LIN: A new algorithm to simulate the dynamics of biomolecules by combining implicit-integration and normal mode techniques

A central goal in molecular dynamics simulations is increasing the integration time-step to allow the capturing of biomolecular motion on biochemically interesting time frames. We previously made a step in that direction by developing the Langevin/implicit–Euler scheme. Here, we present a modified Langevin/implicit–Euler formulation for molecular dynamics. The new method still maintains the major advantage of the original scheme, namely, stability over a wide range of time-steps. However, it substantially reduces the damping effect of the high-frequency modes inherent in the original implicit scheme. The new formulation involves separation of the solution into two components, one of which is solved exactly using normal-mode techniques, the other of which is solved by implicit numerical integration. In this way, the high-frequency and fast-varying components are well resolved in the analytic solution component, while the remaining components of the motion are obtained by a large time-step integration phase. Full details of the new scheme are presented, accompanied by illustrative examples for a simple pendulum system. An application to liquid butane demonstrates stability of the simulations at time-steps up to 50 fs, still with activation of the high-frequency modes. © John Wiley & Sons, Inc.     

Galois Theory and a New Homotopy Double Groupoid of a Map of Spaces

The authors have used generalised Galois Theory to construct a homotopy double groupoid of a surjective fibration of Kan simplicial sets. Here we apply this to construct a new homotopy double groupoid of a map of spaces, which includes constructions by others of a 2-groupoid, cat¹-group or crossed module. An advantage of our construction is that the double groupoid can give an algebraic model of a foliated bundle.     

Electrochemically patterning sol-gel structures on conducting and insulating surfaces

A new approach for the local deposition of sol-gel films on conducting and insulating surfaces using scanning electrochemical microscopy (SECM) via the feedback and direct modes is presented. Patterning is based on enhancing sol-gel condensation by altering the local pH due to water electrolysis as a result of applying negative potentials.     

Deposition of Au and Ag nanoparticles on PEDOT

The deposition of Au and Ag, locally and from bulk solution, on poly(3,4-ethylenedioxythiophene) (PEDOT) was studied. Specifically, PEDOT was electrochemically polymerized onto a glassy carbon (GC) electrode and used for bulk deposition of Au and Ag from their respective ions dissolved in the solution as well as for the local deposition of these metals using scanning electrochemical microscopy (SECM). These two sets of experiments were utilized to investigate the difference between Au and Ag electrochemical deposition on PEDOT. In particular, SECM experiments, which were conducted by the controlled anodic dissolution of Au and Ag microelectrodes close to GC/PEDOT, probed the effect of different PEDOT oxidation states on local deposition. The current-time transients recorded during the deposition, combined with scanning electron microscopy and EDX analysis provided insight into the reduction processes. AuCl(4)(-) and Ag(+) ions were electrochemically reduced at a potential equal to and more negative than the ions redox potentials (0.4 and 0.2 V, respectively) and more positive than -0.7 V, where the PEDOT starts transforming into the reduced, i.e. insulating, state. We found that the electroreduction of Ag(+) ions was diffusion-controlled and the PEDOT film served as a simple conductor. On the other hand, the reduction of AuCl(4)(-) ions was enhanced on GC/PEDOT as compared with bare GC, indicating that PEDOT catalyzes the reduction of AuCl(4)(-) to Au.     

Coherent control of molecular torsion

We propose a coherent, strong-field approach to control the torsional modes of biphenyl derivatives, and develop a numerical scheme to simulate the torsional dynamics. By choice of the field parameters, the method can be applied either to drive the torsion angle to an arbitrary configuration or to induce free internal rotation. Transient absorption spectroscopy is suggested as a probe of torsional control and the usefulness of this approach is numerically explored. Several consequences of our ability to manipulate molecular torsional motions are considered. These include a method for the inversion of molecular chirality and an ultrafast chiral switch.     

Communication: toward ultrafast, reconfigurable logic in the nanoscale

We propose and illustrate numerically a class of nanoscale, ultrafast logic gates with the further advantage of reconfigurability. Underlying the operation of the gates and their versatility is the concept of polarization control of the electromagnetic energy propagating via metal nanoparticle arrays. Specifically, a set of different logic gates is shown to obtain from a single metal nanoparticle junction by modification of the polarization properties of the input light sources. Implications and extensions of the gates are discussed.