Potential of Mean Force of Short‐Chain Surface Adsorption using Non‐Uniform Sampling Windows for Optimal Computational Efficiency

Processive binding mechanism of Cel9G from Clostridium cellulovorans: molecular dynamics and free energy landscape investigations

(2022) Penghui Li et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Molecular Dynamics Simulations of Human Beta-Defensin Type 3 Crossing Different Lipid Bilayers

(2021) Rabeta Yeasmin et al.   ACS Omega

Surfactant desorption and scission free energies for cylindrical and spherical micelles from umbrella-sampling molecular dynamics simulations

(2021) Boyao Wen et al.   JOURNAL OF COLLOID AND INTERFACE SCIENCE

Adsorption of Epoxy Oligomers on Iron Oxide Surfaces: The Importance of Surface Treatment and the Role of Entropy

(2021) Charlie R. Wand et al.   LANGMUIR

Effects of Nanoparticle Electrostatics and Protein–Protein Interactions on Corona Formation: Conformation and Hydrodynamics

(2020) Hwankyu Lee   Small

Theoretical Rationalization of Self-Assembly of Cellulose Nanocrystals: Effect of Surface Modifications and Counterions

(2020) Mohit Garg et al.   BIOMACROMOLECULES

Cellulose nanocrystal structure in the presence of salts

(2019) Aref Abbasi Moud et al.   CELLULOSE

Efficient Construction of Free Energy Profiles of Breathing Metal–Organic Frameworks Using Advanced Molecular Dynamics Simulations

(2017) Ruben Demuynck et al.   Journal of Chemical Theory and Computation

Sampling errors in free energy simulations of small molecules in lipid bilayers

(2016) Chris Neale et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Stable Aqueous Foams from Cellulose Nanocrystals and Methyl Cellulose

(2016) Zhen Hu et al.   BIOMACROMOLECULES

Gaining insight into cell wall cellulose macrofibril organisation by simulating microfibril adsorption

(2015) Daniel P. Oehme et al.   CELLULOSE

Calculating the free energy of transfer of small solutes into a model lipid membrane: Comparison between metadynamics and umbrella sampling

(2015) Davide Bochicchio et al.   JOURNAL OF CHEMICAL PHYSICS

Temperature and Loading-Dependent Diffusion of Light Hydrocarbons in ZIF-8 as Predicted Through Fully Flexible Molecular Simulations

(2015) Ross J. Verploegh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Theory of Adaptive Optimization for Umbrella Sampling

(2014) Soohyung Park et al.   Journal of Chemical Theory and Computation

Tuning Cellulose Nanocrystal Gelation with Polysaccharides and Surfactants

(2014) Zhen Hu et al.   LANGMUIR

Hierarchical Multiscale Modeling of Polymer–Solid Interfaces: Atomistic to Coarse-Grained Description and Structural and Conformational Properties of Polystyrene–Gold Systems

(2013) Karen Johnston et al.   MACROMOLECULES

Using collective variables to drive molecular dynamics simulations

(2013) Giacomo Fiorin et al.   MOLECULAR PHYSICS

Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly

(2012) Soohyung Park et al.   Journal of Chemical Theory and Computation

Cellulose-Builder: A toolkit for building crystalline structures of cellulose

(2012) Thiago C. F. Gomes et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Transmembrane Helix Assembly by Window Exchange Umbrella Sampling

(2012) Soohyung Park et al.   PHYSICAL REVIEW LETTERS

Convergence of the Restricted Nelder--Mead Algorithm in Two Dimensions

(2012) Jeffrey C. Lagarias et al.   SIAM JOURNAL ON OPTIMIZATION

Potential of mean force for separation of the repeating units in cellulose and hemicellulose

(2011) Suma Peri et al.   CARBOHYDRATE RESEARCH

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

(2011) Fangqiang Zhu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Decrystallization of Oligosaccharides from the Cellulose Iβ Surface with Molecular Simulation

(2011) Christina M. Payne et al.   Journal of Physical Chemistry Letters

Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance

(2011) Hyung Min Cho et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

PACKMOL: A package for building initial configurations for molecular dynamics simulations

(2009) L. Martínez et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water

(2009) Halvor S. Hansen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

On the Mechanism of Surfactant Adsorption on Solid Surfaces: Free-Energy Investigations

(2008) Zhijun Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B