A hard-sphere quasicrystal stabilized by configurational entropy

Due to their aperiodic nature, quasicrystals are one of the least understood phases in statistical physics. One significant complication they present in comparison to their periodic counterparts is the fact that any quasicrystal can be realized as an exponentially large number of different tilings, resulting in a significant contribution to the quasicrystal entropy. Here, we use free-energy calculations to demonstrate that it is this configurational entropy which stabilizes a dodecagonal quasicrystal in a binary mixture of hard spheres on a plane. Our calculations also allow us to quantitatively confirm that in this system all tiling realizations are essentially equally likely, with free-energy differences less than 0.0001$k_BT$ per particle -- an observation that could be the related to the observation of only random tilings in soft matter quasicrystals. Owing to the simplicity of the model and its available counterparts in colloidal experiments, we believe that this system is a excellent candidate to achieve the long-awaited quasicrystal self-assembly on the micron scale.Comment: Contains an SI as ancillary fil

PENERTIBAN PENDIRIAN BANGUNAN DI SEPANJANG AREA SEMPADAN SUNGAI IRIGASI GUNUNG NAGO KECAMATAN PAUHKOTA PADANG

ABSTRAK Berdasarkan Lampiran VI Matriks Ketentuan Umum Peraturan Zonasi Pemanfaatan Ruang Peraturan Daerah Kota Padang Nomor 3 Tahun 2019 tentang Perubahan atas Peraturan Daerah Nomor 4 Tahun 2012 tentang Rencana Tata Ruang dan Wilayah Kota Padang Tahun 2010-2030, melarang beberapa kegiatan diantaranya: semua kegiatan yang berpotensi terjadinya perubahan lingkungan fisik alamiah ruang, seluruh kegiatan dan bangunan yang mengancam kerusakan dan menurunkan kualitas sungai, didalam sempadan sungai terdapat tanggul untuk kepentingan pengendalian banjir, perlindungan badan tanggul dilakukan dengan larangan; menanam tanaman selain rumput, mendirikan bangunan, dan mengurangi dimensi tanggul. Namun, fakta dilapangan ditemukan sejumlah bangunan yang berdiri diatas area sempadan sungai tersebut. Berdasarkan latar belakang diatas, maka permasalah yang akan diteliti adalah: 1) Bagaimana penertiban pendirian bangunan di sepanjang area sempadan Sungai Irigasi Gunung Nago, Kecamatan Pauh, Kota Padang? 2) Bagaimana upaya pemerintah dalam menangani permasalahan penertiban pendirian bangunan yang bediri di area sempadan Sungai Irigasi Gunung Nago, Kecamatan Pauh, Kota Padang? Metode penelitian ini adalah yuridis empiris. Data yang digunakan dalam penelitian ini adalah primer dan data sekunder. Teknik pengumpulan data yang digunakan yaitu studi dokumen dan wawancara. Berdasarkan penelitian yang telah dilakukan maka disimpulkan bahwa : Pertama, penertiban bangunan di area Sempadan Sungai Gunung Nago, Kecamatan Pauh, Kota Padang seperti yang diatur dalam Keputusan Wali Kota Padang Nomor 101 Tahun 2016 Tentang Standar Operasional Prosedur Penertiban Di Kota Padang masih belum dilakukan secara maksimal dan belum ditanggapi secara serius oleh Pemerintah Kota Padang. Kedua, Upaya pemerintah terhadap permasalah ini adalah dengan melaksanakan upaya preventif dan upaya represif. Upaya preventif dengan mengadakan sosialisasi dan pengawasan bersama pihak Kecamatan, dan upaya represif dengan mengadakan pembongkaran terhadap banguna

Historic Resources Study of Pullman National Monument, Illinois

This Historic Resource Study is a Baseline Research Report for Pullman National Monument. This HRS summarizes the historical writings about Pullman, provides context for the significant themes identified in its founding document, collates collections of primary documents and historical resources that are important sources of information on those themes, and recommends questions that will require additional study. These cultural resources include primary historical materials in archives and oral history collections, as well as architectural, archaeological, museum collections, or landscape resources. While this report includes new historical narrative based in original archival research, other sections present synthetic reviews of existing publications. National Park Service staff will use this document and included resources as they make management decisions and design interpretive programming. In addition to this report and its appendices—which are only published digitally—the research team deposited its entire library with the monument staff, including nearly 2,000 references and thousands of pages of digitally-imaged archival documents

Quasicrystal of Binary Hard Spheres on a Plane Stabilized by Configurational Entropy

Because of their aperiodic nature, quasicrystals are one of the least understood phases in statistical physics. One significant complication they present in comparison to their periodic counterparts is the fact that any quasicrystal can be realized as an exponentially large number of different tilings, resulting in a significant contribution to the quasicrystal entropy. Here, we use free-energy calculations to demonstrate that it is this configurational entropy which stabilizes a dodecagonal quasicrystal in a binary mixture of hard spheres on a plane. Our calculations also allow us to quantitatively confirm that in this system all tiling realizations are essentially equally likely, with free-energy differences less than 0.0001kBT per particle - an observation that could be related to the observation of only random tilings in soft-matter quasicrystals. Owing to the simplicity of the model and its available counterparts in colloidal experiments, we believe that this system is an excellent candidate to achieve the long-awaited quasicrystal self-assembly on the micron scale

Self-assembly of dodecagonal and octagonal quasicrystals in hard spheres on a plane

Hard spheres are one of the most fundamental model systems in soft matter physics, and have been instrumental in shedding light on nearly every aspect of classical condensed matter. Here, we add one more important phase to the list that hard spheres form: quasicrystals. Specifically, we use simulations to show that an extremely simple, purely entropic model system, consisting of two sizes of hard spheres resting on a flat plane, can spontaneously self-assemble into two distinct random-tiling quasicrystal phases. The first quasicrystal is a dodecagonal square-triangle tiling, commonly observed in a large variety of colloidal systems. The second quasicrystal has, to our knowledge, never been observed in either experiments or simulations. It exhibits octagonal symmetry, and consists of three types of tiles: triangles, small squares, and large squares, whose relative concentration can be continuously varied by tuning the number of smaller spheres present in the system. The observed tile composition of the self-assembled quasicrystals agrees very well with the theoretical prediction we obtain by considering the four-dimensional (lifted) representation of the quasicrystal. Both quasicrystal phases form reliably and rapidly over a significant part of parameter space. Our results demonstrate that entropy combined with a set of geometrically compatible, densely packed tiles can be sufficient ingredients for the self-assembly of colloidal quasicrystals

Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes

Detection of somatic mutations in human leukocyte antigen (HLA) genes using whole-exome sequencing (WES) is hampered by the high polymorphism of the HLA loci, which prevents alignment of sequencing reads to the human reference genome. We describe a computational pipeline that enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using the inferred alleles as a reference. Analysis of WES data from 7,930 pairs of tumor and healthy tissue from the same patient revealed 298 nonsilent HLA mutations in tumors from 266 patients. These 298 mutations are enriched for likely functional mutations, including putative loss-of-function events. Recurrence of mutations suggested that these \u27hotspot\u27 sites were positively selected. Cancers with recurrent somatic HLA mutations were associated with upregulation of signatures of cytolytic activity characteristic of tumor infiltration by effector lymphocytes, supporting immune evasion by altered HLA function as a contributory mechanism in cancer

Temporal transcriptome changes induced by MDV in marek's disease-resistant and -susceptible inbred chickens

<p>Abstract</p> <p>Background</p> <p>Marek's disease (MD) is a lymphoproliferative disease in chickens caused by Marek's disease virus (MDV) and characterized by T cell lymphoma and infiltration of lymphoid cells into various organs such as liver, spleen, peripheral nerves and muscle. Resistance to MD and disease risk have long been thought to be influenced both by genetic and environmental factors, the combination of which contributes to the observed outcome in an individual. We hypothesize that after MDV infection, genes related to MD-resistance or -susceptibility may exhibit different trends in transcriptional activity in chicken lines having a varying degree of resistance to MD.</p> <p>Results</p> <p>In order to study the mechanisms of resistance and susceptibility to MD, we performed genome-wide temporal expression analysis in spleen tissues from MD-resistant line 6₃, susceptible line 7₂and recombinant congenic strain M (RCS-M) that has a phenotype intermediate between lines 6₃and 7₂after MDV infection. Three time points of the MDV life cycle in chicken were selected for study: 5 days post infection (dpi), 10dpi and 21dpi, representing the early cytolytic, latent and late cytolytic stages, respectively. We observed similar gene expression profiles at the three time points in line 6₃and RCS-M chickens that are both different from line 7₂. Pathway analysis using Ingenuity Pathway Analysis (IPA) showed that MDV can broadly influence the chickens irrespective of whether they are resistant or susceptible to MD. However, some pathways like cardiac arrhythmia and cardiovascular disease were found to be affected only in line 7₂; while some networks related to cell-mediated immune response and antigen presentation were enriched only in line 6₃and RCS-M. We identified 78 and 30 candidate genes associated with MD resistance, at 10 and 21dpi respectively, by considering genes having the same trend of expression change after MDV infection in lines 6₃and RCS-M. On the other hand, by considering genes with the same trend of expression change after MDV infection in lines 7₂and RCS-M, we identified 78 and 43 genes at 10 and 21dpi, respectively, which may be associated with MD-susceptibility.</p> <p>Conclusions</p> <p>By testing temporal transcriptome changes using three representative chicken lines with different resistance to MD, we identified 108 candidate genes for MD-resistance and 121 candidate genes for MD-susceptibility over the three time points. Genes included in our resistance or susceptibility genes lists that are also involved in more than 5 biofunctions, such as <it>CD8α</it>, <it>IL8</it>, <it>USP18</it>, and <it>CTLA4</it>, are considered to be important genes involved in MD-resistance or -susceptibility. We were also able to identify several biofunctions related with immune response that we believe play an important role in MD-resistance.</p