Publications

Publication:The Journal of Chemical Physics
Authors:Dr. Huimin Cheng, Dr. Dong Fang, Dr Mingjun Yang et al.
Date:Jan. 31, 2019

Enhanced QM/MM sampling for free energy calculation of chemical reactions: A case study of double proton transfer

J. Chem. Phys. 150, 044111 (2019)

Free energy calculations for chemical reactions with a steep energy barrier require well defined reaction coordinates (RCs). However, when multiple parallel channels exist along selected RC, the application of conventional enhanced samplings is difficult to generate correct sampling within li…

Publication:Catalysis Science & Technology
Authors:Dr. Mingjun Yang et al.
Date:Dec. 6, 2018

Understanding the entropic effect in chorismate mutase reaction catalyzed by isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB)

Catal. Sci. Technol., 2019,9, 957-965

Elucidation of the role of entropy in enzymatic reactions can be utilized in the de novo design of enzymes or protein engineering. Recently, the change in entropy in the enzyme-catalyzed chorismate mutase reaction brought about uncertainty as a result of an experiment using PchB, in …

Publication:Crystal Growth Design
Authors:Dr. Peiyu Zhang et al.
Date:Nov. 18, 2018

Harnessing Cloud Architecture for Crystal Structure Prediction Calculations

Cryst. Growth Des. 2018, 18, 11, 6891-6900

Accurate and rapid crystal structure predictions have the potential to transform the development of new materials, particularly in fields with highly complex molecular structures (such as in drug development). In this work we present a novel cloud-computing crystal structure prediction (CSP) platform with the capability of scheduling hundreds of thousands CPU cores and integrating cutting-edge computational chemistry algorithms.…

Publication:Science Advances
Authors:Dr. Peiyu Zhang et al.
Date:May 11, 2018

Tuning Peptide Self-Assembly by An In-Tether Chiral Center

Sci. Adv. 2018;4: eaar5907

The self-assembly of peptides into ordered nanostructures is important for understanding both peptide molecular interactions and nanotechnological applications. However, because of the complexity and various self-assembling pathways of peptide molecules, design of self-assembling helical pepti…

Publication:Journal of Chemical Theory and Computation
Authors:Dr. Mingjun Yang et al.
Date:April 25, 2018

CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses

J. Chem. Theory Comput. 2018, 14, 6, 3132-3143

We present an extension of the CHARMM Drude polarizable force field to enable modeling of polysaccharides containing pyranose and furanose monosaccharides. The new force field parameters encompass 1↔2, 1→3, 1→4, and 1→6 pyranose–furanose linkages, 2→1 and 2→…

Publication:Carbohydrate Research
Authors:Dr. Mingjun Yang et al.
Date:March 2, 2018

Proper Balance of Solvent-Solute and Solute-Solute Interactions in the Treatment of the Diffusion of Glucose Using the Drude Polarizable Force Field

Carbohydrate Research, Volume 457, 2018, pp. 41-50

Motivated by underestimation of the diffusion constant of glucose in aqueous solution at high glucose concentrations we performed additional optimization of the Drude polarizable hexopyranose monosaccharide force field. This indicated aggregation of the glucose at higher concentrations, which …