Community detection (CD) algorithms are applied to Hi-C data to discover new communities of loci in the 3D conformation of human and mouse DNA. We find that CD has some distinct advantages over pre-existing methods: (...
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Community detection (CD) algorithms are applied to Hi-C data to discover new communities of loci in the 3D conformation of human and mouse DNA. We find that CD has some distinct advantages over pre-existing methods: (1) it is capable of finding a variable number of communities, (2) it can detect communities of DNA loci either adjacent or distant in the 1D sequence, and (3) it allows us to obtain a principled value of k, the number of communities present. Forcing k = 2, our method recovers earlier findings of Lieberman-Aiden, et al. (2009), but letting k be a parameter, our method obtains as optimal value k* = 6, discovering new candidate communities. In addition to discovering large communities that partition entire chromosomes, we also show that CD can detect small-scale topologically associating domains (TADs) such as those found in Dixon, et al. (2012). CD thus provides a natural and flexible statistical framework for understanding the folding structure of DNA at multiple scales in Hi-C data.
By analyzing the momentum distribution obtained from path integral and phonon calculations we find that the protons in hexagonal ice experience an anisotropic quasiharmonic effective potential with three distinct prin...
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By analyzing the momentum distribution obtained from path integral and phonon calculations we find that the protons in hexagonal ice experience an anisotropic quasiharmonic effective potential with three distinct principal frequencies that reflect molecular orientation. Due to the importance of anisotropy, anharmonic features of the environment cannot be extracted from existing experimental distributions that involve the spherical average. The full directional distribution is required, and we give a theoretical prediction for this quantity that could be verified in future experiments. Within the quasiharmonic context, anharmonicity in the ground-state dynamics of the proton is substantial and has quantal origin, a finding that impacts the interpretation of several spectroscopies.
The performance of the i-line AZ Spectralith resist under typical working conditions is examined. A study of primary lens aberrations including spherical aberration, coma, and astigmatism is presented for a lines and ...
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We present two interatomic potentials for hydrogen in α–iron based on the embedded atom method potentials for iron developed by Mendelev et al. [Philos. Mag. 83, 3977 (2003)] and Ackland et al. [J. Phys.: Condens....
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We present two interatomic potentials for hydrogen in α–iron based on the embedded atom method potentials for iron developed by Mendelev et al. [Philos. Mag. 83, 3977 (2003)] and Ackland et al. [J. Phys.: Condens. Matter 16, S2629 (2004)]. Since these latter potentials are unique among existing iron potentials in their ability to produce the same core structure for screw dislocations as density functional theory (DFT) calculations, our interatomic potentials for hydrogen in iron also inherit this important feature. We use an extensive database of energies and atomic configurations from DFT calculations to fit the cross interaction of hydrogen with iron. Detailed tests on the dissolution and diffusion of hydrogen in bulk α–iron, as well as the binding of H to vacancies, free surfaces, and dislocations, indicate that our potentials are in excellent overall agreement with DFT calculations.
In the context of the recently developed “equation-free” approach to computer-assisted analysis of complex systems, we extract the self-similar solution describing core collapse of a stellar system from numerical ex...
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In the context of the recently developed “equation-free” approach to computer-assisted analysis of complex systems, we extract the self-similar solution describing core collapse of a stellar system from numerical experiments. The technique allows us to sidestep the core “bounce” that occurs in direct N-body simulations due to the small-N correlations that develop in the late stages of collapse, and hence to follow the evolution well into the self-similar regime.
Localized states in the discrete two-dimensional (2D) nonlinear Schrödinger equation is found: vortex solitons with an integer vorticity S. While Hamiltonian lattices do not conserve angular momentum or the topol...
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Localized states in the discrete two-dimensional (2D) nonlinear Schrödinger equation is found: vortex solitons with an integer vorticity S. While Hamiltonian lattices do not conserve angular momentum or the topological invariant related to it, we demonstrate that the soliton’s vorticity may be conserved as a dynamical invariant. Linear stability analysis and direct simulations concur in showing that fundamental vortex solitons, with S=1, are stable if the intersite coupling C is smaller than some critical value Ccr(1). At C>Ccr(1), an instability sets in through a quartet of complex eigenvalues appearing in the linearized equations. Direct simulations reveal that an unstable vortex soliton with S=1 first splits into two usual solitons with S=0 (in accordance with the prediction of the linear analysis), but then an instability-induced spontaneous symmetry breaking takes place: one of the secondary solitons with S=0 decays into radiation, while the other one survives. We demonstrate that the usual (S=0) 2D solitons in the model become unstable, at C>Ccr(0)≈2.46Ccr(1), in a different way, via a pair of imaginary eigenvalues ω which bifurcate into instability through ω=0. Except for the lower-energy S=1 solitons that are centered on a site, we also construct ones which are centered between lattice sites which, however, have higher energy than the former. Vortex solitons with S=2 are found too, but they are always unstable. Solitons with S=1 and S=0 can form stable bound states.
We use an “equation-free,” coarse-grained computational approach to accelerate molecular dynamics-based computations of demixing (segregation) of dissimilar particles subject to an upward gas flow (gas-fluidized bed...
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We use an “equation-free,” coarse-grained computational approach to accelerate molecular dynamics-based computations of demixing (segregation) of dissimilar particles subject to an upward gas flow (gas-fluidized beds). We explore the coarse-grained dynamics of these phenomena in gently fluidized beds of solid mixtures of different densities, typically a slow process for which reasonable continuum models are currently unavailable.
The strength of collisional effects in a plasma can be summarized by the non-dimensional Knudsen number Kn. For very small values of Kn, plasma behavior is well-described by the 5N moment fluid model, including the Br...
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A recent numerical study observed that neural network classifiers enjoy a large degree of symmetry in the penultimate layer. Namely, if h(x) = Af(x) + b where A is a linear map and f is the output of the penultimate l...
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