© 2019 American Chemical Society. A model for carboxylic acids, in both the protonated and deprotonated states, is developed in which hydrogen interaction sites are not used and all interactions are short-ranged. A method for constant pH simulations, which exploits these features of the model, is developed. The constant pH method samples protonation states by making discrete Monte Carlo steps and is able to efficiently move between states in two steps. The method is applied to the polymer poly(methacrylic acid), a pH-responsive polymer that undergoes structural changes as a function of pH. The model is able to reproduce the structural changes induced by pH
The role of protonated nucleotides in modulating the pH-dependent properties of nucleic acids is one...
pH is a ubiquitous regulator of biological activity, with widespread impact ranging from its role in...
A central problem in computational biophysics is the treatment of titratable residues in molecular d...
In this work, we deliver a proof of concept for a fast method that introduces pH effects into classi...
ABSTRACT: By utilizing Graphics Processing Units, we show that constant pH molecular dynamics simula...
The accuracy of computational models for simulating biomolecules under specific solution pH conditio...
An accurate description of the protonation state of amino acids is essential to correctly simulate t...
In constant pH molecular dynamics simulations, the protonation states of titratable sites can respon...
Long chain fatty acids are biologically important molecules with complex and pH sensitive aggregatio...
pH dependence abounds in biochemical systems; however, many simulation methods used to investigate t...
Solvent pH is an important property that defines the protonation state of the amino acids and, there...
Protonation states of titratable amino acids play a key role in many biomolecular processes. Knowled...
AbstractThe current article describes a new two-dimensional λ-dynamics method to include proton taut...
pH is an important parameter in condensed-phase systems, because it determines the protonation state...
We present a simulation method that allows us to calculate the titration curves for systems undergoi...
The role of protonated nucleotides in modulating the pH-dependent properties of nucleic acids is one...
pH is a ubiquitous regulator of biological activity, with widespread impact ranging from its role in...
A central problem in computational biophysics is the treatment of titratable residues in molecular d...
In this work, we deliver a proof of concept for a fast method that introduces pH effects into classi...
ABSTRACT: By utilizing Graphics Processing Units, we show that constant pH molecular dynamics simula...
The accuracy of computational models for simulating biomolecules under specific solution pH conditio...
An accurate description of the protonation state of amino acids is essential to correctly simulate t...
In constant pH molecular dynamics simulations, the protonation states of titratable sites can respon...
Long chain fatty acids are biologically important molecules with complex and pH sensitive aggregatio...
pH dependence abounds in biochemical systems; however, many simulation methods used to investigate t...
Solvent pH is an important property that defines the protonation state of the amino acids and, there...
Protonation states of titratable amino acids play a key role in many biomolecular processes. Knowled...
AbstractThe current article describes a new two-dimensional λ-dynamics method to include proton taut...
pH is an important parameter in condensed-phase systems, because it determines the protonation state...
We present a simulation method that allows us to calculate the titration curves for systems undergoi...
The role of protonated nucleotides in modulating the pH-dependent properties of nucleic acids is one...
pH is a ubiquitous regulator of biological activity, with widespread impact ranging from its role in...
A central problem in computational biophysics is the treatment of titratable residues in molecular d...