The mechanism of DNA elongation in nanochannels was explored by Monte Carlo simulations as a function of the channel dimension D, DNA length, and stiffness. Simulations were based on the bead-spring model, representing double-stranded DNA chains of moderate length at a high salt concentration. As a rule, the channel-induced elongation profiles of R( parallel) vs D from the simulations were in qualitative agreement with those from microfluidic measurements of DNA. The longitudinal chain elongation in narrow channels was found to be correctly predicted by the Odijk relation for the deflection regime. The scaling relation of R( parallel) vs D(-1), based on the statistics of ideal-chain blobs, was used to explain the simulation data at the intermediate channel widths. Contrary to the blob-theory presumption, the nonlinear dependence of DNA elongation R( parallel) on the chain length N was observed in simulations at moderate confinement. It was suggested that discrepancies found between the simulations and the blob theory arose from the formation of various DNA hairpin structures within channels.

Following the recent studies of basis sets explicitly dependent on oscillatory external electric field we have investigated the possibility of some further truncation of the so-called polarized basis sets without any major deterioration of the computed data for molecular dipole moments, dipole polarizabilities, and related electric properties of molecules. It has been found that basis sets of contracted Gaussian functions of the form [3s1p] for H and [4s3p1d] for the first-row atoms can satisfy this requirement with particular choice of contractions in their polarization part. With m denoting the number of primitive GTOs in the contracted polarization function, the basis sets devised in this article will be referred to as the ZmPol sets. In comparison with earlier, medium-size polarized basis sets (PolX), these new ZmPol basis sets are reduced by 2/3 in their size and lead to the order of magnitude computing time savings for large molecules. Simultaneously, the dipole moment and polarizability data remain at almost the same level of accuracy as in the case of the PolX sets. Among a variety of possible applications in computational chemistry, the ZmPolX are also to be used for calculations of frequencies and intensities in the Raman spectra of large organic molecules (see Part II, this issue).

The behaviour of semiflexible chains, modelling biopolymers such as DNA and actin in confined spaces, was investigated by means of Monte Carlo simulations. Simulations, based on the coarse-grained worm-like chain (WLC) model, assumed confinement length-scales comparable to those used in micro- and nanofluidic devices. The end-to-end chain elongation R was determined as a function of the channel dimensions and chain bending rigidity. Three regions of chain elongation R, identified in simulations in a cylinder and a slit, were described by current theoretical concepts. In harmony with the measurements of confined DNA, an abrupt transition between the blob region at moderate confinement and the deflection region at strong cylindrical confinement was found. The conditions for hairpin formation were elucidated as a trade-off between confinement and chain stiffness. The intrinsic persistence length of unconfined polymers was calculated by four methods that provided practically identical results. However, in confined geometries only the rigorous and WLC methods predicted the dependence of apparent persistence length P on confinement in a qualitatively correct way. It was found that the simple exponential function, suitable for the description of orientation correlations in free chains is, in confined systems, limited only to short distances along the chain contour and, thus, the apparent persistence length determined by this method just reproduces the intrinsic value of P. The orientation correlations from simulations were compared with analytical predictions in the deflection regime under strong confinement and with the measurements of actin filaments.

The influence of confinement on the persistence length of dsDNA molecules under a high ionic strength environment was explored by coarse-grained Monte Carlo simulations in channels of different profiles. It was found that under confinement three definitions of the persistence length of DNA molecules were not equivalent and represented different properties. In case of the global quantities, the projection and the WLC persistence lengths, the apparent values up to several hundred nanometres are observed for DNA confined in narrow channels. The orientational correlation function cos theta(s) of confined DNA shows a complex pattern, distinctive for semiflexible polymers. At weak and moderate confinements the function cos theta(s) suggests an unexpected increase in the apparent DNA flexibility. The orientational persistence length computed from the initial slope of the function cos theta(s) mirrors only short-scale correlations and gives the value close to the intrinsic persistence length of DNA. The simulation data of direct relevance to experimental studies of DNA in microfluidic devices are compared with analytical theories for stiff chains.

The behavior of semiflexible chains modeling wormlike polymers such as DNA and actin in confined spaces was explored by coarse-grained Monte Carlo simulations. The persistence length P, mean end-to-end distance R2, mean radius of gyration Rg2, and the size ratio R2/Rg2 were computed for chains in slits, cylinders, and spheres. It was found that the intrinsic persistence length of a free chain undergoes on confinement substantial alteration into the apparent persistence length. The qualitative differences were found in trends of the apparent persistence lengths between slits and cylinders on one side and spheres on the other side. The quantities P, R2, Rg2, and R2/Rg2 display similar dependences upon squeezing the chains in nanopores. The above quantities change nonmonotonically with confinement in slits and cylinders, whereas they drop smoothly with decreasing radius of a sphere. For elongation of a chain in a cylinder, two regimes corresponding to strong and moderate confinements were found and compared to experiments and predictions of the blob and Odijk theories. In a spherical cavity, the toroidal chain structure with a hole in the center was detected under strong confinements. The scattering form factor S(q) computed for semiflexible confined chains revealed three regimes of behavior in a slit and a cylinder that matched up well with the scaling theory. The complex form of the function S(q) computed for a sphere was interpreted as a sign of the toroidal structure. A reasonable agreement was found between the simulations and measurements of DNA and actin filaments, confined in nano- and microfluidic channels and spherical droplets, pertaining to the changes of the persistence lengths, chain elongation, and toroidal structure formation.

The constraints due to the chain closure in combination with the geometrical constraints of a DNA molecule are inevitable for many biological processes. In this work, structural properties of flexible and semiflexible cyclic chains and their linear analogues confined in cylindrical channels were studied using the coarse-grained Metropolis Monte Carlo simulations. The radius of gyration satisfactorily represents the longitudinal stretching of both chain topologies. Transition between the moderate and strong confinement regime of semiflexible cyclic chains is described for the first time. Qualitatively similar response of the chain elongation to the confinement strength variation R g(D) is obtained in the case of cyclic chains. However, the relative chain extension is stronger, the Odijk strong confinement regime is extended to larger channel diameters D, and under moderate confinement the chain extension declines less steeply for cyclic chains. All three findings are explained in terms of the strong self-avoidance of confined chains relative to their linear analogues and the last finding is consistent with the reported experimental measurements. In the Odijk regime, the relative chain extension is governed by the same analytical functions provided half of the contour length for a cyclic chain is considered at the full extension. The orientation correlations for a cyclic chain in narrow channels are characterized by a typical sharp central minimum. Upon increasing the channel cross-sectional area, the minimum is broadened, turns into a negative maximum and, ultimately, the orientation correlations merge with those for a free cycle. Confined flexible and less stiff chains resemble their linear analogues more readily. The static structure factor for tightly confined chains provides better differentiation between the chain architecture than for free chains.

No abstract

In this work, hydrated poly(ethylene oxide) (PEO) chains composed of varying length N irreversibly grafted to an amorphous siloxane surface by one chain end at different coverage densities σ were studied using atomistic molecular dynamics simulations. We have assessed beginning of the extended overlapping chains (brush regime) at σ = 0.437 nm−2 and identified the mushroom-like conformation of nonoverlapping chains. For the studied systems, the specific interactions lead to density distributions different from the functions analytically derived for model systems. The brush regime demonstrates itself in the density distribution functions and the reduced height h/N evolution with σ. Since the latter dependence indicates h ∼ Nσ1/2 scaling, the brush regime corresponds to the situation of a concentrated aqueous PEO solution with a correlation length σ−1/2. The extrapolated thickness of PEO brushes reproduces experimental results fairly well. Water molecules prevent EO monomers from an adsorption to the siloxane surface.