Multiscale methods framework: self-consistent coupling of molecular theory of solvation with quantum chemistry, molecular simulations, and dissipative particle dynamics

Computational ‘microscopy’ of cellular membranes

(2016) Helgi I. Ingólfsson et al.   JOURNAL OF CELL SCIENCE

MTS-MD of Biomolecules Steered with 3D-RISM-KH Mean Solvation Forces Accelerated with Generalized Solvation Force Extrapolation

(2015) Igor Omelyan et al.   Journal of Chemical Theory and Computation

A review of methods for the calculation of solution free energies and the modelling of systems in solution

(2015) R. E. Skyner et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The Subtle Balance between Lipolysis and Lipogenesis: A Critical Point in Metabolic Homeostasis

(2015) Chiara Saponaro et al.   Nutrients

An Analysis Platform for Multiscale Hydrogeologic Modeling with Emphasis on Hybrid Multiscale Methods

(2014) Timothy D. Scheibe et al.   Groundwater

Dissipative Particle Dynamics with an Effective Pair Potential from Integral Equation Theory of Molecular Liquids

(2014) Alexander E. Kobryn et al.   JOURNAL OF PHYSICAL CHEMISTRY B

What is a Multiscale Problem in Molecular Dynamics?

(2013) Luigi Site   Entropy

Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: Accelerating with advanced extrapolation of effective solvation forces

(2013) Igor Omelyan et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale modeling of solvation in chemical and biological nanosystems and in nanoporous materials

(2013) Andriy Kovalenko   PURE AND APPLIED CHEMISTRY

Efficient treatment of solvation shells in 3D molecular theory of solvation

(2012) Sergey Gusarov et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Coarse-Grained Modeling of Polystyrene in Various Environments by Iterative Boltzmann Inversion

(2012) Beste Bayramoglu et al.   MACROMOLECULES

Generalised canonical–isokinetic ensemble: speeding up multiscale molecular dynamics and coupling with 3D molecular theory of solvation

(2012) Igor Omelyan et al.   MOLECULAR SIMULATION

Interpretation of atomic motion in flexible molecules: Accelerating molecular dynamics simulations

(2012) Igor Omelyan et al.   PHYSICAL REVIEW E

Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules

(2011) Guillaume Chevrot et al.   JOURNAL OF CHEMICAL PHYSICS

Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. I. Microcanonical ensemble

(2011) Igor P. Omelyan et al.   JOURNAL OF CHEMICAL PHYSICS

Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. II. Canonical and isokinetic ensembles

(2011) Igor P. Omelyan et al.   JOURNAL OF CHEMICAL PHYSICS

Overcoming the Barrier on Time Step Size in Multiscale Molecular Dynamics Simulation of Molecular Liquids

(2011) Igor P. Omelyan et al.   Journal of Chemical Theory and Computation

Multiscale methods for nanochemistry and biophysics in solution

(2011) Andriy Kovalenko et al.   JOURNAL OF MOLECULAR LIQUIDS

3D-RISM-KH approach for biomolecular modelling at nanoscale: thermodynamics of fibril formation and beyond

(2011) Nikolay Blinov et al.   MOLECULAR SIMULATION

Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

(2010) Tyler Luchko et al.   Journal of Chemical Theory and Computation

Modeling Solvatochromic Shifts Using the Orbital-Free Embedding Potential at Statistically Mechanically Averaged Solvent Density

(2010) Jakub W. Kaminski et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Spatial Decomposition of Solvation Free Energy Based on the 3D Integral Equation Theory of Molecular Liquid: Application to Miniproteins

(2010) Takeshi Yamazaki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Anesthetic Sensitivity of the Gloeobacter violaceus Proton-Gated Ion Channel

(2009) Yun Weng et al.   ANESTHESIA AND ANALGESIA

Structural Water Drives Self-assembly of Organic Rosette Nanotubes and Holds Host Atoms in the Channel

(2009) Takeshi Yamazaki et al.   CHEMPHYSCHEM

Spatial Decomposition Analysis of the Thermodynamics of Cyclodextrin Complexation

(2009) Takeshi Yamazaki et al.   Journal of Chemical Theory and Computation

Ab Initio Study of Ionic Liquids by KS-DFT/3D-RISM-KH Theory

(2009) Marco Malvaldi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

One-Pot Nucleation, Growth, Morphogenesis, and Passivation of 1.4 nm Au Nanoparticles on Self-Assembled Rosette Nanotubes

(2009) Rahul Chhabra et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Concurrently coupled atomistic and XFEM models for dislocations and cracks

(2008) Robert Gracie et al.   INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING

Eckart axis conditions, Gauss’ principle of least constraint, and the optimal superposition of molecular structures

(2008) Gerald R. Kneller   JOURNAL OF CHEMICAL PHYSICS

Molecular Recognition in Biomolecules Studied by Statistical-Mechanical Integral-Equation Theory of Liquids

(2008) Norio Yoshida et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hierarchical Self-Assembly of Organic Prolate Nanospheroids from Hydrophobic Rosette Nanotubes

(2008) Grigory Tikhomirov et al.   LANGMUIR

X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation

(2008) Nicolas Bocquet et al.   NATURE

Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution

(2007) Tatsuhiko Miyata et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY