Enhancing important fluctuations: Rare events and metadynamics from a conceptual viewpoint
Atomistic simulations play a central role in many fields of science. However, their usefulness
is often limited by the fact that many systems are characterized by several metastable states …
is often limited by the fact that many systems are characterized by several metastable states …
Physics of base-pairing dynamics in DNA
M Manghi, N Destainville - Physics Reports, 2016 - Elsevier
As a key molecule of life, Deoxyribo-Nucleic Acid (DNA) is the focus of numbers of
investigations with the help of biological, chemical and physical techniques. From a physical …
investigations with the help of biological, chemical and physical techniques. From a physical …
Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps
The ability to predict the mechanisms and the associated rate constants of protein–ligand
unbinding is of great practical importance in drug design. In this work we demonstrate how a …
unbinding is of great practical importance in drug design. In this work we demonstrate how a …
Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/1H Replacement in DNA
A Basov, M Drobotenko, A Svidlov, E Gerasimenko… - Molecules, 2020 - mdpi.com
In the present study, the effect of 2H/1H isotopic exchange in hydrogen bonds between
nitrogenous base pairs on occurrence and open states zones dynamics is investigated …
nitrogenous base pairs on occurrence and open states zones dynamics is investigated …
Position-dependent diffusion from biased simulations and Markov state model analysis
A variety of enhanced statistical and numerical methods are now routinely used to extract
important thermodynamic and kinetic information from the vast amount of complex, high …
important thermodynamic and kinetic information from the vast amount of complex, high …
DNA‐doxorubicin interaction: New insights and peculiarities
We have investigated the interaction of the DNA molecule with the anticancer drug
doxorubicin (doxo) by using three different experimental techniques: single molecule …
doxorubicin (doxo) by using three different experimental techniques: single molecule …
A review of enhanced sampling approaches for accelerated molecular dynamics
P Tiwary, A van de Walle - Multiscale materials modeling for …, 2016 - Springer
Molecular dynamics (MD) simulations have become a tool of immense use and popularity
for simulating a variety of systems. With the advent of massively parallel computer resources …
for simulating a variety of systems. With the advent of massively parallel computer resources …
Kinetics of ligand binding through advanced computational approaches: a review
Ligand residence times and binding rates have been found to be useful quantities to
consider during drug design. The underlying structural and dynamic determinants of these …
consider during drug design. The underlying structural and dynamic determinants of these …
Ideas and methods of nonlinear mathematics and theoretical physics in DNA science: the McLaughlin-Scott equation and its application to study the DNA open state …
LV Yakushevich, LA Krasnobaeva - Biophysical Reviews, 2021 - Springer
The review is devoted to a new and rapidly developing area related to the application of
ideas and methods of nonlinear mathematics and theoretical physics to study the internal …
ideas and methods of nonlinear mathematics and theoretical physics to study the internal …
Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations
Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a
prototypical nucleation event. As such it is challenging to compute its rate from atomistic …
prototypical nucleation event. As such it is challenging to compute its rate from atomistic …