Thermodynamics and structure of macromolecules from flat-histogram Monte Carlo simulations

W Janke, W Paul - Soft matter, 2016 - pubs.rsc.org
Over the last decade flat-histogram Monte Carlo simulations, especially multi-canonical and
Wang–Landau simulations, have emerged as a strong tool to study the statistical mechanics …

Quantum-inspired encoding enhances stochastic sampling of soft matter systems

F Slongo, P Hauke, P Faccioli, C Micheletti - Science Advances, 2023 - science.org
Quantum advantage in solving physical problems is still hard to assess due to hardware
limitations. However, algorithms designed for quantum computers may engender …

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 …

Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins

YW Li, T Wüst, DP Landau - Physical Review E—Statistical, Nonlinear, and …, 2013 - APS
The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice
proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling …

From polymers to proteins: the effect of side chains and broken symmetry on the formation of secondary structures within a Wang–Landau approach

T Škrbić, A Badasyan, TX Hoang, R Podgornik… - Soft Matter, 2016 - pubs.rsc.org
We use a micro-canonical Wang–Landau technique to study the equilibrium properties of a
single flexible homopolymer where consecutive monomers are represented by impenetrable …

Constraint-handling through multi-objective optimization: The hydrophobic-polar model for protein structure prediction

M Garza-Fabre, E Rodriguez-Tello… - Computers & Operations …, 2015 - Elsevier
In the multi-objective approach to constraint-handling, a constrained problem is transformed
into an unconstrained one by defining additional optimization criteria to account for the …

Multi-objectivization, fitness landscape transformation and search performance: A case of study on the hp model for protein structure prediction

M Garza-Fabre, G Toscano-Pulido… - European Journal of …, 2015 - Elsevier
Multi-objectivization represents a current and promising research direction which has led to
the development of more competitive search mechanisms. This concept involves the …

Applications of the Wang-Landau algorithm to phase transitions of a single polymer chain

MP Taylor, W Paul, K Binder - Polymer Science Series C, 2013 - Springer
Abstract The Wang-Landau (WL) algorithm is a Monte Carlo simulation technique providing
a direct computation of the density of states of a many-body system. The temperature …

Wang–landau reaction ensemble method: Simulation of weak polyelectrolytes and general acid–base reactions

J Landsgesell, C Holm, J Smiatek - Journal of Chemical Theory …, 2017 - ACS Publications
We present a novel method for the study of weak polyelectrolytes and general acid–base
reactions in molecular dynamics and Monte Carlo simulations. The approach combines the …

Stochastic approximation Monte Carlo and Wang–Landau Monte Carlo applied to a continuum polymer model

B Werlich, T Shakirov, MP Taylor, W Paul - Computer Physics …, 2015 - Elsevier
Abstract We discuss Stochastic Approximation Monte Carlo (SAMC) simulations, and Wang–
Landau Monte Carlo (WLMC) simulations as one form of SAMC simulations, in an …