Article
Forestry
Bryce Frank, Vicente J. Monleon
Summary: The study compared six alternative variance estimators under two point estimation regimes. Alternative estimators showed better bias and efficiency performance than the simple random sampling estimator. Two promising alternative estimators were identified that offer clear improvements over a wide range of attributes and estimation regimes.
Article
Chemistry, Physical
Zhaoxi Sun, Qiaole He
Summary: 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. In this work, the possibility of further accelerating the nonequilibrium free energy simulation is explored by employing unidirectional pulling and using a selection criterion. Numerical tests are performed to provide insights and guidelines for using this selection-criterion-based scheme.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Operations Research & Management Science
Jose Andre Brito, Leonardo de Lima, Pedro Henrique Gonzalez, Breno Oliveira, Nelson Maculan
Summary: An optimization method based on variable neighborhood search metaheuristic was proposed in this study to minimize sample size in stratification problem, outperforming 94% of considered cases. An enumeration algorithm was also developed to find optimal global solutions in certain populations and scenarios, and the majority of cases yielded optimal global solutions.
RAIRO-OPERATIONS RESEARCH
(2021)
Article
Mathematics
Anqi Zou, Jiajie Wang, Chiye Wu
Summary: In this paper, we creatively price the discretely sampled variance swaps under the mean-reverting Gaussian model with regime-switching asymmetric double exponential jump diffusion. We extend the traditional MRG model by considering the trend of the financial market and unexpected events. Our new model uses observable Markov chains to adjust parameters and captures market movement and asset price fluctuations. Analytical solutions for pricing formulae are obtained using characteristic functions and conditional transition characteristic functions. The closed-form solution offers high computational accuracy and efficiency.
Article
Ecology
Ira L. Parsons, Melanie R. Boudreau, Brandi B. Karisch, Amanda E. Stone, Durham A. Norman, Stephen L. Webb, Kristine O. Evans, Garrett M. Street
Summary: This study explores the relationship between sampling density, interpolation method, and landscape heterogeneity, and evaluates their impact on interpolation accuracy and precision. The results show that decreasing landscape heterogeneity and increasing sampling density can improve accuracy and precision. There is a need for structured tools to determine the most appropriate sampling design for interpolation methods in landscapes with different levels of heterogeneity.
Article
Social Sciences, Mathematical Methods
Robert H. Lyles, Yuzi Zhang, Lin Ge, Cameron England, Kevin Ward, Timothy L. Lash, Lance A. Waller
Summary: The application of serial principled sampling designs is considered ideal for monitoring prevalence and case counts of infectious or chronic diseases. By using creative designs and statistical methods, surveillance efforts can be improved to provide more precise estimates and reduce the necessary sample size. The use of capture-recapture methodology can provide alternative case total estimates for closed populations, such as long-term care facilities or patient registries. Weighted averaging and a novel single capture-recapture estimator can further improve the precision of estimates. A variant on a Dirichlet-multinomial-based credible interval is proposed for accompanying case count estimates.
JOURNAL OF SURVEY STATISTICS AND METHODOLOGY
(2022)
Editorial Material
Mathematical & Computational Biology
Robbie C. M. van Aert
Summary: The partial correlation coefficient (PCC) is commonly used in meta-analysis, but the assumptions of equal-effect and random-effects meta-analysis models are violated. To address this, applying Fisher's z transformation to PCCs can improve the meta-analysis by removing the dependency on sampling variance and approaching a normal distribution. A simulation study shows that meta-analyzing Fisher's z transformed PCCs has lower bias and error compared to meta-analyzing PCCs directly. Therefore, it is recommended to include meta-analyses using Fisher's z transformed PCCs to assess result robustness in any meta-analysis based on PCCs.
RESEARCH SYNTHESIS METHODS
(2023)
Article
Chemistry, Medicinal
Zhe Huai, Zhaoxi Shen, Zhaoxi Sun
Summary: This study employed advanced protein force fields to determine the binding thermodynamics of MUP-inhibitor systems and investigate the inter- and intramolecular interaction patterns. The results showed that AMBER14SB provided better performance in predicting binding affinities compared to the newer AMBER19SB force field, suggesting that AMBER14SB may still be the preferred option for accurate free-energy calculations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Medicinal
Zhaoxi Sun, Zhe Huai, Qiaole He, Zhirong Liu
Summary: Describing, understanding, and designing complex interaction networks within macromolecular systems remain challenging in modern chemical research. Host-guest systems, despite their relative simplicity in both the structural feature and interaction patterns, still pose problems in theoretical modeling. The barrel-shaped supramolecular container cucurbit[8]uril (CB8) shows promising functionalities in various areas.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Statistics & Probability
Bhuwaneshwar Kumar Gupt, Irphan Ahamed
Summary: This article investigates the problem of optimum stratification for the generalized auxiliary variable proportional allocation (GAVPA) under the heteroscedastic regression superpopulation (HRS) model. The equations and approximate methods for finding optimum points of stratification (OPS) are derived. Numerical illustrations show that these methods can efficiently stratify populations with different levels of skewness and heteroscedasticity.
COMMUNICATIONS IN STATISTICS-THEORY AND METHODS
(2022)
Article
Statistics & Probability
Bhuwaneshwar Kumar Gupt, Md Irphan Ahamed, Manoshi Phukon
Summary: This paper discusses the problem of optimum stratification for an auxiliary variable optimum allocation in sampling with simple random sampling with replacement under a superpopulation model. It critiques the general perception of replacing unknown proportionate values of a study variable with known proportionate values of a highly correlated auxiliary variable in the computation of optimum allocation. The proposed methods of stratification are empirically examined and found to be efficient.
ADVANCES AND APPLICATIONS IN STATISTICS
(2021)
Article
Statistics & Probability
Bhuwaneshwar Kumar Gupt, Mankupar Swer, Md Irphan Ahamed, B. K. Singh
Summary: This paper discusses the problem of optimum stratification for two study variables based on an auxiliary variable, and presents equations for obtaining the optimum points of stratification. Additionally, approximate solutions for the optimum points are also provided. Empirical examinations show that the proposed methods are highly efficient, and they can be applied to simple random sampling designs.
ADVANCES AND APPLICATIONS IN STATISTICS
(2022)
Article
Biochemistry & Molecular Biology
Zhaoxi Sun
Summary: This study retrospectively examines the TrimerTrip host-guest systems using the same protocol in the SAMPL7 challenge, achieving good agreement between calculated binding affinities and experimental values, with obtained binding poses serving as a starting point for further research.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Biochemistry & Molecular Biology
Zhe Huai, Huaiyu Yang, Xiao Li, Zhaoxi Sun
Summary: In this study, predictive modeling of host-guest binding affinities was conducted, with satisfactory results achieved using alchemical predictions with specific charge schemes. However, the end-point estimates performed poorly in reproducing the experimental binding affinities.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Cell Biology
Linh Gia Hoang, Jonas Gossen, Riccardo Capelli, Toan T. Nguyen, Zhaoxi Sun, Ke Zuo, Jorg B. Schulz, Giulia Rossetti, Paolo Carloni
Summary: Human NEET proteins play a crucial role in various diseases, and understanding their structure and ligands is important. This study introduces a new method to identify the binding site of a ligand with NEET proteins.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xiaohui Wang, Bin Chong, Zhaoxi Sun, Hao Ruan, Yingguang Yang, Pengbo Song, Zhirong Liu
Summary: In statistical mechanics, the nature of binding affinity can be simplified by ensemble averaging from the vast conformations of intrinsically disordered proteins (IDPs), which can be decomposed into the ligandability of IDP and the capacity of the ligand. This regularity allows for easier virtual screening of IDPs and provides essential insight into the specificity difference between IDPs and conventional ordered proteins.
Article
Multidisciplinary Sciences
Zhaoxi Sun, Mao Wang, Qiaole He, Zhirong Liu
Summary: In molecular modelling of novel solvents such as ionic liquids, scaling atomic charges is a common practice to improve the agreement between experiments and simulations. This study presents a large-scale calculation of solvation free energies in scaled ionic liquids and compares the results obtained from density-derived choices and solvation-thermodynamics-derived choices. The findings reveal that scaling factors affect the intermolecular interactions and density monotonically decreases with decreasing scaling factor. However, solvation free energies do not show consistent monotonic behaviors due to competing electrostatic and vdW responses. Interestingly, the solvation-free-energy-derived scaling factor is generally slightly higher than the density-derived one.
ADVANCED THEORY AND SIMULATIONS
(2022)
Article
Biochemistry & Molecular Biology
Xiao Liu, Lei Zheng, Chu Qin, John Z. H. Zhang, Zhaoxi Sun
Summary: This study presents a comprehensive benchmark calculation of end-point free energy techniques in host-guest binding. The performance of different modeling schemes is compared with experimental references, and practical guidelines for maximizing the performance of end-point methods in practical systems are summarized.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2022)
Article
Chemistry, Applied
Zhaoxi Sun, Lei Zheng, Kai Wang, Zhe Huai, Zhirong Liu
Summary: This article discusses the computational modelling of cyclodextrin host-guest binding, focusing on the challenge of accurately modelling the primary-secondary equilibrium. The author presents an analysis of fixed-charge modelling and finds that while the GAFF2 parameter set is reliable, accurately reproducing electrostatics remains difficult. Enhanced sampling simulations are used to improve accuracy and explore different binding modes. The predicted binding affinities have a moderate error size, and only a fraction of the predicted primary-secondary preferences agree with experimental results.
CARBOHYDRATE POLYMERS
(2022)
Article
Biochemistry & Molecular Biology
Xiao Liu, Lei Zheng, Yalong Cong, Zhihao Gong, Zhixiang Yin, John Z. H. Zhang, Zhirong Liu, Zhaoxi Sun
Summary: End-point free energy calculations are widely used in protein-ligand and protein-protein interactions, but they may not be accurate in simple host-guest systems. This study suggests that improvements in the performance of end-point techniques can be achieved through regression and the consideration of additional variables, such as the dielectric constant. These methods manipulate the end-point equation by altering the contributions of different energy terms, leading to improved accuracy in predicting binding affinities.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2022)
Article
Chemistry, Physical
Zhaoxi Sun, Abhijit Kayal, Zhihao Gong, Lei Zheng, Qiaole He
Summary: Validation of basic issues in molecular modelling of ionic liquids using fixed-charge force fields has been conducted through extensive free energy calculations, component-specific force-field refitting, and box-size dependence analysis. It is found that a combination of scaled RESP charges and GAFF2 parameter set provides an accurate and efficient option for atomistic simulations of ionic liquids derivatives.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Zhaoxi Sun, Lei Zheng, Zuo-Yuan Zhang, Yalong Cong, Mao Wang, Xiaohui Wang, Jingjing Yang, Zhirong Liu, Zhe Huai
Summary: Charge scaling is an effective method for improving the agreement between computational and experimental results in molecular modelling of ionic liquids. A charge-scaling factor of 0.8 is generally applicable to most ILs, but system-dependent adjustments may be needed for better performance. In some cases, the vdW radius is tuned as an additional parameter to minimize the deviation between simulation and experiment.
Article
Biochemistry & Molecular Biology
Xiao Liu, Lei Zheng, Chu Qin, Yalong Cong, John Z. H. Zhang, Zhaoxi Sun
Summary: Host-guest binding is challenging to model computationally, but a modification of the three-trajectory realization shows promise by incorporating structural reorganization and minimizing internal fluctuations. Investigation of different force potentials reveals significant differences in binding thermodynamics and dynamic behaviors. When combined with other modification of interior dielectric constant, this method outperforms existing end-point methods in binding affinity ranking.
Article
Biochemistry & Molecular Biology
Zhaoxi Sun, Qiaole He, Zhihao Gong, Payam Kalhor, Zhe Huai, Zhirong Liu
Summary: Atomic-level understanding of host-guest interactions is crucial in supramolecular chemistry. The remarkable guest binding behavior of Cucurbiturils makes them promising drug carriers. Computational investigations and comparisons of charge models and force fields provide guidelines for theoretical modeling of host-guest binding.
Article
Quantum Science & Technology
Zuo-Yuan Zhang, Zhaoxi Sun, Jie-Ru Hu, Jin-Ming Liu
Summary: Theoretical schemes for implementing the Grover search algorithm using ultracold polar molecules in an electric field are proposed. Various logic operations, such as Hadamard gates and conditional phase gates, are designed using optimal control theory. The factorized Grover algorithm is demonstrated with coupled CH3CN molecules, and techniques to reduce imprecision and decoherence in the gates are explored. Additionally, optimal pulse sequences for a four-level molecular qudit are designed for simulating high fidelity quantum search on a single CH3CN molecule.
ADVANCED QUANTUM TECHNOLOGIES
(2023)
Article
Biochemistry & Molecular Biology
Xiaohui Wang, Zhe Huai, Zhaoxi Sun
Summary: This paper profiles the energetics and dynamics of four types of popular macrocycles and provides general guidelines on force field parametrization and selection in host-guest modeling.
Article
Chemistry, Physical
Zhaoxi Sun, Qiaole He
Summary: 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. In this work, the possibility of further accelerating the nonequilibrium free energy simulation is explored by employing unidirectional pulling and using a selection criterion. Numerical tests are performed to provide insights and guidelines for using this selection-criterion-based scheme.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Sergey Yu. Ketkov, Sheng-Yuan Tzeng, Elena A. Rychagova, Anton N. Lukoyanov, Wen-Bih Tzeng
Summary: Metallocenes, including methylcobaltocene, play important roles in various fields of chemistry. The ionization energy and vibrational structure of (Cp ')(Cp)Co can be influenced by introducing methyl substituents. The mass-analyzed threshold ionization spectrum and DFT calculations provide accurate information about the properties and transformations of (Cp ')(Cp)Co.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Review
Chemistry, Physical
Qifeng Mu, Jian Hu
Summary: Polymer mechanochemistry has experienced a renaissance due to the rapid development of mechanophores and principles governing mechanochemical transduction or material strengthening. It has not only provided fundamental guidelines for converting mechanical energy into chemical output, but also found applications in engineering and smart devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Da Hye Yang, Francesco Ricci, Fredrik L. Nordstrom, Na Li
Summary: Through systematic evaluation of the oiling-out behavior of procaine, we identified both stable and metastable liquid-liquid phase separation, and established phase diagrams to assist in rational selection of crystallization strategies.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Vikki Anand Varma, Simmie Jaglan, Mohd Yasir Khan, Sujin B. Babu
Summary: Designing engineering structures like nanocages, shells, and containers through self-assembly of colloids is a challenging problem. This work proposes a simple model for the subunit, which leads to the formation of monodispersed spherical cages or containers. The model with only one control parameter can be used to design cages with the desired radius.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Hainan Jiang, Yaolong He, Xiaolin Li, Zhiyao Jin, Huijie Yu, Dawei Li
Summary: The cycling lifespan and coulombic efficiency of lithium-ion batteries are crucial for high C-rate applications. The Li-ion concentration plays a crucial role in determining the mechanical integrity and structural stability of electrodes. This study focuses on graphite as the working electrode and establishes an experimental system to investigate the mechanical properties of composite graphite electrode at different C-rates. Considering the effect of Li-ion concentration in stress analysis is found to be significant.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Zhiye Wang, Yunchuan Li, Mingjun Sun
Summary: This study investigates the influence of intramolecular pi-pi interactions on the electronic transport capabilities of molecules. By designing and analyzing three pi-conjugated molecules, the researchers observe that different pi-conjugated structures have varying effects on electron transport. The findings provide a theoretical foundation for designing single-molecule electronic devices with multiple electron channels based on intramolecular pi-pi interactions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Yuandong Xu, Haoyang Feng, Chaoyang Dong, Yuqing Yang, Meng Zhou, Yajun Wei, Hui Guo, Yaqing Wei, Jishan Su, Yingying Ben, Xia Zhang
Summary: Hollow MoS2 cubes and spheres were successfully synthesized using a one-step hydrothermal method with the hard template method. The hollow MoS2 cubes exhibited higher specific capacitance and energy density compared to the hollow MoS2 spheres. The symmetrical supercapacitors assembled with these hollow structures showed good performance and high capacity retention after multiple cycles. These findings suggest that controlling the pore structure and surface characteristics of MoS2 is crucial for enhancing its electrochemical properties.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Ainhoa Oliden-Sanchez, Rebeca Sola-Llano, Joaquin Perez-Pariente, Luis Gomez-Hortiguela, Virginia Martinez-Martinez
Summary: The combination of photoactive molecules and inorganic structures is important for the development of advanced materials in optics. In this study, bulky dyes were successfully encapsulated in a zeolitic framework, resulting in emission throughout the visible spectrum.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Miaomiao Zhang, Cunyuan Pei, Qiqi Xiang, Lintao Liu, Zhongxu Dai, Huijuan Ma, Shibing Ni
Summary: The design of a solid electrolyte interphase (SEI) plays a crucial role in improving the electrochemical performance of anode materials. In this study, lithium difluoro(oxalate)borate (LiDFOB) is used as an electrolyte additive to form a protective SEI film on Li3VO4 (LVO) anodes. The addition of LiDFOB results in a dense, uniform, stable, and LiF-richer SEI, which enhances the Li-ion storage kinetics. The generated SEI also prevents further decomposition of the electrolyte and maintains the morphology of LVO anodes during charge/discharge processes. This work demonstrates the effectiveness of LiDFOB as a multi-functional additive for LiPF6 electrolytes and provides insights into SEI construction for high-performance LVO anodes.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
B. V. Andryushechkin, T. V. Pavlova, V. M. Shevlyuga
Summary: The atomic structure of the Ag(111)-p(4 x 4)-O phase was reexamined and two phases with the same periodicity were discovered. It was demonstrated that the accepted Ag6 model is incompatible with high-resolution oxygen-sensitive STM images.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
S. L. Romo-Avila, D. Marquez-Ruiz, R. A. Guirado-Lopez
Summary: In this study, we used density functional theory (DFT) calculations to investigate the interaction between model graphene oxide (GO) nanostructures and chlorine monoxide ClO. We aimed to understand the role of this highly oxidizing species in breaking C-C bonds and forming significant holes on GO sheets. Our results showed that C-C bonds in a single graphene oxide sheet can be broken through a simple mechanism involving the dissociation of two chemically attached ClO molecules. The formation of carbonyl groups and holes on the GO surface was also observed. This study provides important insights into the degradation of carbon nanotubes and the stability of GO during the myeloperoxidase (MPO) catalytic cycle.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Alberto Garcia-Fernandez, Birgit Kammlander, Stefania Riva, Hakan Rensmo, Ute B. Cappel
Summary: In this study, the X-ray stability of five different lead halide perovskite compositions (MAPbI3, MAPbCl3, MAPbBr3, FAPbBr3, CsPbBr3) was investigated using photoelectron spectroscopy. Different degradation mechanisms and resistance to X-ray were observed depending on the crystal composition. Overall, perovskite compositions based on the MA+ cation were found to be less stable than those based on FA+ or Cs+. Metallic lead formation was most easily observed in the chloride perovskite, followed by bromide, and very little in MAPbI3. Multiple degradation processes were identified for the bromide compositions, including ion migration, formation of volatile and solid products, as well as metallic lead. CsBr was formed as a solid degradation product on the surface of CsPbBr3.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Timofei Rostilov, Vadim Ziborov, Alexander Dolgoborodov, Mikhail Kuskov
Summary: The shock-loading behavior of nanomaterials is investigated in this study. It is found that shock compaction waves exhibit a distinct two-step structure, with the formation of faster precursor waves that travel ahead of the main compaction waves. The complexity of the shock Hugoniot curve of the tested nanomaterial is described, and the effect of initial porosity on the compressed states is demonstrated.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Sergey S. Nikitin, Alexander D. Koryakov, Elizaveta A. Antipinskaya, Alexey A. Markov, Mikhail V. Patrakeev
Summary: The stability of La1/3Sr2/3Fe1-xMnxO3-delta, a perovskite-type oxide, under reducing conditions is dependent on the manganese content. Increasing the manganese content leads to a decrease in stability. The behavior of iron and manganese in the oxide shows distinct differences, which can be attributed to the difference in the enthalpy of oxidation reactions. Additionally, the change in the La/Sr ratio affects the concentration of iron and manganese ions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
Article
Chemistry, Physical
Mosayeb Naseri, Shirin Amirian, Mehrdad Faraji, Mohammad Abdur Rashid, Maicon Pierre Lourenco, Venkataraman Thangadurai, D. R. Salahub
Summary: Inspired by the successful transfer of freestanding ultrathin films of SrTiO3 and BiFeO3, this study assessed the structural stability and investigated the electronic, optical, and thermoelectric properties of a group of two-dimensional perovskite-type materials called perovskenes. The findings revealed that these materials are wide bandgap semiconductors with potential application in UV shielding. Moreover, they exhibit better electrical and thermal conductivity at high temperatures, enabling efficient power generation in thermoelectric devices.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2024)
