Molecular Modeling for Nanomaterial–Biology Interactions: Opportunities, Challenges, and Perspectives

Computational Modeling of Realistic Cell Membranes

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

In Silico Study of Gold Nanoparticle Uptake into a Mammalian Cell: Interplay of Size, Shape, Surface Charge, and Aggregation

(2019) Thodsaphon Lunnoo et al.   Journal of Physical Chemistry C

Design and Development of Biomimetic Nanovesicles Using a Microfluidic Approach

(2018) Roberto Molinaro et al.   ADVANCED MATERIALS

Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation

(2018) Arushi Prakash et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Fixed-Charge Atomistic Force Fields for Molecular Dynamics Simulations in the Condensed Phase: An Overview

(2018) Sereina Riniker   Journal of Chemical Information and Modeling

Modular assembly of proteins on nanoparticles

(2018) Wenwei Ma et al.   Nature Communications

Atomistic Details of Chymotrypsin Conformational Changes upon Adsorption on Silica

(2018) Nils Hildebrand et al.   ACS Biomaterials-Science & Engineering

Au Nanoparticles in Lipid Bilayers: A Comparison between Atomistic and Coarse-Grained Models

(2017) Sebastian Salassi et al.   Journal of Physical Chemistry C

Effect of Concentration on the Supramolecular Polymerization Mechanism via Implicit-Solvent Coarse-Grained Simulations of Water-Soluble 1,3,5-Benzenetricarboxamide

(2017) Davide Bochicchio et al.   Journal of Physical Chemistry Letters

Probing the modulated formation of gold nanoparticles–beta-lactoglobulin corona complexes and their applications

(2017) Jiang Yang et al.   Nanoscale

Exploring Protein-Nanoparticle Interactions with Coarse-Grained Protein Folding Models

(2017) Shuai Wei et al.   Small

Protein corona and nanoparticles: how can we investigate on?

(2017) Francesca Pederzoli et al.   Wiley Interdisciplinary Reviews-Nanomedicine and Nanobiotechnology

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

Validating lipid force fields against experimental data: Progress, challenges and perspectives

(2016) David Poger et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Computational ‘microscopy’ of cellular membranes

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

Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model

(2016) Karl T. Debiec et al.   Journal of Chemical Theory and Computation

Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations

(2016) Mickaël Lelimousin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling

(2016) Callum J. Dickson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Understanding of the Penetration of Functionalized Gold Nanoparticles into Asymmetric Membranes

(2016) Xuebo Quan et al.   LANGMUIR

Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

(2016) Yinglong Miao et al.   MOLECULAR SIMULATION

The interaction with gold suppresses fiber-like conformations of the amyloid β (16–22) peptide

(2016) Luca Bellucci et al.   Nanoscale

Understanding the curvature effect of silica nanoparticles on lysozyme adsorption orientation and conformation: a mesoscopic coarse-grained simulation study

(2016) Gaobo Yu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Reduced Cytotoxicity of Graphene Nanosheets Mediated by Blood-Protein Coating

(2015) Yu Chong et al.   ACS Nano

Contribution of Electrostatics in the Fibril Stability of a Model Ionic-Complementary Peptide

(2015) Marta Owczarz et al.   BIOMACROMOLECULES

Coarse-grained model of adsorption of blood plasma proteins onto nanoparticles

(2015) Hender Lopez et al.   JOURNAL OF CHEMICAL PHYSICS

A Comprehensive Computational Study of the Interaction between Human Serum Albumin and Fullerenes

(2015) Georgios Leonis et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Competitive Binding of Proteins to Gold Nanoparticles Disclosed by Molecular Dynamics Simulations

(2015) Francesco Tavanti et al.   Journal of Physical Chemistry C

Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps

(2015) Pratyush Tiwary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Glycan Role in the Glycopeptide Immunogenicity Revealed by Atomistic Simulations and Spectroscopic Experiments on the Multiple Sclerosis Biomarker CSF114(Glc)

(2015) Agostino Bruno et al.   Scientific Reports

Surface Curvature Relation to Protein Adsorption for Carbon-based Nanomaterials

(2015) Zonglin Gu et al.   Scientific Reports

Protein Interactions with Polymer Coatings and Biomaterials

(2014) Qiang Wei et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Dissipative Particle Dynamics (DPD): An Overview and Recent Developments

(2014) M. B. Liu et al.   ARCHIVES OF COMPUTATIONAL METHODS IN ENGINEERING

Computer simulation of the role of protein corona in cellular delivery of nanoparticles

(2014) Hong-ming Ding et al.   BIOMATERIALS

Endocytosis of PEGylated nanoparticles accompanied by structural and free energy changes of the grafted polyethylene glycol

(2014) Ying Li et al.   BIOMATERIALS

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

(2014) Jason M. Swails et al.   Journal of Chemical Theory and Computation

Modeling the effect of nano-sized polymer particles on the properties of lipid membranes

(2014) Giulia Rossi et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Lipid Organization of the Plasma Membrane

(2014) Helgi I. Ingólfsson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Histidine Adsorption on TiO2 Nanoparticles: An Integrated Spectroscopic, Thermodynamic, and Molecular-Based Approach toward Understanding Nano–Bio Interactions

(2014) Imali A. Mudunkotuwa et al.   LANGMUIR

Can small hydrophobic gold nanoparticles inhibit β2-microglobulin fibrillation?

(2014) Giorgia Brancolini et al.   Nanoscale

Theoretical and Computational Investigations of Nanoparticle-Biomembrane Interactions in Cellular Delivery

(2014) Hong-ming Ding et al.   Small

Computational investigation of the influence of chain length on the shielding effect of PEGylated nanoparticles

(2014) Yang Li et al.   RSC Advances

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

Revealing the Binding Structure of the Protein Corona on Gold Nanorods Using Synchrotron Radiation-Based Techniques: Understanding the Reduced Damage in Cell Membranes

(2013) Liming Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Exhaustively Sampling Peptide Adsorption with Metadynamics

(2013) Michael Deighan et al.   LANGMUIR

Funnel metadynamics as accurate binding free-energy method

(2013) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Understanding and modulating the competitive surface-adsorption of proteins through coarse-grained molecular dynamics simulations

(2013) Pol Vilaseca et al.   Soft Matter

Role of physicochemical properties of coating ligands in receptor-mediated endocytosis of nanoparticles

(2012) Hong-ming Ding et al.   BIOMATERIALS

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble

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

Beyond the lipid-bilayer: interaction of polymers and nanoparticles with membranes

(2012) Matthias Schulz et al.   Soft Matter

Understanding and controlling the interaction of nanomaterials with proteins in a physiological environment

(2011) Carl D. Walkey et al.   CHEMICAL SOCIETY REVIEWS

Molecular Dynamics Simulations of the Adsorption of Bone Morphogenetic Protein-2 on Surfaces with Medical Relevance

(2011) Tillmann Utesch et al.   LANGMUIR

The dynamic behaviours of protein BMP-2 on hydroxyapatite nanoparticles

(2011) Xiu-Li Dong et al.   MOLECULAR SIMULATION

Binding of blood proteins to carbon nanotubes reduces cytotoxicity

(2011) C. Ge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Penetration of Lipid Membranes by Gold Nanoparticles: Insights into Cellular Uptake, Cytotoxicity, and Their Relationship

(2010) Jiaqi Lin et al.   ACS Nano

Computer simulation of the translocation of nanoparticles with different shapes across a lipid bilayer

(2010) Kai Yang et al.   Nature Nanotechnology

Modeling the Time Evolution of the Nanoparticle-Protein Corona in a Body Fluid

(2010) Daniele Dell'Orco et al.   PLoS One

Understanding biophysicochemical interactions at the nano–bio interface

(2009) Andre E. Nel et al.   NATURE MATERIALS

Protein adsorption on tailored substrates: long-range forces and conformational changes

(2008) M Bellion et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Nanoparticle size and surface properties determine the protein corona with possible implications for biological impacts

(2008) M. Lundqvist et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA