Thermal Rectification in Graphene-Boron Nitride Nanotube Hybrid Structures: An Independent Control Mechanism for Forward and Backward Heat Flux.

The weak van der Waals interactions in the out-of-plane direction result in markedly low thermal conductivity in one-dimensional (1D) and two-dimensional (2D) materials, which substantially restricts their applications. Developing three-dimensional (3D) columnar hybrid structures, featuring high thermal conductivity both within and beyond the plane, effectively addresses this challenge. This study investigated a 3D hybrid structure composed of graphene and boron nitride nanotubes (GR-BNNTs) using non-equilibrium molecular dynamics simulations. This approach allowed the examination of the formation mechanisms and key factors influencing thermal rectification (TR) in these materials. Our findings reveal a novel mechanism for independently regulating forward and backward heat fluxes in GR-BNNTs. By manipulating the thermal properties of the BNNTs and the graphene layer, the TR ratio can be controlled flexibly. Additionally, we identify specific strategies for independently adjusting the heat flux, such as altering the intercolumn distance of BNNTs, which impacts the backward flux merely, while applying strain to affect the forward flux merely. This research introduces a novel concept of independent regulation of forward and backward heat fluxes, providing significant insights into phonon thermal transport in 3D hybrid structures.

Phonon transport in vacancy induced defective stanene/hBN van der Waals heterostructure.

In this study, Non-Equilibrium Molecular Dynamics (NEMD) simulation is employed to investigate the phonon thermal conductivity (PTC) of Sn/hBN van der Waals heterostructures with different vacancy-induced defects. We deliberately introduce three types of vacancies in Sn/hBN bilayer point vacancies, bivacancies, and edge vacancies at various concentrations ranging from 0.25% to 2%, to examine their effects on PTC across temperatures from 100 K to 600 K. The key findings of our work are (i) PTC declines monotonically with increasing vacancy concentration for all types of vacancies, with a maximum reduction of ∼62% observed at room temperature compared to its pristine form. (ii) The position of defects has an impact on PTC, with a larger decrease observed when defects are present in the hBN layer and a smaller decrease when defects are in the Sn layer. (iii) The type of vacancy also influences PTC, with point vacancies causing the most substantial reduction, followed by bivacancies, and edge vacancies having the least effect. A 2% defect concentration results in a ∼62% decrease in PTC for point vacancies, ∼51% for bivacancies, and ∼32% for edge vacancies. (iv) Finally, our results indicate that for a given defect concentration, PTC decreases as temperature increases. The impact of temperature on thermal conductivity is less pronounced compared to the effect of vacancies for the defective Sn/hBN bilayer. The presence of vacancies and elevated temperatures enhance phonon-defect and phonon-phonon scattering, leading to changes in the phonon density of states (PDOS) profile and the distribution of phonons across different frequencies of Sn/hBN bilayer, thus affecting its thermal conductivity. This work offers new insights into the thermal behavior of vacancy-filled Sn/hBN heterostructures, suggesting potential pathways for modulating thermal conductivity in bilayer van der Waals heterostructures for applications in thermoelectric, optoelectronics, and nanoelectronics in future.

A molecular dynamics simulation study of thermal transport in hydrazinium cyclo-pentazolate.

Cyclo-pentazolate salts (CPSs) as a new type of high-energy-density materials (HEDMs) with high nitrogen content have attracted considerable research attention. In contrast to the extensive studies on their energy properties, the thermal transport process in CPSs has been less studied which relates closely to the thermal safety of this material. Concerning the hydrazinium cyclo-pentazolate (HCP), we conduct a computational study to estimate the thermal conductivity of HCP by means of the non-equilibrium molecular dynamics (NEMD) simulation. To achieve that, we have customized interaction parameters based on the default OPLS force field for the HCP, as benchmarked by its crystal structure. Our simulations have revealed surprisingly anisotropic thermal conductivity for the HCP, while the thermal conductivity becomes highest roughly in the direction perpendicular tocyclo-N5-with its value notably higher than common high explosives. By modulating the interaction parameters within the HCP molecule, we have further captured a dominant role of the interaction betweencyclo-N5-in regulating the thermal conductivity of the HCP. The attractive Lennard-Jones (LJ) potential may restrict the relative motion betweencyclo-N5-, which forms a long-range order thus enhances thermal transport in the direction perpendicular tocyclo-N5-. Our simulations result on the effect of (cyclo-N5-)-(cyclo-N5-) interaction provide insights to engineer thermal transport in CPSs at the molecular level.

Comparative Study of the Orientation and Order Effects on the Thermoelectric Performance of 2D and 3D Perovskites.

Calcium titanium oxide has emerged as a highly promising material for optoelectronic devices, with recent studies suggesting its potential for favorable thermoelectric properties. However, current experimental observations indicate a low thermoelectric performance, with a significant gap between these observations and theoretical predictions. Therefore, this study employs a combined approach of experiments and simulations to thoroughly investigate the impact of structural and directional differences on the thermoelectric properties of two-dimensional (2D) and three-dimensional (3D) metal halide perovskites. Two-dimensional (2D) and three-dimensional (3D) metal halide perovskites constitute the focus of examination in this study, where an in-depth exploration of their thermoelectric properties is conducted via a comprehensive methodology incorporating simulations and experimental analyses. The non-equilibrium molecular dynamics simulation (NEMD) was utilized to calculate the thermal conductivity of the perovskite material. Thermal conductivities along both in-plane and out-plane directions of 2D perovskite were computed. The NEMD simulation results show that the thermal conductivity of the 3D perovskite is approximately 0.443 W/mK, while the thermal conductivities of the parallel and vertical oriented 2D perovskites increase with n and range from 0.158 W/mK to 0.215 W/mK and 0.289 W/mK to 0.309 W/mK, respectively. Hence, the thermal conductivity of the 2D perovskites is noticeably lower than the 3D ones. Furthermore, the parallel oriented 2D perovskites exhibit more effective blocking of heat transfer behavior than the perpendicular oriented ones. The experimental results reveal that the Seebeck coefficient of the 2D perovskites reaches 3.79 × 102 µV/K. However, the electrical conductivity of the 2D perovskites is only 4.55 × 10-5 S/cm, which is one order of magnitude lower than that of the 3D perovskites. Consequently, the calculated thermoelectric figure of merit for the 2D perovskites is approximately 1.41 × 10-7, slightly lower than that of the 3D perovskites.

A Molecular Dynamics Simulation Study of In- and Cross-Plane Thermal Conductivity of Bilayer Graphene.

Efficient thermal management of modern electronics requires the use of thin films with highly anisotropic thermal conductivity. Such films enable the effective dissipation of excess heat along one direction while simultaneously providing thermal insulation along the perpendicular direction. This study employs non-equilibrium molecular dynamics to investigate the thermal conductivity of bilayer graphene (BLG) sheets, examining both in-plane and cross-plane thermal conductivities. The in-plane thermal conductivity of 10 nm × 10 nm BLG with zigzag and armchair edges at room temperature is found to be around 204 W/m·K and 124 W/m·K, respectively. The in-plane thermal conductivity of BLG increases with sheet length. BLG with zigzag edges consistently exhibits 30-40% higher thermal conductivity than BLG with armchair edges. In addition, increasing temperature from 300 K to 600 K decreases the in-plane thermal conductivity of a 10 nm × 10 nm zigzag BLG by about 34%. Similarly, the application of a 12.5% tensile strain induces a 51% reduction in its thermal conductivity compared to the strain-free values. Armchair configurations exhibit similar responses to variations in temperature and strain, but with less sensitivity. Furthermore, the cross-plane thermal conductivity of BLG at 300 K is estimated to be 0.05 W/m·K, significantly lower than the in-plane results. The cross-plane thermal conductance of BLG decreases with increasing temperatures, specifically, at 600 K, its value is almost 16% of that observed at 300 K.

The thermodynamic-pathway-determined microstructure evolution of copper under shock compression.

Shock-induced structural transformations in copper exhibit notable directional dependence and anisotropy, but the mechanisms that govern the responses of materials with different orientations are not yet well understood. In this study, we employ large-scale non-equilibrium molecular dynamics simulations to investigate the propagation of a shock wave through monocrystal copper and analyse the structural transformation dynamics in detail. Our results indicate that anisotropic structural evolution is determined by the thermodynamic pathway. A shock along the [Formula: see text] orientation causes a rapid and instantaneous temperature spike, resulting in a solid-solid phase transition. Conversely, a liquid metastable state is observed along the [Formula: see text] orientation due to thermodynamic supercooling. Notably, melting still occurs during the [Formula: see text]-oriented shock, even if it falls below the supercooling line in the thermodynamic pathway. These results highlight the importance of considering anisotropy, the thermodynamic pathway and solid-state disordering when interpreting phase transitions induced by shock. This article is part of the theme issue 'Dynamic and transient processes in warm dense matter'.

Molecular insights into the effects of focused ultrasound mechanotherapy on lipid bilayers: Unlocking the keys to design effective treatments.

Administration of focused ultrasounds (US) represents an attractive complement to classical therapies for a wide range of maladies, from cancer to neurological pathologies, as they are non-invasive, easily targeted, their dosage is easy to control, and they involve low risks. Different mechanisms have been proposed for their activity but the direct effect of their interaction with cell membranes is not well understood at the molecular level. This is in part due to the difficulty of designing experiments able to probe the required spatio-temporal resolutions. Here we use Molecular Dynamics (MD) simulations at two resolution levels and machine learning (ML) classification tools to shed light on the effects that focused US mechanotherapy methods have over a range of lipid bilayers. Our results indicate that the dynamic-structural response of the membrane models to the mechanical perturbations caused by the sound waves strongly depends on the lipid composition. The analyses performed on the MD trajectories contribute to a better understanding of the behavior of lipid membranes, and to open up a path for the rational design of new therapies for the long list of diseases characterized by specific lipid profiles of pathological membrane cells.

Prediction of ionic conductivity from adiabatic heating in non-equilibrium molecular dynamics on various test systems.

CONTEXT: The evaluation of ionic conductivity through atomistic modeling typically involves calculating diffusion coefficients, which often necessitates simulations spanning several hundreds of nanoseconds. This study introduces a less computationally demanding approach based on non-equilibrium molecular dynamics applicable to a wide range of systems. METHOD: Ionic conductivity is determined by evaluating the Joule heating effect recorded during non-equilibrium molecular dynamics (NEMD) simulations. These simulations which involve applying a uniform electric field using classical force fields in LAMMPS are conducted within the MedeA software environment. The conductivity value for a specific temperature can thus be obtained from a single simulation together with an estimation of the associated uncertainty. Guidelines for selecting NEMD parameters such as electric field intensity and initial temperature are proposed to satisfy linear irreversible transport. RESULTS: The protocol presented in this study is applied to four different types of systems, namely, (i) molten NaCl, (ii) NaCl and LiCl aqueous solutions, (iii) solution of ionic liquid with two solvents, and (iv) NaX zeolites in the anhydrous and hydrated states. The main advantages of the proposed protocol are simplicity of implementation (eliminating the need to store individual ion trajectories), reliability (low electric field, linear response, no perturbation of the equations of motion by a thermostat), and a wide range of applications. The estimated contribution of field-induced drift motion of ions to kinetic energy appears very low, justifying the use of standard kinetic energy in the method. For each system, the reported influence of temperature, ion concentration, solvent nature, or hydration is correctly predicted.

Solvent-Solute Interaction Effect on Permeation Flux through Forward Osmosis Membranes Investigated by Non-Equilibrium Molecular Dynamics.

The relationship between the solvent-solute interaction and permeation properties is fundamental in the development of the forward osmosis (FO) membrane. In this study, we report on the quantitative reproduction of the permeation flux, which has different solvent-solute interactions, through the modeled FO membrane by non-equilibrium molecular dynamics (NEMD). The interaction effect was investigated by changing the interatomic interaction between the solute and the solvent. The calculated permeation through the semi-permeable modeled FO membrane, in which the interaction between solvent and solution is equal to that between solutions, was consistent with the theoretical curve derived from the combination of the permeation flux and Van't Hoff equations. These results validate the NEMD for the evaluation of permeation in FO. On the other hand, the permeation is much derived from the theoretical values when the interaction between the solvent and solute atoms is relatively large. However, the simulated permeation was consistent with the theoretical curve, correcting the solution concentration by the coordination number of the solvent atoms to the solute atoms. Our results imply that permeation flux through the FO membrane is significantly changed by the interaction between the solute and the solvent and can be theoretically predicted by calculating the coordination number of the solvent to the solute, which can be readily estimated by equilibrium molecular dynamics simulation.

Prediction of Thermal Conductivities of Rubbers by MD Simulations-New Insights.

In this article, two main approaches to the prediction of thermal conductivities by molecular dynamics (MD) simulations are discussed, namely non-equilibrium molecular dynamics simulations (NEMD) and the application of the Green-Kubo formula, i.e., EMD. NEMD methods are more affected by size effects than EMD methods. The thermal conductivities of silicone rubbers in special were found as a function of the degree of crosslinking. Moreover, the thermal conductivities of thermoplastic polyurethane as function of the mass fraction of soft segments were obtained by those MD simulations. All results are in good agreement with data from the experimental literature. After the analysis of normalized heat flux autocorrelation functions, it has been revealed that heat in the polymers is mainly transferred by low-frequency phonons. Simulation details as well as advantages and disadvantages of the single methods are discussed in the article.

Putting Forward NUS-8-CO2H/PIM-1 as a Mixed Matrix Membrane for CO2 Capture.

Mixed matrix membranes (MMMs) composed of NUS-8 metal-organic framework (MOF) nanosheets dispersed into a polymer of intrinsic microporosity 1 (PIM-1) polymer matrix are known to be promising candidates for CO2/N2 separation because of a solubility-driven separation mechanism. In this work, we predict that a chemical functionalization of the organic linker of NUS-8 by a CO2-philic function confers an even better separation performance to the resulting MMM. Our simulations revealed that the NUS-8-CO2H/PIM-1 composite exhibits a 3-fold increase in CO2/N2 selectivity versus the NUS-8/PIM-1 analogue while achieving a high CO2 permeability (6700 barrer). We demonstrated that this improved level of performance is due to an increase both in the total MOF/polymer interfacial pore volume and in the CO2-affinity due to the chemical functionalization. These results suggest that an appropriate choice of chemical functionalization of a MOF is a promising strategy to improve gas separation performances for MMM composites that exhibit a solubility-driven separation mechanism.

Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules.

Non-equilibrium molecular dynamics (NEMD) simulation has been recognized as a powerful tool for examining biomolecules and provides fruitful insights into not only non-equilibrium but also equilibrium processes. We review recent advances in NEMD simulation and relevant, fundamental results of non-equilibrium statistical mechanics. We first introduce Crooks fluctuation theorem and Jarzynski equality that relate free energy difference to work done on a physical system during a non-equilibrium process. The theorems are beneficial for the analysis of NEMD trajectories. We then describe rate theory, a framework to calculate molecular kinetics from a non-equilibrium process; this theoretical framework enables us to calculate a reaction time-mean-first passage time-from NEMD trajectories. We, in turn, present recent NEMD techniques that apply an external force to a system to enhance molecular dissociation and introduce their application to biomolecules. Lastly, we show the current status of an appropriate selection of reaction coordinates for NEMD simulation.

Molecular modeling on the pressure-driven methane desorption in illite nanoslits.

Understanding to the pressure-driven desorption of methane in shale formations is crucial for the establishment of predictive models used in shale gas development. Based on the grand canonical Monte-Carlo simulations of methane adsorption in illite slits of 1-5-nm wide, the pressure-driven desorption processes of methane in the nanoslits are studied with non-equilibrium molecular dynamics simulations. External forces are applied to the methane molecules to mimic a pressure drop that releases the adsorbed molecules and pushes them flowing directionally. Effect of pressure drop and slit aperture on the interchange between adsorbed and free phases of methane is investigated by a statistic analysis on the velocity and density distributions of methane molecules in the nanoslits under various conditions. A minimum pressure drop that initiates the methane desorption in the illite slit exists and varies with slit aperture. Our simulations reveal the microscopic mechanism of pressure-driven methane desorption, which would be useful for subsequent studies on the prediction of mineable yields for shale formations. Under pressure drop, adsorbed methane molecules are desorbed to free phase and then transported to wellbore. The criterion of pressure drop for desorption increases with decreasing slit aperture.

Investigation of Interface Thermal Resistance between Polymer and Mold Insert in Micro-Injection Molding by Non-Equilibrium Molecular Dynamics.

Micro-injection molding has attracted a wide range of research interests to fabricate polymer products with nanostructures for its advantages of cheap and fast production. The heat transfer between the polymer and the mold insert is important to the performance of products. In this study, the interface thermal resistance (ITR) between the polypropylene (PP) layer and the nickel (Ni) mold insert layer in micro-injection molding was studied by using the method of non-equilibrium molecular dynamics (NEMD) simulation. The relationships among the ITR, the temperature, the packing pressure, the interface morphology, and the interface interaction were investigated. The simulation results showed that the ITR decreased obviously with the increase of the temperature, the packing pressure and the interface interaction. Both rectangle and triangle interface morphologies could enhance the heat transfer compared with the smooth interface. Moreover, the ITR of triangle interface was higher than that of rectangle interface. Based on the analysis of phonon density of states (DOS) for PP-Ni system, it was found that the mismatch between the phonon DOS of the PP atoms and Ni atoms was the main cause of the interface resistance. The frequency distribution of phonon DOS also affected the interface resistance.

Viscosity prediction of Pongamia pinnata (Karanja) oil by molecular dynamics simulation using GAFF and OPLS force field.

The increasing concern on the harmful effects caused by mineral oil-based lubricants towards the environment has given impetus to the evolution of green-lubricants. Vegetable oils are highly biodegradable, renewable, and possesses good lubricating property. In the present study Pongamia pinnata, non-edible vegetable oil, also known as Karanja Oil (KO) was used as the base oil for a lubricant. The preliminary properties, such as fatty acid profile and viscosity, which has a vital role in governing the performance of lubricants were evaluated experimentally as per international standards. The shear viscosity of KO which constitutes 8 major fatty acids were predicted using non-equilibrium molecular dynamics (NEMD) and periodic perturbation (PP) method using Optimised Potentials for Liquid Simulations (OPLS) and Generalized Amber Force Field (GAFF). The shear viscosities were evaluated at temperatures ranging from 313K to 373 K and pressure P = 0.1 MPa. The experimental and simulation data of KO shear viscosity are in line with each other using OPLS. The kinematic viscosities were calculated using the shear viscosities and densities obtained from simulation. The variation between experimental and simulation data is less while using OPLS, while GAFF force fields resulted in higher deviations.

Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations.

Checkpoint kinase 1 (CHK1) is a serine/threonine-protein kinase that is involved in cell cycle regulation in eukaryotes. Inhibition of CHK1 is thus considered as a promising approach in cancer therapy. In this study, the fast pulling of ligand (FPL) process was applied to predict the relative binding affinities of CHK1 inhibitors using non-equilibrium molecular dynamics (MD) simulations. The work of external harmonic forces to pull the ligand out of the binding cavity strongly correlated with the experimental binding affinity of CHK1 inhibitors with the correlation coefficient of R = -0.88 and an overall root mean square error (RMSE) of 0.99 kcal/mol. The data indicate that the FPL method is highly accurate in predicting the relative binding free energies of CHK1 inhibitors with an affordable CPU time. A new set of molecules were designed based on the molecular modeling of interactions between the known inhibitor and CHK1 as inhibitory candidates. Molecular docking and FPL results exhibited that the binding affinities of developed ligands were similar to the known inhibitor in interaction with the catalytic site of CHK1, producing very potential CHK1 inhibitors of that the inhibitory activities should be further evaluated in vitro.

A non-equilibrium approach to allosteric communication.

While the theory of protein folding is well developed, including concepts such as rugged energy landscape, folding funnel, etc., the same degree of understanding has not been reached for the description of the dynamics of allosteric transitions in proteins. This is not only due to the small size of the structural change upon ligand binding to an allosteric site, but also due to challenges in designing experiments that directly observe such an allosteric transition. On the basis of recent pump-probe-type experiments (Buchli et al. 2013 Proc. Natl Acad. Sci. USA110, 11 725-11 730. (doi:10.1073/pnas.1306323110)) and non-equilibrium molecular dynamics simulations (Buchenberg et al. 2017 Proc. Natl Acad. Sci. USA114, E6804-E6811. (doi:10.1073/pnas.1707694114)) studying an photoswitchable PDZ2 domain as model for an allosteric transition, we outline in this perspective how such a description of allosteric communication might look. That is, calculating the dynamical content of both experiment and simulation (which agree remarkably well with each other), we find that allosteric communication shares some properties with downhill folding, except that it is an 'order-order' transition. Discussing the multiscale and hierarchical features of the dynamics, the validity of linear response theory as well as the meaning of 'allosteric pathways', we conclude that non-equilibrium experiments and simulations are a promising way to study dynamical aspects of allostery.This article is part of a discussion meeting issue 'Allostery and molecular machines'.

Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work.

The fast pulling ligand (FPL) out of binding cavity using non-equilibrium molecular dynamics (MD) simulations was demonstrated to be a rapid, accurate and low CPU demand method for the determination of the relative binding affinities of a large number of HIV-1 protease (PR) inhibitors. In this approach, the ligand is pulled out of the binding cavity of the protein using external harmonic forces, and the work of pulling force corresponds to the relative binding affinity of HIV-1 PR inhibitor. The correlation coefficient between the pulling work and the experimental binding free energy of R=-0.95 shows that FPL results are in good agreement with experiment. It is thus easier to rank the binding affinities of HIV-1 PR inhibitors, that have similar binding affinities because the mean error bar of pulling work amounts to δW=7%. The nature of binding is discovered using the FPL approach. © 2016 Wiley Periodicals, Inc.