Pawel Pomorski

Dynamical scaling exponents for polymer translocation through a nanopore

Kaifu Luo,1 Tapio Ala-Nissila, 1, 2 See-Chen Ying, 2 Pawel Pomorski, 3 and Mikko Karttunen3 Laboratory of Physics, Helsinki University of Technology, P.O. Box 1100, FIN-02015 TKK, Espoo, Finland Department of Physics, Box 1843, Brown University, Providence, Rhode Island 02912-1843, USA Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada (Dated: August 21, 2007)We determine the scaling exponents of polymer translocation (PT) through a nanopore by extensive computer simulations of various microscopic models for chain lengths extending up to N=800 in some cases. We focus on the scaling of the average PT time tau approximately Nalpha and the mean-square change of the PT coordinate, approximately tbeta. We find alpha=1+2nu and beta=2/alpha for unbiased PT in two dimensions (2D) and three dimensions (3D). The relation alphabeta=2 holds for driven PT in 2D, with a crossover from alpha approximately 2nu for short chains to alpha approximately 1+nu for long chains. This crossover is, however, absent in 3D where alpha=1.42+/-0.01 and alphabeta approximately 2.2 for N approximately 40-800.

Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations

It has long been known that accurate electrostatics is a key issue for improving current force fields for large-scale biomolecular simulations. Typically, this calls for an improved and more accurate description of the molecular electrostatic potential, which eliminates the artifacts associated with current point charge-based descriptions. In turn, this involves the partitioning of the extended molecular charge distribution, so that charges and multipole moments can be assigned to different atoms. As an alternate to current approaches, we have investigated a charge partitioning scheme that is based on the maximally localized Wannier functions. This has the advantage of partitioning the charge, and placing it around the molecule in a chemically meaningful manner. Moreover, higher order multipoles may all be calculated without any undue numerical difficulties. Tests on isolated molecules and water dimers, show that the molecular electrostatic potentials generated by such a Wannier-function based approach are in excellent agreement with the density functional-based calculations.

Chapter 7 Nonequilibrium Green's function modeling of the quantum transport of molecular electronic devices

Publisher Summary This chapter discusses the nonequilibrium Greens function (NEGF) modeling of the quantum transport of molecular electronic devices. All the theoretical approaches to the accurate modeling of quantum transport of molecular devices fall into four main categories: semi-empirical methods, supercell methods, the open-jellium Lippman-Schwinger approach, and the NEGF approach. The key feature of the NEGF formalism is that the self-consistent charge density is not constructed out of the eigenstates of the system. Rather, the charge density is determined via the Keldysh NEGFs that provide an efficient framework for dealing with an open quantum system. The NEGF–DFT formalism for quantum transport provides important contributions toward calculating the device properties of real materials systems, especially when combined with the power of parallel supercomputers. The incorporation of spin-dependent effects opens up the important field of nanoscale magnetoelectronics or “spintronics.” In magnetoelectronics, both the charge and the spin degrees of freedom are utilized for the operation of a functional device.