Force fields for simulating the interaction of surfaces with biological molecules

Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene

(2015) Tigran M. Abramyan et al.   Biointerphases

Facet selectivity in gold binding peptides: exploiting interfacial water structure

(2015) Louise B. Wright et al.   Chemical Science

Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene

(2015) Tigran M. Abramyan et al.   Biointerphases

Biofunctionalization of surfaces by energetic ion implantation: Review of progress on applications in implantable biomedical devices and antibody microarrays

(2014) Marcela M.M. Bilek   APPLIED SURFACE SCIENCE

Surface plasma modification and tropoelastin coating of a polyurethane co-polymer for enhanced cell attachment and reduced thrombogenicity

(2014) Daniel V. Bax et al.   BIOMATERIALS

Prediction of Specific Biomolecule Adsorption on Silica Surfaces as a Function of pH and Particle Size

(2014) Fateme S. Emami et al.   CHEMISTRY OF MATERIALS

Force Field and a Surface Model Database for Silica to Simulate Interfacial Properties in Atomic Resolution

(2014) Fateme S. Emami et al.   CHEMISTRY OF MATERIALS

Perspectives on the simulation of protein–surface interactions using empirical force field methods

(2014) Robert A. Latour   COLLOIDS AND SURFACES B-BIOINTERFACES

Interaction with a Gold Surface Reshapes the Free Energy Landscape of Alanine Dipeptide

(2014) Luca Bellucci et al.   Journal of Physical Chemistry C

Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model

(2014) Jing Huang et al.   Journal of Physical Chemistry Letters

Computational Prediction of Circular Dichroism Spectra and Quantification of Helicity Loss upon Peptide Adsorption on Silica

(2014) Robert H. Meißner et al.   LANGMUIR

Molecular dynamics simulation of protein effects on interfacial energy between HA surfaces and solutions

(2014) Kefeng Wang et al.   MATERIALS LETTERS

Efficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model

(2014) Zak E. Hughes et al.   Nanoscale

Bio-Activation of Polyether Ether Ketone Using Plasma Immersion Ion Implantation: A Kinetic Model

(2014) Edgar A. Wakelin et al.   Plasma Processes and Polymers

Electronic Properties of a Graphene Device with Peptide Adsorption: Insight from Simulation

(2013) Brahim Akdim et al.   ACS Applied Materials & Interfaces

Perspective on the Martini model

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

On the Calculation of Solid-Fluid Contact Angles from Molecular Dynamics

(2013) Erik Santiso et al.   Entropy

GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100)

(2013) Louise B. Wright et al.   Journal of Chemical Theory and Computation

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

Free Energy of Adsorption for a Peptide at a Liquid/Solid Interface via Nonequilibrium Molecular Dynamics

(2013) Milan Mijajlovic et al.   LANGMUIR

Biomolecular Adsorption at Aqueous Silver Interfaces: First-Principles Calculations, Polarizable Force-Field Simulations, and Comparisons with Gold

(2013) Zak E. Hughes et al.   LANGMUIR

Circular Dichroism Analysis of Cyclic β-Helical Peptides Adsorbed on Planar Fused Quartz

(2013) Kenan P. Fears et al.   LANGMUIR

Exhaustively Sampling Peptide Adsorption with Metadynamics

(2013) Michael Deighan et al.   LANGMUIR

Thermodynamically Consistent Force Fields for the Assembly of Inorganic, Organic, and Biological Nanostructures: The INTERFACE Force Field

(2013) Hendrik Heinz et al.   LANGMUIR

Principles of Biofouling Protection in Marine Sponges: A Model for the Design of Novel Biomimetic and Bio-inspired Coatings in the Marine Environment?

(2013) Werner E. G. Müller et al.   MARINE BIOTECHNOLOGY

From macromolecules to electrons—grand challenges in theoretical and computational chemistry

(2013) Thomas S. Hofer   Frontiers in Chemistry

The Gold Standard: Gold Nanoparticle Libraries To Understand the Nano–Bio Interface

(2012) Alaaldin M. Alkilany et al.   ACCOUNTS OF CHEMICAL RESEARCH

Development of a Tuned Interfacial Force Field Parameter Set for the Simulation of Protein Adsorption to Silica Glass

(2012) James A. Snyder et al.   Biointerphases

Comparison Between Empirical Protein Force Fields for the Simulation of the Adsorption Behavior of Structured LK Peptides on Functionalized Surfaces

(2012) Galen Collier et al.   Biointerphases

Influence of pH on yeast immobilization on polystyrene surfaces modified by energetic ion bombardment

(2012) Clara T.H. Tran et al.   COLLOIDS AND SURFACES B-BIOINTERFACES

Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior

(2012) Pradip K. Biswas et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Biomimetic and bioinspired silica: recent developments and applications

(2011) Siddharth V. Patwardhan   CHEMICAL COMMUNICATIONS

Molecular Simulation on the Interactions of Water with Polypropylene Surfaces

(2011) Zheng-Wei Dai et al.   Journal of Physical Chemistry C

Development of the CHARMM Force Field for Lipids

(2011) R. W. Pastor et al.   Journal of Physical Chemistry Letters

Structure of Peptides on Metal Oxide Surfaces Probed by NMR

(2011) Peter A. Mirau et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Probing surface tension additivity on chemically heterogeneous surfaces by a molecular approach

(2011) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent developments and applications of the CHARMM force fields

(2011) Xiao Zhu et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Peptide Interactions with Metal and Oxide Surfaces

(2010) Anne Vallee et al.   ACCOUNTS OF CHEMICAL RESEARCH

How Can Hydrophobic Association Be Enthalpy Driven?

(2010) Piotr Setny et al.   Journal of Chemical Theory and Computation

The temperature intervals with global exchange of replicas empirical accelerated sampling method: Parameter sensitivity and extension to a complex molecular system

(2010) Xianfeng Li et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Polarization at metal-biomolecular interfaces in solution

(2010) H. Heinz et al.   Journal of the Royal Society Interface

Assessment of the Transferability of a Protein Force Field for the Simulation of Peptide-Surface Interactions

(2010) Nadeem A. Vellore et al.   LANGMUIR

Influence of nanoscale surface topography on protein adsorption and cellular response

(2010) Megan S. Lord et al.   Nano Today

The linker-free covalent attachment of collagen to plasma immersion ion implantation treated polytetrafluoroethylene and subsequent cell-binding activity

(2009) Daniel V. Bax et al.   BIOMATERIALS

TIGER2: An improved algorithm for temperature intervals with global exchange of replicas

(2009) Xianfeng Li et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of the Extended Isotropic Periodic Sum and Particle Mesh Ewald Methods for Simulations of Lipid Bilayers and Monolayers

(2009) Richard M. Venable et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Nature of Molecular Interactions of Peptides with Gold, Palladium, and Pd−Au Bimetal Surfaces in Aqueous Solution

(2009) Hendrik Heinz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Benchmark Experimental Data Set and Assessment of Adsorption Free Energy for Peptide−Surface Interactions

(2009) Yang Wei et al.   LANGMUIR

Dewetting and Hydrophobic Interaction in Physical and Biological Systems

(2008) Bruce J. Berne et al.   Annual Review of Physical Chemistry

Potential of mean force calculations of ligand binding to ion channels from Jarzynski’s equality and umbrella sampling

(2008) Turgut Baştuğ et al.   JOURNAL OF CHEMICAL PHYSICS

GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water

(2008) F. Iori et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12−6 and 9−6 Lennard-Jones Potentials

(2008) Hendrik Heinz et al.   Journal of Physical Chemistry C

Determination of the Surface pKof Carboxylic- and Amine-Terminated Alkanethiols Using Surface Plasmon Resonance Spectroscopy

(2008) Kenan P. Fears et al.   LANGMUIR

Modelling the nanoscale patterning of nucleic acid base pairs deposited on graphite

(2008) T. R. Walsh   MOLECULAR PHYSICS

Innate and adaptive immune responses in tissue engineering

(2008) Michael V. Sefton et al.   SEMINARS IN IMMUNOLOGY