[HTML][HTML] Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook
S Hussain, A Haji-Akbari - The Journal of Chemical Physics, 2020 - pubs.aip.org
Rare events are processes that occur upon the emergence of unlikely fluctuations. Unlike
what their name suggests, rare events are fairly ubiquitous in nature, as the occurrence of …
what their name suggests, rare events are fairly ubiquitous in nature, as the occurrence of …
An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization
A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model
includes anisotropic potentials between bases involved in base stacking and base pair …
includes anisotropic potentials between bases involved in base stacking and base pair …
DNA hybridization kinetics: zippering, internal displacement and sequence dependence
Although the thermodynamics of DNA hybridization is generally well established, the
kinetics of this classic transition is less well understood. Providing such understanding has …
kinetics of this classic transition is less well understood. Providing such understanding has …
Coarse-graining DNA for simulations of DNA nanotechnology
To simulate long time and length scale processes involving DNA it is necessary to use a
coarse-grained description. Here we provide an overview of different approaches to such …
coarse-grained description. Here we provide an overview of different approaches to such …
Computer Aided Development of Nucleic Acid Applications in Nanotechnologies
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology‐related
applications is a growing field with broad application potential, ranging from biosensing up …
applications is a growing field with broad application potential, ranging from biosensing up …
Determining sequence-dependent DNA oligonucleotide hybridization and dehybridization mechanisms using coarse-grained molecular simulation, markov state …
A robust understanding of the sequence-dependent thermodynamics of DNA hybridization
has enabled rapid advances in DNA nanotechnology. A fundamental understanding of the …
has enabled rapid advances in DNA nanotechnology. A fundamental understanding of the …
Intermediate states of molecular self-assembly from liquid-cell electron microscopy
Traditional single-molecule methods do not report whole-molecule kinetic conformations,
and their adaptive shape changes during the process of self-assembly. Here, using …
and their adaptive shape changes during the process of self-assembly. Here, using …
Coarse-grained modeling of DNA oligomer hybridization: length, sequence, and salt effects
A recently published coarse-grained DNA model [DM Hinckley, GS Freeman, JK Whitmer,
and JJ de Pablo, J. Chem. Phys. 139, 144903 (2013)] is used to study the hybridization …
and JJ de Pablo, J. Chem. Phys. 139, 144903 (2013)] is used to study the hybridization …
Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models
We investigate the influence of nonlocal couplings on the torsional and bending elasticities
of DNA. Such couplings have been observed in the past by several simulation studies. Here …
of DNA. Such couplings have been observed in the past by several simulation studies. Here …
DNA strand replacement mechanism in molecular beacons encoded for the detection of cancer biomarkers
M Stobiecka, A Chalupa - The Journal of Physical Chemistry B, 2016 - ACS Publications
Signaling properties of a fluorescent hairpin oligonucleotide molecular beacon (MB)
encoded to recognize protein survivin (Sur) mRNA have been investigated. The process of …
encoded to recognize protein survivin (Sur) mRNA have been investigated. The process of …