Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes

What are the true values of the bending modulus of simple lipid bilayers?

(2015) John F. Nagle et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Dynamic Kerr Effect Study on Six-Membered-Ring Molecular Liquids: Benzene, 1,3-Cyclohexadiene, 1,4-Cyclohexadiene, Cyclohexene, and Cyclohexane

(2015) Shohei Kakinuma et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Recent developments in the field of bending rigidity measurements on membranes

(2014) Rumiana Dimova   ADVANCES IN COLLOID AND INTERFACE SCIENCE

Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations

(2014) Zachary A. Levine et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Experimental Support for Tilt-Dependent Theory of Biomembrane Mechanics

(2014) M. S. Jablin et al.   PHYSICAL REVIEW LETTERS

A guiding potential method for evaluating the bending rigidity of tensionless lipid membranes from molecular simulation

(2013) Shuhei Kawamoto et al.   JOURNAL OF CHEMICAL PHYSICS

Determining the bending modulus of a lipid membrane by simulating buckling

(2013) Patrick Diggins et al.   JOURNAL OF CHEMICAL PHYSICS

CHARMM36 United Atom Chain Model for Lipids and Surfactants

(2013) Sarah Lee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Molecular Structure of the Liquid-Ordered Phase of Lipid Bilayers

(2013) Alexander J. Sodt et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Plasma membrane organization and function: moving past lipid rafts

(2013) Mary L. Kraft   MOLECULAR BIOLOGY OF THE CELL

Using collective variables to drive molecular dynamics simulations

(2013) Giacomo Fiorin et al.   MOLECULAR PHYSICS

Computer simulation studies of self-assembling macromolecules

(2012) Wataru Shinoda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Heating and flooding: A unified approach for rapid generation of free energy surfaces

(2012) Ming Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids

(2012) Joakim P. M. Jämbeck et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Determining Biomembrane Bending Rigidities from Simulations of Modest Size

(2012) Max C. Watson et al.   PHYSICAL REVIEW LETTERS

Interpretation of Fluctuation Spectra in Lipid Bilayer Simulations

(2011) Erik G. Brandt et al.   BIOPHYSICAL JOURNAL

Determination of Electron Density Profiles and Area from Simulations of Undulating Membranes

(2011) Anthony R. Braun et al.   BIOPHYSICAL JOURNAL

Premicelles and monomer exchange in aqueous surfactant solutions above and below the critical micelle concentration

(2011) David N. LeBard et al.   CHEMICAL PHYSICS LETTERS

Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics

(2011) Benjamin G. Levine et al.   Journal of Chemical Theory and Computation

Update of the Cholesterol Force Field Parameters in CHARMM

(2011) Joseph B. Lim et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-grained force field for ionic surfactants

(2011) Wataru Shinoda et al.   Soft Matter

Raft registration across bilayers in a molecularly detailed model

(2011) Diego A. Pantano et al.   Soft Matter

A Structurally Relevant Coarse-Grained Model for Cholesterol

(2010) K.R. Hadley et al.   BIOPHYSICAL JOURNAL

Implementing molecular dynamics on hybrid high performance computers – short range forces

(2010) W. Michael Brown et al.   COMPUTER PHYSICS COMMUNICATIONS

Parametrization and Application of a Coarse Grained Force Field for Benzene/Fullerene Interactions with Lipids

(2010) Russell DeVane et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field

(2010) Wataru Shinoda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Cholesterol Flip-Flop: Insights from Free Energy Simulation Studies

(2010) Sunhwan Jo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Lipid Rafts As a Membrane-Organizing Principle

(2010) D. Lingwood et al.   SCIENCE

Self-Assembly of Janus Dendrimers into Uniform Dendrimersomes and Other Complex Architectures

(2010) V. Percec et al.   SCIENCE

Effect of cholesterol on the rigidity of saturated and unsaturated membranes: fluctuation and electrodeformation analysis of giant vesicles

(2010) Rubèn Serral Gracià et al.   Soft Matter

Stiffening Effect of Cholesterol on Disordered Lipid Phases: A Combined Neutron Spin Echo + Dynamic Light Scattering Analysis of the Bending Elasticity of Large Unilamellar Vesicles

(2009) Laura R. Arriaga et al.   BIOPHYSICAL JOURNAL

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

Systematic coarse graining from structure using internal states: Application to phospholipid/cholesterol bilayer

(2009) Teemu Murtola et al.   JOURNAL OF CHEMICAL PHYSICS

Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids

(2009) Russell DeVane et al.   Journal of Chemical Theory and Computation

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables

(2009) Jérome Hénin et al.   Journal of Chemical Theory and Computation

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

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

The Functional Significance of Lipid Diversity: Orientation of Cholesterol in Bilayers Is Determined by Lipid Species

(2009) Norbert Kučerka et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular View of Cholesterol Flip-Flop and Chemical Potential in Different Membrane Environments

(2009) W. F. Drew Bennett et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Effect of cholesterol on structural and mechanical properties of membranes depends on lipid chain saturation

(2009) Jianjun Pan et al.   PHYSICAL REVIEW E

Effect of cholesterol on the structure of a phospholipid bilayer

(2009) F. de Meyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detailed molecular dynamics simulations of model biological membranes containing cholesterol

(2008) Max L. Berkowitz   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Polyunsaturated fatty acid–cholesterol interactions: Domain formation in membranes

(2008) Stephen R. Wassall et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Energetics of Cholesterol Transfer between Lipid Bilayers

(2008) Zhancheng Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Cholesterol Perturbs Lipid Bilayers Nonuniversally

(2008) Jianjun Pan et al.   PHYSICAL REVIEW LETTERS

The molecular face of lipid rafts in model membranes

(2008) H. J. Risselada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems

(2008) M. L. Klein et al.   SCIENCE

A Quantitative Coarse-Grain Model for Lipid Bilayers

(2007) Mario Orsi et al.   JOURNAL OF PHYSICAL CHEMISTRY B