Density functional tight binding-based free energy simulations in the DFTB+ program

Metadynamics Enhanced Markov Modeling of Protein Dynamics

(2018) Mithun Biswas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Metadynamics combined with auxiliary density functional and density functional tight-binding methods: alanine dipeptide as a case study

(2017) Jerome Cuny et al.   JOURNAL OF MOLECULAR MODELING

Corannulene–fullerene C70 noncovalent interactions and their effect on the behavior of charge transport and optical property

(2017) Yan-Zhi Liu et al.   RSC Advances

Implementation of replica-exchange umbrella sampling in the DFTB+ semiempirical quantum chemistry package

(2016) Shingo Ito et al.   COMPUTER PHYSICS COMMUNICATIONS

A global reaction route mapping-based kinetic Monte Carlo algorithm

(2016) Izaac Mitchell et al.   JOURNAL OF CHEMICAL PHYSICS

QM/MM free energy simulations: recent progress and challenges

(2016) Xiya Lu et al.   MOLECULAR SIMULATION

Porphyrins bearing corannulene pincers: outstanding fullerene receptors

(2016) Pablo A. Denis et al.   RSC Advances

On-the-Fly Kinetic Monte Carlo Simulation of Aqueous Phase Advanced Oxidation Processes

(2015) Xin Guo et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solution based upon a mixed quantum–classical approximation. II. Proton transfer reaction in non-polar solvent

(2015) H. Kojima et al.   JOURNAL OF CHEMICAL PHYSICS

Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

(2015) Riccardo Petraglia et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Inversion and rotation processes involving non-planar aromatic compounds catalyzed by extended polycyclic aromatic hydrocarbons

(2014) Amir Karton   CHEMICAL PHYSICS LETTERS

A molecular dynamics study of intramolecular proton transfer reaction of malonaldehyde in solutions based upon mixed quantum-classical approximation. I. Proton transfer reaction in water

(2014) Atsushi Yamada et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models

(2014) Puja Goyal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

3-Dimensional atomic scale structure of the ionic liquid–graphite interface elucidated by AM-AFM and quantum chemical simulations

(2014) Alister J. Page et al.   Nanoscale

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

(2013) Michele Ceriotti et al.   COMPUTER PHYSICS COMMUNICATIONS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Adsorption and Diffusion of Oxygen on Single-Layer Graphene with Topological Defects

(2013) Faisal Mehmood et al.   Journal of Physical Chemistry C

Quantum chemical investigation of epoxide and ether groups in graphene oxide and their vibrational spectra

(2013) Alister J. Page et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations

(2013) Yoshiharu Mori et al.   PHYSICAL REVIEW E

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

(2013) D. Granata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origin of the Chemical and Kinetic Stability of Graphene Oxide

(2013) Si Zhou et al.   Scientific Reports

Parametrization and Benchmark of DFTB3 for Organic Molecules

(2012) Michael Gaus et al.   Journal of Chemical Theory and Computation

Establishing Uniform Acceptance in Force Biased Monte Carlo Simulations

(2012) E. C. Neyts et al.   Journal of Chemical Theory and Computation

Two-dimensional nucleation and growth mechanism explaining graphene oxide structures

(2012) Manh-Thuong Nguyen et al.   PHYSICAL REVIEW B

Domain formation on oxidized graphene

(2012) M. Topsakal et al.   PHYSICAL REVIEW B

New advances in metadynamics

(2012) Ludovico Sutto et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Oxygen migration on the graphene surface. 2. Thermochemistry of basal-plane diffusion (hopping)

(2011) Ljubisa R. Radovic et al.   CARBON

DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)

(2011) Michael Gaus et al.   Journal of Chemical Theory and Computation

Mechanisms for Oxidative Unzipping and Cutting of Graphene

(2011) Tao Sun et al.   NANO LETTERS

Gate-Voltage Control of Oxygen Diffusion on Graphene

(2011) Alejandro M. Suarez et al.   PHYSICAL REVIEW LETTERS

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS