Generic, hierarchical framework for massively parallel Wang-Landau sampling

T Vogel, YW Li, T Wüst, DP Landau - Physical review letters, 2013 - APS
We introduce a parallel Wang-Landau method based on the replica-exchange framework for
Monte Carlo simulations. To demonstrate its advantages and general applicability for …

Scalable replica-exchange framework for Wang-Landau sampling

T Vogel, YW Li, T Wüst, DP Landau - Physical Review E, 2014 - APS
We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations
based on the Wang-Landau method. To demonstrate its advantages and general …

[BOOK][B] Thermodynamics and statistical mechanics of macromolecular systems

M Bachmann - 2014 - books.google.com
The structural mechanics of proteins that fold into functional shapes, polymers that
aggregate and form clusters, and organic macromolecules that bind to inorganic matter can …

Effect of grafting density on the adsorption of end-grafted polymer chains

HK Qi, X Yang, QH Yang, MB Luo - Polymer, 2022 - Elsevier
The critical adsorption temperature (T CAP) and adsorption process of end-grafted polymer
chains with grafting density f on a homogeneous, attractive surface are studied using …

A new paradigm for petascale Monte Carlo simulation: Replica exchange Wang-Landau sampling

YW Li, T Vogel, T Wüst, DP Landau - Journal of Physics …, 2014 - iopscience.iop.org
We introduce a generic, parallel Wang-Landau method that is naturally suited to
implementation on massively parallel, petaflop supercomputers. The approach introduces a …

Effects of knots on protein folding properties

MA Soler, PFN Faisca - PloS one, 2013 - journals.plos.org
This work explores the impact of knots, knot depth and motif of the threading terminus in
protein folding properties (kinetics, thermodynamics and mechanism) via extensive Monte …

Height switching in mixed polymer brushes with polymers of different stiffnesses

X Yang, JH Huang, IV Mikhailov, AA Polotsky… - …, 2020 - ACS Publications
The conformational properties of mixed polymer brushes made of polymers with different
stiffnesses are studied by using Monte Carlo computer simulations and the Scheutjens …

Effect of single-site mutations on hydrophobic-polar lattice proteins

G Shi, T Vogel, T Wüst, YW Li, DP Landau - Physical Review E, 2014 - APS
We developed a heuristic method for determining the ground-state degeneracy of
hydrophobic-polar (HP) lattice proteins, based on Wang-Landau and multicanonical …

Study on the adsorption process of a semi-flexible polymer onto homogeneous attractive surfaces

X Yang, QH Yang, Y Fu, F Wu, JH Huang, MB Luo - Polymer, 2019 - Elsevier
The dynamic adsorption process of a semi-flexible polymer onto homogeneous attractive
surfaces is studied using dynamic Monte Carlo simulations. The adsorption time increases …

Designs to improve capability of neural networks to make structural predictions

TY Wang, JF Li, HD Zhang, JZY Chen - Chinese Journal of Polymer …, 2023 - Springer
A deep neural network model generally consists of different modules that play essential
roles in performing a task. The optimal design of a module for use in modeling a physical …