Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History

Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole evolution history becomes a challenging problem in computational biology. In this paper, we present a likelihood-based approach to inferring network evolution history from the topology of PPI networks and the duplication relationship among the paralogs. Simulations show that our approach outperforms the existing ones in terms of the accuracy of reconstruction. Moreover, the growth parameters of several real PPI networks estimated by our method are more consistent with the ones predicted in literature.Comment: 15 pages, 5 figures, submitted to ISBRA 201

Refinding is Not Finding Again

A challenging problem for Internet users today is how to refind information that they have seen before. We believe that finding and refinding are different user activities and require different types of support. The problem of how to find information on the web is studied extensively---new search algorithms, support for natural language queries, and innovative document indexing techniques are common topics in information retrieval research; visualizations of documents, and task support for finding are topics in human-computer interaction. But refinding has only recently begun to receive attention. In this article, we present evidence to support the claim that information refinding is a different activity than information finding. We present results that show how refinding is different from finding and suggest ways to improve web information seeking tools and designs tosupport refinding information

Structure in sheared supercooled liquids:Dynamical rearrangements of an effective system of icosahedra

We consider a binary Lennard-Jones glassformer whose super-Arrhenius dynamics are correlated with the formation of particles organized into icosahedra under simple steady state shear. We recast this glassformer as an effective system of icosahedra [Pinney et al. J. Chem. Phys. 143 244507 (2015)]. From the observed population of icosahedra in each steady state, we obtain an effective temperature which is linearly dependent on the shear rate in the range considered. Upon shear banding, the system separates into a region of high shear rate and a region of low shear rate. The effective temperatures obtained in each case show that the low shear regions correspond to a significantly lower temperature than the high shear regions. Taking a weighted average of the effective temperature of these regions (weight determined by region size) yields an estimate of the effective temperature which compares well with an effective temperature based on the global mesocluster population of the whole system.Comment: accepted by J. Chehm. Phy

Analysis of signalling pathways using continuous time Markov chains

We describe a quantitative modelling and analysis approach for signal transduction networks. We illustrate the approach with an example, the RKIP inhibited ERK pathway [CSK+03]. Our models are high level descriptions of continuous time Markov chains: proteins are modelled by synchronous processes and reactions by transitions. Concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis such as what is the probability that if a concentration reaches a certain level, it will remain at that level thereafter? or how does varying a given reaction rate affect that probability? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

Geometric Phases, Symmetries of Dynamical Invariants, and Exact Solution of the Schr\"odinger Equation

We introduce the notion of the geometrically equivalent quantum systems (GEQS) as quantum systems that lead to the same geometric phases for a given complete set of initial state vectors. We give a characterization of the GEQS. These systems have a common dynamical invariant, and their Hamiltonians and evolution operators are related by symmetry transformations of the invariant. If the invariant is $T$-periodic, the corresponding class of GEQS includes a system with a $T$-periodic Hamiltonian. We apply our general results to study the classes of GEQS that include a system with a cranked Hamiltonian $H(t)=e^{-iKt}H_0e^{iKt}$. We show that the cranking operator $K$ also belongs to this class. Hence, in spite of the fact that it is time-independent, it leads to nontrivial cyclic evolutions and geometric phases. Our analysis allows for an explicit construction of a complete set of nonstationary cyclic states of any time-independent simple harmonic oscillator. The period of these cyclic states is half the characteristic period of the oscillator.Comment: Accepted for publication in J. Phys.

Unified Treatment of Heterodyne Detection: the Shapiro-Wagner and Caves Frameworks

A comparative study is performed on two heterodyne systems of photon detectors expressed in terms of a signal annihilation operator and an image band creation operator called Shapiro-Wagner and Caves' frame, respectively. This approach is based on the introduction of a convenient operator $\hat \psi$ which allows a unified formulation of both cases. For the Shapiro-Wagner scheme, where $[\hat \psi, \hat \psi^{\dag}] =0$, quantum phase and amplitude are exactly defined in the context of relative number state (RNS) representation, while a procedure is devised to handle suitably and in a consistent way Caves' framework, characterized by $[\hat \psi, \hat \psi^{\dag}] \neq 0$, within the approximate simultaneous measurements of noncommuting variables. In such a case RNS phase and amplitude make sense only approximately.Comment: 25 pages. Just very minor editorial cosmetic change

Backlund transformations for many-body systems related to KdV

We present Backlund transformations (BTs) with parameter for certain classical integrable n-body systems, namely the many-body generalised Henon-Heiles, Garnier and Neumann systems. Our construction makes use of the fact that all these systems may be obtained as particular reductions (stationary or restricted flows) of the KdV hierarchy; alternatively they may be considered as examples of the reduced sl(2) Gaudin magnet. The BTs provide exact time-discretizations of the original (continuous) systems, preserving the Lax matrix and hence all integrals of motion, and satisfy the spectrality property with respect to the Backlund parameter.Comment: LaTeX2e, 8 page

Solutions to Maxwell's Equations using Spheroidal Coordinates

Analytical solutions to the wave equation in spheroidal coordinates in the short wavelength limit are considered. The asymptotic solutions for the radial function are significantly simplified, allowing scalar spheroidal wave functions to be defined in a form which is directly reminiscent of the Laguerre-Gaussian solutions to the paraxial wave equation in optics. Expressions for the Cartesian derivatives of the scalar spheroidal wave functions are derived, leading to a new set of vector solutions to Maxwell's equations. The results are an ideal starting point for calculations of corrections to the paraxial approximation

2H and 27Al Solid-State NMR Study of the Local Environments in Al-Doped 2-Line Ferrihydrite, Goethite, and Lepidocrocite.

Although substitution of aluminum into iron oxides and oxyhydroxides has been extensively studied, it is difficult to obtain accurate incorporation levels. Assessing the distribution of dopants within these materials has proven especially challenging because bulk analytical techniques cannot typically determine whether dopants are substituted directly into the bulk iron oxide or oxyhydroxide phase or if they form separate, minor phase impurities. These differences have important implications for the chemistry of these iron-containing materials, which are ubiquitous in the environment. In this work, 27Al and 2H NMR experiments are performed on series of Al-substituted goethite, lepidocrocite, and 2-line ferrihydrite in order to develop an NMR method to track Al substitution. The extent of Al substitution into the structural frameworks of each compound is quantified by comparing quantitative 27Al MAS NMR results with those from elemental analysis. Magnetic measurements are performed for the goethite series to compare with NMR measurements. Static 27Al spin-echo mapping experiments are used to probe the local environments around the Al substituents, providing clear evidence that they are incorporated into the bulk iron phases. Predictions of the 2H and 27Al NMR hyperfine contact shifts in Al-doped goethite and lepidocrocite, obtained from a combined first-principles and empirical magnetic scaling approach, give further insight into the distribution of the dopants within these phases.J.K., A.J.I., D.M. and N.P. were supported by an NSF grant collaborative research grant in chemistry CHE0714183. An allocation of time upon the NANO computer cluster at the Center for Functional Nanomaterials, Brookhaven National Laboratory, U.S.A., which is supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, under Contract No. DE-AC02-98CH10886 is also acknowledged. D.S.M. and C.P.G. thank the EPSRC and the EU-ERC for support.This is the final version of the article. It first appeared from the American Chemical Society via http://dx.doi.org/10.1021/acs.chemmater.5b0085