Exploring the Molecular Dynamics of a Lipid-A Vesicle at the Atom Level: Morphology and Permeation Mechanism

Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape

(2022) Denys E. S. Santos et al.   Journal of Chemical Information and Modeling

Distinguishing Weak and Strong Hydrogen Bonds in Liquid Water—A Potential of Mean Force-Based Approach

(2021) Aswin V. Muthachikavil et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Simulations of Gram-Negative Bacterial Membranes Come of Age

(2020) Wonpil Im et al.   Annual Review of Physical Chemistry

Aggregation of Lipid A variants: A hybrid particle-field model

(2020) Antonio De Nicola et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Outermembrane lipid secretion and the innate immune response to Gram-negative bacteria.

(2020) Nicole P. Giordano et al.   INFECTION AND IMMUNITY

Computational Modeling of Realistic Cell Membranes

(2019) Siewert J. Marrink et al.   CHEMICAL REVIEWS

SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces

(2019) Denys E. S. Santos et al.   Journal of Chemical Information and Modeling

Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment

(2018) Hima Bindu Kolli et al.   Journal of Chemical Theory and Computation

Polymyxin Binding to the Bacterial Outer Membrane Reveals Cation Displacement and Increasing Membrane Curvature in Susceptible but Not in Resistant Lipopolysaccharide Chemotypes

(2017) Denys E. S. Santos et al.   Journal of Chemical Information and Modeling

CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

(2017) Pin-Chia Hsu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Toward Chemically Resolved Computer Simulations of Dynamics and Remodeling of Biological Membranes

(2017) Thereza A. Soares et al.   Journal of Physical Chemistry Letters

Structure and function: Lipid A modifications in commensals and pathogens

(2016) Alex Steimle et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

A MARTINI extension for Pseudomonas aeruginosa PAO1 lipopolysaccharide

(2016) Brad Van Oosten et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Hybrid particle–field molecular dynamics simulation for polyelectrolyte systems

(2016) You-Liang Zhu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Simulating Gram-Negative Bacterial Outer Membrane: A Coarse Grain Model

(2015) Huilin Ma et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics

(2013) Emilia L. Wu et al.   BIOPHYSICAL JOURNAL

Hydration, ionic valence and cross-linking propensities of cations determine the stability of lipopolysaccharide (LPS) membranes

(2013) Agrinaldo Nascimento et al.   CHEMICAL COMMUNICATIONS

A multiscale approach to triglycerides simulations: from atomistic to coarse-grained models and back

(2012) Antonio Brasiello et al.   FARADAY DISCUSSIONS

The Effect of Temperature, Cations, and Number of Acyl Chains on the Lamellar to Non-Lamellar Transition in Lipid-A Membranes: A Microscopic View

(2012) Frederico J. S. Pontes et al.   Journal of Chemical Theory and Computation

A Glycam-Based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation

(2012) Karl N. Kirschner et al.   Journal of Chemical Theory and Computation

Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks

(2012) Ying Zhao et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Effects of Specific versus Nonspecific Ionic Interactions on the Structure and Lateral Organization of Lipopolysaccharides

(2011) Christoph Jeworrek et al.   BIOPHYSICAL JOURNAL

Hybrid Particle-Field Coarse-Grained Models for Biological Phospholipids

(2011) Antonio De Nicola et al.   Journal of Chemical Theory and Computation

Electroporation of the E. coli and S. Aureus Membranes: Molecular Dynamics Simulations of Complex Bacterial Membranes

(2011) Thomas J. Piggot et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Pressure calculation in hybrid particle-field simulations

(2010) Giuseppe Milano et al.   JOURNAL OF CHEMICAL PHYSICS

Hybrid particle-field molecular dynamics simulations for dense polymer systems

(2009) Giuseppe Milano et al.   JOURNAL OF CHEMICAL PHYSICS

Effect of Cations on the Structure of Bilayers Formed by Lipopolysaccharides Isolated from Pseudomonas aeruginosa PAO1

(2008) Norbert Kučerka et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Assessment of the convergence of molecular dynamics simulations of lipopolysaccharide membranes

(2008) T.A. Soares et al.   MOLECULAR SIMULATION