Related papers: Molecular dynamics simulations with grand-canonica…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
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…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…
Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental approaches, a promising candidate is the "chemical modification…
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of \emph{forward models} that relate measured SAXS intensities and structural features, and that are suitable to model either…
Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg$^{2+}$ on a RNA duplex, including both…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and some properties of water-methanol liquid mixture. The TIP4P/2005 and SPC/E water models are combined with the united atom TraPPE and the…
Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively…
Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining the ensemble of conformations that they populate is crucial…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
There is a lack of scalable quantitative measures of reactivity for functional groups in organic chemistry. Measuring reactivity experimentally is costly and time-consuming and does not scale to the astronomical size of chemical space. In…
We consider cooperative reactions and we study the effects of the interaction strength among the system components on the reaction rate, hence realizing a connection between microscopic and macroscopic observables. Our approach is based on…
We use molecular dynamic simulations to investigate the relation between the presence of packing defects in a glass-former and the spontaneous cooperative motions called dynamic heterogeneity. For that purpose we use a simple diatomic…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Cooperative interactions among sensory receptors provide a general mechanism to increase the sensitivity of signal transduction. In particular, bacterial chemotaxis receptors interact cooperatively to produce an ultrasensitive response to…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…