arXiv subjects

Minghong G. Wu

Publications and source records attributed to Minghong G. Wu.

4 recordsLinked to original sources

arXiv2001

Calculating the r^{-n} Interactions, 1<= n< 3, in a Periodic System with a Neutralizing Background Charge Density

The $r^{-n}$ interaction energy, $1\leq n< 3$, for a infinitely periodic system with explicit charges and a neutralizing, uniform background charge density is derived. An Ewald based expression for this energy has an extra term proportional to the square of the total explicit charges of the system. This expression may be useful for simulations in which explicit charge neutrality does not hold or for which the total explicit charges is a fluctuating quantity.

cond-mat.mtrl-sci↗

arXiv2001

Monte Carlo Study of the Nucleation Process during Zeolite Synthesis

An atomic-scale model for silicate solutions is introduced for investigation of the nucleation process during zeolite synthesis in the absence of a structure directing agent. Monte Carlo schemes are developed to determine the equilibrium distribution of silicate cluster sizes within the context of this model. How the nucleation barrier and critical cluster size change with Si monomer concentration is discussed. Distance and angle histograms as well as ring size distributions are calculated and compared with known zeolite structures. The free energies of critical clusters are compared with those for small clusters of alpha-quartz.

cond-mat.stat-mech↗

arXiv1999

Analytical Rebridging Monte Carlo: Application to cis/trans Isomerization in Proline-Containing, Cyclic Peptides

We present a new method, the analytical rebridging scheme, for Monte Carlo simulation of proline-containing, cyclic peptides. The cis/trans isomerization is accommodated by allowing for two states of the amide bond. We apply our method to five peptides that have been previously characterized by NMR methods. Our simulations achieve effective equilibration and agree well with experimental data in all cases. We discuss the importance of effective equilibration and the role of bond flexibility and solvent effects on the predicted equilibrium properties.

physics.chem-ph↗

arXiv1999

Efficient Monte Carlo Methods for Cyclic Peptides

We present a new, biased Monte Carlo scheme for simulating complex, cyclic peptides. Backbone atoms are equilibrated with a biased rebridging scheme, and side-chain atoms are equilibrated with a look-ahead configurational bias Monte Carlo. Parallel tempering is shown to be an important ingredient in the construction of an efficient approach.

physics.bio-ph↗