Denys Biriukov

Peptide Sequence Features that Reduce Membrane Pore Line Tension

The paper identifies sequence features of α-helical peptides that reduce membrane line tension through computational simulations and evolutionary optimization.

Quantitative Mapping of Sulfation, Iduronic Acid, and Secondary Structure in Glycosaminoglycans

The paper uses molecular dynamics simulations to study how sulfation and monosaccharide composition affect GAG secondary structures and introduces a classification metric.

The Origins of Arginine "Magic": Guanidinium Like-Charge Ion Pairing and Oligoarginine Aggregation in Water by NMR, Cryoelectron Microscopy, and Molecular Dynamics Simulations

This study quantifies weak like-charge pairing of guanidinium ions in water using NMR, MD simulations, and cryo-EM, contrasting with ammonium ions and showing oligoarginine aggregation.

Transient Formation of Supramolecular Complexes Between Hyaluronan and Oligopeptides at Submicromolar Concentration

This study investigates HA-peptide interactions at submicromolar concentrations using multiple techniques, revealing selective multivalent binding and dynamic supramolecular complex formation.

Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters for Glycosaminoglycans via Ab Initio Molecular Dynamics Simulations

This study evaluates force fields for sulfated glycosaminoglycans using ab initio MD simulations, finding that charge-scaled models better capture Ca2+ binding than others.

Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field

prosECCo75 improves MD simulations by incorporating electronic polarization, enhancing accuracy in modeling electrostatic interactions in biological systems without increasing computational cost.