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Publications (190)
An investigation of novel Ba 2 TiMxO 6 (Mx = Ge, Sn, Se, Te), highlighting promising candidates for UV optoelectronics and solar cell applications.
When using solid oxide fuel cells (SOFCs) as the auxiliary power unit (APU) of automobiles, a stringent thermal control to limit the temperature and thermal stress of all components of the SOFC system is required. Various thermal management methods have been proposed, mostly involving the use of cooling air (CA). To avoid the thermal shock associat...
Heterojunction catalysts in the field of hydrogen evolution reaction (HER) from electrocatalytic water splitting have recently become a hot research topic. In this paper, we systematically calculated the HER catalytic performance of a MoS2/CoS2 heterojunction for the first time, considering the effect of edge sites regulation, strain and electric f...
Predicting protein‐ligand binding affinity is a crucial and challenging task in structure‐based drug discovery. With the accumulation of complex structures and binding affinity data, various machine‐learning scoring functions, particularly those based on deep learning, have been developed for this task, exhibiting superiority over their traditional...
Machine learning has boosted the remarkable development of crystal structure prediction (CSP), greatly accelerating modern materials design.The state-of-the-art methods, however, rely on a giant training dataset, and there is a trend to keep increasing the dataset, as triggered by the great success of artificial intelligence models.Here, we show th...
Barium-based periodate double perovskites Ba 2 NaHaO 6 (Ha = Cl, Br, I) are strong candidates for novel optoelectronic applications. The structural stability, electronic, and thermodynamic properties of Ba 2 NaHaO 6 are examined systematically here...
Structural prediction for the discovery of novel materials is a long sought-after goal of computational physics and materials sciences. The success is rather limited for methods such as the simulated annealing method (SA) that require expensive density functional theory (DFT) calculations and follow unintelligent search paths. Here a machine-learni...
Although the perovskite (Nd,Sr)CoO3 (NSC113)/Ruddlesden-Popper (R-P) oxide (Nd,Sr)2CoO4 (NSC214) heterostructure is reported to improve the oxygen reduction reaction (ORR) activity by 2-3 orders of magnitude, the enhancement mechanism remains unclear. For the first time, we conclude that there are two main factors that can enhance the ORR activity:...
Structural prediction for the discovery of novel materials is a long sought after goal of computational physics and materials sciences. The success is rather limited for methods such as the simulated annealing method (SA) that require expensive density functional theory (DFT) calculations and follow unintelligent search paths. Here a machine-learni...
Structural search and feature extraction are a central subject in modern materials design, the efficiency of which is currently limited, but can be potentially boosted by machine learning (ML). Here, we develop an ML-based prediction-analysis framework, which includes a symmetry-based combinatorial crystal optimization program (SCCOP) and a feature...
Thermal stress-induced mechanical failure is a critical issue for practical application of solid oxide fuel cells (SOFCs). Due to the lack of study on the thermo-mechanical behavior of SOFC with different methane steam pre-reforming ratios (R), a 3D thermo-mechanical model is developed to systematically evaluate the mechanical performance of SOFC r...
Aim
Developing a method for use in computer aided drug design
Background
Predicting the structure of enzyme-ligand binding mode is essential for understanding the properties, functions, and mechanisms of the bio-complex, but is rather difficult due to the enormous sampling space involved.
Objective
Accurate prediction of enzyme-ligand binding mod...
Proline is an important amino acid that plays unique roles in the structures of peptides and proteins. The conformations of proline are searched by a thorough method, generating 3888 trial structures optimized at the B97D/6-311++G** level. A total of 23 conformations are found and their structural and energetic data are presented. All the proline c...
To reduce the dimensionality of the potential energy surface (PES) necessary for finding the low energy conformations (LECs) of peptides, the sidechain dihedral angles (DAs) of 3548 LECs of 17 amino acids (AAs) and related peptides are examined. The analysis reveals that most DAs can be discretized into 3 states. Moreover, the fact that many DA com...
To improve the successful prediction rate of the existing molecular docking methods, a new docking approach is proposed that consists of three steps: generating an ensemble of docked poses with a conventional docking method, performing clustering analysis of the ensemble to select the representative poses, and optimizing the representative structur...
An external electric field (EEF) can impact a broad range of catalytic processes beyond redox systems. Computational design of catalysts under EEFs targeting specific operation conditions essentially requires accurate predictions of the response of a complex physicochemical system to collective parameters such as EEF strength/direction and temperat...
Here, the combination of theoretical computations followed by rapid experimental screening and in situ diffraction studies is demonstrated as a powerful strategy for novel compounds discovery. When applied for the previously “empty” Na−Zn−Bi system, such an approach led to four novel phases. The compositional space of this system was rapidly screen...
Predicting the binding structure of bio-complex is essential for understanding its properties, functions, and mechanisms, but is rather difficult due to the huge sampling space involved. A new computational protocol, MDO, for finding the ligand binding structure is proposed. MDO consists of global sampling via MD simulation and clustering of the re...
Solid oxide cells are an exciting technology for energy conversion. Fuel cells, based on solid oxide technology, convert hydrogen or hydrogen-rich fuels into electrical energy, with potential applications in stationary power generation. Conversely, solid oxide electrolysers convert electricity into chemical energy, thereby offering the potential to...
Three new sodium zinc antimonides Na11Zn2Sb5, Na4Zn9Sb9, and NaZn3Sb3 were synthesized utilizing sodium hydride NaH as a reactive sodium source. In comparison to the synthesis using sodium metal, salt-like NaH can be ball-milled, leading to the easy and uniform mixing of precursors in the desired stoichiometric ratios. Such comprehensive compositio...
Fe, Mg, and O are among the most abundant elements in terrestrial planets. While the behavior of the Fe–O, Mg–O, and Fe–Mg binary systems under pressure have been investigated, there are still very few studies of the Fe–Mg–O ternary system at relevant Earth’s core and super-Earth’s mantle pressures. Here, we use the adaptive genetic algorithm (AGA)...
Mechanical performance analysis is important for ensuring the long-term reliability of solid oxide fuel cells (SOFCs). Thermal-mechanical models are constructed to conduct time-dependent mechanical performance analysis of SOFC stack with temperature field obtained by multiphysics modeling. The volume-averaged temperature field is used as comparison...
The computational determination of peptide conformations is a challenging task of finding minima in a high dimensional space. By combining the sampling efficiency of the genetic algorithm (GA) and the dimensionality reduction resulted from the backbone dihedral angle correlations, named as the path matrix (PM) method, a new searching algorithm, par...
Fe, Mg, and O are among the most abundant elements in terrestrial planets. While the behavior of the Fe-O, Mg-O, and Fe-Mg binary systems under pressure have been investigated, there are still very few studies of the Fe-Mg-O ternary system at relevant Earth's core and super-Earth's mantle pressures. Here, we use the adaptive genetic algorithm (AGA)...
Multiphysics models are important tools for the design and optimization of solid oxide fuel cells (SOFCs). The computational efficiency of a sophisticated multiphysics model is improved by a factor of 4 by symmetry utilization and grid optimization, allowing its routine use for the analysis and diagnosis of industrial-sized SOFC stacks. The predict...
Structure design is of great value for the performance improvement of solid oxide electrolysis cells (SOECs) to diminish the gap between scientific research and industrial application. A comprehensive multi-physics coupled model is constructed to conduct parameter sensitivity analysis to reveal the primary and secondary factors on the SOEC performa...
Valley polarized transport was studied in graphene cross junctions consisting of a bilayer graphene device region connected to 4 monolayer graphene leads. Electrons injected from the armchair leads to the zigzag leads can be valley polarized in a range of Fermi energies. The valley polarization is produced by quantum interference and the Fano reson...
Due to the high cost and insufficient resource of lithium, alternative sodium-ion batteries are widely investigated for large-scale applications. NaFePO4 has the highest theoretical capacity of 154 mAh g-1 among the iron-based phosphates, which makes it an attractive cathode material for Na-ion batteries. Experimentally, LiFePO4 has been highly suc...
Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principledriven met...
Sr3Fe2O7-δ (SFO) with two-layer Ruddlesden-Popper (R–P) structure has recently been proved to be a promising material for the single phase cathode in proton conducting solid oxide fuel cells (P–SOFCs). To investigate the hydration reactions and proton conducting mechanisms of SFO and cobalt doped SFO (SFCO), both bulk and surface properties were ca...
Dehydrogenation of H3COH and H2O are key steps of methanol steam reforming on transition metal surfaces. Oxhydryl dehydrogenation reactions of HxCOH (x = 0–3) and OH on Ni (111) were investigated by DFT calculations with the OptB88-vdW functional. The transition states were searched by the climbing image nudged elastic band method and the dimer met...
The intrinsic mechanism of Ni-catalyzed methanol steam reforming (MSR) is examined by considering 54 elementary reaction steps involved in MSR over Ni(111). Density functional theory computations and transition state theory analyses are performed on the elementary reaction network. A microkinetic model is constructed by combining the quantum chemic...
The structural diversity of rare-earth and transition metal borides indicates that alkali-transition metal borides (A-T-B) show tremendous promise in exhibiting a variety of crystal structures with different dimensionalities of T-B frameworks. On the other hand, the A-T-B ternary systems are severely underexplored because of the synthetic challenge...
Ni-catalyzed steam methane reforming (SMR) is widely used in energy and chemical engineering, but the confusion about vastly different SMR kinetic data has lasted for half a century. Towards solving the puzzle, the intrinsic mechanism of SMR is examined by performing density functional theory computations and transition state theory analyses on 80...
By analyzing the Fe-Ni-B compositional diagram, we predict an energetically and dynamically stable FeNiB2 compound. This system belongs to the class of highly responsive state of materials, as it is very sensitive to the external perturbations. This state is also characterized by a high level of spin fluctuations, which strongly influence possible...
By analyzing Fe-Ni-B compositional diagram we predicte a new energetically and dynamically stable FeNiB2 compound. This system belongs to the class of highly response state of material, as it is very sensitive to the external perturbations. This state is also characterized by a high level of spin fluctuations which strongly influence possible magne...
We studied the valley dependent transport properties of bilayer-monolayer graphene junctions consisting of a device region of bilayer zigzag ribbon connected to monolayer zigzag ribbon leads. We determined numerically using the python package Kwant the valley dependent conductance through the junctions in an energy range in which each valley has at...
Long-term performance stability is essential for the commercialization of solid oxide fuel cell (SOFC) technology. The performance degradations of SOFCs induced by the microstructure evolutions of cell component materials are examined by multi-physics numerical simulations. Explicit considerations are given to the typical material set: nickel (Ni)...
Damage by mismatch of thermal expansion coefficients and temperature gradient is a major factor limiting the long-term stability of solid oxide fuel cell (SOFC). Numerical simulations are performed to provide in-depth information about the mechanical stress, mechanical failure probability and creep strain rate of planar SOFC. The dependences of the...
Doped CeO2 is a very promising electrolyte for intermediate temperature solid oxide fuel cells (IT-SOFCs). To further improve the performance of the CeO2-based electrolyte, co-doping two different elements into CeO2 is a feasible method, however the co-doping effect on the ionic conductivity is not well understood and whether it is synergistic or a...
Internal reformation of low steam methane fuel is highly beneficial for improving the energy efficiency and reducing the system complexity and cost of solid oxide fuel cells (SOFCs). However, anode coking for the Ni-based anode should be prevented before the technology becomes a reality. A multi-physics fully coupled model is employed to simulate t...
Mechanical damage is a major factor limiting the long-term stability of solid oxide fuel cells (SOFCs). Here, the mechanical stability of planar SOFCs consisting of Ni-YSZ anode/YSZ electrolyte/LSM-YSZ cathode (Ni=Nickel, YSZ=yttria-stabilized zirconia, LSM=lanthanum strontium manganite) is analyzed by a structural mechanics model with composition...
Computational determination of peptide conformations is challenging as it is a problem of finding minima in a high-dimensional space. The "divide and conquer" approach is promising for reliably reducing the search space size. A random forest learning model is proposed here to expand the scope of applicability of the "divide and conquer" approach. A...
The maximum electrical efficiency of fuel cell system, ηemax, is important for the understanding and development of the fuel cell technology. Attempt is made to build a theory for ηemax by considering the energy requirement of heating the fuel and air streams to the fuel cell operating temperature T. A general thermodynamic analysis is performed an...
Structural phase transitions of electrode materials are responsible for poor reversibility during charge/discharge cycling in Li-ion batteryies. Using previously-developed structural databases, we investigate the structural landscape for LixFeSiO4 systems at x=1. Starting with the low-energy Li2FeSiO4 crystal structures, we explore the crystal stru...
Solid oxide fuel cells (SOFCs) have been attracting people's attention for their high energy conversion efficiency, good fuel compatibility, no precious metal catalysts, and pollution-free emissions. However, the high operating temperature (800-1200℃) of the traditional SOFC can reduce the long-term stability and cause the difficulties in either th...
The Al–Sm system is selected as a model system to study the transition process from liquid and amorphous to crystalline states. In recent work, we have shown that, in addition to long-range translational periodicity, crystal structures display well-defined short-range local atomic packing motifs that transcends liquid, amorphous and crystalline sta...
Quantum chemistry calculations play a fundamental role in revealing the molecular structures observed in gas-phase spectroscopic measurements. The supersonic jet cooling widely used in single molecular spectroscopy experiment is a non-equilibrium process and often causes confusion on the theoretical and experimental comparison. A computational appr...
High volumetric power density (VPD) is the basis for the commercial success of micro-tubular solid oxide fuel cells (mtSOFCs). To find maximal VPD (MVPD) for anode-supported mtSOFC (as-mtSOFC), the effects of geometric parameters on VPD are analyzed and the anode thickness, tan, and the cathode length, lca, are identified as the key design paramete...
We present in this paper a network scheme to explore the structural diversity of LiFePO4 which is an important cathode material in Li-ion batteries. In our scheme, networks of Fe and P atoms are initially constructed as backbone structures using structural motifs for FePx and FePx vertices obtained from existing structural databases. Then Oxygen at...
A multiphysics model for a production scale planar solid oxide fuel cell(SOFC) stack is important for the SOFC technology, but usually requires an unpractical amount of computing resource. The major cause for the huge computing resource requirement is identified as the need to solve the cathode O2 transport and the associated electrochemistry. To o...
Predictions of structures of biomolecules are challenging due to the high dimensionalities of the potential energy surfaces (PESs) involved. Reducing the necessary PES dimensionality is helpful for improving the computational efficiency of all relevant structure prediction methods. For that purpose, a systematic analysis of the backbone dihedral an...
A planar SOFC stack is an integral but basic power generation unit with physical conditions completely different from that of a laboratory button cell. The ability to reliably predict the operating behaviors of SOFC stacks is crucial for the technology advancement. The existing stack models either rely on simplified geometries, or handle a few sele...
Conformations of biomolecules are the basis for their property studies and the predictions of peptide structures are of high interest in life science but very difficult in practice. The potential energy surfaces of five tetrapeptides, GGGG, GVGG, GTGG, GGYG and GSDG, are thoroughly explored here by considering all combinations of their internal sin...
Solid oxide fuel cell (SOFC) fueled by methane with low steam content is desirable from the energy efficiency and power density point of view. Improved understanding about the low steam methane fuel operation is required for advancing the technology. A rigorous and comprehensive multiphysics model for methane fueled SOFCs is described for the first...
Using a combination of adaptive genetic algorithm search, motif-network search scheme and first-principles calculations, we have systematically studied the low-energy crystal structures of Na2FeSiO4. We show that the low-energy crystal structures with different space group symmetries can be classified into several families based on the topologies o...
The intermolecular hydrogen bond (H-bond) interactions play vital roles in many biological systems. Despite continued interest, the nature of their electronic structures has remained elusive. Based on the unique features of aqueous solution, a simple model depicting the H-bond electronic states by orbital hybridizations is developed. The model is d...
There is a growing interest in the study of structures and properties of biomolecules in gas phase. Applications of force fields are highly desirable for the computational efficiency of the gas phase study. To help the selection of force fields, the performances of five representative force fields for gaseous neutral, protonated, deprotonated and c...
The genetic algorithm (GA) is an intelligent approach for finding minima in a highly dimensional parametric space. However, the success of GA searches for low energy conformations of biomolecules is rather limited so far. Herein an improved GA scheme is proposed for the conformational search of oligopeptides. A systematic analysis of the backbone d...
Based on the fundamental definition of the electrical efficiency and the thermodynamics principle, a theoretical expression for the maximum electricity efficiency of a fuel cell system was derived. The characteristics of cell voltage operating at the maximum electrical efficiency and the energy required for heating the fuel and air were considered...
Methane steam reforming (MSR) reaction rate is an important factor affecting the performance of methane fueled solid oxide fuel cell (SOFC). Ni is the most common catalyst for MSR in SOFC. There are large discrepancies in the Ni catalyzed MSR kinetic models proposed by different experiments. Moreover, the experiments for all the MSR kinetic models...
Using a motif-network search scheme, we studied the tetrahedral structures of
the dilithium/disodium transition metal orthosilicates A2MSiO4 with A = Li or
Na and M = Mn, Fe or Co. In addition to finding all previously reported
structures, we discovered many other different tetrahedral-network-based
crystal structures which are highly degenerate in...
The energy differences between canonical and zwitterionic isomers of arginylglycine (ArgGly) at the CCSD/aug-cc-pVDZ level are too small (less than 1 kcal mol(-1)) to determine the dominant form in the gas phase from the energetic point of view. First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS)...
Mechanical damage is a major factor limiting the long-term stability of SOFCs. It is a common practice to perform the stress analysis by isolating the interested component of an SOFC stack. This approach is questionable as it is difficult or even impossible to properly define the boundary condition for the isolated component. Here we show that the...
We report a successful development of a high space resolution multi-physics mathematical model for full scale planar SOFC stacks which is, to the best of our knowledge, the first of its kind. This 3D 30-cell stack model takes into account the coupled physical processes, applicable for both methane and hydrogen based fuels. Every cell consists of 30...
Mechanical damage induced by operation under high stress conditions is one of the major factors limiting the long-term stability of SOFCs. Stress analysis is therefore important for the development the SOFC technology. To date, it is a common practice to focus the stress analysis at some interested component of an SOFC stack, e.g., PEN, glass-ceram...
An SOFC stack is the basic functioning unit of SOFC as an electrical power generation device. The physical condition of an operating SOFC stack is vastly different from that of a laboratory button cell. The ability to analyze the performance characteristics of SOFC stacks is immensely helpful for advancing the SOFC technology for large scale commer...
Internal reformation of low steam methane fuel is important for the high efficiency and low cost operation of solid oxide fuel cell. Understanding and overcoming carbon deposition is crucial for the technology development. Here a multi-physics model is established for the relevant experimental cells. Balance of electrochemical potentials for the el...
An extensive computational study on the conformations of gaseous dipeptide glycine-arginine, GlyArg, has been performed. A large number of trail structures were generated by systematically sampling the potential energy surface (PES) of GlyArg. The trial structures were successively optimized with the methods of PM3, HF/3-21G*, BHandHLYP/6-31G* and...
We studied the pure valley current generated by adiabatic quantum pumping in a monolayer graphene with a gap generated by a substrate. The generation of the quantum-pumped pure valley current requires the presence of the antiparallel magnetic fields of two magnetic strips and the electrical potential barriers of three metal gates. The Fabry–Perot r...
The analysis of π/π and H/π interactions in complexes are a challenging aspect of theoretical research. Due to the different approximations of different levels of theory, results tend to be inconsistent. We compared the reliabilities of HF, SVWN, M06L, PW91, BLYP, B3LYP, BHandHLYP, B97D, MP2, and DFTB-D approaches in researching π/π and H/π interac...
The stability of the ZnO polar surfaces which is crucial for their applications is still being debated intensely. Here, we demonstrate that O extrusion outside the outermost bilayer is a universal reconstruction behavior of the Zn-terminated (0001) surface (with or without terraces) to compensate the well-known instability of such polar surfaces. T...
We study the generation of spin polarization in monolayer graphene in the presence of Rashba spin?orbit interaction (SOI) and a ferromagnetic (FM) stripe. It is shown that Rashba SOI alone can generate an in-plane (x?y plane) spin polarization, but a FM stripe with magnetization parallel to the current direction cannot generate any spin polarizatio...
Oxygen ion conductivities of acceptor-doped ZrO2 and CeO2 are important for their solid oxide full cell applications. A quantitative model accounting for the widely observed grain size dependence of the conductivity is of significant interest. A concise model for the grain size dependence of Schottky barrier is proposed here. The model is deduced f...
A nano-composite electrode with a core-shell structure is superior to the traditional design in terms of performance and durability. But the theory for the electrical conductivities influenced by the core-shell structure is lacking, hindering its theoretical analysis and modeling activity. Combining the physical picture of the core-shell structure...
Single- and binary-phase nano-particle infiltrated electrodes (SIE and BIE) have been actively studied experimentally. To properly understand the experimental results and the benefits of SIE and BIE designs, new models for electrical conductivities of BIE and TPB lengths of SIE and BIE are proposed here. The models agree with experiments on the var...
We investigate the thermal expansion behaviors of monolayer graphene and three configurations of graphene with point defects, namely the replacement of one carbon atom with a boron or nitrogen atom, or of two neighboring carbon atoms by boron-nitrogen atoms, based on calculations using first-principles density functional theory. It is found that th...
For biomolecules of increased size and flexibility, more efficient and reliable strategies are always needed to determine their stable low-energy conformers. Here, we propose a fragment based step-by-step strategy to search for the full conformational space of biomolecules. In this strategy, the molecule is divided into several fragments and each o...
Triplet nano-composite electrodes are actively examined experimentally, but there is a shortage of theoretical study. Theoretical models are helpful for understanding the experiments and provide guidance for design optimization of the novel electrode. Here new models for computing the electrode electronic and ionic conductivities, TPB length and hy...
Employing density functional theory and Grüneisen formalism, the layer dependence of zinc oxide (ZnO) sheet thermal expansion coefficients (TECs) is investigated. The monolayer ZnO sheet contracts significantly across the entire range of temperatures investigated. The negative TEC with maximum absolute value is determined, which implies that the mo...
Structures and binding energies are important information for describing the interactions between biomolecules and metal ions. The gas phase coordination properties of the metal cations, Li+, Na+, K-+,K- Mg2+, and Ca2+, with glutamic acid (Glu) are thoroughly examined by considering all the likely cation coordination modes and through the first pri...
