A coarse-grained MARTINI-like force field for DNA unzipping in nanopores

Coarse-Grained Model for Predicting RNA Folding Thermodynamics

(2013) Natalia A. Denesyuk et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study

(2012) Andrew T. Guy et al.   BIOPHYSICAL JOURNAL

Sequence-dependent thermodynamics of a coarse-grained DNA model

(2012) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

A comparison of the value of viscosity for several water models using Poiseuille flow in a nano-channel

(2012) A. P. Markesteijn et al.   JOURNAL OF CHEMICAL PHYSICS

On developing coarse-grained models for biomolecular simulation: a review

(2012) Sereina Riniker et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations

(2012) Ari Zeida et al.   PHYSICAL REVIEW E

Recent successes in coarse-grained modeling of DNA

(2012) Davit A. Potoyan et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems

(2011) Shina C.L. Kamerlin et al.   Annual Review of Physical Chemistry

Moving beyond Watson–Crick models of coarse grained DNA dynamics

(2011) Margaret C. Linak et al.   JOURNAL OF CHEMICAL PHYSICS

Coarse-Grained Molecular Dynamics Simulation of DNA Translocation in Chemically Modified Nanopores

(2011) Abhijit Ramachandran et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Nanopore sensors for nucleic acid analysis

(2011) Bala Murali Venkatesan et al.   Nature Nanotechnology

Simulating water with rigid non-polarizable models: a general perspective

(2011) Carlos Vega et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Capturing the essence of folding and functions of biomolecules using coarse-grained models

(2011) Changbong Hyeon et al.   Nature Communications

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

(2010) Alex Morriss-Andrews et al.   JOURNAL OF CHEMICAL PHYSICS

A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics

(2010) Pablo D. Dans et al.   Journal of Chemical Theory and Computation

Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?

(2010) Leonardo Darré et al.   Journal of Chemical Theory and Computation

A Coarse-Grained Model of DNA with Explicit Solvation by Water and Ions

(2010) Robert C. DeMille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

(2010) Semen O. Yesylevskyy et al.   PLoS Computational Biology

Microscopic Mechanics of Hairpin DNA Translocation through Synthetic Nanopores

(2009) Jeffrey Comer et al.   BIOPHYSICAL JOURNAL

The persistence length of double stranded DNA determined using dark field tethered particle motion

(2009) Sanneke Brinkers et al.   JOURNAL OF CHEMICAL PHYSICS

Stretching and twisting of the DNA duplexes in coarse-grained dynamical models

(2009) Szymon Niewieczerzał et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

3D-DART: a DNA structure modelling server

(2009) M. van Dijk et al.   NUCLEIC ACIDS RESEARCH

PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy

(2009) Srinivasa M. Gopal et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

What ice can teach us about water interactions: a critical comparison of the performance of different water models

(2008) C. Vega et al.   FARADAY DISCUSSIONS

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

Insights on protein-DNA recognition by coarse grain modelling

(2008) P. Poulain et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

DNA and lipid bilayers: self-assembly and insertion

(2008) S. Khalid et al.   Journal of the Royal Society Interface

Stretching and unzipping nucleic acid hairpins using a synthetic nanopore

(2008) Q. Zhao et al.   NUCLEIC ACIDS RESEARCH