223 research outputs found
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 Vs 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 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
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