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$^2$ 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

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 $\AA$ or 17 %) leading to a melted DNA state. In contrast, for 3'end1-3'end2 pulling it takes almost 32$\AA$ (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