33 research outputs found
Simulation of Noncircular Rigid Bodies: Machine Learning Based Overlap Calculation Technique with System Size Independent Computational Cost
Standard molecular dynamics (MD) and Monte Carlo (MC) simulation deals with
spherical particles. Extending these standard simulation methodologies to the
non-spherical cases is non-trivial. To circumvent this problem, non-spherical
bodies are considered as a collection of constituent spherical objects. As the
number of these constituent objects becomes large, the computational burden to
simulate the system also increases. In this article, we propose an alternative
way to simulate non-circular rigid bodies in two dimensions having pairwise
repulsive interactions. Our approach is based on a machine learning (ML) based
model which predicts the overlap between two non-circular bodies. The machine
learning model is easy to train and the computation cost of its implementation
remains independent of the number of constituents disks used to represent a
non-circular rigid body. When used in MC simulation, our approach provides
significant speed up in comparison to the standard implementation where overlap
determination between two rigid bodies is done by calculating the distance of
their constituent disks. Our proposed ML based MC method provided very similar
structural features (in comparison to standard implementation) of the systems.
We believe this work is a very first step towards a time-efficient simulation
of non-spherical rigid bodies
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
Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA
We report a structural polymorphism of the S-DNA when a canonical B-DNA is
stretched under different pulling protocols and provide a fundamental molecular
understanding of the DNA stretching mechanism. Extensive all atom molecular
dynamics simulations reveal a clear formation of S-DNA when the B-DNA is
stretched along the 3' directions of the opposite strands (OS3) and is
characterized by the changes in the number of H-bonds, entropy and free energy.
Stretching along 5' directions of the opposite strands (OS5) leads to force
induced melting form of the DNA. Interestingly, stretching along the opposite
ends of the same strand (SS) leads to a coexistence of both the S- and melted
M-DNA structures. We also do the structural characterization of the S-DNA by
calculating various helical parameters. We find that S-DNA has a twist of ~10
degrees which corresponds to helical repeat length of ~ 36 base pairs in close
agreement with the previous experimental results. Moreover, we find that the
free energy barrier between the canonical and overstretched states of DNA is
higher for the same termini (SE) pulling protocol in comparison to all other
protocols considered in this work. Overall, our observations not only reconcile
with the available experimental results qualitatively but also enhance the
understanding of different overstretched DNA structures.Comment: To be published in the The Journal of Chemical Physics (AIP
Charge Transport in Dendrimer Melt using Multiscale Modeling Simulation
In this paper we present a theoretical calculation of the charge carrier
mobility in two different dendrimeric melt system (Dendritic phenyl azomethine
with Triphenyl amine core and Dendritic Carbazole with Cyclic Phenylazomethine
as core), which have recently been reported1 to increase the efficiency of
Dye-Sensitized solar cells (DSSCs) by interface modification. Our mobility
calculation, which is a combination of molecular dynamics simulation, first
principles calculation and kinetic Monte Carlo simulation, leads to mobilities
that are in quantitative agreement with available experimental data. We also
show how the mobility depends on the dendrimer generation. Furthermore, we
examine the variation of mobility with external electric field and external
reorganization energy. Physical mechanisms behind observed electric field and
generation dependencies of mobility are also explored
Dramatic changes in DNA conductance with stretching: structural polymorphism at a critical extension
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3′end1–3′end2 ends, which find a sharp conductance jump for a very short (4.5%) stretching length, we carried out multiscale modeling to predict the conductance of dsDNA as it is mechanically stretched to promote various structural polymorphisms. We calculate the current along the stretched DNA using a combination of molecular dynamics simulations, non-equilibrium pulling simulations, quantum mechanics calculations, and kinetic Monte Carlo simulations. For 5′end1–5′end2 attachments we find an abrupt jump in the current within a very short stretching length (6 Å or 17%) leading to a melted DNA state. In contrast, for 3′end1–3′end2 pulling it takes almost 32 Å (84%) of stretching to cause a similar jump in the current. Thus, we demonstrate that charge transport in DNA can occur over stretching lengths of several nanometers. We find that this unexpected behaviour in the B to S conformational DNA transition arises from highly inclined base pair geometries that result from this pulling protocol. We found that the dramatically different conductance behaviors for two different pulling protocols arise from how the hydrogen bonds of DNA base pairs break
Dramatic changes in DNA Conductance with stretching: Structural Polymorphism at a critical extension
In order to interpret recent experimental studies of the dependence of
conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which
find a sharp conductance jump for a very short (4.5 %) stretching length, we
carried out multiscale modeling, to predict the conductance of dsDNA as it is
mechanically stretched to promote various structural polymorphisms. We
calculate the current along the stretched DNA using a combination of molecular
dynamics simulations, non-equilibrium pulling simulations, quantum mechanics
calculations, and kinetic Monte Carlo simulations. For 5'end1-5'end2
attachments we find an abrupt jump in the current within a very short
stretching length (6 or 17 %) leading to a melted DNA state. In
contrast, for 3'end1-3'end2 pulling it takes almost 32 (84 %) of
stretching to cause a similar jump in the current. Thus, we demonstrate that
charge transport in DNA can occur over stretching lengths of several
nanometers. We find that this unexpected behaviour in the B to S conformational
DNA transition arises from highly inclined base pair geometries that result
from this pulling protocol. We find that the dramatically different conductance
behaviors for two different pulling protocols arise from the nature of how
hydrogen bonds of DNA base pairs break