Related papers: Ion Condensation onto Ribozyme is Site-Specific an…
Dynamic fluctuations in hydrogen-bond network of water occur from femto- to nano-second timescale and provides insights into structural/dynamical aspects of water at ion-water interfaces. Employing terahertz spectroscopy assisted with…
Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape that cannot be easily explored using conventional…
In contrast to proteins much less attention has been focused on development of computational models for describing RNA molecules, which are being recognized as playing key roles in many cellular functions. Current atomically detailed force…
A recent Monte Carlo simulation determined the potential of mean force between two lysozyme molecules in various aqueous solutions [M. Lund et al. Phys. Rev. Lett. 100, 258105 (2008)]. The study involved a combination of explicit solvent…
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…
Sodium-ion batteries are a cost-effective and sustainable alternative to lithium-ion systems for large-scale energy storage. Hard carbon (HC) anodes, composed of disordered graphitic and amorphous domains, offer high capacity but exhibit…
The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in…
Correlated anion and cation motion can significantly reduce the overall ion conductivity in electrolytes versus the ideal conductivity calculated based on the diffusion constants alone. Using coarse-grained molecular dynamics simulations,…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
This paper studies mechanism of preconcentration of charged particles in a straight micro-channel embedded with permselective membranes, by numerically solving coupled transport equations of ions, charged particles and solvent fluid without…
Lithium zirconium chlorides (LZCs) present a promising class of cost-effective solid electrolyte for next-generation all-solid-state batteries. The unique crystal structure of LZCs plays a crucial role in facilitating lithium-ion mobility,…
Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well…
The ionic atmospheres around nucleic acids play important roles in biological function. Large-scale explicit solvent simulations coupled to experimental assays such as anomalous small-angle X-ray scattering (ASAXS) can provide important…
Strongly correlated electrostatics of DNA systems has drawn the interest of many groups, especially the condensation and overcharging of DNA by multivalent counterions. By adding counterions of different valencies and shapes, one can…
Upon the addition of multivalent cations, a giant DNA chain exhibits a large discrete transition from an elongated coil into a folded compact state. We performed single-chain observation of long DNAs in the presence of a tetravalent cation…
We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca$^{2+}$, Ba$^{2+}$, Sr$^{2+}$, Cd$^{2+}$, Pb$^{2+}$, and Hg$^{2+}$. The underlying data set consists…
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…
We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…
Through molecular dynamics simulations considering thermal vibration of surface atoms, ionic behaviors in concentrated NaCl solutions confined between discretely charged silicon surfaces have been investigated. The electric double layer…
Acid-base equilibria directly influence the functionality and behavior of particles in a system. Due to the ionizing effects of acid-base functional groups, particles will undergo charge exchange. The degree of ionization and their…