Nonequilibrium Simulations Research Articles

Thermal conductance of the water-gold interface: The impact of the treatment of surface polarization in non-equilibrium molecular simulations.

Interfacial thermal conductance (ITC) quantifies heat transport across material-fluid interfaces. It is a property of crucial importance to study heat transfer processes at both macro- and nanoscales. Therefore, it is essential to accurately model the specific interactions between solids and liquids. Here, we investigate the thermal conductance of gold-water interfaces using polarizable and non-polarizable models. Both models have been fitted to reproduce the interfacial tension of the gold-water interface, but they predict significantly different ITCs. We demonstrate that the treatment of polarization using Drude-like models, widely employed in molecular simulations, leads to a coupling of the solid and liquid vibrational modes that give rise to a significant overestimation of the ITCs. We analyze the dependence of the vibrational coupling with the mass of the Drude particle and propose a solution to the artificial enhancement of the ITC, preserving at the same time the polarization response of the solid. Based on our calculations, we estimate ITCs of 200 MW/(m2 K) for the water-gold interface. This magnitude is comparable to that reported recently for gold-water interfaces [279 ± 16 MW/(m2 K)] using atomic fluctuating charges to account for the polarization contribution.

PIC-DSMC simulation of nonequilibrium capacitively coupled plasma in low pressure

In recent years, the interaction of electrons with the electromagnetic field in plasma at low pressure has received significant attention because of its high application. In low-pressure plasma, electrons can move long distances without any collisions in physical dimensions of the problem. This causes nonlocal dynamics, which leads to strong time and space dependence on and anisotropy of the distribution function. In this paper, a hybrid Particle-in-Cell (PIC) method with Direct Monte Carlo Simulation (DSMC) was proposed to investigate electron interactions with the electrostatic field. A capacitively coupled plasma (CCP) reactor at low pressure (0.01–10Pa) was also investigated. The effect of electric field was studied on electrons and field distribution in the computational domain at different times. Also, the amplitude current was investigated in a complete radio frequency (RF) cycle. As a result, this work proposed tools to examine the discharge flow for accurate knowledge of CCP discharge for optimization of reactors and its related processes.

Investigating the wet-to-dry expansion of organic fluids for power generation

The successful and economic conversion of waste heat into electricity requires new, innovative, power cycles to be developed. The proposed wet-to-dry cycle, in which the working fluid transitions across the saturation dome during expansion, has been shown to offer significant thermodynamic benefits. However, the feasibility of achieving wet-to-dry expansion when non-equilibrium effects, which are expected during a high-speed two-phase expansion, are taken into account has not been previously established. This paper first introduces a simple method to assess the thermodynamic potential of a fluid for the wet-to-dry cycle, which confirms that the siloxanes MM and MDM are excellent contenders and under ideal conditions can achieve second law efficiencies approaching 90% whilst operating with heat-source temperatures around 200 ∘C. The second part of this paper presents a one-dimensional nozzle design tool that accounts for thermal and mechanical non-equilibrium effects, which has been verified against previous studies and non-equilibrium computational-fluid dynamic simulations of the two-phase expansion of the refrigerant R1233zd(E). The model is then applied to the wet-to-dry expansion of MM under operating conditions directly relevant for the wet-to-dry cycle. The results firstly indicate the importance of accounting for non-equilibrium effects when designing nozzles for wet-to-dry expansion and the importance of having a realistic model that accounts for the break-up of droplets during the expansion. More importantly, the results reveal that for eight of the twelve cases considered it is still possible to achieve the full vapourisation of the working fluid within the nozzle when non-equilibrium effects are considered. This confirms the potential of the wet-to-dry cycle to enhance the performance of waste-heat recovery systems, which, in turn, necessitates further investigation, including experimental investigation, to further explore the concept.

Effect of lattice distortion and nanovoids on the shock compression behavior of (Co-Cr-Cu-Fe-Ni) high entropy alloy

In this article, non-equilibrium molecular dynamics-based simulations were performed to study the effect of shock compression on the deformation governing mechanism of high entropy alloys (HEA). Quinary configuration of the alloy containing (Co-Cr-Cu-Fe-Ni) as primary elements were considered, and interaction between them was simulated with the help of embedded atom method potential. Hugoniot curves between P-Up and Us-Up were captured for HEA that agrees qualitatively and quantitatively with results reported using higher fidelity simulations and experimental techniques. Single-crystal HEA was subjected to shock compression and ultra-short pulse at piston velocities above and below the Hugoniot elastic limit. To capture the dynamics of the shock wave propagation in single-crystal HEA, spectra-temporal distribution of pressure and velocities were captured as a function of time from the onset of the shock wave. It was predicted from atomistic simulations that the insertion of voids in the path of shock front helps in dispersing the energy, as well as reducing the speed of shock propagation. Voids significantly affect the shock deformation governing mechanism in the crystal of HEA, and onset plastic deformation, even at piston velocities below the Hugoniot elastic limit. To capture the effect of lattice distortion in HEA, average atom configuration was also developed. It was predicted from the simulations that the effect of lattice distortion helps in blunting the shock front and diluting its speed of propagation. The lattice distortion effect is more dominant at lower simulation temperatures and lower piston impact velocities.

Gate- versus defect-induced voltage drop and negative differential resistance in vertical graphene heterostructures

To enable the computer-aided design of vertically stacked two-dimensional (2D) van der Waals (vdW) heterostructure devices, we here introduce a non-equilibrium first-principles simulation method based on the multi-space constrained-search density functional formalism. Applying it to graphene/few-layer hBN/graphene field-effect transistors, we show that the negative differential resistance (NDR) characteristics can be produced not only from the gating-induced mismatch between two graphene Dirac cones in energy-momentum space but from the bias-dependent energetic shift of defect levels. Specifically, for a carbon atom substituted for a nitrogen atom (CN) within inner hBN layers, the increase of bias voltage is found to induce a self-consistent electron filling of in-gap CN states, which in turn changes voltage drop profiles and produces symmetric NDR characteristics. With the CN placed on outer hBN layers, however, the pinning of CN states to nearby graphene significantly modifies device characteristics, demonstrating the critical impact of atomic details for 2D vdW devices.

Non-equilibrium free-energy calculation of phase-boundaries using LAMMPS

We present a guide to compute the phase-boundaries of classical systems using a dynamic Clausius–Clapeyron integration (dCCI) method within the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) code. The advantage of the dCCI method is because it provides coexistence curves spanning a wide range of thermodynamic states using relatively short single non-equilibrium simulations. We describe the state-of-the-art of non-equilibrium free-energy methods that allow us to compute the Gibbs free-energy in a wide interval of pressure and/or temperature. We present the dCCI method in details, discuss its implementation in the LAMMPS package and make available source code, scripts, as well as auxiliary files. As an illustrative example, we determine the phase diagram of silicon in a range of pressures covering from 0 to 15 GPa and temperatures as low as 400 K up to the liquid phase, in order to obtain the phase boundaries and triple point between diamond, liquid and β-Sn phases.

Hydrodynamics and transport in the long-range-interacting φ 4 chain

We present a simulation study of the one-dimensional φ 4 lattice theory with long-range interactions decaying as an inverse power r −(1+σ) of the intersite distance r, σ > 0. We consider the cases of single and double-well local potentials with both attractive and repulsive couplings. The double-well, attractive case displays a phase transition for 0 < σ ⩽ 1 analogous to the Ising model with long-range ferromagnetic interactions. A dynamical scaling analysis of both energy structure factors and excess energy correlations shows that the effective hydrodynamics is diffusive for σ > 1 and anomalous for 0 < σ < 1, where fluctuations propagate superdiffusively. We argue that this is accounted for by a fractional diffusion process and we compare the results with an effective model of energy transport based on Lévy flights. Remarkably, this result is fairly insensitive on the phase transition. Nonequilibrium simulations with an applied thermal gradient are in quantitative agreement with the above scenario.

A new model of solid-phase effective thermal conductivity in local thermal non-equilibrium simulation for packed beds of rough spheres in convective flow

This work proposes a new method to calculate the solid-phase effective conductivity in a two-equation local thermal non-equilibrium (LTNE) model for a packed sphere bed under convection. Considered parameters include the surface roughness, the slope of the surface asperity, the applied force, and the hardness of the sphere. The framework of this method is described and constructed both numerically and mathematically. First, structured unit cells in simple cubic and face-centered cubic arrangements are considered to represent mono-sized packed spheres of different porosities. The inter-sphere apparent contact region is found to be surrounded by a stagnant-fluid ring whose outer boundary divides the inner conductive region from the uncoupled outer convective region. Both the apparent contact region and the stagnant-fluid ring are included in the calculation of the solid-phase effective conductivity. Numerical simulations accounting for the inter-sphere contact resistance and the interior constriction/spreading resistance are conducted to evaluate the effective thermal conductivity over a unit cell with respect to various parameters. In addition, a semi-empirical mathematical equation is formulated with deviations from the numerical results within 3%. The present semi-empirical model for the prediction of the solid-phase effective conductivity associated with packed rough spheres is validated by the excellent agreement with experiments under a stagnant environment. The present method is expected to provide accurate evaluation of the solid-phase effective conductivity in a two-equation LTNE convective heat transfer model for packed beds of mono-sized spheres.

Electric Field Effects on Photoelectrochemical Water Splitting: Perspectives and Outlook

The grand challenges in renewable energy lie in our ability to comprehend efficient energy conversion systems, together with dealing with the problem of intermittency via scalable energy storage systems. Relatively little progress has been made on this at grid scale and two overriding challenges still need to be addressed: (i) limiting damage to the environment and (ii) the question of environmentally friendly energy conversion. The present review focuses on a novel route for producing hydrogen, the ultimate clean fuel, from the Sun, and renewable energy source. Hydrogen can be produced by light-driven photoelectrochemical (PEC) water splitting, but it is very inefficient; rather, we focus here on how electric fields can be applied to metal oxide/water systems in tailoring the interplay with their intrinsic electric fields, and in how this can alter and boost PEC activity, drawing both on experiment and non-equilibrium molecular simulation.

Interfacial characteristics of P91 steel - Inconel 740H bimetallic structure fabricated using wire-arc additive manufacturing

Although bimetallic structures can offer unique solutions to engineering problems with varying functionality, joining two dissimilar alloys using additive manufacturing involves challenges such as cracking and segregation. In this work, bimetallic structures of Inconel 740H superalloy and P91 steel are processed using wire-arc additive manufacturing (WAAM) for the first time. P91 steel is directly deposited over 740H with a cooling time of 20 min in between the two depositions. During microstructure characterization, a large gradient zone with coarse grains spanning for ∼2200 μm is observed. Moreover, the microhardness of the gradient zone is the least in comparison with the P91 and 740H deposits. No deleterious phase formation is found; however, intergranular cracks are observed along the gradient zone. In order to deduce the reason for cracking, non-equilibrium solidification simulations are performed for the mixed compositions of P91 and 740H in the gradient zone. The reasons for crack formation in the gradient zone are the sudden change in the volumetric coefficient of thermal expansion due to the formation of MC carbides as well as the development of local strains from the thermal residual stresses. Therefore, altering the deposition sequence and introducing gradient layers with mixed composition between the P91 and 740H deposits will be beneficial in achieving defect-free builds. Through the integration of experiments and simulation, this work gains valuable insights into the processability of dissimilar alloy manufacturing using the WAAM technique.

Vibrational-Specific Model of Simultaneous and Relaxation Under Postshock Conditions

The present paper discusses the development of an aerothermochemistry model that can be efficiently coupled with fluid dynamics simulations and retains the accuracy of the quantum-mechanical and molecular dynamic principles from which it is derived. The present model allows simulations of thermochemical nonequilibrium in nitrogen without relying on the existence of a vibrational temperature. A series of verification tests suggest that the vibrational-specific master equation model is sufficiently accurate and computationally efficient when applied to the modeling of dissociating nitrogen flows under adiabatic conditions. Toward this end, a kinetic dataset describing vibrational energy transfer and dissociation in and collisions is obtained on a high-fidelity potential energy surface, and curve fit coefficients are reported. Validation against shock-tube data indicates that the inclusion of electronically excited and ionic species is potentially required when computing and comparing relaxation parameters with the experimental data derived from the radiative signatures of nitrogen shock flows.

A Liquid State Perspective on Dynamics of Chromatin Compartments.

The interior of the eukaryotic cell nucleus has a crowded and heterogeneous environment packed with chromatin polymers, regulatory proteins, and RNA molecules. Chromatin polymer, assisted by epigenetic modifications, protein and RNA binders, forms multi-scale compartments which help regulate genes in response to cellular signals. Furthermore, chromatin compartments are dynamic and tend to evolve in size and composition in ways that are not fully understood. The latest super-resolution imaging experiments have revealed a much more dynamic and stochastic nature of chromatin compartments than was appreciated before. An emerging mechanism explaining chromatin compartmentalization dynamics is the phase separation of protein and nucleic acids into membraneless liquid condensates. Consequently, concepts and ideas from soft matter and polymer systems have been rapidly entering the lexicon of cell biology. In this respect, the role of computational models is crucial for establishing a rigorous and quantitative foundation for the new concepts and disentangling the complex interplay of forces that contribute to the emergent patterns of chromatin dynamics and organization. Several multi-scale models have emerged to address various aspects of chromatin dynamics, ranging from equilibrium polymer simulations, hybrid non-equilibrium simulations coupling protein binding and chromatin folding, and mesoscopic field-theoretic models. Here, we review these emerging theoretical paradigms and computational models with a particular focus on chromatin’s phase separation and liquid-like properties as a basis for nuclear organization and dynamics.

On phase stability of Mo-Nb-Ta-W refractory high entropy alloys

Refractory high entropy alloys (RHEAs) emerge as promising candidate materials for ultrahigh-temperature applications. Accurate phase stability is the prerequisite for design of high-performance RHEAs, but still missing in the literature due to the big challenge in experiments. In this paper, the reliable 3rd-generation Gibbs energy expressions for pure Mo, Nb, Ta and W were firstly evaluated by integrating the physical based Segmented Regression model with thermal vacancy description from 0 K to high temperatures. The thermodynamic database of the Mo-Nb-Ta-W quaternary system was then developed by combining the established 3rd-generation Gibbs energies with the phase equilibrium and thermodynamic data by using the CALPHAD (CALculation of PHAse Diagram) approach. The calculated phase equilibria, thermodynamic properties as well as the A2/B2 ordering transition behaviors show good agreement with those from experimental determination and theoretical calculation. The phase constitutes and elemental distributions in an equiatomic MoNbTaW as-cast alloy were experimentally investigated and compared with the non-equilibrium solidification simulations to further verify the database reliability. The high-throughput mapping of phase stability within the composition-temperature space in various Mo-Nb-Ta-W alloys was then constructed by applying thermodynamic calculations. The alloying effects on the formation of B2 phase were systematically analyzed. The Mo-Nb-Ta-W alloys have a wide temperature region with a single A2 phase, while the A2 + B2 phase regions exist at very low temperatures. It is highly anticipated that the present accurate 3rd-generation thermodynamic database provides an important basis for efficient design and development of novel Mo-Nb-Ta-W RHEAs.

Seeding the multi-dimensional nonequilibrium pulling for Hamiltonian variation: indirect nonequilibrium free energy simulations at QM levels.

The combination of free energy simulations in the alchemical and configurational spaces provides a feasible route to access the thermodynamic profiles under a computationally demanding target Hamiltonian. Normally, due to the significant differences between the computational cost of ab initio quantum mechanics (QM) calculations and those of semi-empirical quantum mechanics (SQM) and molecular mechanics (MM), this indirect method could be used to obtain the QM thermodynamics by combining the SQM or MM results and the SQM-to-QM or MM-to-QM corrections. In our previous work, a multi-dimensional nonequilibrium pulling framework for Hamiltonian variations was introduced based on bidirectional pulling and bidirectional reweighting. The method performs nonequilibrium free energy simulations in the configurational space to obtain the thermodynamic profile along the conformational change pathway under a selected computationally efficient Hamiltonian, and uses the nonequilibrium alchemical method to correct or perturb the thermodynamic profile to that under the target Hamiltonian. The BAR-based method is designed to achieve the best generality and transferability and thus leads to modest (∼20 fold) speedup. In this work, we explore the possibility of further accelerating the nonequilibrium free energy simulation by employing unidirectional pulling and using the selection criterion to obtain the initial configurations used to initiate nonequilibrium trajectories following the idea of adaptive steered molecular dynamics (ASMD). A single initial condition is used to seed the whole multi-dimensional nonequilibrium free energy simulation and the sampling is performed fully in the nonequilibrium ensemble. Introducing very short ps-length equilibrium sampling to grab more initial seeds could also be helpful. The ASMD scheme estimates the free energy difference with the unidirectional exponential average (EXP), but it does not follow exactly the requirements of the EXP estimator. Another deficiency of the seeding simulation is the inherently sequential or serial pulling due to the inter-segment dependency, which triggers some problems in the parallelizability of the simulation. Numerical tests are performed to grasp some insights and guidelines for using this selection-criterion-based ASMD scheme. The presented selection-criterion-based multi-dimensional ASMD scheme follows the same perturbation network of the BAR-based method, and thus could be used in various Hamiltonian-variation cases.

All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations.

Protein aggregates are associated with more than 40 serious human diseases. To understand the formation mechanism of protein aggregates at atomic level, all-atom molecular dynamics (MD) simulation is a powerful computational tool. In this chapter, we review the all-atom MD simulation methods that are useful for study on the protein aggregation. We first explain conventional MD simulation methods in physical statistical ensembles, such as the canonical and isothermal-isobaric ensembles. We then describe the generalized-ensemble algorithms such as replica-exchange and replica-permutation MD methods. These methods can overcome a difficulty, in which simulations tend to get trapped in local-minimum free-energy states. Finally we explain the nonequilibrium MD method. Some simulation results based on these methods are also presented.

Thermal non-equilibrium simulation of diffuse and constricted anode attachments of a high intensity transferred arc

The arc attachment modes on anode of a high intensity argon arc with water-cooled constrictor are numerically investigated by a two-temperature model. An inelastic electron energy loss factor, representing the energy loss due to non-equilibrium chemical kinetic processes, is introduced to the electron energy equation. Two different attachment modes, i.e., diffuse and constricted anode attachments, are obtained based on the experimental conditions. Results for both anode attachment modes indicate that the temperature discrepancy between electrons and heavy particles is very pronounced in the arc fringes and in the regions close to the anode. By comparing the axial and radial Lorentz forces between the diffuse and constricted anode attachments, it is found that the larger axial and radial Lorentz forces in a constricted anode attachment are the main cause for the formation and maintenance of anode jet. The effects of inelastic electron energy loss on different anode attachment modes are discussed and the results indicate that it is very important to consider the chemical non-equilibrium processes in an appropriate way for predicting arc attachment modes on anode reasonably.

Redox Potentials of Disulfide Bonds in LOXL2 Studied by Nonequilibrium Alchemical Simulation.

Lysyl oxidase-like 2 (LOXL2) is a metalloenzyme that catalyzes the oxidative deamination ε-amino group of lysine. It is found that LOXL2 is a promotor for the metastasis and invasion of cancer cells. Disulfide bonds are important components in LOXL2, and they play a stabilizing role for protein structure or a functional role for regulating protein bioactivity. The redox potential of disulfide bond is one important property to determine the functional role of disulfide bond. In this study, we have calculated the reduction potential of all the disulfide bonds in LOXL2 by non-equilibrium alchemical simulations. Our results show that seven of seventeen disulfide bonds have high redox potentials between −182 and −298 mV and could have a functional role, viz., Cys573–Cys625, Cys579–Cys695, Cys657–Cys673, and Cys663–Cys685 in the catalytic domain, Cys351–Cys414, Cys464–Cys530, and Cys477–Cys543 in the scavenger receptor cysteine-rich (SRCR) domains. The disulfide bond of Cys351–Cys414 is predicted to play an allosteric function role, which could affect the metastasis and invasion of cancer cells. Other functional bonds have a catalytic role related to enzyme activity. The rest of disulfide bonds are predicted to play a structural role. Our study provides an important insight for the classification of disulfide bonds in LOXL2 and can be utilized for the drug design that targets the cysteine residues in LOXL2.

Nonequilibrium Vibrational, Rotational, and Translational Thermometry via Megahertz Laser Absorption of CO

A mid-infrared laser absorption strategy for simultaneously measuring translational, rotational, and vibrational temperatures of carbon monoxide (CO) at high speeds was developed for application to high-temperature nonequilibrium environments relevant to Mars atmosphere entry. Rapid-tuning scanned wavelength techniques were used to spectrally resolve the R(0,66), P(0,31), P(2,20), and P(3,14) lines of the CO fundamental vibrational bands at a rate of 1 MHz to infer multiple temperatures of CO behind incident and reflected shock waves in a shock tube. A distributed feedback quantum cascade laser was used to probe the P-branch transitions near and an external cavity quantum cascade laser was used to probe the R-branch transition near , both using bias-tee circuitry. The sensing method is shown to resolve each targeted transition with temporal and spectral resolution sufficient for quantitative multi-temperature measurements over a wide range of temperatures and pressures (2100–5500 K, 0.03–1.02 atm), including behind incident shock waves traveling up to 3.3 km/s. Measured temperature results were compared to equilibrium and nonequilibrium simulations.

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.