Monte Carlo molecular simulation of solution and surface-bound DNA hybridization of short oligomers at varying surface densities.

DNA microarrays utilize surface bound sequences to probe for target sequences in samples of interest, and density of surface coverage plays an important role in any duplex formation and subsequent detection. Here, Monte Carlo molecular simulations utilize a modified coarse-grained DNA model to calculate the impact of binding density and arrangement as well as temperature on duplex structure and hydrogen bonding patterns for two different undecamer sequences. Results indicate a modest, sequence-dependent increase in dissociation related to the proximity of neighboring duplexes but little impact on duplex structure or hydrogen bonding pattern.

Effect of surface binding on heterogeneous DNA melting equilibria: a Monte Carlo simulation study.

Deoxyribonucleic acid (DNA) microarrays are constructed with a surface-immobilized single-stranded probe sequence that hydrogen bonds with its complementary target strand from solution and is subsequently detected, making their hybridization equilibrium of central importance. Unexpectedly, the effect of surface immobilization is that if the sequences of probe and target are exchanged, the hybridization equilibrium shifts. Here, configurational-bias Monte Carlo simulations using a coarse-grained model for DNA were carried out for an undecamer double helix both in solution and bound to a surface to determine dissociation equilibria. Four possible surface binding orientations were independently investigated. Analysis shows that the effect of surface binding is to destabilize hydrogen-bonding interactions of bases proximal to the binding site and enhance those of distal bases due to the double helix lying flat on the surface. Results have implications for predicting surface-bound DNA hybridization equilibria.

Partial molar volume and solvation structure of naphthalene in supercritical carbon dioxide: a Monte Carlo simulation study.

Monte Carlo simulations were used to investigate the solvation of naphthalene in supercritical carbon dioxide at a temperature of 308.38 K just above the solvent's critical temperature and at pressures of 74.6, 79.7, 87.8, and 310.2 bar covering a range from just below to far above the solvent's critical pressure and at a slightly elevated temperature of 318.15 K and a pressure of 93.0 bar. The Monte Carlo simulations were carried out in the isobaric-isothermal ensemble and employed the transferable potentials for phase equilibria (TraPPE) force field. Systems containing 2000 carbon dioxide molecules and from 0 to 4 solute molecules were used for all five state points, and additional simulations with 16 000 solvent molecules were carried out at the lower temperature and p = 79.7 bar. In agreement with experiment, the simulations yield large, negative partial molar volumes of naphthalene near the critical pressure at 79.7 bar, with values of -4340 +/- 750 and -3400 +/- 620 cm(3) mol(-1) for the 2000 and 16 000 molecule systems, respectively. Structural analysis through radial distribution functions and the corresponding number integrals yields good agreement with neutron diffraction data and shows evidence for a long-range density enhancement around solutes but lacking any specific solute-solvent clustering. Solvatochromic shifts estimated from the local solvent structure correlate well with the experimental data over the entire pressure range.

Binary phase behavior and aggregation of dilute methanol in supercritical carbon dioxide: a Monte Carlo simulation study.

Configurational-bias Monte Carlo simulations in the Gibbs and isobaric-isothermal ensembles using the transferable potentials for phase equilibria force field were carried out to investigate the thermophysical properties of mixtures containing supercritical carbon dioxide and methanol. The binary vapor-liquid coexistence curves were calculated at 333.15 and 353.15 K and are in excellent agreement with experimental measurements. The self-association of methanol in supercritical carbon dioxide was investigated over a range of temperatures and pressures near the mixture critical point. The temperature dependence of the equilibrium constants for the formation of hydrogen-bonded aggregates (from dimer to heptamer) allowed for the determination of the enthalpy of hydrogen bonding, DeltaHHB, in supercritical carbon dioxide with values for DeltaHHB of about 15 kJ mol(-1) falling within the range of previously proposed values. No strong pressure dependence was observed for the formation of aggregates. Apparently the decrease of the entropic penalty and of the enthalpic benefit upon increasing pressure or solvent density mostly cancel each other's effect on aggregate formation.