The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in
generating pathways and rate constants for rare events such as protein folding and protein …

Helices are essential building blocks of living organisms, be they molecular fragments of
proteins (α-helices), macromolecules (DNA and collagen), or multimolecular assemblies …

It has been known for decades that DNA is extremely flexible and polymorphic, but our
knowledge of its accessible conformational space remains limited. Structural data, primarily …

We study here a DNA oligonucleotide having the ability to form two different i-motif structures
whose relative stability depends on pH and temperature. The major species at neutral pH is …

We present the first microsecond MD simulation of B-DNA. Trajectory shows good
agreement with available data and clarifies the μs dynamics of DNA. The duplex is sampling …

The reorientation and hydrogen-bond dynamics of water molecules within the hydration
shell of a B-DNA dodecamer, which are of interest for many of its biochemical functions, are …

Counterions play a significant role in DNA structure and function, and molecular dynamics
(MD) simulations offer the prospect of detailed description of the dynamical structure of ions …

Biomolecular simulations are typically performed in an aqueous environment where the
number of ions remains fixed for the duration of the simulation, generally with either a …

Proteins are fascinating supramolecular structures, which are able to recognize ligands
transforming binding information into chemical signals. They can transfer information across …

We present a new method for analyzing ion, or molecule, distributions around helical nucleic
acids and illustrate the approach by analyzing data derived from molecular dynamics …