Yu Liu

University of California, Riverside, Riverside, California, United States

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Publications (28)89.72 Total impact

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    ABSTRACT: Most chemical engineering processes involve complex multiphase fluid systems, and their evolution depends on the mechanism by which the inhomogeneous subsystems exchange information at different length scales. Whereas numerous theoretical methods with specific description accuracies have been developed for investigating physicochemical properties of various fluid systems, a unified theory that enables the investigation of mesoscale problems is still needed. Here, we introduce a unified framework of multiscale density functional theories (DFTs). With the same physical concept and mathematical framework four different versions of DFTs, covering quantum, atomic, molecular, and polymeric DFTs, are presented complemented with their illustrative applications at individual scales. In addition, the combinations of those DFTs with each other and with other conventional theories and simulation approaches are also discussed. Finally, general discussions on the up-to-date progress of DFTs and the expectations on their further extensions are given. The introduction of this unified framework of DFTs is expected to advance the theoretical study of mesoscale problems.
    No preview · Article · Dec 2015
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    ABSTRACT: High-throughput screening of desulfurization adsorbent has been implemented by introducing a classical density functional theory (CDFT). The screening is focused on the adsorption capacity of dibenzothiophene (DBT) in 458 types of metal–organic frameworks (MOFs). Comparing to the state of art desulfurization adsorbent, the best MOF for low concentration (BMLC) shows an uptake 27 times of HKUST-1 while the best MOF for high concentration (BMHC) shows an uptake twice of HKUST-1. Hierarchical porous structure has been found in BMLC and BMHC, respectively. According to the radial distribution function, a layered adsorption mechanism has been found in BMLC instead of BMHC; and the thermodynamic differences between BMLC and BMHC can be understood by this lamellar adsorption mechanism.
    No preview · Article · Dec 2015 · Chemical Engineering Science
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    ABSTRACT: DNA melting has attracted much attention due to its importance in understanding the life-reproduction and metabolism and in the applications of modern DNA-based technologies. While numerous works have been contributed to the determination of melting profiles in diverse environments, the understanding of DNA melting dynamics is still limited. By employing three-site-per-nucleotide (3SPN) double-stranded DNA (dsDNA) model, we here demonstrate the melting dynamics of an isolated short dsDNA under different conditions (different temperatures, ionic concentrations and DNA chain lengths) can be accessed by coarse-grained simulation studies. We particularly show that at dilute ionic concentration the dsDNA, regardless being symmetric or asymmetric, opens at both ends with roughly equal probabilities, while at high ionic concentration the asymmetric dsDNA chain opens at the A-T-rich end. The comparisons of our simulation results to available data are discussed, and overall good agreements have been found.
    Preview · Article · Dec 2015 · SpringerPlus
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    Jia Fu · Yu Liu · Jianzhong Wu
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    ABSTRACT: Recent developments in physical and computer sciences enable quantitative predictions the kinetics of chemical reactions and thermodynamic data from first principles by multiscale modeling. The hierarchical approach integrates different theoretical frameworks ranging from those describing physical phenomena at the electronic length and time scales to those pertinent to complex biomolecular systems and macroscopic phase transitions, promising broad applications to problems of practical concern. Whereas multiscale modeling has been emerging as a popular computational tool, the connection between calculations at different scales is far from being coherent, and the multiple choices of quantum/classical methods at each scale renders numerous combinations that have been rarely calibrated against extensive experimental data. In this work, we have examined a multiscale procedure for predicting the solvation free energies of a large set of small molecules in liquid water at ambient conditions. Using the experimental data for the hydration free energies as a benchmark, we find that the theoretical results are sensitive to selection of quantum-mechanical methods for determining atomic charges and solute configurations, assignment of the force-field parameters in particular the atomic partial charges, and approximations in the statistical–mechanical calculations. Because of significant uncertainties in quantum-mechanical calculations and the semi-empirical nature of force-field models, computational efficiency makes the classical density functional theory a valuable alternative to molecular simulations for future development and application of multiscale modeling methods.
    Full-text · Article · Apr 2015 · Chemical Engineering Science
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    ABSTRACT: High-throughput prediction of H2 adsorption in MOF materials has been extended from a few specific conditions to the whole T, p space. The prediction is based on a classical density functional theory and has been implemented over 712 MOFs in 441 different conditions covering a wide range. Some testing materials show excellent behavior at low temperatures and obvious improvement at high temperatures compared to conventional MOFs. The structures of the best MOFs at high and low temperatures are totally different. Linear and nonlinear correlations between the two Langmuir parameters have been found at high and low temperatures, respectively. According to the analysis of the excess uptake, we found that the saturated pressure increases along with temperature in the low temperature region but decreases in the high temperature region. This article is protected by copyright. All rights reserved.
    No preview · Article · Apr 2015 · AIChE Journal
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    Jia Fu · Yu Liu · Yun Tian · Jianzhong Wu
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    ABSTRACT: Classical density functional theory (DFT) has been routinely used for the characterization of pore size distribution and specific surface area of porous materials by gas physisorption. However, its application to large-scale screening of materials for gas storage has been largely unexplored because it is commonly believed that the DFT calculations are applicable only to one-dimensional systems and highly sensitive to the approximations introduced in the free-energy functionals. In this work, we have investigated four representative versions of nonlocal density functionals for predicting H2 adsorption using both the slit pore model and a large library of metal-organic frameworks (MOFs) under a broad range of temperatures and pressures. The four versions of DFT share a common functional from the modified fundamental measure theory to account for the molecular excluded volume effects while differing in their approximations to represent the intermolecular attractions, viz., mean-field approximation, two versions of weighted-density approximations (WDA), and the quadratic functional expansion method. We have tested these functionals by extensive comparison with Monte Carlo simulation data for H2 adsorption at conditions of practical interest. Overall all four versions of DFT are reasonably accurate in comparison with the simulation results. While the density expansion method performs rather well at the DOE target condition for hydrogen storage, the WDA methods are found most accurate at low temperature, a condition typically used in materials characterization. In addition to rapid prediction of the adsorption isotherms, DFT is able to generate molecular density profiles revealing microscopic details such as favorable adsorption sites. From a computational perspective, the DFT calculation is at least 1 order of magnitude faster than conventional simulation methods, promising for large-scale screening of nanostructured materials for gas storage.
    Full-text · Article · Sep 2014 · The Journal of Physical Chemistry C
  • Yu Liu · Jianzhong Wu
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    ABSTRACT: We introduce a modified classical mapping method to predict the exchange-correlation free energy and the structure of homogeneous electron gases (HEG) at finite temperature. With the classical map temperature parameterized on the basis of the quantum Monte Carlo simulation data for the correlation energy and exact results at high and low temperature limits, the new theoretical procedure greatly improves the classical mapping method for correlating the energetic properties HEG over a broad range of thermodynamic conditions. Improvement can also be identified in predicting the long-range components of the spin-averaged pair correlation functions.
    No preview · Article · Aug 2014 · The Journal of Chemical Physics
  • Yu Liu · Jianzhong Wu
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    ABSTRACT: Predicting the correct binding curves of H2(+) and H2 systems presents a great challenge in current applications of electronic density functional theory. Here we report a new functional for the exchange-correlation energy based on the weighted density approximation and the classical mapping method. With the exact sum rule for the exchange-correlation hole and accurate correlation functions of uniform electrons as the input, the new functional is free of delocalization and static correlation errors. It yields the exact results for any one-electron systems and the correct asymptotic limit of the binding energy between hydrogen atoms.
    No preview · Article · Jul 2014 · Physical Chemistry Chemical Physics
  • Yu Liu · Jianzhong Wu
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    ABSTRACT: Relativistic effect is important in many quantum systems but theoretically complicated from both fundamental and practical perspectives. Herein we introduce an efficient computational procedure to predict the structure and energetic properties of relativistic quantum systems by mapping the Pauli principle into an effective pairwise-additive potential such that the properties of relativistic nonquantum systems can be readily predicted from conventional liquid-state methods. We applied our theoretical procedure to relativistic uniform electron gases and compared the pair correlation functions with those for systems of nonrelativistic electrons. A simple analytical expression has been developed to correlate the exchange-correlation free energy of relativistic uniform electron systems.
    No preview · Article · Jul 2014 · Physical Review E
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    Jia Fu · Yu Liu · Jianzhong Wu
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    ABSTRACT: We report the performance of a classical density functional theory (CDFT) in the competition for the solvation free-energy category of the SAMPL4 blind prediction event. The theoretical calculations were carried out with the TIP3P water model and different combinations of solute configurations and molecular force fields. In comparison with the experimental data, the blind test yields an average unsigned error of 2.38 kcal/mol and the root mean square deviation of 2.99 kcal/mol. Whereas these numbers are significantly larger than the best results from explicit-solvent MD simulations, we find that the theoretical performance is sensitive to both the molecular force fields and solute configurations and that a comparable level of accuracy can be achieved by a judicious selection of the solute configurations and the force-field parameters. Most importantly, CDFT reduces the computational cost of MD simulation by almost 3 orders of magnitude, making it very attractive for large-scale hydration free-energy calculations (e.g., screening the aqueous solubility of drug-like molecules).
    Full-text · Article · Mar 2014 · Journal of Computer-Aided Molecular Design
  • Yu Liu · Jianzhong Wu
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    ABSTRACT: Efficient and accurate prediction of the correlation functions of uniform electron gases is of great importance for both practical and theoretical applications. This paper presents a bridge-functional-based classical mapping method for calculating the correlation functions of uniform spin-unpolarized electron gases at finite temperature. The bridge functional is formulated by following Rosenfeld's universality ansatz in combination with the modified fundamental measure theory. The theoretical predictions are in good agreement with recent quantum Monte Carlo results but with negligible computational cost, and the accuracy is better than a previous attempt based on the hypernetted-chain approximation. We find that the classical mapping method is most accurate if the effective mass of electrons increases as the density falls.
    No preview · Article · Feb 2014 · The Journal of Chemical Physics
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    Yu Liu · Jia Fu · Jianzhong Wu
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    ABSTRACT: The classical density functional theory (DFT) is proposed as an efficient computational tool for high-throughput prediction of the solvation free energies of small molecules in liquid water under the ambient condition. With the solute molecules represented by the AMBER force field and the TIP3P model for the solvent, the new theoretical method predicts the hydration free energies of 500 neutral molecules with average unsigned errors of 0.96 and 1.04 kcal/mol in comparison with the experimental and simulation data, respectively. The DFT predictions are orders of magnitude faster than conventional molecular dynamics simulations, and the theoretical performance can be further improved by taking into account the molecular flexibility of large solutes.
    Full-text · Article · Oct 2013 · Journal of Physical Chemistry Letters
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    Yu Liu · Jia Fu · Jianzhong Wu
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    ABSTRACT: We present an efficient computation procedure for rapid prediction of the self-diffusivity of gas molecules in nanoporous materials by a combination of the Knudsen model, Rosenfeld's excess entropy scaling method, and a classical density functional theory (DFT). The self-diffusivity conforms to the Knudsen model at low density, and the effects of intermolecular interactions at higher densities are accounted for by Rosenfeld's excess-entropy scaling method. The classical DFT provides a convenient way to calculate the excess entropy used in the scaling analysis. The hybrid computational procedure has been calibrated with MD simulation for the adsorption of H2, He, Ne and Ar gases in several nanoporous materials over a broad range of pressure. It predicts adsorption isotherms and different types of diffusion behavior in excellent agreement with the simulation results. While simulation of gas diffusion in nanoporous materials is extremely time consuming, the new procedure is computationally very efficient because it uses only single molecular and thermodynamic parameters.
    Full-text · Article · Sep 2013 · Langmuir
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    ABSTRACT: Direct correlation functions (DCFs) play a pivotal role in the applications of classical density functional theory (DFT) to addressing the thermodynamic properties of inhomogeneous systems beyond the local-density or mean-field approximations. Whereas numerous studies have been dedicated to the radial distribution functions of liquid water - the most important solvent on earth, relatively little attention has been given to the site-site DCFs. The water DCFs are long-ranged and difficult to calculate directly by simulation, and the predictions from conventional liquid-state theories have been rarely calibrated. Here we report a computational procedure for accurate evaluation of the site-site DCFs of liquid water based on three popular molecular models (viz., SPC, SPC∕E, and TIP3P). The numerical results provide a benchmark for calibration of conventional liquid-state theories and fresh insights into development of new DFT methods. We show that: (1) the long-range behavior of the site-site DCFs depends on both the molecular model and the thermodynamic condition; (2) the asymptotic limit of DCFs at large distance does not follow the mean-spherical approximation (MSA); (3) individual site-site DCFs are long ranged (∼40 nm) but a summation of all DCF pairs exhibits only short-range behavior (∼1 nm or a few water diameters); (4) the site-site bridge correlation functions behave as the DCFs, i.e., they are also long-ranged while the summation of all bridge correlation functions is short ranged. Our analytical and numerical analyses of the DCFs provide some simple strategies for possible improvement of the numerical performance of conventional liquid-state theories.
    Full-text · Article · Aug 2013 · The Journal of Chemical Physics
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    Yu Liu · Jianzhong Wu
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    ABSTRACT: At ambient conditions the intermolecular correlation in liquid water is generally believed to be short ranged as shown in the atomic pair distribution functions (PDFs) obtained from scattering experiments or from theoretical predictions. However, atom-atom PDFs provide only a partial description of the higher dimensional intermolecular correlation function that depends on both the positions and orientations of water molecules. Here we study the atomic PDFs of liquid water as well as the angular correlation function (ACF) using a classical density functional theory. We demonstrate that, different from the PDFs, the ACF exhibits long-range oscillatory decay extending up to tens of molecular diameters. The theoretical predictions are in good agreement with molecular simulations and corroborate recent experimental results from the second harmonic light scattering experiments.
    Full-text · Article · Jul 2013 · The Journal of Chemical Physics
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    ABSTRACT: A novel method for real-time monitoring of the oxidative response of a membrane-channel biomimetic system (MCBS) to free radicals is developed and the deduction of the buffering effect of MCBS is discussed.
    Full-text · Article · Apr 2013 · Chemical Communications
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    ABSTRACT: We report a site density functional theory (SDFT) based on the conventional atomistic models of water and the universality ansatz of the bridge functional. The excess Helmholtz energy functional is formulated in terms of a quadratic expansion with respect to the local density deviation from that of a uniform system and a universal functional for all higher-order terms approximated by that of a reference hard-sphere system. With the atomistic pair direct correlation functions of the uniform system calculated from MD simulation and an analytical expression for the bridge functional from the modified fundamental measure theory, the SDFT can be used to predict the structure and thermodynamic properties of water under inhomogeneous conditions with a computational cost negligible in comparison to that of brute-force simulations. The numerical performance of the SDFT has been demonstrated with the predictions of the solvation free energies of 15 molecular analogs of amino acid side chains in water represented by SPC/E, SPC, and TIP3P models. For theTIP3P model, a comparison of the theoretical predictions with MD simulation and experimental data shows agreement within 0.64 and 1.09 kcal/mol on average, respectively.
    No preview · Article · Mar 2013 · Journal of Chemical Theory and Computation
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    ABSTRACT: Many important cellular events, including protein-DNA interactions, are attributed to weak interactions. Almost all of the known biological functions of P53 depend critically upon its DNA-binding properties via numerous weak interactions. At the single-molecule level, information about the weak interactions between each residue of the P53 DNA binding domain (P53 DBD) and DNA is essential for understanding the biological function of P53 and for anti-cancer drug design. Here, we used the alpha-hemolysin (alpha-HL) pore to detect the weak interaction between a peptide of the P53 DBD (P53-P) and a 40-bp double-stranded DNA (B40) that includes the p21(wafl/cipl) DNA response element. The weak interactions in the complex of p53-P and B40 (p53-P:B40) produce a unique current trace through an alpha-HL nanopore with diagnostic ionic current blockages. Each current trace at a particular potential is related to the characterized behavior of captured p53-P:B40. Nanopore analysis indicates that the conformation of B40 might be changed by binding to p53-P, this change is confirmed by the molecule docking simulation. In the presence of the weak interactions between p53-P and B40, the analyte exhibits an increase in the rate constant of association with the nanopore vestibule. This reveals that the analyte-pore interactions could be enhanced by the weak interactions between p53-P and B40. The distorted B40 might be prone to translocate through the narrow constriction in the nanopore at the higher potential (> + 120 mV). Moreover, our findings demonstrate that the structure of distorted B40 in p53-P:B40 could be broken by the electric force. Our results support the possibility of identifying the weak interaction between two biomolecules. In addition, the analyte-pore association rate constant could be used to estimate the weak binding energy between different parts of the p53 binding domain and the target sequence. The signatures of the current trace may assist in the prediction of the conformational changes of biomolecules at the single-molecule level. Our observations suggest that a biological alpha-HL nanopore could be a candidate biosensor for predicting the conformational changes that result from weak interactions.
    Preview · Article · Jan 2013 · Acta Chimica Sinica -Chinese Edition-
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    ABSTRACT: A molecular thermodynamic model is developed to examine crowding effect on DNA melting. Each pair of nucleotides in double-stranded DNA and each nucleotide in single-stranded DNA are represented by two types of charged Lennard-Jones segments, respectively. Water molecules are mimicked explicitly as spherical particles, embedded in a dielectric continuum. Crowders with varying concentration, size, interaction strength, and chain length are considered. For DNA with a sequence of A(20), the melting temperature is predicted to increase by 1 K in the presence of Ficoll70 and by 7.5 K in the presence of Ficoll70-polyvinyl pyrrolidone360 mixture. The predictions agree well with experimental data. Furthermore, the melting temperature is found to increase with increasing crowder size, but reduce with increasing interaction strength and crowder length. The predicted changes of Gibbs energy, entropy and enthalpy are consistent with experimentally measured values. The study reveals that DNA melting in a crowded environment is influenced by both entropic and enthalpic effects.
    No preview · Article · Oct 2012 · Physical Chemistry Chemical Physics
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    ABSTRACT: Two peptide-oligonucleotide conjugates are studied using an α-hemolysin nanopore to investigate their structural properties at the single-molecule level.
    No preview · Article · Jul 2012 · Chemical Communications

Publication Stats

269 Citations
89.72 Total Impact Points

Institutions

  • 2013-2015
    • University of California, Riverside
      • Department of Chemical and Environmental Engineering
      Riverside, California, United States
  • 2009-2015
    • East China University of Science and Technology
      • School of Chemistry and Molecular Engineering
      Shanghai, Shanghai Shi, China
  • 2008
    • National University of Singapore
      • Department of Chemical & Biomolecular Engineering
      Tumasik, Singapore