J. A. Lemkul

Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer

The paper uses polarizable molecular dynamics simulations to quantify how induced dipole effects influence small molecule permeation through a model phospholipid bilayer, comparing results with nonpolarizable simulations.

Dynamics, Electrostatics, and Thermodynamics ofBase Pairing at the LTR-III Quadruplex:Duplex Junction

The paper uses molecular dynamics simulations to study base pair formation at the HIV-1 LTR-III G-quadruplex:duplex junction, revealing electrostatic and geometric factors influencing base pair stability.

Structural dynamics of the methyl-coenzyme M reductase active site are influenced by coenzyme F430 modifications

This study uses molecular dynamics simulations to analyze how coenzyme F430 modifications affect the structural dynamics and electric fields of methyl-coenzyme M reductase (MCR) active sites.

Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes

The paper quantifies ion binding effects on G-quadruplex dynamics and free energies, revealing differences between telomeric and TERRA GQs.

An in silico approach to determine inter-subunit affinities in human septin complexes

The paper uses molecular dynamics to calculate inter-subunit binding free energies in human septin complexes, identifying GTP as a stabilizing element in the G interface.

FusoPortal: An interactive repository of hybrid MinION sequenced Fusobacterium genomes improves gene identification and characterization

FusoPortal provides a repository of hybrid MinION sequenced Fusobacterium genomes, improving gene identification and characterization by correcting misannotations and offering downloadable genomic data.