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- Boaz Ilan, Emad Tajkhorshid, Klaus Schulten, Gregory A Voth
- Proteins
- 2004

The mechanism of proton exclusion in aquaporin channels is elucidated through free energy calculations of the pathway of proton transport. The second generation multistate empirical valence bond (MS-EVB2) model was applied to simulate the interaction of an excess proton with the channel environment. Jarzynski's equality was employed for rapid convergence of… (More)

- Hanning Chen, Boaz Ilan, Yujie Wu, Fangqiang Zhu, Klaus Schulten, Gregory A Voth
- Biophysical journal
- 2007

The explicit contribution to the free energy barrier and proton conductance from the delocalized nature of the excess proton is examined in aquaporin channels using an accurate all-atom molecular dynamics computer simulation model. In particular, the channel permeation free energy profiles are calculated and compared for both a delocalized (fully Grotthuss… (More)

- Yujie Wu, Boaz Ilan, Gregory A Voth
- Biophysical journal
- 2007

In this study, the minimalist synthetic LS2 channel is used as a prototype to examine the selectivity of protons over other cations. The free-energy profiles along the transport pathway of LS2 are calculated for three cation species: a realistic delocalized proton (including Grotthuss shuttling)--H(+), a classical (nonshuttling) hydronium--H(3)O(+), and a… (More)

- B. Ilan, Michael I. Weinstein
- Multiscale Modeling & Simulation
- 2010

We consider a class of nonlinear Schrödinger/Gross–Pitaevskii (NLS/GP) equations with periodic potentials having an even symmetry. We construct " solitons, " centered about any point of symmetry of the potential. For focusing (attractive) nonlinearities, these solutions bifurcate from the zero state at the lowest band-edge frequency into the semi-infinite… (More)

- M. A. Hoefer, B. Ilan
- 2009

Dispersive shock waves ͑DSWs͒ are studied theoretically in the context of two-dimensional ͑2D͒ supersonic flow of a superfluid. Employing Whitham averaging theory for the repulsive Gross-Pitaevskii ͑GP͒ equation, suitable jump and entropy conditions are obtained for an oblique DSW, a fundamental building block for 2D flows with boundaries. In analogy to… (More)

- M. A. Hoefer, B. Ilan
- 2016

We investigate propagating dark soliton solutions of the two-dimensional defocusing nonlinear Schrödinger or Gross-Pitaevskii (NLS-GP) equation that are transversely confined to propagate in an infinitely long channel. Families of single, vortex, and multilobed solitons are computed using a spectrally accurate numerical scheme. The multilobed solitons are… (More)

- M. A. Hoefer, B. Ilan
- Multiscale Modeling & Simulation
- 2012

The nature of transverse instabilities of dark solitons for the (2+1)-dimensional defo-cusing nonlinear Schrödinger/Gross–Pitaevski ˘ i (NLS/GP) equation is considered. Special attention is given to the small (shallow) amplitude regime, which limits to the Kadomtsev–Petviashvili (KP) equation. We study analytically and numerically the eigenvalues of the… (More)

We compute and study localized nonlinear modes (solitons) in the semi-infinite gap of the focusing two-dimensional nonlinear Schrödinger (NLS) equation with various irregular lattice-type potentials. The potentials are characterized by large variations from periodicity, such as vacancy defects, edge dislocations, and a quasicrystal structure. We use a… (More)

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