Penghua Ying

Penghua Ying

Postdoc in School of Chemistry, Tel Aviv University.

Publications

X. Wu, W. Zhou, H. Dong, P. Ying, Y. Wang, B. Song, Z. Fan, S. Xiong, Correcting force error-induced underestimation of lattice thermal conductivity in machine learning molecular dynamics. The Journal of Chemical Physics 161, 014103 (2024).

Published in The Journal of Chemical Physics, 2024

We reveal that the fitting errors in the machine-learned forces against the reference ones are responsible for the underestimated LTC as they constitute external perturbations to the interatomic forces. Since the force errors of a NEP model and the random forces in the Langevin thermostat both follow a Gaussian distribution, we propose an approach to correcting the LTC by intentionally introducing different levels of force noises via the Langevin thermostat and then extrapolating to the limit of zero force error.

H. Dong, Y. Shi, P. Ying, K. Xu, T. Liang, Y. Wang, Z. Zeng, X. Wu, W. Zhou, S. Xiong, S. Chen, Z. Fan, Molecular dynamics simulations of heat transport using machine-learned potentials: A mini-review and tutorial on GPUMD with neuroevolution potentials. Journal of Applied Physics 135, 161101 (2024).

Published in Journal of Applied Physics, 2024

In this mini-review and tutorial, we delve into the fundamentals of heat transport, explore pertinent MD simulation methods, and survey the applications of MLPs in MD simulations of heat transport. Furthermore, we provide a step-by-step tutorial on developing MLPs for highly efficient and predictive heat transport simulations, utilizing the neuroevolution potentials as implemented in the GPUMD package.

X. Wang, J. Yang, P. Ying, Z. Fan, J. Zhang, H. Sun, Dissimilar thermal transport properties in κ-Ga2O3 and β-Ga2O3 revealed by homogeneous nonequilibrium molecular dynamics simulations using machine-learned potentials. Journal of Applied Physics 135, 065104 (2024).

Published in Journal of Applied Physics, 2024

In this work, we develop machine-learned neuroevolution potentials (NEPs) for single-crystalline $\beta$-Ga$_2$O$_3$ and $\kappa$-Ga$_2$O$_3$, and demonstrate their accuracy in modeling thermal transport properties. Combining NEP-driven homogeneous non-equilibrium molecular dynamics (HNEMD) simulations with tensor analysis, we determine the spatial distributions of lattice thermal conductivities (LTCs) for two Ga$_2$O$_3$ crystals, showing dissimilar thermal behaviors.

B. Wang, P. Ying, J. Zhang, The thermoelastic properties of monolayer covalent organic frameworks studied by machine-learning molecular dynamics. Nanoscale 16, 237-248 (2023).

Published in Nanoscale, 2023

With the aid of the obtained NEP, molecular dynamics (MD) simulations together with a strain-fluctuation method were employed to evaluate the elastic constants of the considered 2D COFs at different temperatures. The elastic constants of COF-1 and COF-5 monolayers were found to decrease with an increase in the temperature, though they were almost isotropic irrespective of the temperature. The thermally induced softening of 2D COFs below a critical temperature was observed, which is mainly attributed to their inherent ripple configurations at finite temperatures, while above the critical temperature, the damping effect of anharmonic vibrations became the dominant factor. Based on the proposed mechanisms, analytical models were developed for capturing the temperature dependence of elastic constants, which were found to agree with the MD simulation results well.

T. Liang, P. Ying, K. Xu, Z. Ye, C. Ling, Z. Fan, J. Xu, Mechanisms of temperature-dependent thermal transport in amorphous silica from machine-learning molecular dynamics. Physical Review B 108, 184203 (2023).

Published in Physical Review B, 2023

Using the homogeneous nonequilibrium MD method and a proper quantum-statistical correction to the classical MD results, quantitative agreement with experiments is achieved for the thermal conductivities of bulk and 190-nm-thick a-SiO2 films over a wide range of temperatures.

X. Chen, B. Wang, P. Ying, J. Zhang, Indentation Depth-Dependent Hardness of Metal-Organic Framework Crystals: The Effect of Local Amorphization Induced by Indentation. ChemPhysChem 25, e202300647 (2024).

Published in ChemPhysChem, 2023

In order to explain the effect of the indentation depth on the hardness of MOFs, we conducted nanoindentation simulations on HKUST-1 by using reactive molecular dynamics simulations. Our simulations reveal that the HKUST-1 material near the indenter can transform from the parent crystalline phase to a new amorphous phase due to the high pressure generated, while its counterpart far from the indenter remains in the crystalline phase.

P. Ying, T. Liang, K. Xu, J. Zhang, J. Xu, Z. Zhong, Z. Fan, Sub-Micrometer Phonon Mean Free Paths in Metal-Organic Frameworks Revealed by Machine Learning Molecular Dynamics Simulations. ACS Appl Mater Interfaces 15, 36412-36422 (2023).

Published in ACS Applied Materials & Interfaces, 2023

We develop a set of accurate yet highly efficient machine-learned potentials for three typical MOFs and perform extensive MD simulations to study thermal transport in the three MOFs. We found the phonon mean free paths (MFPs) of MOFs can reach the sub-micrometer scale in the low-frequency region. The sub-micrometer phonon MFPs are also found to be correlated with a moderate temperature dependence of thermal conductivity between those in typical crystalline and amorphous materials.

J. Li, P. Ying, T. Liang, Y. Du, J. Zhou, J. Zhang, Mechanical and thermal properties of graphyne-coated carbon nanotubes: a molecular dynamics simulation on one-dimensional all-carbon van der Waals heterostructures. Phys Chem Chem Phys 25, 8651-8663 (2023).

Published in Physical Chemistry Chemical Physics, 2023

The mechanical and thermal properties of a hybrid nanotube consisting of a coaxial carbon nanotube (CNT) inside a graphyne nanotube (GNT), i.e., CNT@GNT, are investigated in this paper by using molecular dynamics simulations.

H. Dong, C. Cao, P. Ying, Z. Fan, P. Qian, Y. Su, Anisotropic and high thermal conductivity in monolayer quasi-hexagonal fullerene: A comparative study against bulk phase fullerene. International Journal of Heat and Mass Transfer 206, 123943 (2023).

Published in International Journal of Heat and Mass Transfer, 2023

Recently a novel two-dimensional (2D) C$_{60}$ based crystal called quasi-hexagonal-phase fullerene (QHPF) has been fabricated and demonstrated to be a promising candidate for 2D electronic devices [Hou et al. Nature 606, 507–510 (2022)]. We construct an accurate and transferable machine-learned potential to study heat transport and related properties of this material, with a comparison to the face-centered-cubic bulk-phase fullerene (BPF).

B. Wang, P. Ying, J. Zhang, Effects of Missing Linker Defects on the Elastic Properties and Mechanical Stability of the Metal–Organic Framework HKUST-1. The Journal of Physical Chemistry C 127, 2533-2543 (2023).

Published in The Journal of Physical Chemistry C, 2023

The defects can naturally exist or be artificially designed in metal–organic frameworks (MOFs), which could significantly affect their mechanical properties. In this paper, the elastic properties of HKUST-1 with randomly distributed missing linker defects are investigated by reactive molecular dynamics simulations together with the strain-fluctuation method.

P. Ying, H. Dong, T. Liang, Z. Fan, Z. Zhong, J. Zhang, Atomistic insights into the mechanical anisotropy and fragility of monolayer fullerene networks using quantum mechanical calculations and machine-learning molecular dynamics simulations. Extreme Mechanics Letters 58, 101929 (2023).

Published in Extreme Mechanics Letters, 2022

In this work, we comprehensively study the mechanical properties of the newly synthesized monolayer quasi-hexagonal-phase fullerene (qHPF) membrane [Hou et al., 2022] under uniaxial tension by using quantum mechanical density-functional-theory (DFT) calculations and molecular dynamics (MD) simulations with a machine-learned neuroevolution potential (NEP).

P. Ying, T. Liang, K. Xu, J. Xu, Z. Fan, T. Ala-Nissila, Z. Zhong, Variable thermal transport in black, blue, and violet phosphorene from extensive atomistic simulations with a neuroevolution potential. International Journal of Heat and Mass Transfer 202, 123681 (2023).

Published in International Journal of Heat and Mass Transfer, 2022

Phosphorus has diverse chemical bonds, and even in its two-dimensional form, there are three stable allotropes: black phosphorene (Black-P), blue phosphorene (Blue-P), and violet phosphorene (Violet-P). Due to the complexity of these structures, no efficient and accurate classical interatomic potential has been developed for them. In this paper, we develop an efficient machine-learned neuroevolution potential model for these allotropes and apply it to study thermal transport in them via extensive molecular dynamics (MD) simulations.

X. Wu, P. Ying, C. Li, Q. Han, Dual effects of hetero-interfaces on phonon thermal transport across graphene/C3N lateral superlattices. International Journal of Heat and Mass Transfer 201, 123643 (2023).

Published in International Journal of Heat and Mass Transfer, 2022

Two-dimensional (2D) lateral superlattices, a typical artificial nano-phononic crystal, have stimulated widespread interests and potential application prospects in terms of their physically interesting features. Herein, we have found wave-particle crossover of phonon transport in the graphene (Gr)/2D polyaniline (C N) lateral superlattices, which is an indication of a transition in the phonon transport mechanism from the incoherent to coherent regime.

H. Song, P. Ying, P. Zhu, Y. Zhou, Z. Zhong, Modeling of load responses and aging of high strength fibers considering UV-radiation. Composites Science and Technology 231, 109806 (2023).

Published in Composites Science and Technology, 2022

Long-term illumination can damage the mechanical properties of high strength fiber composites, resulting in the material aging and loss of mechanical properties. To reveal the mechanism of ultraviolet- (UV-) induced damage, in this paper, a nonlinear constitutive model is developed to describe the elastic and inelastic deformation behavior of high strength fibers under UV-radiation and mechanical loadings.

Z. Fan, Y. Wang, P. Ying, K. Song, J. Wang, Y. Wang, Z. Zeng, K. Xu, E. Lindgren, J. M. Rahm, A. J. Gabourie, J. Liu, H. Dong, J. Wu, Y. Chen, Z. Zhong, J. Sun, P. Erhart, Y. Su, T. Ala-Nissila, GPUMD: A package for constructing accurate machine-learned potentials and performing highly efficient atomistic simulations. J Chem Phys 157, 114801 (2022).

Published in The Journal of Chemical Physics, 2022

We present our latest advancements of machine-learned potentials (MLPs) based on the neuroevolution potential (NEP) framework introduced in [Fan et al., Phys. Rev. B 104, 104309 (2021)] and their implementation in the open-source package GPUMD.We increase the accuracy of NEP models both by improving the radial functions in the atomic-environment descriptor using a linear combination of Chebyshev basis functions and by extending the angular descriptor with some four-body and five-body contributions as in the atomic cluster expansion approach.

P. Ying, X. Li, X. Qiang, Y. Du, J. Zhang, L. Chen, Z. Zhong, Tension-induced phase transformation and anomalous Poisson effect in violet phosphorene. Materials Today Physics 27, 100755 (2022).

Published in Materials Today Physics, 2022

Two-dimensional violet phosphorene (VP) nanosheets are promising semiconductor materials with unique cross structures distinct from those of their allotropes such as black phosphorene and blue phosphorene, but their mechanical behaviors remain almost unexplored. By using the first-principles calculations, in this paper we investigate the mechanical behaviors of monolayer, bilayer, and bulk VP under uniaxial tension. A phase transformation from the open-pore phase to closed-pore phase is observed in VP structures when under a specific tensile strain.

J. Ke, P. Ying, Y. Du, B. Zou, H. Sun, J. Zhang, Delamination of MoS(2)/SiO(2) interfaces under nanoindentation. Phys Chem Chem Phys 24, 15991-16002 (2022).

Published in Physical Chemistry Chemical Physics, 2022

Molybdenum disulphide (MoS2) mounted on silicon dioxide (SiO2) constitutes the fundamental functional components of many nanodevices, but its mechanical properties, which are crucial for the device design and fabrication, remain almost unexplored. Here, the mechanical properties of the multilayer MoS2/SiO2 system are investigated via nanoindentation experiments and molecular dynamics simulations. In terms of the mechanical properties, a comparative study of MoS2/SiO2 and graphene/SiO2 systems is presented.

Y. Zhou, S. Zhou, P. Ying, Q. Zhao, Y. Xie, M. Gong, P. Jiang, H. Cai, B. Chen, S. Tongay, J. Zhang, W. Jie, T. Wang, P. Tan, D. Liu, M. Kuball, Unusual Deformation and Fracture in Gallium Telluride Multilayers. J Phys Chem Lett 13, 3831-3839 (2022).

Published in Journal of Physical Chemistry Letters, 2022

The deformation and fracture mechanism of two-dimensional (2D) materials are still unclear and not thoroughly investigated. Given this, mechanical properties and mechanisms are explored on example of gallium telluride (GaTe), a promising 2D semiconductor with an ultrahigh photoresponsivity and a high flexibility. Hereby, the mechanical properties of both substrate-supported and suspended GaTe multilayers were investigated through Berkovich-tip nanoindentation instead of the commonly used AFM-based nanoindentation method.

P. Ying, T. Liang, Y. Du, J. Zhang, X. Zeng, Z. Zhong, Thermal transport in planar sp2-hybridized carbon allotropes: A comparative study of biphenylene network, pentaheptite and graphene. International Journal of Heat and Mass Transfer 183, 122060 (2022).

Published in International Journal of Heat and Mass Transfer, 2021

The biphenylene network with periodically arranged four-, six-, and eight-membered rings has been successfully synthesized in very recent experiments. This novel two-dimensional (2D) carbon allotrope has potentials in applications of lithium storage and carbon-based circuitry. Understanding the thermal transport properties of biphenylene network is of critical importance for the performance and reliability of its practical applications. To this end, the thermal transport in biphenylene network is comprehensively investigated in this paper with the aid of molecular dynamics simulations together with first-principles calculations.

Y. Du, P. Ying, J. Zhang, Prediction and optimization of the thermal transport in hybrid carbon-boron nitride honeycombs using machine learning. Carbon 184, 492-503 (2021).

Published in Carbon, 2021

The recently discovered carbon honeycombs (CHCs) and boron nitride honeycombs (BNHCs) are found to have the similar molecular structures but different thermal properties. Thus, through appropriately patching together CHCs and BNHCs, the hybrid carbon-boron nitride honeycombs (C–BNHCs) with tunable thermal conductivity can be achieved. In this paper, the machine learning (ML) method together with molecular dynamics simulations is employed to study the thermal transport property of C–BNHCs, and also utilized to design the structures of C–BNHCs for the specific thermal conductivity.

P. Ying, J. Zhang, Z. Zhong, Effect of Phase Transition on the Thermal Transport in Isoreticular DUT Materials. The Journal of Physical Chemistry C 125, 12991-13001 (2021).

Published in The Journal of Physical Chemistry C, 2021

Soft porous crystals (SPCs) or flexible metal–organic frameworks have great potential applications in gas storage and separation, in which SPCs can undergo phase transition due to external stimuli. Thus, understanding the effect of phase transition on the thermal transport in SPCs becomes extremely crucial because the latent heat generated in aforementioned applications is needed to be effectively removed. In this paper, taking the isorecticular DUT series as an example, the thermal transport property of SPCs during the phase transition from a large pore (lp) phase to a narrow pore (np) phase is comprehensively investigated by molecular dynamics simulations together with the Gree–Kubo method.

P. Ying, J. Zhang, Y. Du, Z. Zhong, Effects of coating layers on the thermal transport in carbon nanotubes-based van der Waals heterostructures. Carbon 176, 446-457 (2021).

Published in Carbon, 2021

In this paper, we conduct a comprehensive investigation on the thermal transport in one-dimensional (1D) van der Waals (vdW) heterostructures by using non-equilibrium molecular dynamics simulations. As for the considered 1D vdW heterostructures having a base of (40,40) carbon nanotube (CNT), we find that the boron nitride nanotube (BNNT) coating can increase the thermal conductance of inner CNT base by 36%, while the molybdenum disulfide nanotube (MSNT) coating can reduce the thermal conductance by 47%.

P. Ying, J. Zhang, Z. Zhong, Pressure-induced phase transition of isoreticular MOFs: Mechanical instability due to ligand buckling. Microporous and Mesoporous Materials 312, 110765 (2021).

Published in Microporous and Mesoporous Materials, 2020

Since MOFs are often upon varied pressures in gas adsorption/desorption process, understanding the mechanical stability of these ultraporous frameworks becomes extremely crucial. In this paper, taking the isoreticular DUT material as an example, the relation between the mechanical stability of isoreticular MOFs and their ligands is investigated by real-time molecular dynamics simulations as well as three state of art computational approaches including Born stability criteria, anisotropy in elastic moduli and pressure-versus-volume equations.

Y. Du, J. Zhou, P. Ying, J. Zhang, Effects of cell defects on the mechanical and thermal properties of carbon honeycombs. Computational Materials Science 187, 110125 (2021).

Published in Computational Materials Science, 2020

Cell defects are inevitable during the fabrication of carbon honeycombs (CHCs), which, however, were tacitly ignored in previous studies. In this work, the effects of defects including Stone-Wales (SW) defect and single-wall vacancy (SV) defect on the mechanical and thermal properties of CHCs are investigated by using molecular dynamics simulations.

P. Ying, J. Zhang, J. Zhou, Q. Liang, Z. Zhong, Mechanical behaviors of MoS nanowires under tension from molecular dynamics simulations. Computational Materials Science 179, 109691 (2020).

Published in Computational Materials Science, 2020

As a new class of one-dimensional (1D) transition-metal monochalcogenides (TMMs) nanowires (NWs), the recently synthesized MoS NWs exhibit potential applications in two-dimensional integrated circuit. However, their mechanical behaviors remain almost unexplored. In this paper, the mechanical behaviors of MoS NWs under tensile loading are studied by classical molecular dynamics simulations together with first-principles calculations.

P. Ying, J. Zhang, X. Zhang, Z. Zhong, Impacts of Functional Group Substitution and Pressure on the Thermal Conductivity of ZIF-8. The Journal of Physical Chemistry C 124, 6274-6283 (2020).

Published in The Journal of Physical Chemistry C, 2020

Metal–organic frameworks (MOFs) are promising candidates as natural gas adsorbents because of their porous feature and high structural tunability. In the gas adsorption/desorption process, MOFs are often under complicated physical environments, such as varied pressure and temperature; however, limited attention has been paid to the effect of pressure on their thermal properties. In this work, taking ZIF-8 with four different functional groups (−H, −CH3, −Cl, and −Br) as an example, we investigate the influence of functional group substitution and pressure on the thermal conductivity of MOFs through equilibrium molecular dynamics simulations.

J. Zhang, Y. Zhou, P. Ying, H. Sun, J. Zhou, T. Wang, W. Jie, M. Kuball, Effects of interlayer interactions on the nanoindentation response of freely suspended multilayer gallium telluride. Nanotechnology 31, 165706 (2020).

Published in Nanotechnology, 2020

Freestanding indentation is a widely used method to characterise the elastic properties of two-dimensional (2D) materials. However, many controversies and confusion remain in this field due to the lack of appropriate theoretical models in describing the indentation responses of 2D materials. Taking the multilayer gallium telluride (GaTe) as an example, in this paper we conduct a series of experiments and simulations to achieve a comprehensive understanding of its freestanding indentation behaviours.

P. Ying, J. Zhang, Z. Zhong, Mechanical properties of monolayer ternary transitional metal dichalogenides MoS2xTe2(1 − x): A molecular dynamics study. Journal of Applied Physics 126, 215105 (2019).

Published in Journal of Applied Physics, 2019

In this paper, the mechanical behaviors of recently synthesized monolayer ternary transitional metal dichalogenides (TMDs) MoS2xTe2(1 − x) (0 < x < 1) under tensile loading are studied by classical molecular dynamics simulations. Particular attention is paid to the fundamental mechanical properties such as Young’s modulus and fracture behaviors of monolayer MoS2xTe2(1 − x).

P. Ying, Y. Zhao, H. Tan, Study on collapse controlling of single-wall carbon nanotubes by helium storage. Computational Materials Science 164, 133-138 (2019).

Published in Computational Materials Science, 2019

In this paper, we propose a method to control the collapsed nanostructurings of single-walled carbon nanotubes (SWCNTs) by helium storage and the key mechanism is elaborated from the potential energy aspect. The molecular dynamics simulation shows that enough helium atoms could restore the collapsing configuration of (40, 40) carbon nanotubes back to the circular cross section.