Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session B26: Focus Session: Computational Nanoscience II: Mechanics, Dynamics, and Assembly |
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Sponsoring Units: DMP DCOMP Chair: Dennis Rapaport,, Bar-Ilan University Room: 328 |
Monday, March 16, 2009 11:15AM - 11:51AM |
B26.00001: An atomistic approach to viral mechanical oscillations Invited Speaker: Viruses are the simplest ``life'' form. These parasites reproduce by borrowing the machinery of their host cell. Many are pathogenic to plants, animals, and humans. Viruses possess an outer protein coat (capsid) that protects its genomic material that resides inside. We have developed a theoretical technique to model the very low frequency mechanical modes of the viral capsid with atomic resolution. The method uses empirical force fields and a mathematical framework borrowed from electronic structure theory for finding low energy states. The low frequency modes can be ``pinged'' with an ultra-short laser pulse and the aim of the light/vibrational coupling is to interfere with the viral life cycle. The theoretical work here is motivated by the recent work of Tsen et al. [2] who have used ultra-short pulsed laser scattering to inactivate viruses. The methodology can be applied to many systems, and the coupled mechanical oscillations of other floppy biomolecules such as a complete ATP binding cassette (ABC transporter) will also be discussed. Co-authors of this work are Dr. Eric Dykeman, Prof. K.-T. Tsen and Daryn Benson. \\[4pt] [1] E.C. Dykeman et al., Phys. Rev. Lett., 100, 028101 (2008). \\[0pt] [2] K-T. Tsen et al., J. of Physics -- Cond. Mat. 19, 472201 (2007). [Preview Abstract] |
Monday, March 16, 2009 11:51AM - 12:03PM |
B26.00002: A new paradigm for self-assembly: The role of reversibility in viral capsid growth Dennis Rapaport The phenomenon of supramolecular self-assembly, despite its importance, remains an enigma. The formation of virus capsids -- the exquisitely designed protein shells of spherical viruses -- is a well-known example, and there are numerous potential applications for nanotechnology. The capsid assembly process can be modeled using molecular dynamics simulation of simplified particles that are designed to form polyhedral shells. New insights into the mechanism of self-assembly have emerged from simulations carried out using particles immersed in an explicit solvent. Contrary to expectation, self-assembly is found to proceed via a cascade of strongly reversible steps, a feature that helps avoid growth-impeding kinetic traps because partial shells generally tend to lose rather than gain members. This ensures a robust process leading, under suitable conditions, to a high yield of complete shells. Furthermore, despite the large variety of possible intermediate structures, the assembly pathways are found to involve only a small fraction of highly bonded (low energy) forms. [Preview Abstract] |
Monday, March 16, 2009 12:03PM - 12:15PM |
B26.00003: Calculation of the free energy of binding of DNA bases on a single-wall carbon nanotube Robert Johnson, A.T. Charlie Johnson, Michael Klein Biological molecules can be combined with inorganic nanostructures to form multifunctional hybrid materials with unique properties that will drives advances in nanoelectronics, environmental safety, medicine and homeland security. One such material of contemporary interest is the DNA-carbon nanotube hybrid (DNA-CN), which consists of a single-wall carbon nanotube (SWCN) coated with a self-assembled monolayer of single-stranded DNA (ssDNA). Computation and experiment indicate that DNA-CN self-assembles with DNA bases binding to SWCN sidewall. However, the nature, strength and solvation effects of base-SWCN binding have not been studied in detail. To address these issues and expand our understanding of DNA-CN, we have computed the binding free energy of individual DNA bases with SWCN using alchemical free energy methods. Such calculations provide detailed information about the importance of electrostatic, van der Waals and hydrophobic interactions in base-SWCN binding. [Preview Abstract] |
Monday, March 16, 2009 12:15PM - 12:27PM |
B26.00004: Simulations of the self-assembly of CdTe nanoparticles into large pitch helices Aaron Santos, Sudhanshu Srivastava, Sharon Glotzer, Nicholas Kotov Recent experiments have shown that CdTe nanoparticles can self- assemble into wires, sheets, or helical nanoribbons with a large pitch length (300-400 nm) depending on the amount and type of capping group used. While conventional Monte Carlo simulations of electrically charged truncated tetrahedrons successfully predict the formation of wires and sheets, they are inadequate to describe the formation of helical nanoribbons, which require a large number of particles and a long run time to observe their characteristic features. We use a newly developed energy minimization technique, ``binary hierarchical assembly,'' to predict the packing structure of tetrahedral CdTe nanoparticles within the helix. From this packing structure, we construct nanoribbons of various widths and minimize the energy to determine the width of the stable structure. We find the stable width of the ribbon is charge dependent with values that correspond to ribbons observed in experiments. [Preview Abstract] |
Monday, March 16, 2009 12:27PM - 12:39PM |
B26.00005: Sensitivity Limits of Nanomechanical Resonance Spectroscopy P. Alex Greaney The sensitivity limit of the recently proposed chemical sensing method, nanomechanical resonance spectroscopy (NRS) \footnote{P.A. Greaney and J.C. Grossman, \emph{Nano Letters}, {\bf 8}, 2648-2652, (2008).}, is investigated using classical molecular dynamics simulations. The NRS method exploits the preferential transfer of energy between resonant modes, using an array of nanomechanical resonators to interrogate the vibrational spectrum of an analyte directly. We report on the effects of solvent and complex analytes. [Preview Abstract] |
Monday, March 16, 2009 12:39PM - 12:51PM |
B26.00006: Enhancing Molecuar Dynamics to Capture Electronic Effects N.A. Modine, R.E. Jones, D.L. Olmsted, J.A. Templeton, G.J. Wagner, R.M. Hatcher, M.J. Beck In modeling non-equilibrium thermal transport in nanoscale systems, classical molecular dynamics (MD) has the primary strength of explicitly representing phonon modes and scattering mechanisms. On the other hand, electrons and their role in energy transport are missing. Our goal is to couple a MD treatment of the ionic subsystem with a partial differential equation based model of the electronic subsystem in order to accurately capture aggregate behavior at the nanoscale. Along these lines, we have enhanced the LAMMPS MD package by coupling the ionic motions to a finite element based representation of electronic heat transport. The coupling between the subsystems occurs via a local version of the two-temperature model. Key parameters describing the coupling are calculated using Time Dependent Density Functional Theory (TDDFT) calculations with either explicit or implicit energy flow. We will discuss initial demonstrations of our approach focusing on nanowires and carbon nanotubes. [Preview Abstract] |
Monday, March 16, 2009 12:51PM - 1:03PM |
B26.00007: Rotary molecular motion at the nanoscale: motors, propellers, wheels Lela Vukovic, Boyang Wang, Petr Kral We describe by molecular dynamics simulations nanoscale systems that could realize rotary motion. First, we study molecular propellers formed by carbon nanotube rotors with attached aromatic blades [1]. We show that these propellers could pump different types of liquids, and their pumping efficiency strongly depends on the chemistry of the (hydrophobic or hydrophilic) liquid-blade interface. We also investigate nanoscopic wheels with hydrophobic surfaces that show rolling activity on water when driven. Finally, we model efficient molecular motors driven by electron tunneling, which could drive rotary molecular systems [2]. \\[3pt] [1] B. Wang and P. Kr\'{a}l, . Rev. Lett. 98, 266102 (2007).\\[0pt] [2] B. Wang, L. Vukovic and P. Kr\'{a}l, Phys. Rev. Lett. 101, 186808 (2008). [Preview Abstract] |
Monday, March 16, 2009 1:03PM - 1:15PM |
B26.00008: Long-Range Hydrodynamic Interactions Implemented into LAMMPS (Parallel MD) Frances Mackay, Colin Denniston We use an explicit solvent method to study the interaction between particles and a fluid. Similar to the Particle-Mesh-Ewald schemes for electrodynamics, the long range hydrodynamic interactions are treated by interpolating the particle density onto a mesh. This is then coupled to the fluid, which we model using a thermal lattice Boltzmann scheme. Mass and momentum conserving noise in the lattice Boltzmann fluid scheme provides a thermostat for both the fluid and the particles. This work has been fully parallelized and implemented into LAMMPS, an open-source molecular dynamics code. We demonstrate the scheme with some examples from colloidal physics and flow over rough surfaces. [Preview Abstract] |
Monday, March 16, 2009 1:15PM - 1:27PM |
B26.00009: Atomistic Simulations of Hydrodynamic and Interaction Forces on Functionalized Silica Nanoparticles J. Matthew D. Lane, Ahmed E. Ismail, Michael Chandross, Christian D. Lorenz, Gary S. Grest It is often desired to prevent the flocculation and phase separation of nanoparticles in solution. This can be accomplished either by manipulating the solvent or by tailoring the surface chemistry of the nanoparticles through functionalization with a monolayer of oligomer chains. Since it is not known how these functionalized coatings affect the interactions between nanoparticles and with the surrounding solvent, we present results from a series of molecular dynamics simulations of polyethylene oxide (PEO) coated silica nanoparticles of varying size (5 to 20 nm diameter) in water. For a single nanoparticle we determined the Stokes drag on the nanoparticle as it moves through the solvent and as it approaches a wall. Due to hydrodynamic interactions there are large finite size effects which we estimate by varying the size of the simulation cell. We also determined both solvent-mediated (velocity-independent) and lubrication (velocity-dependent) forces between two nanoparticles as a function of the coverage and chain length of the PEO chains. [Preview Abstract] |
Monday, March 16, 2009 1:27PM - 1:39PM |
B26.00010: Water Flow in Carbon Nanotubes: Transition from Continuum to Subcontinuum Transport John Thomas, Alan McGaughey Water flow through carbon nanotubes (CNTs) with diameters ranging from 0.83 nm to 4.98 nm is examined using molecular dynamics simulation. A reflecting particle membrane is used to drive the flow and the relationship between the axial pressure gradient, CNT diameter, and volumetric flow rate is examined. The flow enhancement, defined as the ratio of the observed flow rate to that predicted from the no-slip Hagen-Poiseuille relation, is calculated for each CNT. In CNTs with diameters greater than 1.39 nm, flow can be accurately described in terms of continuum mechanics and the enhancement agrees with predictions from the slip-modified Hagen-Poiseuille flow relation. In CNTs with diameters smaller then 1.39 nm, we find that the liquid structure varies with CNT diameter and a continuum-based description of the fluid flow is inappropriate. The flow enhancement for these CNTs do not agree with predictions from the slip-modified Hagen-Poiseuille flow relation. They can, however, be correlated to the diameter-specific liquid structure. [Preview Abstract] |
Monday, March 16, 2009 1:39PM - 1:51PM |
B26.00011: Fluid flow through carbon nanotubes: a new modeling and simulation approach Michael A. Avon, Alper Buldum The flow of fluids through carbon nanotubes was investigated in order to get a better understanding of the unique properties and phenomena of nanofluidics. The previous modeling and simulation efforts were based on diffusion of atoms or molecules that were thrown to the nanotubes with initial velocities. Here, we present molecular dynamics simulations of carbon nanotubes that were embedded in liquid argon. The fluid was pushed through the nanotubes using a moving wall piston of graphene.Single-walled, double-walled, rigid and relaxed nanotubes in different diameters were considered. In order to achieve more continuous flow of fluid through the nanotube, several rounds of pumping were simulated. Pressure difference in different regions was analyzed. [Preview Abstract] |
Monday, March 16, 2009 1:51PM - 2:03PM |
B26.00012: Accelerated Molecular Dynamics Simulation on Friction of Incommensurate Interfaces Woo Kyun Kim, Michael Falk We apply a molecular dynamics (MD) methodology to study the friction of incommensurate interfaces. While the traditional Tomlinson model assumes a single, repeatable transition, the sliding at the real incommensurate interface is comprised of a multitude of transition modes. This may account for recent Atomic Force Microscope (AFM) experimental results that indicate more complex temperature and velocity dependence of friction that deviate from the Tomlinson predictions. Conventional MD simulations are unable to simulate a wide range of sliding rates due to time scale limitations. In this study, we achieve decreases in the simulated sliding velocity by several orders of magnitude compared with conventional MD simulations using Voter's hyperdynamics scheme. This method uses a biased potential to reduce the barrier heights of the original potential to decrease the simulated time between slip events. The decrease in the sliding velocity makes it possible to see the atomic level processes during sliding speeds much closer to the experimental time scale. We carefully analyze the simulation results to elucidate the transition mechanisms. [Preview Abstract] |
Monday, March 16, 2009 2:03PM - 2:15PM |
B26.00013: Molecular dynamics study of the phase transition in the bcc metal nanoparticles Yasushi Shibuta, Toshio Suzuki The phase transition between liquid and solid phases in bcc metal nanoparticles was investigated using a molecular dynamics simulation. The nucleation from an undercooled liquid droplet was observed during cooling in all nanoparticles considered. A nucleus was generated near one side of the particle and solidification spread toward the other side the during nucleation process. On the other hand, the surface melting and subsequent inward melting of the solid core of the nanoparticles were observed during heating. The depression of the melting point was proportional to the inverse of the particle radius due to the Gibbs--Thomson effect [1]. However, the depression of the nucleation temperature during cooling was not monotonic with respect to the particle radius since the nucleation from an undercooled liquid depends on the event probability of an embryo or a nucleus. \\[3pt] [1] Y. Shibuta, T. Suzuki, J. Chem. Phys. 129 (2008) 144102. [Preview Abstract] |
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