112 research outputs found
Geometry Selects Highly Designable Structures
By enumerating all sequences of length 20, we study the designability of
structures in a two-dimensional Hydrophobic-Polar (HP) lattice model in a wide
range of inter-monomer interaction parameters. We find that although the
histogram of designability depends on interaction parameters, the set of highly
designable structures is invariant. So in the HP lattice model the High
Designability should be a purely geometrical feature. Our results suggest two
geometrical properties for highly designable structures, they have maximum
number of contacts and unique neighborhood vector representation. Also we show
that contribution of perfectly stable sequences in designability of structures
plays a major role to make them highly designable.Comment: 6 figure, To be appear in JC
A model universe with variable dimension: Expansion as decrumpling
We propose a model universe, in which the dimension of the space is a
continuous variable, which can take any real positive number. The dynamics
leads to a model in which the universe has no singularity. The difference
between our model and the standard Friedman-Robertson-Walker models become
effective for times much before the presently accepted age of the universe.Comment: 12 pages, emTeX version 3.0, no figure
Directed motion of C60 on a graphene sheet subjected to a temperature gradient
Nonequilibrium molecular dynamics simulations is used to study the motion of
a C60 molecule on a graphene sheet subjected to a temperature gradient. The C60
molecule is actuated and moves along the system while it just randomly dances
along the perpendicular direction. Increasing the temperature gradient
increases the directed velocity of C60. It is found that the free energy
decreases as the C60 molecule moves toward the cold end. The driving mechanism
based on the temperature gradient suggests the construction of nanoscale
graphene-based motors
Extreme bendability of DNA double helix due to bending asymmetry
Experimental data of the DNA cyclization (J-factor) at short length scales,
as a way to study the elastic behavior of tightly bent DNA, exceed the
theoretical expectation based on the wormlike chain (WLC) model by several
orders of magnitude. Here, we propose that asymmetric bending rigidity of the
double helix in the groove direction can be responsible for extreme bendability
of DNA at short length scales and it also facilitates DNA loop formation at
these lengths. To account for the bending asymmetry, we consider the asymmetric
elastic rod (AER) model which has been introduced and parametrized in an
earlier study (B. Eslami-Mossallam and M. Ejtehadi, Phys. Rev. E 80, 011919
(2009)). Exploiting a coarse grained representation of DNA molecule at base
pair (bp) level, and using the Monte Carlo simulation method in combination
with the umbrella sampling technique, we calculate the loop formation
probability of DNA in the AER model. We show that, for DNA molecule has a
larger J-factor compared to the WLC model which is in excellent agreement with
recent experimental data.Comment: 8 pages, 9 figure
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