Characterizing Residue-Bilayer Interactions Using Gramicidin A as a Scaffold and Tryptophan Substitutions as Probes

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1021/acs.jctc.7b00400.Previous experiments have shown that the lifetime of a gramicidin A dimer channel (which forms from two non-conducting monomers) in a lipid bilayer is modulated by mutations of the tryptophan (Trp) residues at the bilayer-water interface. We explore this further using extensive molecular dynamics simulations of various gA dimer and monomer mutants at the Trp positions in phosphatidylcholine bilayers with different tail lengths. gA interactions with the surrounding bilayer are strongly modulated by mutating these Trp residues. There are three principal effects: eliminating residue hydrogen bonding ability (i.e., reducing the channel-monolayer coupling strength) reduces the extent of the bilayer deformation caused by the assembled dimeric channel; a residue’s size and geometry affects its orientation, leading to different hydrogen bonding partners; and increasing a residue’s hydrophobicity increases the depth of gA monomer insertion relative to the bilayer center, thereby increasing the lipid bending frustration

Pfaffian-like ground states for bosonic atoms and molecules in one-dimensional optical lattices

We study ground states and elementary excitations of a system of bosonic atoms and diatomic Feshbach molecules trapped in a one-dimensional optical lattice using exact diagonalization and variational Monte Carlo methods. We primarily study the case of an average filling of one boson per site. In agreement with bosonization theory, we show that the ground state of the system in the thermodynamic limit corresponds to the Pfaffian-like state when the system is tuned towards the superfluid-to-Mott insulator quantum phase transition. Our study clarifies the possibility of the creation of exotic Pfaffian-like states in realistic one-dimensional systems. We also present preliminary evidence that such states support non-Abelian anyonic excitations that have potential application for fault-tolerant topological quantum computation.Comment: 10 pages, 10 figures. Matching the version published Phys.Rev.

Polynomially filtered exact diagonalization approach to many-body localization

Polynomially filtered exact diagonalization method (POLFED) for large sparse matrices is introduced. The algorithm finds an optimal basis of a subspace spanned by eigenvectors with eigenvalues close to a specified energy target by a spectral transformation using a high order polynomial of the matrix. The memory requirements scale better with system size than in the state-of-the-art shift-invert approach. The potential of POLFED is demonstrated examining many-body localization transition in 1D interacting quantum spin-1/2 chains. We investigate the disorder strength and system size scaling of Thouless time. System size dependence of bipartite entanglement entropy and of the gap ratio highlights the importance of finite-size effects in the system. We discuss possible scenarios regarding the many-body localization transition obtaining estimates for the critical disorder strength.Comment: 4+5 pages, version accepted in Physical Review Letters, comments welcom

Nearly extensive sequential memory lifetime achieved by coupled nonlinear neurons

Many cognitive processes rely on the ability of the brain to hold sequences of events in short-term memory. Recent studies have revealed that such memory can be read out from the transient dynamics of a network of neurons. However, the memory performance of such a network in buffering past information has only been rigorously estimated in networks of linear neurons. When signal gain is kept low, so that neurons operate primarily in the linear part of their response nonlinearity, the memory lifetime is bounded by the square root of the network size. In this work, I demonstrate that it is possible to achieve a memory lifetime almost proportional to the network size, "an extensive memory lifetime", when the nonlinearity of neurons is appropriately utilized. The analysis of neural activity revealed that nonlinear dynamics prevented the accumulation of noise by partially removing noise in each time step. With this error-correcting mechanism, I demonstrate that a memory lifetime of order $N/\log N$ can be achieved.Comment: 21 pages, 5 figures, the manuscript has been accepted for publication in Neural Computatio

Open system quantum annealing in mean field models with exponential degeneracy

Real life quantum computers are inevitably affected by intrinsic noise resulting in dissipative non-unitary dynamics realized by these devices. We consider an open system quantum annealing algorithm optimized for a realistic analog quantum device which takes advantage of noise-induced thermalization and relies on incoherent quantum tunneling at finite temperature. We analyze the performance of this algorithm considering a p-spin model which allows for a mean field quasicalssical solution and at the same time demonstrates the 1st order phase transition and exponential degeneracy of states. We demonstrate that finite temperature effects introduced by the noise are particularly important for the dynamics in presence of the exponential degeneracy of metastable states. We determine the optimal regime of the open system quantum annealing algorithm for this model and find that it can outperform simulated annealing in a range of parameters.Comment: 11 pages, 5 figure

Incremental eigenpair computation for graph Laplacian matrices: theory and applications

The smallest eigenvalues and the associated eigenvectors (i.e., eigenpairs) of a graph Laplacian matrix have been widely used for spectral clustering and community detection. However, in real-life applications, the number of clusters or communities (say, K) is generally unknown a priori. Consequently, the majority of the existing methods either choose K heuristically or they repeat the clustering method with different choices of K and accept the best clustering result. The first option, more often, yields suboptimal result, while the second option is computationally expensive. In this work, we propose an incremental method for constructing the eigenspectrum of the graph Laplacian matrix. This method leverages the eigenstructure of graph Laplacian matrix to obtain the Kth smallest eigenpair of the Laplacian matrix given a collection of all previously compute

Predicting the wake structure of the HART II rotor using the vorticity transport model

Brown’s Vorticity Transport Model has been used to predict the wake structure and resultant blade loading of the rotor that was studied during the HART II experimental programme. The descending flight condition of the experiment yields significant high-frequency content to the blade loading due to the presence of blade-vortex interactions. PIV images of the wake structure were compared against numerical predictions of the detailed geometry of the rotor wake using three different computational resolutions of the flow. This was done to investigate the origin of inaccuracies exposed in an earlier study of the system in capturing the effects of blade vortex interactions on the loading on the rotor. The predicted positions of the vortex cores agree with measured data to within a fraction of the blade chord, and the strength of the vortices is preserved to well downstream of the rotor, essentially independently of the resolution of the calculation. Nevertheless the amplitude of the loading impulses induced on the blade by vortex interaction are strongly influenced by the resolution of the calculation through the effect of cell density on the minimum vortex core size that can be supported. It would appear thus that the inaccuracies in predicting the high-frequency loading on the rotor are not due to any inherent deficiency in the representation of the wake, although viscous effects may need to be considered in future in order to decouple the vortex core size from the cell size, but rather due to the inherent deficiencies of the lifting line approach used to model the blade aerodynamics