B. Ilan

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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)
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)
Scanning tunneling microscopy (STM) images of self-assembled monolayers of close-packed alkane chains on highly oriented pyrolitic graphite often display an alternating bright and dark spot pattern. Classical simulations suggest that a tilt of the alkane backbone is unstable and, therefore, unlikely to account for the contrast variation. First principles(More)
Semiconductor nanoparticles have a wide absorption band and small reabsorption probability, which makes them great candidates for luminescent solar concentrators (LSCs). We use Monte-Carlo simulations of photon transport to predict the performance of LSCs based on " type-II " CdSe-CdTe quantum dots. These computations suggest that semiconductor-based LSCs(More)
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)
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)
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)
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)
and found it satisfactory in all respects, and that any and all revisions required by the examining committee have been made. Abstract We explore methods that allow us to change an existing network's structure to achieve a desired PageRank. Being able to change the ranking of the nodes is desirable for any network for which the PageRank determines the(More)