Metassembler: merging and optimizing de novo genome assemblies

Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. We apply it to the four genomes from the Assemblathon competitions and show it consistently and substantially improves the contiguity and quality of each assembly. We also develop guidelines for meta-assembly by systematically evaluating 120 permutations of merging the top 5 assemblies of the first Assemblathon competition. The software is open-source at http://metassembler.sourceforge.net

Calculating Nonlocal Optical Properties of Structures with Arbitrary Shape

In a recent Letter [Phys. Rev. Lett. 103, 097403 (2009)], we outlined a computational method to calculate the optical properties of structures with a spatially nonlocal dielectric function. In this Article, we detail the full method, and verify it against analytical results for cylindrical nanowires. Then, as examples of our method, we calculate the optical properties of Au nanostructures in one, two, and three dimensions. We first calculate the transmission, reflection, and absorption spectra of thin films. Because of their simplicity, these systems demonstrate clearly the longitudinal (or volume) plasmons characteristic of nonlocal effects, which result in anomalous absorption and plasmon blueshifting. We then study the optical properties of spherical nanoparticles, which also exhibit such nonlocal effects. Finally, we compare the maximum and average electric field enhancements around nanowires of various shapes to local theory predictions. We demonstrate that when nonlocal effects are included, significant decreases in such properties can occur.Comment: 30 pages, 12 figures, 1 tabl

AFM pulling and the folding of donor-acceptor oligorotaxanes: phenomenology and interpretation

The thermodynamic driving force in the self-assembly of the secondary structure of a class of donor-acceptor oligorotaxanes is elucidated by means of molecular dynamics simulations of equilibrium isometric single-molecule force spectroscopy AFM experiments. The oligorotaxanes consist of cyclobis(paraquat-\emph{p}-phenylene) rings threaded onto an oligomer of 1,5-dioxynaphthalenes linked by polyethers. The simulations are performed in a high dielectric medium using MM3 as the force field. The resulting force vs. extension isotherms show a mechanically unstable region in which the molecule unfolds and, for selected extensions, blinks in the force measurements between a high-force and a low-force regime. From the force vs. extension data the molecular potential of mean force is reconstructed using the weighted histogram analysis method and decomposed into energetic and entropic contributions. The simulations indicate that the folding of the oligorotaxanes is energetically favored but entropically penalized, with the energetic contributions overcoming the entropy penalty and effectively driving the self-assembly. In addition, an analogy between the single-molecule folding/unfolding events driven by the AFM tip and the thermodynamic theory of first-order phase transitions is discussed and general conditions, on the molecule and the cantilever, for the emergence of mechanical instabilities and blinks in the force measurements in equilibrium isometric pulling experiments are presented. In particular, it is shown that the mechanical stability properties observed during the extension are intimately related to the fluctuations in the force measurements.Comment: 42 pages, 17 figures, accepted to the Journal of Chemical Physic

Semiclassical Nonadiabatic Dynamics Using a Mixed Wave-Function Representation

Nonadiabatic effects in quantum dynamics are described using a mixed polar/coordinate space representation of the wave function. The polar part evolves on dynamically determined potential surfaces that have diabatic and adiabatic potentials as limiting cases of weak localized and strong extended diabatic couplings. The coordinate space part, generalized to a matrix form, describes transitions between the surfaces. Choice of the effective potentials for the polar part and partitioning of the wave function enables one to represent the total wave function in terms of smooth components that can be accurately propagated semiclassically using the approximate quantum potential and small basis sets. Examples are given for two-state one-dimensional problems that model chemical reactions that demonstrate the capabilities of the method for various regimes of nonadiabatic dynamics

Semiclassical Nonadiabatic Dynamics Based on Quantum Trajectories for the O(\u3csup\u3e3\u3c/sup\u3eP,\u3csup\u3e1\u3c/sup\u3eD)+H\u3csub\u3e2\u3c/sub\u3e System

The O(3P,1D)+H2→OH+H reaction is studied using trajectory dynamics within the approximate quantum potential approach. Calculations of the wave-packet reaction probabilities are performed for four coupled electronic states for total angular momentum J = 0 using a mixed coordinate/polar representation of the wave function. Semiclassical dynamics is based on a single set of trajectories evolving on an effective potential-energy surface and in the presence of the approximate quantum potential. Population functions associated with each trajectory are computed for each electronic state. The effective surface is a linear combination of the electronic states with the contributions of individual components defined by their time-dependent average populations. The wave-packet reaction probabilities are in good agreement with the quantum-mechanical results. Intersystem crossing is found to have negligible effect on reaction probabilities summed over final electronic states

Proton Drip-Line Calculations and the Rp-process

One-proton and two-proton separation energies are calculated for proton-rich nuclei in the region $A=41-75$. The method is based on Skyrme Hartree-Fock calculations of Coulomb displacement energies of mirror nuclei in combination with the experimental masses of the neutron-rich nuclei. The implications for the proton drip line and the astrophysical rp-process are discussed. This is done within the framework of a detailed analysis of the sensitivity of rp process calculations in type I X-ray burst models on nuclear masses. We find that the remaining mass uncertainties, in particular for some nuclei with $N=Z$, still lead to large uncertainties in calculations of X-ray burst light curves. Further experimental or theoretical improvements of nuclear mass data are necessary before observed X-ray burst light curves can be used to obtain quantitative constraints on ignition conditions and neutron star properties. We identify a list of nuclei for which improved mass data would be most important.Comment: 20 pages, 9 figures, 2 table

On the linear response and scattering of an interacting molecule-metal system

A many-body Green's function approach to the microscopic theory of plasmon-enhanced spectroscopy is presented within the context of localized surface-plasmon resonance spectroscopy and applied to investigate the coupling between quantum-molecular and classical-plasmonic resonances in monolayer-coated silver nanoparticles. Electronic propagators or Green's functions, accounting for the repeated polarization interaction between a single molecule and its image in a nearby nanoscale metal, are explicitly computed and used to construct the linear-response properties of the combined molecule-metal system to an external electromagnetic perturbation. Shifting and finite lifetime of states appear rigorously and automatically within our approach and reveal an intricate coupling between molecule and metal not fully described by previous theories. Self-consistent incorporation of this quantum-molecular response into the continuum-electromagnetic scattering of the molecule-metal target is exploited to compute the localized surface-plasmon resonance wavelength shift with respect to the bare metal from first principles.Comment: under review at Journal of Chemical Physic

Ab-initio study of the relation between electric polarization and electric field gradients in ferroelectrics

The hyperfine interaction between the quadrupole moment of atomic nuclei and the electric field gradient (EFG) provides information on the electronic charge distribution close to a given atomic site. In ferroelectric materials, the loss of inversion symmetry of the electronic charge distribution is necessary for the appearance of the electric polarization. We present first-principles density functional theory calculations of ferroelectrics such as BaTiO3, KNbO3, PbTiO3 and other oxides with perovskite structures, by focusing on both EFG tensors and polarization. We analyze the EFG tensor properties such as orientation and correlation between components and their link with electric polarization. This work supports previous studies of ferroelectric materials where a relation between EFG tensors and polarization was observed, which may be exploited to study ferroelectric order when standard techniques to measure polarization are not easily applied.Comment: 9 pages, 6 figures, 5 tables, corrected typos, as published in Phys. Rev.

Statistical inference of the generation probability of T-cell receptors from sequence repertoires

Stochastic rearrangement of germline DNA by VDJ recombination is at the origin of immune system diversity. This process is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions between, and deletions from, genes. We use large sequence repertoires of the variable CDR3 region of human CD4+ T-cell receptor beta chains to infer the statistical properties of these basic biochemical events. Since any given CDR3 sequence can be produced in multiple ways, the probability distribution of hidden recombination events cannot be inferred directly from the observed sequences; we therefore develop a maximum likelihood inference method to achieve this end. To separate the properties of the molecular rearrangement mechanism from the effects of selection, we focus on non-productive CDR3 sequences in T-cell DNA. We infer the joint distribution of the various generative events that occur when a new T-cell receptor gene is created. We find a rich picture of correlation (and absence thereof), providing insight into the molecular mechanisms involved. The generative event statistics are consistent between individuals, suggesting a universal biochemical process. Our distribution predicts the generation probability of any specific CDR3 sequence by the primitive recombination process, allowing us to quantify the potential diversity of the T-cell repertoire and to understand why some sequences are shared between individuals. We argue that the use of formal statistical inference methods, of the kind presented in this paper, will be essential for quantitative understanding of the generation and evolution of diversity in the adaptive immune system.Comment: 20 pages, including Appendi