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RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly…
Using coarse-grained model we have explored forced-unfolding of RNA hairpin as a function of $f_S$ and the loading rate ($r_f$). The simulations and theoretical analysis have been done without and with the handles that are explicitly…
Machine-learning force fields (MLFFs) have emerged as a promising solution for speeding up ab initio molecular dynamics (MD) simulations, where accurate force predictions are critical but often computationally expensive. In this work, we…
Predictive computational modeling of polymer materials is necessary for the efficient design of composite materials and the corresponding processing methods. Molecular dynamics (MD) modeling is especially important for establishing accurate…
Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle…
We review the basic concepts and tools for mechanically unzipping RNA hairpins using force spectroscopy. By pulling apart the ends of an RNA molecule using optical tweezers, it is possible to measure the folding free energy at varying…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
Recently, we introduced a new force field (FF) to simulate transport properties of imidazolium-based room-temperature ionic liquids (RTILs) using a solid physical background. In the present work, we apply this FF to derive thermodynamic,…
We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and…
Gaussian process (GP) emulator has been used as a surrogate model for predicting force field and molecular potential, to overcome the computational bottleneck of molecular dynamics simulation. Integrating both atomic force and energy in…
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
Atomic force microscopy (AFM) enables high-resolution imaging and quantitative force measurement, which is critical for understanding nanoscale mechanical, chemical, and biological interactions. In dynamic AFM modes, however, interaction…
Molecular dynamics simulations have been performed to understand true atomic resolution, which has been observed on the Si(111)-7$\times$7 surface by dynamic force microscopy in ultra high vacuum(UHV). Stable atomic-scale contrast is…
We present results of a systematic study of the capture process through the barrier penetration model. The nucleus-nucleus interaction potential is calculated using the double-folding model (DFM) with the M3Y Paris NN forces. The nucleon…
The force field describing the calculated interaction between atoms or molecules is the key to the accuracy of many molecular dynamics (MD) simulation results. Compared with traditional or semi-empirical force fields, machine learning force…
Atomistic modeling of thin-film processes provides an avenue not only for discovering key chemical mechanisms of the processes but also to extract quantitative metrics on the events and reactions taking place at the gas-surface interface.…
Machine learned chemical potentials have shown great promise as alternatives to conventional computational chemistry methods to represent the potential energy of a given atomic or molecular system as a function of its geometry. However,…
Atomic force microscopes (AFMs) are ubiquitous in research laboratories and have recently been priced for use in teaching laboratories. Here we review several AFM platforms (Dimension 3000 by Digital Instruments, EasyScan2 by Nanosurf,…
In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since…