Theory of phase segregation in DNA assemblies containing two different base pair sequence types

Spontaneous pairing of homologous DNA sequences – a challenging subject in molecular biophysics, often referred to as ‘homology recognition’ – ha s been observed in vitro for several DNA system s a . One of th e se experiments involved liquid crystalline quasi - columnar phases formed by a mixture of two kinds of oligo mer of double stranded DNA . Both oligomer types were of the same length and identical stoichiometric base - pair composition , but the base - pairs followed a different order . Phase segregation of the two DNA types was observed in the experiments , wit h the formation of boundaries between domai ns rich in molecules of one type (order) of base pair sequence . We formulate here a modified ‘ X - Y model ’ for phase segregation in such assemblies , obtain approximate solutions of the model , compare analytical results to Monte Carlo simulations, and rationalize past experimental observations . This study, furthermore , reveals the factors that affect the degree of segregat ion . Such information c ould be used in planning new versions of similar segregation experiments , needed for deepen i ng our understanding of forces that might be involved , e.g., in gene - gene recognition

Charging Ultra-nanoporous Electrodes with Size-asymmetric Ions Assisted by Apolar Solvent

We develop a statistical theory of charging quasi single-file pores with cations and anions of different sizes as well as solvent molecules or voids. This is done by mapping the charging onto a one-dimensional Blume–Emery–Griffith model with variable coupling constants. The results are supported by three-dimensional Monte Carlo simulations in which many limitations of the theory are lifted. We explore the different ways of enhancing the energy storage which depend on the competitive adsorption of ions and solvent molecules into pores, the degree of ionophilicity and the voltage regimes accessed. We identify new solvent-related charging mechanisms and show that the solvent can play the role of an “ionophobic agent”, effectively controlling the pore ionophobicity. In addition, we demonstrate that the ion-size asymmetry can significantly enhance the energy stored in a nanopore

Theory of the Double Layer in Water-in-Salt Electrolytes.

One challenge in developing the next generation of lithium-ion batteries is the replacement of organic electrolytes, which are flammable and most often contain toxic and thermally unstable lithium salts, with safer, environmentally friendly alternatives. Recently developed water-in-salt electrolytes (WiSEs), which are nonflammable, nontoxic, and also have enhanced electrochemical stability, are promising alternatives. In this work, we develop a simple modified Poisson-Fermi theory for WiSEs, which demonstrates the fine interplay between electrosorption, solvation, and ion correlations. The phenomenological parameters are extracted from molecular dynamics simulations, also performed here. The theory reproduces the WiSEs' electrical double-layer structure with remarkable accuracy

Cracking Ion Pairs in the electrical double layer of ionic liquids

Here we investigate a limiting case of the theory for aggregation and gelation in the electrical double layer (EDL) of ionic liquids (ILs). The limiting case investigated only accounts for ion pairs, ignoring the possibility of larger clusters and a percolating ionic network. This simplification, permits analytical solutions for the properties of the EDL. The resulting equations demonstrate the competition between the free energy of an association and the electrostatic potential in the EDL. For small electrostatic potentials and large negative free energies of associations, ion pairs dominate in the EDL. Whereas, for electrostatic potential energies larger than the free energy of an association, electric-field-induced cracking of ion pairs occurs. The differential capacitance for this consistent ion pairing theory has a propensity to have a “double hump camel” shape. We compare this theory against previous free ion approaches, which do not consistently treat the reversible associations in the EDL

Current-generating 'double layer shoe' with a porous sole

We present a principle and a simple theory of a novel reverse electroactuator, in which the electrical current is generated by pumping an electrolytic liquid into nonwetting pores of a polarized electrode. The theory establishes the relationship between the variation of external pressure and the electrical current. The effective current density is amplified by the high porosity of the electrode. The suggested principle can be implemented into the design of a shoe which will generate an AC current simply by walking. Estimates of typical parameters and operation regimes of such a device suggest that one can easily generate a peak current density of ~17 mA cm−2. This would produce some 1.7 A from each shoe at 0.65 W average power density, without hampering walking

Electrotunable lubrication with ionic liquids: the effects of cation chain length and substrate polarity.

Electrotunable lubrication with ionic liquids (ILs) provides dynamic control of friction with the prospect to achieve superlubrication. We investigate the dependence of the frictional and structural forces with 1-n,2-methyl-imidazolium tetrafluoroborate [C n MIM]+[BF4]- (n = 2, 4, 6) ILs as a lubricant on the molecular structure of the liquid, normal load, and polarity of the electrodes. Using non-equilibrium molecular dynamics simulations and coarse-grained force-fields, we show that the friction force depends significantly on the chain length of the cation. ILs containing cations with shorter aliphatic chains show lower friction forces, ∼40% for n = 2 as compared to the n = 6 case, and more resistance to squeeze-out by external loads. The normal load defines the dynamic regime of friction, and it determines maxima in the friction force at specific surface charges. At relatively low normal loads, ∼10 MPa, the velocity profile in the confined region resembles a Couette type flow, whereas at high loads, >200 MPa, the motion of the ions is highly correlated and the velocity profile resembles a "plug" flow. Different dynamic regimes result in distinctive slippage planes, located either at the IL-electrode interface or in the interior of the film, which ultimately lead, at high loads, to the observation of maxima in the friction force at specific surface charge densities. Instead, at low loads the maxima are not observed, and the friction is found to monotonously increase with the surface charge. Friction with [C n MIM]+[BF4]- as a lubricant is reduced when the liquid is confined between positively charged electrodes. This is due to better lubricating properties and enhanced resistance to squeeze out when the anion [BF4]- is in direct contact with the electrode

Theory and simulations of ionic liquids in nanoconfinement.

Room-temperature ionic liquids (RTILs) have exciting properties such as nonvolatility, large electrochemical windows, and remarkable variety, drawing much interest in energy storage, gating, electrocatalysis, tunable lubrication, and other applications. Confined RTILs appear in various situations, for instance, in pores of nanostructured electrodes of supercapacitors and batteries, as such electrodes increase the contact area with RTILs and enhance the total capacitance and stored energy, between crossed cylinders in surface force balance experiments, between a tip and a sample in atomic force microscopy, and between sliding surfaces in tribology experiments, where RTILs act as lubricants. The properties and functioning of RTILs in confinement, especially nanoconfinement, result in fascinating structural and dynamic phenomena, including layering, overscreening and crowding, nanoscale capillary freezing, quantized and electrotunable friction, and superionic state. This review offers a comprehensive analysis of the fundamental physical phenomena controlling the properties of such systems and the current state-of-the-art theoretical and simulation approaches developed for their description. We discuss these approaches sequentially by increasing atomistic complexity, paying particular attention to new physical phenomena emerging in nanoscale confinement. This review covers theoretical models, most of which are based on mapping the problems on pertinent statistical mechanics models with exact analytical solutions, allowing systematic analysis and new physical insights to develop more easily. We also describe a classical density functional theory, which offers a reliable and computationally inexpensive tool to account for some microscopic details and correlations that simplified models often fail to consider. Molecular simulations play a vital role in studying confined ionic liquids, enabling deep microscopic insights otherwise unavailable to researchers. We describe the basics of various simulation approaches and discuss their challenges and applicability to specific problems, focusing on RTIL structure in cylindrical and slit confinement and how it relates to friction and capacitive and dynamic properties of confined ions

Connections matter: On the importance of pore percolation for nanoporous supercapacitors

Nanoporous supercapacitors play a key role in energy storage and thereby attract growing interest from the research community. Development of porous electrodes for supercapacitors is of the paramount importance, but their characterization still remains a challenge. Herein, we analyze two examples of the popular carbide-derived and activated carbon electrodes from the point of view of interpore connectivity and ion permeation. Due to limited percolation, the effective porosity, as seen by an ion, decreases with an increase in the ion size, which can reduce the stored energy density substantially. Our results highlight the importance of high quality well-percolated porous electrodes for supercapacitors and suggest that the interpore connectivity is an important characteristic to consider when optimizing the existing and developing new electrode materials

Gelation, clustering, and crowding in the electrical double layer of ionic liquids.

Understanding the bulk and interfacial properties of super-concentrated electrolytes, such as ionic liquids (ILs), has attracted significant attention lately for their promising applications in supercapacitors and batteries. Recently, McEldrew et al. [J. Phys. Chem. B 125, 2677 (2021)] developed a theory for reversible ion associations in bulk ILs, which accounted for the formation of all possible (Cayley tree) clusters and a percolating ionic network (gel). Here, we adopt and develop this approach to understand the associations of ILs in the electrical double layer at electrified interfaces. With increasing charge of the electrode, the theory predicts a transition from a regime dominated by a gelled or clustered state to a crowding regime dominated by free ions. This transition from gelation to crowding is conceptually similar to the overscreening to crowding transition