Water-silica force field for simulating nanodevices

Amorphous silica is an inorganic material that is central for many nanotechnology applications, such as nanoelectronics, microfluidics, and nanopore sensors. To use molecular dynamics (MD) simulations to study the behavior of biomolecules interacting with silica, we developed a force field for amorphous silica surfaces based on their macroscopic wetting properties that is compatible with the CHARMM force field and TIP3P water model. The contact angle of a water droplet on a silica surface served as a criterion to tune the intermolecular interactions. The resulting force field was used to study the permeation of water through silica nanopores, illustrating the influence of the surface topography and the intermolecular parameters on permeation kinetics. We find that minute modeling of the amorphous surface is critical for MD studies, since the particular arrangement of surface atoms controls sensitively electrostatic interactions between silica and water.     

Strain softening in stretched DNA

The microscopic mechanics of DNA stretching was characterized using extensive molecular dynamics simulations. By employing an anisotropic pressure-control method, realistic force-extension dependences of effectively infinite DNA molecules were obtained. A coexistence of B and S DNA domains was observed during the overstretching transition. The simulations revealed that strain softening may occur in the process of stretching torsionally constrained DNA. The latter observation was qualitatively reconciled with available experimental data using a random-field Ising model.     

Sulfur-Containing Foldamer-Based Artificial Lithium Channels

Unlike many other biologically relevant ions (Na⁺, K⁺, Ca²⁺, Cl⁻, etc) and protons, whose cellular concentrations are closely regulated by highly selective channel proteins, Li⁺ ion is unusual in that its concentration is well tolerated over many orders of magnitude and that no lithium-specific channel proteins have so far been identified. While one naturally evolved primary pathway for Li⁺ ions to traverse across the cell membrane is through sodium channels by competing with Na⁺ ions, highly sought-after artificial lithium-transporting channels remain a major challenge to develop. Here we show that sulfur-containing organic nanotubes derived from intramolecularly H-bonded helically folded aromatic foldamers of 3.6 Å in hollow cavity diameter could facilitate highly selective and efficient transmembrane transport of Li⁺ ions, with high transport selectivity factors of 15.3 and 19.9 over Na⁺ and K⁺ ions, respectively.     

Swelling and shrinking of polymer chains in homopolymer blends

The radius of gyration, R, of polymer chains in homopolymer blends is studied in the framework of a self-consistent one-loop approximation. We show that the polymer chains can shrink or swell in comparison to the Gaussian chain. Swelling of the polymer chains in a region far away from the critical point is caused by the steric repulsive forces that were included in the model as the constraint of incompressibility. The chains shrink progressively, as we approach the critical region passing through the Gaussian limit, $ R_0 = \sqrt{\frac{N}{6}}l $, far away from the critical point (N − degree of polymerization, l − length of monomer). The correction responsible for the swelling and the shrinking is small when the concentrations of components ϕ are comparable ($ N = 1000,\bar\phi = 0.5,\frac{{R_0^2 - R^2}}{{R_0^2}} = \pm 0.02\%$). This effect, although small, leads to a local demixing, a sharp shrinking of chains in both components accompanied by a strong change of the global inter-monomer distance, which should be observable experimentally. When the local demixing occurs there is a sudden increase in the scattering intensity (of the order of 30% for N = 1000, and ϕ _A = 0.2). The increase of the degree of polymerization of the same type of chains leads to an increase of the swelling-shrinking effects. In addition, the critical concentration of the shorter chains component is smaller in comparison to the value obtained in the Flory-Huggins theory. The self-consistent determination of the radius of gyration and the upper wave-vector cutoff make our model free from any divergences. In the limit of N → ∞ this theory reduces to the random phase approximation (RPA) of de Gennes.     

Polyhydrazide-Based Organic Nanotubes as Efficient and Selective Artificial Iodide Channels

Reported herein is a series of pore-containing polymeric nanotubes based on a hydrogen-bonded hydrazide backbone. Nanotubes of suitable lengths, possessing a hollow cavity of about a 6.5 Å diameter, mediate highly efficient transport of diverse types of anions, rather than cations, across lipid membranes. The reported polymer channel, having an average molecular weight of 18.2 kDa and 3.6 nm in helical height, exhibits the highest anion-transport activities for iodide (EC₅₀=0.042 μm or 0.028 mol % relative to lipid), whcih is transported 10 times more efficiently than chlorides (EC₅₀=0.47 μm ). Notably, even in cholesterol-rich environment, iodide transport activity remains high with an EC₅₀ of 0.37 μm . Molecular dynamics simulation studies confirm that the channel is highly selective for anions and that such anion selectivity arises from a positive electrostatic potential of the central lumen rendered by the interior-pointing methyl groups.     

MORPHOLOGICAL TRANSFORMATIONS DURING PHASE-SEPARATION/ORDERING PHENOMENA

Abstract

The quantitative analysis of the morphological transformations in asymmetric and symmetric binary mixtures undergoing the phase separation has been reported. The general features of the bicontinuous morphology evolution have been discussed from the standpoint of the dynamic scaling hypothesis. The method for the quantitative characterization of the percolation transition by calculating the Euler characteristic has been described. It has been shown that the transformation of the bicontinuous morphology into droplets involves formation of the transient “cylindric” morphology composed of highly elongated, disconnected droplets.     

Scaling of the Euler characteristic, surface area, and curvatures in the phase separating or ordering systems

We present robust scaling laws for the Euler characteristic and curvatures applicable to any symmetric system undergoing phase separating or ordering kinetics. We apply it to the phase ordering in a system of the nonconserved scalar order parameter and find three scaling regimes. The appearance of the preferred nonzero curvature of an interface separating +/- domains marks the crossover to the late stage regime characterized by the Lifshitz-Cahn-Allen scaling.     

Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics

It has become possible to distinguish DNA molecules of different nucleotide sequences by measuring ion current passing through a narrow pore containing DNA. To assist experimentalists in interpreting the results of such measurements and to improve the DNA sequence detection method, we have developed a computational approach that has both the atomic-scale accuracy and the computational efficiency required to predict DNA sequence-specific differences in the nanopore ion current. In our Brownian dynamics method, the interaction between the ions and DNA is described by three-dimensional potential of mean force maps determined to a 0.03 nm resolution from all-atom molecular dynamics simulations. While this atomic-resolution Brownian dynamics method produces results with orders of magnitude less computational effort than all-atom molecular dynamics requires, we show here that the ion distributions and ion currents predicted by the two methods agree. Finally, using our Brownian dynamics method, we find that a small change in the sequence of DNA within a pore can cause a large change in the ion current, and validate this result with all-atom molecular dynamics.     

DNA attraction in monovalent and divalent electrolytes

The dependence of the effective force on the distance between two DNA molecules was directly computed from a set of extensive all-atom molecular dynamics simulations. The simulations revealed that in a monovalent electrolyte the effective force is repulsive at short and long distances but can be attractive in the intermediate range. This attractive force is, however, too weak (approximately 5 pN per turn of a DNA helix) to induce DNA condensation in the presence of thermal fluctuations. In divalent electrolytes, DNA molecules were observed to form a bound state, where Mg(2+) ions bridged minor groves of DNA. The effective force in divalent electrolytes was predominantly attractive, reaching a maximum of 42 pN per one turn of a DNA helix.