David Aristoff

Bio: David Aristoff is an academic researcher from Colorado State University. The author has contributed to research in topics: Markov chain & Phase transition. The author has an hindex of 13, co-authored 51 publications receiving 379 citations. Previous affiliations of David Aristoff include University of Texas at Austin & University of Minnesota.

On the phase transition curve in a directed exponential random graph model

Abstract: We consider a family of directed exponential random graph models parametrized by edges and outward stars. Much of the important statistical content of such models is given by the normalization constant of the models, and in particular, an appropriately scaled limit of the normalization, which is called the free energy. We derive precise asymptotics for the normalization constant for finite graphs. We use this to derive a formula for the free energy. The limit is analytic everywhere except along a curve corresponding to a first order phase transition. We examine unusual behavior of the model along the phase transition curve.

Emergent structures in large networks

Abstract: We consider a large class of exponential random graph models and prove the existence of a region of parameter space corresponding to the emergent multipartite structure, separated by a phase transition from a region of disordered graphs. An essential feature is the formalism of graph limits as developed by Lovasz et al. for dense random graphs.

A Mathematical Framework for Exact Milestoning

Abstract: We give a mathematical framework for exact milestoning, a recently introduced algorithm for mapping a continuous time stochastic process into a Markov chain or semi-Markov process that can be efficiently simulated and analyzed. We generalize the setting of exact milestoning and give explicit error bounds for the error in the milestoning equation for mean first passage times.

Random Loose Packing in Granular Matter

Abstract: We introduce and simulate a two-dimensional Edwards-style model of granular matter at vanishing pressure. The model incorporates some of the effects of gravity and friction, and exhibits a random loose packing density whose standard deviation vanishes with increasing system size, a phenomenon that should be verifiable for real granular matter.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

An Introduction To The Theory Of Point Processes

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Stochastic Differential Equations And Applications

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QuantumATK: an integrated platform of electronic and atomic-scale modelling tools.

Abstract: QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented,a#13; the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings,a#13; simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more.a#13; Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation detailsa#13; not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys.a#13;