Kinetics of Phase ordering in Microemulsions and Micellar Solutions

We review the models developed and techniques used in recent years to study the kinetics of phase ordering in a class of complex fluids, namely, ternary microemulsions and micellar solutions.Comment: 10 pages in REVTEX, 4 Postscript figures. To appear in "Phase Transitions in Complex Fluids", Eds. P. Toledano and A. M. Figueiredo Neto (World Scientific, 1997

Translocation and encapsulation of siRNA inside carbon nanotubes

We report spontaneous translocation of small interfering RNA (siRNA) inside carbon nanotubes (CNTs) of various diameters and chirality using all atom molecular dynamics (MD) simulations with explicit solvent. We use Umbrella sampling method to calculate the free energy landscape of the siRNA entry and translocation event. Free energy profiles shows that siRNA gains free energy while translocating inside CNT and barrier for siRNA exit from CNT ranges from 40 to 110 kcal/mol depending on CNT chirality and salt concentration. The translocation time \tau decreases with the increase of CNT diameter with a critical diameter of 24 \AA for the translocation. In contrast, double strand DNA (dsDNA) of the same sequence does not translocate inside CNT due to large free energy barrier for the translocation. This study helps in understanding the nucleic acid transport through nanopores at microscopic level and may help designing carbon nanotube based sensor for siRNA.Comment: Accepted for the Journal of Chemical Physics; 24 pages, 6 figures and 1 tabl

A Microscopic Model of Gemini Surfactants: Self-assemblies in Water and at Air-Water Interface

We report the results of large scale Monte Carlo (MC) simulations of novel microscopic models of gemini surfactants to elucidate (i) their spontaneous aggregation in bulk water and (ii) their spatial organization in a system where water is separated from the air above it by a sharp well defined interface. We study the variation of the critical micellar concentration (CMC) with the variation of the (a) length of the spacer, (b) length of the hydrophobic tail and (c) the bending rigidity of the hydrocarbon chains forming the spacer and the tail; some of the trends of variation are counter-intuitive but are in excellent agreement with the available experimental results. Our simulations elucidate the effects of the geometrical shape, size and density of the surfactant molecules, the ionic nature of the heads and hydrophobicity/hydrophilicity of the spacer not only on the shapes of the micellar aggregates and the magnitude of the CMC, but also on their conformations close to the air-water interface.Comment: 19 pages in REVTEX, 25 Postscript Figures (now included

Ultrahigh Charge Carrier Mobility in Nanotube Encapsulated Coronene Stack

Achieving high charge carrier mobility is the holy grail of organic electronics. In this letter we report a record charge carrier mobility of 14.93 cm$^2$ V$^{-1}$s$^{-1}$ through a coronene stack encapsulated in a single walled carbon nanotube (CNT) by using a multiscale modeling technique which combines MD simulations, first principle calculations and Kinetic Monte Carlo simulations. For the CNT having a diameter of 1.56 nm we find a highly ordered defect free organization of coronene molecules inside the CNT which is responsible for the high charge carrier mobility. The encapsulated coronene molecules are correlated with a large correlation length of $\sim$18 {\AA} which is independent of the length of the coronene column. Our simulation further suggests that coronene molecules can spontaneously enter the CNT, suggesting that the encapsulation is experimentally realizable

Force Induced DNA Melting

When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very cooperative. Applying force perpendicular to the DNA axis (unzipping), double-strand DNA can also be separated into two single-stranded DNA which is a fundamental process in DNA replication. We study the DNA overstretching and unzipping transition using fully atomistic molecular dynamics (MD) simulations and argue that the conformational changes of double strand DNA associated with either of the above mentioned processes can be viewed as force induced DNA melting. As the force at one end of the DNA is increased the DNA start melting abruptly/smoothly after a critical force depending on the pulling direction. The critical force fm, at which DNA melts completely decreases as the temperature of the system is increased. The melting force in case of unzipping is smaller compared to the melting force when the DNA is pulled along the helical axis. In the cases of melting through unzipping, the double-strand separation has jumps which correspond to the different energy minima arising due to different base pair sequence. The fraction of Watson-Crick base pair hydrogen bond breaking as a function of force does not show smooth and continuous behavior and consists of plateaus followed by sharp jumps.Comment: 23 pages, 9 figures, accepted for publication in J. Phys.: Condens. Matte

Structure, stability and elasticity of DNA nanotube

DNA nanotubes are tubular structures composed of DNA crossover molecules. We present a bottom up approach for construction and characterization of these structures. Various possible topologies of nanotubes are constructed such as 6-helix, 8-helix and tri-tubes with different sequences and lengths. We have used fully atomistic molecular dynamics simulations to study the structure, stability and elasticity of these structures. Several nanosecond long MD simulations give the microscopic details about DNA nanotubes. Based on the structural analysis of simulation data, we show that 6-helix nanotubes are stable and maintain their tubular structure; while 8-helix nanotubes are flattened to stabilize themselves. We also comment on the sequence dependence and effect of overhangs. These structures are approximately four times more rigid having stretch modulus of ~4000 pN compared to the stretch modulus of 1000 pN of DNA double helix molecule of same length and sequence. The stretch moduli of these nanotubes are also three times larger than those of PX/JX crossover DNA molecules which have stretch modulus in the range of 1500-2000 pN. The calculated persistence length is in the range of few microns which is close to the reported experimental results on certain class of the DNA nanotubes.Comment: Published in Physical Chemistry Chemical Physic

Tunable mechanical and thermal properties of ZnS/CdS core/shell nanowires

Using all atom molecular dynamics (MD) simulations, we have studied the mechanical properties of ZnS/CdS core/shell nanowires. Our results show that the coating of a few atomic layer CdS shell on the ZnS nanowire leads to a significant change in the stiffness of the core/shell nanowires compared to the stiffness of pure ZnS nanowires. The binding energy between the core and shell region decreases due to the lattice mismatch at the core-shell interface. This reduction in binding energy plays an important role in determining the stiffness of a core/shell nanowire. We have also investigated the effects of the shell on the thermal conductivity and melting behavior of the nanowires

Driving force of water entry into hydrophobic channels of carbon nanotubes: entropy or energy?

Spontaneous entry of water molecules inside single-wall carbon nanotubes (SWCNTs) has been confirmed by both simulations and experiments. Using molecular dynamics simulations, we have studied the thermodynamics of filling of a (6,6) carbon nanotube in a temperature range from 273 to 353 K and with different strengths of the nanotube-water interaction. From explicit energy and entropy calculations using the two-phase thermodynamics method, we have presented a thermodynamic understanding of the filling behaviour of a nanotube. We show that both the energy and the entropy of transfer decrease with increasing temperature. On the other hand, scaling down the attractive part of the carbon-oxygen interaction results in increased energy of transfer while the entropy of transfer increases slowly with decreasing the interaction strength. Our results indicate that both energy and entropy favour water entry into (6,6) SWCNTs. Our results are compared with those of several recent studies of water entry into carbon nanotubes.Comment: 18 pages, 5 figures, Molecular Simulation, 201

Coarse-grained simulation of polymer translocation through an artificial nanopore

The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried out a molecular dynamics simulation study of electrophoretic translocation of a charged polymer through an artificial nanopore to explore the feasibility of semiconductor--based nanopore devices for ultra--fast DNA sequencing. The polymer is represented by a simple bead--spring model designed to yield an appropriate coarse-grained description of the phosphate backbone of DNA in salt--free aqueous solution. A detailed analysis of single translocation event is presented to assess whether the passage of individual ions through the pore can be detected by a nanoscale field--effect transistor by measuring variations in electrostatic potential during polymer translocation. We find that it is possible to identify single events corresponding to the passage of counterions through the pore, but that discrimination of individual ions on the polymer chain based on variations in electrostatic potential is problematic. Several distinct stages in the translocation process are identified, characterized by changes in polymer conformation and by variations in the magnitude and direction of the internal electric field induced by the fluctuating charge distribution. The dependence of the condensed fraction of counterions on Bjerrum length leads to significant changes in polymer conformation, which profoundly affect the dynamics of electrophoresis and translocation.Comment: 37 pages Revtex, 11 postscript figure

Structure and Electrical Properties of DNA Nanotubes Embedded in Lipid Bilayer Membranes

Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT) embedded in POPC lipid bilayer using the analysis of 0.2 microsecond long equilibrium MD simulation trajectories. We observe that the head groups of the lipid molecules close to the lumen cooperatively tilt towards the hydrophilic sugar-phosphate backbone of DNA and form a toroidal structure around the patch of DNT protruding in the membrane. Further, we explore the effect of ionic concentrations to the in-solution structure and stability of the lipid-DNT complex. Transmembrane ionic current measurements for the constant electric field MD simulation provide the I-V characteristics of the water filled DNT lumen in lipid membrane. With increasing salt concentrations, the measured values of transmembrane ionic conductance of the porous DNT lumen vary from 4.3 nS to 20.6 nS. Simulations of the DNTs with ssDNA and dsDNA overhangs at the mouth of the pore show gating effect with remarkable difference in the transmembrane ionic conductivities for open and close state nanopores.Comment: Accepted for publication in Nucleic Acid Research, 11 Figures and 3 Table