Molecular Dynamics Simulation of Sympathetic Crystallization of Molecular Ions

It is shown that the translational degrees of freedom of a large variety of molecules, from light diatomic to heavy organic ones, can be cooled sympathetically and brought to rest (crystallized) in a linear Paul trap. The method relies on endowing the molecules with an appropriate positive charge, storage in a linear radiofrequency trap, and sympathetic cooling. Two well--known atomic coolant species, ${}^9{\hbox{Be}}^+$ and ${}^{137}{\hbox{Ba}}^+$, are sufficient for cooling the molecular mass range from 2 to 20,000 amu. The large molecular charge required for simultaneous trapping of heavy molecules and of the coolant ions can easily be produced using electrospray ionization. Crystallized molecular ions offer vast opportunities for novel studies.Comment: Accepted for publication in Phys. Rev.

A Novel A Priori Simulation Algorithm for Absorbing Receivers in Diffusion-Based Molecular Communication Systems

A novel a priori Monte Carlo (APMC) algorithm is proposed to accurately simulate the molecules absorbed at spherical receiver(s) with low computational complexity in diffusion-based molecular communication (MC) systems. It is demonstrated that the APMC algorithm achieves high simulation efficiency since by using this algorithm, the fraction of molecules absorbed for a relatively large time step length precisely matches the analytical result. Therefore, the APMC algorithm overcomes the shortcoming of the existing refined Monte Carlo (RMC) algorithm which enables accurate simulation for a relatively small time step length only. Moreover, for the RMC algorithm, an expression is proposed to quickly predict the simulation accuracy as a function of the time step length and system parameters, which facilitates the choice of simulation time step for a given system. Furthermore, a rejection threshold is proposed for both the RMC and APMC algorithms to significantly save computational complexity while causing an extremely small loss in accuracy.Comment: 11 pages, 14 figures, submitted to IEEE Transactions on NanoBioscience. arXiv admin note: text overlap with arXiv:1803.0463

Molecular mode-coupling theory for supercooled liquids: Application to water

We present mode-coupling equations for the description of the slow dynamics observed in supercooled molecular liquids close to the glass transition. The mode-coupling theory (MCT) originally formulated to study the slow relaxation in simple atomic liquids, and then extended to the analysis of liquids composed by linear molecules, is here generalized to systems of arbitrarily shaped, rigid molecules. We compare the predictions of the theory for the $q$-vector dependence of the molecular nonergodicity parameters, calculated by solving numerically the molecular MCT equations in two different approximation schemes, with ``exact'' results calculated from a molecular dynamics simulation of supercooled water. The agreement between theory and simulation data supports the view that MCT succeeds in describing the dynamics of supercooled molecular liquids, even for network forming ones.Comment: 22 pages 4 figures Late

Molecular Dynamics Simulation of Polymer-Metal Bonds

Molecular simulation is becoming a very powerful tool for studying dynamic phenomena in materials. The simulation yields information about interaction at length and time scales unattainable by experimental measurements and unpredictable by continuum theories. This is especially meaningful when referring to bonding between a polymer and a metal substrate. A very important characteristic of polymers is that their physical properties do not rely on the detailed chemical structure of the molecular chains but only on their flexibility, and accordingly they will be able to adopt different conformations. In this paper, a molecular simulation of the bonding between vinyl ester polymer and steel is presented. Four different polymers with increasing chain lengths have been studied. Atomic co-ordinates are adjusted in order to reduce the molecular energy. Conformational changes in the macromolecules have been followed to obtain the polymer pair correlation function. Radius of gyration and end-to-end distance distributions of the individual chains have been used as a quantitative measurement of their flexibility. There exists a correlation between flexibility of the molecular chains and the energy of adhesion between the polymer and the metal substrate. Close contacts between the two materials are established at certain points but every atom up to a certain distance from the interface contributes to the total value of the adhesion energy of the system