Water dynamics in the hydration shells of biomolecules
D Laage, T Elsaesser, JT Hynes - Chemical Reviews, 2017 - ACS Publications
The structure and function of biomolecules are strongly influenced by their hydration shells.
Structural fluctuations and molecular excitations of hydrating water molecules cover a broad …
Structural fluctuations and molecular excitations of hydrating water molecules cover a broad …
Multiscale simulation of DNA
Highlights•We describe the most recent methods to study DNA from electrons to
chromosomes.•Methods were classified as: electronic, atomistic, coarse grained, and …
chromosomes.•Methods were classified as: electronic, atomistic, coarse grained, and …
[HTML][HTML] A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0]
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 …
generating pathways and rate constants for rare events such as protein folding and protein …
Ethidium bromide interactions with DNA: an exploration of a classic DNA–ligand complex with unbiased molecular dynamics simulations
R Galindo-Murillo, TE Cheatham III - Nucleic acids research, 2021 - academic.oup.com
Visualization of double stranded DNA in gels with the binding of the fluorescent dye
ethidium bromide has been a basic experimental technique in any molecular biology …
ethidium bromide has been a basic experimental technique in any molecular biology …
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
M Pasi, JH Maddocks, D Beveridge… - Nucleic acids …, 2014 - academic.oup.com
We present the results of microsecond molecular dynamics simulations carried out by the
ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct …
ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct …
The structural impact of DNA mismatches
The structure and dynamics of all the transversion and transition mismatches in three
different DNA environments have been characterized by molecular dynamics simulations …
different DNA environments have been characterized by molecular dynamics simulations …
Rolling circle RNA synthesis catalyzed by RNA
RNA-catalyzed RNA replication is widely considered a key step in the emergence of life's
first genetic system. However, RNA replication can be impeded by the extraordinary stability …
first genetic system. However, RNA replication can be impeded by the extraordinary stability …
Twisting DNA by salt
The structure and properties of DNA depend on the environment, in particular the ion
atmosphere. Here, we investigate how DNA twist-one of the central properties of DNA …
atmosphere. Here, we investigate how DNA twist-one of the central properties of DNA …
Dynamical disorder in the DNA hydration shell
E Duboué-Dijon, AC Fogarty, JT Hynes… - Journal of the American …, 2016 - ACS Publications
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 …
shell of a B-DNA dodecamer, which are of interest for many of its biochemical functions, are …
Long-timescale dynamics of the Drew–Dickerson dodecamer
We present a systematic study of the long-timescale dynamics of the Drew–Dickerson
dodecamer (DDD: d (CGCGAATTGCGC) 2) a prototypical B-DNA duplex. Using our newly …
dodecamer (DDD: d (CGCGAATTGCGC) 2) a prototypical B-DNA duplex. Using our newly …