Xiao Zhu

发表

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

Alexander D. MacKerell, Pedro E. M. Lopes, M. Feig, 2012, Journal of chemical theory and computation.

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field.

Alexander D. MacKerell, Pedro E. M. Lopes, B. Roux, 2010, Journal of chemical theory and computation.

Establishing Effective Simulation Protocols for β- and α/β-Mixed Peptides. I. QM and QM/MM Models.

Q. Cui, Xiao Zhu, A. Yethiraj, 2007, Journal of chemical theory and computation.

Complexation process of amylose under different concentrations of linoleic acid using molecular dynamics simulation.

O. Campanella, Xiao Zhu, B. Hamaker, 2019, Carbohydrate polymers.

Modeling DNA-bending in the nucleosome: role of AA periodicity.

J. Widom, G. Schatz, Xiao Zhu, 2011, The journal of physical chemistry. B.

Local DNA dynamics shape mutational patterns of mononucleotide repeats in human genomes

D. Cooper, K. Howells, Xiao Zhu, 2015, Nucleic acids research.

A molecular dynamics simulation study on the conformational stability of amylose-linoleic acid complex in water.

O. Campanella, Xiao Zhu, B. Hamaker, 2018, Carbohydrate polymers.

Toward molecular models of proton pumping: Challenges, methods and relevant applications

Q. Cui, Xiao Zhu, D. Riccardi, 2012, Science China Chemistry.

A modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions.

Q. Cui, Xiao Zhu, M. Elstner, 2012, Journal of chemical theory and computation.

A novel calcium-binding peptide from Antarctic krill protein hydrolysates and identification of binding sites of calcium-peptide complex.

Xiao Zhu, Ba-fang Li, Qiqi Li, 2018, Food chemistry.

Establishing effective simulation protocols for β‐ and α/β‐peptides. III. Molecular mechanical model for acyclic β‐amino acids

Xiao Zhu, Qiang Cui, Peter Koenig, 2010, Journal of computational chemistry.

Recent developments and applications of the CHARMM force fields

Xiao Zhu, Alexander D. MacKerell, Pedro E. M. Lopes, 2012, Wiley interdisciplinary reviews. Computational molecular science.

Molecular Dynamics Simulations and Experimental Verification to Determine Mechanism of Cosolvents on Increased 5-Hydroxymethylfurfural Yield from Glucose

N. Mosier, Xiao Zhu, Jonathan C. Overton, 2019, ACS Sustainable Chemistry & Engineering.

Surface photochemistry 15: On the role of substrate excitation

Xiao Zhu, J. White, A. Campion, 1990 .

Molecular Simulation Study Conformation and Energy of Polyaniline/Graphite Composites

Xiao Zhu, Shengrong Yang, Z. Mo, 2013 .

Characterization of Interactions between Curcumin and Different Types of Lipid Bilayers by Molecular Dynamics Simulation.

Xiao Zhu, J. Mondal, G. Narsimhan, 2018, The journal of physical chemistry. B.

Potential of mean force for insertion of antimicrobial peptide melittin into a pore in mixed DOPC/DOPG lipid bilayer by molecular dynamics simulation.

Ganesan Narsimhan, Xiao Zhu, G. Narsimhan, 2017, The Journal of chemical physics.

Molecular dynamics study of the role of the spine of hydration in DNA A-tracts in determining nucleosome occupancy.

G. Schatz, Xiao Zhu, 2012, The journal of physical chemistry. B.

Atomistic simulations of dilute polyelectrolyte solutions.

Xiao Zhu, Soohyung Park, A. Yethiraj, 2012, The journal of physical chemistry. B.

(Ala)4‐X‐(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side‐chain dihedral empirical force field parameters

Xiao Zhu, Alexander D. MacKerell, Robert B. Best, 2013, J. Comput. Chem..

Intrinsic Energy Landscapes of Amino Acid Side-Chains

Xiao Zhu, Alexander D. MacKerell, Pedro E. M. Lopes, 2012, J. Chem. Inf. Model..

Sequence-dependent pKa shift induced by molecular self-assembly: insights from computer simulation.

Q. Cui, Xiao Zhu, J. Mondal, 2012, The journal of physical chemistry. B.

Effect of immobilization on the antimicrobial activity of a cysteine-terminated antimicrobial Peptide Cecropin P1 tethered to silica nanoparticle against E. coli O157:H7 EDL933.

A. Bhunia, Xiao Zhu, G. Narsimhan, 2017, Colloids and surfaces. B, Biointerfaces.

Molecular Dynamics Study of Pore Formation by Melittin in a 1,2-Dioleoyl-sn-glycero-3-phosphocholine and 1,2-Di(9Z-octadecenoyl)-sn-glycero-3-phospho-(1′-rac-glycerol) Mixed Lipid Bilayer

Xiao Zhu, G. Narsimhan, Ning Xiang, 2015 .

Polarizable empirical force field for sulfur‐containing compounds based on the classical Drude oscillator model

Xiao Zhu, Alexander D. MacKerell, Xiao Zhu, 2010, J. Comput. Chem..

Self-Assembly of β-Peptides: Insight from the Pair and Many-Body Free Energy of Association

Q. Cui, Xiao Zhu, J. Mondal, 2010 .

Sequence-dependent interaction of β-peptides with membranes.

Arun Yethiraj, Jagannath Mondal, Qiang Cui, 2010, The journal of physical chemistry. B.

Complexation of 26-Mer Amylose with Egg Yolk Lipids with Different Numbers of Tails Using a Molecular Dynamics Simulation

Xiao Zhu, Xueming Xu, G. Narsimhan, 2021, Foods.

Development of the Charmm Polarizable Force Field for Polypeptides Based on Drude Oscillators

Alexander D. MacKerell, Pedro E. M. Lopes, B. Roux, 2011 .

A Quantitative Assessment of the Conformational Heterogeneity in Amylose across Force Fields.

Xiao Zhu, J. Mondal, J. Koneru, 2019, Journal of chemical theory and computation.

Polyphenols Weaken Pea Protein Gel by Formation of Large Aggregates with Diminished Noncovalent Interactions.

O. Campanella, Xiao Zhu, J. Ilavsky, 2021, Biomacromolecules.

Sequence-dependent interaction of β-peptides with membranes.

Q. Cui, Xiao Zhu, A. Yethiraj, 2010, The journal of physical chemistry. B.

An implicit solvent model for SCC-DFTB with Charge-Dependent Radii.

Guanhua Hou, Qiang Cui, Q. Cui, 2010, Journal of chemical theory and computation.

Single Conformation Spectroscopy of Suberoylanilide Hydroxamic Acid: A Molecule Bites Its Tail.

Xiao Zhu, Karl N. Blodgett, T. Zwier, 2017, The journal of physical chemistry. A.

Effect of immobilization on the antimicrobial activity of a cysteine-terminated antimicrobial Peptide Cecropin P1 tethered to silica nanoparticle against E. coli O157:H7 EDL933.

A. Bhunia, Xiao Zhu, G. Narsimhan, 2017, Colloids and surfaces. B, Biointerfaces.