相关论文: Ion-mediated RNA structural collapse: effect of sp…
Using non-equilibrium molecular dynamics simulations and a coarse grained model of ionic liquids, we have investigated the impact that the shape and the intramolecular charge distribution of the ions have on the electrotuneable friction…
Urea titration of RNA by urea is an effective approach to investigate the forces stabilizing this biologically important molecule. We used all atom molecular dynamics simulations using two urea force fields and two RNA constructs to…
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively…
In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…
We use Metropolis Monte Carlo and umbrella sampling to calculate the free energies of interaction of two methane molecules and their charged derivatives in cylindrical water-filled pores. Confinement strongly alters the interactions between…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
Transport of ions in molecular-scale confined spaces is central to all aspects of life and technology: into a crack, it may break steel within days; through a membrane separator, it determines the efficiency of electrochemical energy…
As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($\phi_F$) reaches the folded state while the remaining fraction of…
mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…
Nanoconfinement generally leads to drastic effect on the physical and chemical properties of ionic liquids. Here we investigate how the electrochemical reactivity in such media may be impacted inside nanoporous carbon electrodes. To this…
Ionic liquids constrained at interfaces or restricted in subnanometric pores are increasingly employed in modern technologies, including energy applications. Understanding the details of their behavior in these conditions is therefore…
We recast the problem of hydrogel swelling under physical constraints as an energy optimization problem. We apply this approach to compute equilibrium shapes of hydrogel spheres confined within a jammed matrix of rigid beads, and interpret…
Nanoscale confinement of molecules in a fluid can result in enhanced viscosity, local fluidic order, or collective motion. Confinement also affects ion transport and/or the rate and equilibrium concentration in a chemical reaction, all of…
Mechanosensitive ion nanochannels regulate transport by undergoing conformational changes within nanopores. However, achieving precise control over these conformational states remains a major challenge for both artificial soft or solid…
Ion channels form pores across the lipid bilayer, selectively allowing inorganic ions to cross the membrane down their electrochemical gradient. While the study of ion desolvation free-energies have attracted much attention, the role of…
The role of ion-ion correlations in suppressing neutrino-nucleus elastic scattering during stellar core collapse is reinvestigated, using two different equations of state. We test the improved description by Itoh et al. against the…
We review the effects of macromolecular crowding on the folding of RNA by considering the simplest scenario when excluded volume interactions between crowding particles and RNA dominate. Using human telomerase enzyme as an example, we…
Ion transport within confined environments, like nanopores and nanotubes, is pivotal for advancing a range of applications, including biosensors, seawater desalination, and energy storage devices. Existing research does not sufficiently…
Contribution of metal ions on nucleic acids structures and functions is undeniable. Among the available metal ions like Na+, K+, Ca2+, Mg2+ etc., the role that play the Mg2+ ion is very significant related to the stability of the structures…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…