Manifold learning in atomistic simulations: a conceptual review
Analyzing large volumes of high-dimensional data requires dimensionality reduction: finding
meaningful low-dimensional structures hidden in their high-dimensional observations. Such …
meaningful low-dimensional structures hidden in their high-dimensional observations. Such …
Biomolecular infrared spectroscopy: making time for dynamics
NT Hunt - Chemical Science, 2024 - pubs.rsc.org
Time resolved infrared spectroscopy of biological molecules has provided a wealth of
information relating to structural dynamics, conformational changes, solvation and …
information relating to structural dynamics, conformational changes, solvation and …
Simulation‐Assisted Localized DNA Logical Circuits for Cancer Biomarkers Detection and Imaging
DNA‐based nanodevices equipped with localized modules have been promising probes for
biomarker detection. Such devices heavily rely on the intramolecular hybridization reaction …
biomarker detection. Such devices heavily rely on the intramolecular hybridization reaction …
Girsanov reweighting enhanced sampling technique (grest): On-the-fly data-driven discovery of and enhanced sampling in slow collective variables
Molecular dynamics simulations of microscopic phenomena are limited by the short
integration time steps which are required for numerical stability but which limit the practically …
integration time steps which are required for numerical stability but which limit the practically …
Toward a molecular mechanism of complementary RNA duplexes denaturation
A Dabin, G Stirnemann - The Journal of Physical Chemistry B, 2023 - ACS Publications
RNA duplexes are relatively rare but play very important biological roles. As an end-product
of template-based RNA replication, they also have key implications for hypothetical primitive …
of template-based RNA replication, they also have key implications for hypothetical primitive …
Chasing collective variables using temporal data-driven strategies
The convergence of free-energy calculations based on importance sampling depends
heavily on the choice of collective variables (CVs), which in principle, should include the …
heavily on the choice of collective variables (CVs), which in principle, should include the …
Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs
Hybridization of short nucleic acid segments (< 4 nt) to single-strand templates occurs as a
critical intermediate in processes such as nonenzymatic nucleic acid replication and toehold …
critical intermediate in processes such as nonenzymatic nucleic acid replication and toehold …
Transient states during the annealing of mismatched and bulged oligonucleotides
Oligonucleotide hybridization is crucial in various biological, prebiotic and
nanotechnological processes, including gene regulation, non-enzymatic primer extension …
nanotechnological processes, including gene regulation, non-enzymatic primer extension …
Disruption of energetic and dynamic base-pairing cooperativity in DNA duplexes by an abasic site
Wednesday, February 14, 2024 459a short segment cannot overcome the added free-
energy barrier, but moving the AP site inward produces segments long enough to stably …
energy barrier, but moving the AP site inward produces segments long enough to stably …
Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain
The hybridization kinetic of an oligonucleotide to its template is a fundamental step in many
biological processes such as replication arrest, CRISPR recognition, DNA sequencing, DNA …
biological processes such as replication arrest, CRISPR recognition, DNA sequencing, DNA …