Search Results - "Santos, Denys E.S."

Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape by Santos, Denys E. S., Coutinho, Kaline, Soares, Thereza A.

“…The surface assessment via grid evaluation (SuAVE) software was developed to account for the effect of curvature in the calculations of structural properties…”
Get full text

Polymyxin Binding to the Bacterial Outer Membrane Reveals Cation Displacement and Increasing Membrane Curvature in Susceptible but Not in Resistant Lipopolysaccharide Chemotypes by Santos, Denys E. S, Pol-Fachin, Laércio, Lins, Roberto D, Soares, Thereza A

“…Lipid-A is the causative agent of Gram-negative sepsis and is responsible for an increasingly high mortality rate among hospitalized patients. Compounds that…”
Get full text

Conformational Dynamics and Responsiveness of Weak and Strong Polyelectrolyte Brushes: Atomistic Simulations of Poly(dimethyl aminoethyl methacrylate) and Poly(2-(methacryloyloxy)ethyl trimethylammonium chloride) by Santos, Denys E. S, Li, Danyang, Ramstedt, Madeleine, Gautrot, Julien E, Soares, Thereza A

“…The complex solution behavior of polymer brushes is key to control their properties, including for biomedical applications and catalysis. The swelling behavior…”
Get full text

Exploring the Molecular Dynamics of a Lipid‑A Vesicle at the Atom Level: Morphology and Permeation Mechanism by Santos, Denys E. S., De Nicola, Antonio, dos Santos, Vinicius F., Milano, Giuseppe, Soares, Thereza A.

“…Lipid-A was previously shown to spontaneously aggregate into a vesicle via the hybrid particle field approach. We assess the validity of the proposed…”
Get full text

SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces by Santos, Denys E. S, Pontes, Frederico J. S, Lins, Roberto D, Coutinho, Kaline, Soares, Thereza A

“…Curvature is an intrinsic feature of biological membranes underlying vital cellular processes such as endocytosis, membrane fusion–fission, trafficking, and…”
Get full text

Aggregation of Lipid A Variants: A Hybrid Particle-Field Model by De Nicola, Antonio, Soares, Thereza A., Santos, Denys E.S., Bore, Sigbjørn Løland, Sevink, G.J. Agur, Cascella, Michele, Milano, Giuseppe

“…Lipid A is one of the three components of bacterial lipopolysaccharides constituting the outer membrane of Gram-negative bacteria, and is recognized to have an…”
Get full text

Compatibility of GROMOS-Derived Atomic Parameters for Lipopolysaccharide Membranes with the SPC/E Water Model and Alternative Long-Range Electrostatic Treatments Using Single Nonbonded Cutoff and Atom-Based Charge Schemes by Lima, Manoela, Nader, Manuela, Santos, Denys, Soares, Thereza

“…Recent developments of GROMACS v.2016 ceased to support methodological approaches used in the development and validation of the GROMOS force field. We…”
Get full text

Out of Sight, Out of Mind: The Effect of the Equilibration Protocol on the Structural Ensembles of Charged Glycolipid Bilayers by Messias, Andresa, Santos, Denys E S, Pontes, Frederico J S, Lima, Filipe S, Soares, Thereza A

“…Molecular dynamics (MD) simulations represent an essential tool in the toolbox of modern chemistry, enabling the prediction of experimental observables for a…”
Get full text

Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations by Rusu, Victor H, Santos, Denys E. S, Poleto, Marcelo D, Galheigo, Marcelo M, Gomes, Antônio T. A, Verli, Hugo, Soares, Thereza A, Lins, Roberto D

“…Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting an empirical energy profile to a…”
Get full text