is nowhere more apparent than in the case of externally-applied electric fields, where there has been a gradually increasing number of reports in recent years of electro-manipulated crystallisation imparted by such electric fields. Drawing motivations from both natural phenomena, state-of-the-art experiments and, indeed, industrial applications, this review focusses on how non-equilibrium molecular simulation has helped to elucidate crystallisation phenomena from a microscopic perspective, as well as offering an important, predictive molecular-design approach with which to further refine in-field-crystallisation operations.

Simulation of time-dependent resonant inelastic x-ray scattering using nonequilibrium dynamical mean-field theory

We develop a framework to evaluate the time-dependent resonant inelastic X-ray scattering (RIXS) signal with the use of non-equilibrium dynamical mean field theory simulations. The approach is based on the solution of a time-dependent impurity model which explicitly incorporates the probe pulse. It avoids the need to compute four-point correlation functions, and can in principle be combined with different impurity solvers. This opens a path to study time-resolved RIXS processes in multi-orbital systems. The approach is exemplified with a study of the RIXS signal of a melting Mott antiferromagnet.