A5100339736- Spectroscopy and Quantum Chemical Studies
- Protein Structure and Dynamics
- Advanced Chemical Physics Studies
- Computational Drug Discovery Methods
- Advanced Thermodynamics and Statistical Mechanics
- Free Radicals and Antioxidants
- Modeling and Simulation Systems
- Quantum, superfluid, helium dynamics
- Mass Spectrometry Techniques and Applications
- DNA and Nucleic Acid Chemistry
- Advanced Decision-Making Techniques
- Advanced Computational Techniques and Applications
- Chemistry and Chemical Engineering
- Refrigeration and Air Conditioning Technologies
- Building Energy and Comfort Optimization
- Rough Sets and Fuzzy Logic
- thermodynamics and calorimetric analyses
- Real-time simulation and control systems
- stochastic dynamics and bifurcation
- Innovation and Knowledge Management
- interferon and immune responses
- Surface Chemistry and Catalysis
- Protein Kinase Regulation and GTPase Signaling
- Magnetic confinement fusion research
- Advanced Breast Cancer Therapies
University of Iowa
2022
East China Normal University
2011-2021
New York University Shanghai
2017-2021
Shanxi University
2020-2021
University of Oklahoma
2017-2021
Hefei National Center for Physical Sciences at Nanoscale
2020-2021
University of Science and Technology of China
2020-2021
Suzhou Research Institute
2020-2021
Sichuan University
2018
University of Wisconsin–Milwaukee
2009-2011
Predicting protein–ligand binding affinities and the associated thermodynamics of biomolecular recognition is a primary objective structure-based drug design. Alchemical free energy simulations offer highly accurate computationally efficient route to achieving this goal. While AMBER molecular dynamics package has successfully been used for alchemical in academic research groups decades, widespread impact industrial discovery settings minimal because previous limitations within code, coupled...
Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and validation mechanism. For chemical reactions in condensed phase or enzymatic reactions, computation FE at ab initio (ai) quantum mechanical/molecular mechanics (QM/MM) level still far too expensive. Although semiempirical (SE) method can be hundreds thousands times faster than ai methods, accuracy SE methods often unsatisfactory due to approximations that have been adopted these methods. In this...
An efficient and accurate reference potential simulation protocol is proposed for producing <italic>ab initio</italic> quantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles chemical reactions in a solvent or macromolecular environment.
The binding affinity between a drug molecule and its target, measured by absolute free energy (ABFE), is crucial factor in the lead discovery phase of development. Recent research has highlighted potential silico ABFE predictions to directly aid development allowing for ranking prioritization promising candidates. This paper introduces an open-source Python workflow called FEP-SPell-ABFE, designed automate calculations with minimal user involvement. requires only three key inputs: receptor...
The binding affinity between a drug molecule and its target, measured by the absolute free energy (ABFE), is crucial factor in lead discovery phase of development. Recent research has highlighted potential silico ABFE predictions to directly aid development allowing for ranking prioritization promising candidates. This work introduces an open-source Python workflow called FEP-SPell-ABFE, designed automate calculations with minimal user involvement. requires only three key inputs: receptor...
The partitioning of solute molecules between immiscible solvents with significantly different polarities is great importance. polarization the and solvent plays an essential role in determining solubility solute, which makes computational studies utilizing molecular mechanics (MM) rather difficult. In contrast, quantum (QM) can provide more reliable predictions. this work, partition coefficients side chain analogs some amino acids water chloroform were computed. QM solvation free energies...
Although quantum mechanical/molecular mechanics (QM/MM) methods are now routinely applied to the studies of chemical reactions in condensed phases and enzymatic reactions, they may experience technical difficulties when reactive region is varying over time. For instance, solvent molecules directly participating reaction, exchange water between QM MM regions occur on a time scale comparable reaction To cope with this situation, several adaptive QM/MM schemes have been proposed. However, these...
Due to the crucial regulatory mechanism of cyclin-dependent kinase 9 (CDK9) in mRNA transcription, development inhibitors targeting CDK9 holds promise as a potential treatment strategy for cancer. A structure-based virtual screening approach has been employed discovery novel inhibitors. First, compounds with inhibitor characteristics were identified from ZINC15 database
Abstract For simulation of centrifugal chiller system with differential algebraic equations, consistent initial conditions are difficult to obtain due the two-phase refrigerant cycle and connections between several components. Existing rigorous initialization methods not suitable for particular problems in simulation, such as surge instability. In this paper, dynamic model a water-cooled is developed Modelica Dymola TLK/IfT Library (TIL). A preprocessing scheme direct method proposed DAE...
Calculations of the free energy profile, also known as potential mean force (PMF), along a chosen collective variable (CV) are now routinely applied in studies chemical processes, such enzymatic reactions and condensed phases. However, if
The microscopic insight into the endo/exo stereoselectivity of Diels–Alder (DA) reaction between cyclopentadiene and methyl vinyl ketone (MVK) has posed a challenge to computational chemists, which requires an accurate free-energy (FE) landscape. Although ab initio (ai) quantum mechanical/molecular mechanical (QM/MM) calculations are capable providing conformation energies, they far too expensive for calculations, in large-scale sampling phase space is always indispensable. Recently, on...
For Diels⁻Alder (DA) reactions in solution, an accurate and converged free energy (FE) surface at ab initio (ai) quantum mechanical/molecular mechanical (QM/MM) level is imperative for the understanding of reaction mechanism. However, this computation still far too expensive. In a previous work, we proposed new method termed MBAR+wTP, with which ai FE profile can be accelerated by several orders magnitude via three-step procedure: (I) umbrella sampling (US) using semi-empirical (SE) QM/MM...
In this work, IPolQ-Mod charges and the reference potential scheme are used to calculate solvation free energies of a set organic molecules. Both methods could capture phase transfer solute with accompanying polarization cost utilizing fixed-charge model. The charges, which average two charge sets fitted in vacuum state condensed phase, take account effect implicitly. For method, quantum mechanics corrections calculated explicitly by thermodynamic perturbation. captured is an approximation...
Alchemical binding free energy (BFE) calculations offer an efficient and thermodynamically rigorous approach to in silico affinity predictions. As a result of decades methodological improvements recent advances computer technology, alchemical BFE are now widely used drug discovery research. They help guide the prioritization candidate molecules by predicting their affinities for biomolecular target interest (and potentially selectivity against undesirable antitargets). Statistical variance...
In this work, both a molecular mechanical (MM) method and hybrid quantum mechanical/molecular (QM/MM) have been applied in the study of binding affinities methyl-α-<sc>l</sc>-fucoside to<italic>Ralstonia solanacearum</italic>lectins.
In this paper the collective behavior and stochastic resonance (SR) phenomenon in a linear underdamped coupled system with multiplicative dichotomous noise periodical driving is investigated. Firstly, stationary solution of mean field stability conditions are obtained by introducing system. Secondly, behaviors particles discussed through studying their synchronization behavior. Finally, range parameters for which SR occurs given, based on conditions. The synchronous phenomenon, as well...
Horizontal interaction and networking between competitors as opposed to vertical value-chain-based linkages has long been under-conceptualized in the literature on internal external structure of clusters. Combining labor mobility/spill-offs, friendship ties among competitors, role trade fairs/professional conferences, competitive interaction, a framework clusters is developed that focuses horizontal dimension an alternative way interpret local learning. This model applied investigate...
Estimation of protein-ligand binding affinity within chemical accuracy is one the grand challenges in structure-based rational drug design. With efforts over three decades, free energy methods based on equilibrium molecular dynamics (MD) simulations have become mature and are nowadays routinely applied community computational chemistry. On contrary, nonequilibrium MD simulation attracted less attention, despite their underlying rigor mathematics potential advantage efficiency. In this work,...
Abstract Coronavirus disease 2019 (COVID-19) is especially severe in aged populations. Resolution of the COVID-19 pandemic has been advanced by recent development SARS-CoV-2 vaccines, but vaccine efficacy partly compromised emergence variants with enhanced transmissibility. The these emphasizes need for further anti-SARS-CoV-2 therapies, Here, we describe isolation a new set highly virulent mouse-adapted viruses and use them to test novel therapeutic drug useful infections animals. Similar...
The binding affinity between a drug molecule and its target, measured by absolute free energy (ABFE), is crucial factor in the lead discovery phase of development. Recent research has highlighted potential silico ABFE predictions to directly aid development allowing for ranking prioritization promising candidates. This paper introduces an open-source Python workflow called FEP-SPell-ABFE, designed automate calculations with minimal user involvement. requires only three key inputs: receptor...
With the rapid development of supercomputers and advances numerical algorithms, nowadays it is possible to study electronic, structural dynamical properties complicated physical systems containing thousands atoms using density functional theory (DFT). The atomic orbitals are ideal basis sets for large-scale DFT calculations in terms their small base size localized characteristic, can be mostly easily combined with linear scaling methods. Here we introduce a first-principles simulation...
For the heating, ventilating, and air conditioning (HVAC) systems for commercial buildings, cooling coils in handling units (AHU) account a significant fraction of total building energy consumption have major impact on comfort conditions maintenance costs. Development cost-effective advanced control strategies will enhance performance efficiency AHU. The design process can be greatly facilitated with simulation high-fidelity dynamic model prior to experimental validation implementation. This...