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Topological computing of arrangements with (co)chains [article]

Alberto Paoluzzi, Vadim Shapiro, Antonio DiCarlo, Francesco Furiani, Giulio Martella, Giorgio Scorzelli
2019 arXiv   pre-print
This paper introduces computational topology algorithms to discover the 2D/3D space partition induced by a collection of geometric objects of dimension 1D/2D, respectively.  ...  Methods and language are those of basic geometric and algebraic topology.  ...  Acknowledgements We would like to thank the anonymous reviewers who carefully read our manuscript and provided us with many useful comments.  ... 
arXiv:1911.08130v1 fatcat:g73baxybgjbvzo3mb7rbts5bky

Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization

Ivan Junier, Olivier Martin, François Képès, Hanah Margalit
2010 PLoS Computational Biology  
Next, numerical simulations of the polymer reveal a rich variety of phases that are associated with different topological orderings, each providing a way to increase the local concentrations of the interacting  ...  However, the mechanisms underlying the formation of these foci and the resulting topological order of the chromosome remain to be elucidated.  ...  The investigation of gene positions in E. coli and yeast suggests that in these organisms a near periodic arrangement on the DNA of co-regulated genes may be at the base of a good 3-dimensional spatial  ... 
doi:10.1371/journal.pcbi.1000678 pmid:20169181 pmcid:PMC2820526 fatcat:tbfj3nmr5ngptf4epoxdg3bgza

Moduli space actions on the Hochschild Co-Chains of a Frobenius algebra I: Cell Operads [article]

Ralph M. Kaufmann
2006 arXiv   pre-print
This is the first of two papers in which we prove that a cell model of the moduli space of curves with marked points and tangent vectors at the marked points acts on the Hochschild co--chains of a Frobenius  ...  We also prove that a there is dg--PROP action of a version of Sullivan Chord diagrams which acts on the normalized Hochschild co-chains of a Frobenius algebra.  ...  Singular Chains/PL Chains. First it is clear that there are family operations which have as input the singular co-chains of the Arc operad and as output products of these chains.  ... 
arXiv:math/0606064v2 fatcat:kftllqkepvdazpzb6yy5fizqf4

Moduli space actions on the Hochschild co-chains of a Frobenius algebra II: Correlators [article]

Ralph M. Kaufmann
2006 arXiv   pre-print
This is the second of two papers in which we prove that a cell model of the moduli space of curves with marked points and tangent vectors at the marked points acts on the Hochschild co--chains of a Frobenius  ...  We also prove that a there is dg--PROP action of a version of Sullivan Chord diagrams which acts on the normalized Hochschild co-chains of a Frobenius algebra.  ...  in the summer of 2006.  ... 
arXiv:math/0606065v2 fatcat:jzi3o6l2qnhbld7oiwoend74w4

Exploring a Proximity-Coupled Co Chain on Pb(110) as a Possible Majorana Platform

Michael Ruby, Benjamin W. Heinrich, Yang Peng, Felix von Oppen, Katharina J. Franke
2017 Nano letters (Print)  
Here, we study chains of the transition metal cobalt (Co) on Pb(110) and check for topological signatures.  ...  Linear chains of magnetic atoms proximity coupled to an s-wave superconductor are predicted to host Majorana zero modes at the chain ends in the presence of strong spin-orbit coupling.  ...  The uniform contrast along the Co chain suggests that it is in a ferromagnetic state, similar to Fe chains on Pb(110), although we cannot exclude a more complex spin arrangement with the out-of-plane spin  ... 
doi:10.1021/acs.nanolett.7b01728 pmid:28640633 pmcid:PMC5515507 fatcat:5qqasetpizdtpgdakjnu3knici

Moduli space actions on the Hochschild co-chains of a Frobenius algebra I: cell operads

Ralph Kaufmann
2007 Journal of Noncommutative Geometry  
This is the first of two papers in which we prove that a cell model of the moduli space of curves with marked points and tangent vectors at the marked points acts on the Hochschild co-chains of a Frobenius  ...  We also prove that a there is dg-PROP action of a version of Sullivan chord diagrams which acts on the normalized Hochschild co-chains of a Frobenius algebra.  ...  We would like to thank the Max-Planck-Institute for Mathematics where this work was started, a good portion of it was written in the summer of 2005 and the finishing touches were put on in the summer of  ... 
doi:10.4171/jncg/10 fatcat:rj7v4et2gneaxoagsdvemuzm2i

Moduli space actions on the Hochschild co-chains of a Frobenius algebra II: correlators

Ralph Kaufmann
2008 Journal of Noncommutative Geometry  
This is the second of two papers in which we prove that a cell model of the moduli space of curves with marked points and tangent vectors at the marked points acts on the Hochschild co-chains of a Frobenius  ...  We also prove that there is dg-PROP action of a version of Sullivan chord diagrams which acts on the normalized Hochschild co-chains of a Frobenius algebra.  ...  We would like to thank the Max-Planck-Institute for Mathematics where this work was started, a good portion of it was written in the summer of 2005 and the finishing touches were put on in the summer of  ... 
doi:10.4171/jncg/22 fatcat:sf7xvutcpjgr5os3xoical2spq

Machine-Learning Methods to Select Potential Depot Locations for the Supply Chain of Biomass Co-Firing

Diana Goettsch, Krystel K. Castillo-Villar, Maria Aranguren
2020 Energies  
BSC and the computational burden of the stochastic MILP model.  ...  To establish biomass as a viable option, the optimization of the biomass supply chain (BSC) is essential.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/en13246554 fatcat:lrqdtuhiynfhjl6v6ppkmaaceu

Local congruence of chain complexes [article]

Gianmaria DelMonte, Elia Onofri, Giorgio Scorzelli, Alberto Paoluzzi
2020 arXiv   pre-print
While computing the space arrangement generated by a collection of cellular complexes, one may start from independently and efficiently computing the intersection of each single input 2-cell with the others  ...  The topology of these intersections is codified within a set of (0-2)-dimensional chain complexes.  ...  In particular, the (co)boundary chain is produced by merging a set of local coboundary matrices computed independently from each other on every fragmented input 2-cell.  ... 
arXiv:2004.00046v1 fatcat:ie57rku3jrfpnacjkkfistfdxa

Exploring the Kondo effect of an extended impurity with chains of Co adatoms in a magnetic field [article]

Bimla Danu, Fakher Assaad, Frédéric Mila
2019 arXiv   pre-print
of the chain.  ...  Our modeling and numerical simulations provide a theoretical basis for the interpretation of the STM spectrum in terms of level crossings of the Co adatom chains.  ...  FFA thanks the DFG collaborative research centre SFB1170 To CoTronics (project C01) for financial support as well as the Würzburg-Dresden Clus-ter of Excellence on Complexity and Topology in Quantum Matter  ... 
arXiv:1903.08622v1 fatcat:jf6xmpk5tzdpxntx5pnijikj7i

Geometric Computing with Chain Complexes: Design and Features of a Julia Package [article]

Francesco Furiani, Giulio Martella, Alberto Paoluzzi
2017 arXiv   pre-print
Geometric computing with chain complexes allows for the computation of the whole chain of linear spaces and (co)boundary operators generated by a space decomposition into a cell complex.  ...  of geometric computing with any kind of meshes, using linear algebra tools with sparse matrices.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge a partial support 2016-17 from SOGEI, the ICT company of the Italian Ministry of Economy and Finance.  ... 
arXiv:1710.07819v2 fatcat:h4db4gwtp5cpbjsgfox6h3l7dy

Topology of internally constrained polymer chains

Maziar Heidari, Vahid Satarifard, Sander J. Tans, Mohammad Reza Ejtehadi, Samaneh Mashaghi, Alireza Mashaghi
2017 Physical Chemistry, Chemical Physics - PCCP  
An interacting partner can provide external control over folding rates and realized topologies.  ...  Due to the finite size of the chain, loops with the contact order higher than CO Z 0.35 are not investigated.  ...  The contact order of two loops with the topology of k is calculated by CO k ¼ 1=2N k L ð Þ P i2k DL ð1Þ i þ DL ð2Þ i , where N k is the number of double loops which are categorized in the topological state  ... 
doi:10.1039/c7cp02145c pmid:28678226 fatcat:du6arji4fzhcvegfrzauy3wpla

Two magnetic Δ-chain-based Mn(ii) and Co(ii) coordination polymers with mixed carboxylate–phosphinate and μ3-OH−bridges

Zi-Yi Du, Ling Zhang, Bao-Ying Wang, Sui-Jun Liu, Bo Huang, Cai-Ming Liu, Wei-Xiong Zhang
2017 CrysteEngComm  
The hydrothermal reaction of MnIJII) or CoIJII) ions with 2-carboxyethylIJphenyl)phosphinic acid (H 2 L) afforded MnIJII) and CoIJII) carboxylate-phosphinates containing μ 3 -OH − as a co-ligand, namely  ...  [M 3 IJL) 2 IJOH) 2 ] (M = Mn (1) or Co (2) ).  ...  The red solid line is Curie-Weiss fitting; (b) magnetization measured at 2 K for 1.Fig. 5 A proposed arrangement of the magnetic moments in a single chain of 1.  ... 
doi:10.1039/c6ce02537d fatcat:asistijvnjgovnyd7lnjcy2g2e

Proposal for realizing Majorana fermions in chains of magnetic atoms on a superconductor

S. Nadj-Perge, I. K. Drozdov, B. A. Bernevig, Ali Yazdani
2013 Physical Review B  
Model calculations show that such chains can be easily tuned between trivial and topological ground state.  ...  Decoupled Majorana bound states can form even in short magnetic chains consisting of only tens of atoms.  ...  Note that self-assembled chains consisting of ∼ 50 atoms with spiral arrangement of magnetic moments are already reported 37 .  ... 
doi:10.1103/physrevb.88.020407 fatcat:qyo6mhgxhrdvtjzrti7tkx4ba4

Effect of Surface Roughness on Aggregation of Polypeptide Chains: A Monte Carlo Study

Nguyen Truong Co, Mai Suan Li
2021 Biomolecules  
Our goal was to develop a simple lattice model for studying the role of surface roughness in the aggregation kinetics of polypeptide chains and the morphology of aggregates.  ...  The self-assembly of amyloidogenic peptides and proteins into fibrillar structures has been intensively studied for several decades, because it seems to be associated with a number of neurodegenerative  ...  Acknowledgments: We highly appreciate the supercomputer centre TASK in Gdansk, and PLGrid infrastructure, Poland for providing us with computational resources.  ... 
doi:10.3390/biom11040596 pmid:33919640 fatcat:sncgsdaqvbev7imxvc7einntgi
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