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Doubly Stochastic Pairwise Interactions for Agreement and Alignment [article]

Thomas Dagès, Alfred M. Bruckstein
<span title="2021-03-15">2021</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We here propose a very simple stochastic interaction at encounters that leads to agreement or geometric alignment in swarms of simple agents, and analyse the process of converging to consensus.  ...  The interactions are doubly stochastic, in the sense that, at discrete time steps, pairs of agents are randomly selected and their new states are independently and uniformly set at random in (local) domains  ...  The interactions that we define are stochastic and we prove that a desired behaviour eventually emerges.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2012.13727v2">arXiv:2012.13727v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4d7o3xu3k5gfnhs63youte6b7u">fatcat:4d7o3xu3k5gfnhs63youte6b7u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210324192313/https://arxiv.org/pdf/2012.13727v2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cb/7f/cb7fa1d22db44f9c416f1fea67236814ac82fe3b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2012.13727v2" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Global multiple protein-protein interaction network alignment by combining pairwise network alignments

Jakob Dohrmann, Juris Puchin, Rahul Singh
<span title="">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
A wealth of protein interaction data has become available in recent years, creating an urgent need for powerful analysis techniques.  ...  SMAL was also able to retain many important characteristics of the native pairwise alignments, such as the number of aligned nodes and edges, as well as the functional and homologene similarity of aligned  ...  The resulting cost function is optimized through two relaxations, one concave and one convex, over doubly stochastic matrices by PATH; and through permutation in the direction of the gradient starting  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-16-s13-s11">doi:10.1186/1471-2105-16-s13-s11</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26423128">pmid:26423128</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4597059/">pmcid:PMC4597059</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tvpshnsatfdmlggksi2joyli4a">fatcat:tvpshnsatfdmlggksi2joyli4a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170819161730/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-16-S13-S11?site=bmcbioinformatics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1c/1d/1c1db03df93712585e63b0b3c2f74d1393ebf943.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-16-s13-s11"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4597059" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Dressed-state control of effective dipolar interaction between strongly-coupled solid-state spins [article]

Junghyun Lee, Mamiko Tatsuta, Andrew Xu, Erik Bauch, Mark J. H. Ku, Ronald. L. Walsworth
<span title="2022-03-15">2022</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Strong interactions between spins in many-body solid-state quantum system is a crucial resource for exploring and applying non-classical states.  ...  We perform simulations that indicate the promise for this robust scheme to control the distribution of interaction strengths in strongly-interacting spin systems, including interaction strength homogenization  ...  (d) PDF for R dd when pairwise off-axis NV spins are not driven (ND); singly driven with Ω1 = 50 MHz, Ω2 = 0; and doubly driven with Ω1 = 50 MHz, Ω2 = 40 MHz.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2203.07610v1">arXiv:2203.07610v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mczdmgy2y5a2zocniyllqw4lhq">fatcat:mczdmgy2y5a2zocniyllqw4lhq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220320194858/https://arxiv.org/pdf/2203.07610v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/53/92/5392508fd58aa31524a21c29b20af53b4484a215.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2203.07610v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

GLOBAL ALIGNMENT OF MULTIPLE PROTEIN INTERACTION NETWORKS

ROHIT SINGH, JINBO XU, BONNIE BERGER
<span title="">2007</span> <i title="WORLD SCIENTIFIC"> Biocomputing 2008 </i> &nbsp;
Recently, we have proposed the first algorithm for pairwise global alignment of PPI networks.  ...  Contributions One of the main contributions of this paper is the first algorithm for global alignment of multiple protein interaction networks.  ...  (i, j) and column (u, v) (the row and column are doubly-indexed).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789812776136_0030">doi:10.1142/9789812776136_0030</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ulltm7m6ifdb7dlux5ptqk3fly">fatcat:ulltm7m6ifdb7dlux5ptqk3fly</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20150619225611/http://psb.stanford.edu/psb-online/proceedings/psb2008/singh.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ad/c6/adc6bc5761885f9bbc7f33e76dc5828fd6e76001.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9789812776136_0030"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

Global alignment of multiple protein interaction networks with application to functional orthology detection

R. Singh, J. Xu, B. Berger
<span title="2008-08-25">2008</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
The conserved subgraphs in this alignment are larger and more varied than those produced by previous methods, which performed pairwise network alignments.  ...  The network alignment problem can be formulated in various ways, depending on the kind of input (pairwise vs. multiple alignments) and the scope of node mapping desired.  ...  We thank Michael Baym and Michael Schnall-Levin for helpful comments, Leonid Chindelevitch for additionally proving the convergence bound, and the referees for valuable advice and suggestions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.0806627105">doi:10.1073/pnas.0806627105</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18725631">pmid:18725631</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2522262/">pmcid:PMC2522262</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vn3hf3vcljgnlcv5mqclnhb23a">fatcat:vn3hf3vcljgnlcv5mqclnhb23a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20151106021323/http://www.pnas.org:80/content/105/35/12763.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a5/bd/a5bdb1ff0b87de987d1745c02d0c63a2e393cd72.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.0806627105"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2522262" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy

B. Roux, B. Prod'hom, M. Karplus
<span title="">1995</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
The structural and thermodynamic factors responsible for the singly and doubly occupied saturation states of the gramicidin channel are investigated with molecular dynamics simulations and free energy  ...  The calculations reveal that the doubly occupied state is relatively more favorable for the larger ions.  ...  The calculations show a clear tendency for the larger cations to be bound more favorably in doubly occupied channels, in agreement with experiment.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0006-3495(95)80264-x">doi:10.1016/s0006-3495(95)80264-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/7538804">pmid:7538804</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1281812/">pmcid:PMC1281812</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hfufxiowzfdbrdco4e6hhv4d3u">fatcat:hfufxiowzfdbrdco4e6hhv4d3u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190415035628/https://core.ac.uk/download/pdf/82154854.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c1/5b/c15b57f6646af26fe58fd719445d1b465150669e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0006-3495(95)80264-x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1281812" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Effects of Posttranslational Modifications on the Structure and Dynamics of Histone H3 N-Terminal Peptide

Haiguang Liu, Yong Duan
<span title="">2008</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
The calculated melting temperatures showed that the doubly acetylated peptide has the lowest melting temperature (T m ¼ 324 K), which is notably lower than the melting temperatures of the other four peptides  ...  and the stability of the most populated states significantly.  ...  GM64458 and GM67168 to Y.D.). Usage of the Visual Molecular Dynamics graphics package is gratefully acknowledged.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1529/biophysj.107.115824">doi:10.1529/biophysj.107.115824</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18192367">pmid:18192367</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2397375/">pmcid:PMC2397375</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ysv47opdzrax3nrghiwujkn5se">fatcat:ysv47opdzrax3nrghiwujkn5se</a> </span>
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Gossip-Based Centroid and Common Reference Frame Estimation in Multiagent Systems

Mauro Franceschelli, Andrea Gasparri
<span title="">2014</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dg2bd7saqzaj3e4myjqwziwpa4" style="color: black;">IEEE Transactions on robotics</a> </i> &nbsp;
Only asynchronous and random pairwise communications are allowed between neighboring agents.  ...  In this work the decentralized common reference frame estimation problem for multi-agent systems in absence of any common coordinate system is investigated.  ...  only asynchronous and random pairwise communications between pairs of agents.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tro.2013.2291621">doi:10.1109/tro.2013.2291621</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u7aqom7m4jgjlaf5u3xhulf6ke">fatcat:u7aqom7m4jgjlaf5u3xhulf6ke</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809113147/http://gasparri.dia.uniroma3.it/biblio/pdf/GasparriTRO12014.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/10/74/1074a94952e463132a8ebebf20586a970a88b94b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tro.2013.2291621"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Casimir forces on a silicon micromechanical chip

J. Zou, Z. Marcet, A. W. Rodriguez, M. T. H. Reid, A. P. McCauley, I. I. Kravchenko, T. Lu, Y. Bao, S. G. Johnson, H. B. Chan
<span title="2013-05-14">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
Quantum fluctuations give rise to van der Waals and Casimir forces that dominate the interaction between electrically neutral objects at sub-micron separations.  ...  Apart from providing a compact platform for Casimir force measurements, this scheme also opens the possibility of tailoring the Casimir force using lithographically defined components of non-conventional  ...  The element for sensing the force is a doubly-clamped silicon beam that is 100 µm long and ~ 1.42 µm wide, depicted in the top parts of Figs. 1a and 1b.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms2842">doi:10.1038/ncomms2842</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23673630">pmid:23673630</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y5hh5ek7vveq5focqwlxhtzbb4">fatcat:y5hh5ek7vveq5focqwlxhtzbb4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304124838/http://pdfs.semanticscholar.org/dc52/6be0227a77397f23f3a5cd0cc98117771461.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/dc/52/dc526be0227a77397f23f3a5cd0cc98117771461.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms2842"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a>

Recent advances in opinion propagation dynamics: A 2020 Survey [article]

Hossein Noorazar
<span title="2020-06-04">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Local interactions among individuals create interesting dynamics for the system as a whole. Such dynamics are important from a variety of perspectives.  ...  In this paper, we summarize these ground-breaking ideas and their fascinating extensions and introduce newly surfaced concepts.  ...  It is shown in [87] that for the DeGroot-Friedkin model, a democratic configuration will be reached if and only if the relative matrix C is doubly-stochastic.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2004.05286v2">arXiv:2004.05286v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pnflrglcznaqfflea45ergpdaa">fatcat:pnflrglcznaqfflea45ergpdaa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200826215121/https://arxiv.org/pdf/2004.05286v2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/82/07/82078d4c05c9f605db49715f4d703cabab569b5a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2004.05286v2" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

REGAL

Mark Heimann, Haoming Shen, Tara Safavi, Danai Koutra
<span title="">2018</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6g37zvjwwrhv3dizi6ffue642m" style="color: black;">Proceedings of the 27th ACM International Conference on Information and Knowledge Management - CIKM &#39;18</a> </i> &nbsp;
Our results demonstrate the utility and promise of unsupervised representation learning-based network alignment in terms of both speed and accuracy.  ...  Motivated by recent advancements in node representation learning for single-graph tasks, we propose REGAL (REpresentation learning-based Graph ALignment), a framework that leverages the power of automatically-learned  ...  , and P is a permutation matrix or a relaxed version, such as doubly stochastic matrix [32] or some other concave/convex relaxation [35] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/3269206.3271788">doi:10.1145/3269206.3271788</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/cikm/HeimannSSK18.html">dblp:conf/cikm/HeimannSSK18</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fg6x6of7qrbzneeni4sdfg2qoe">fatcat:fg6x6of7qrbzneeni4sdfg2qoe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191012074753/https://arxiv.org/pdf/1802.06257v2.pdf" title="fulltext PDF download [not primary version]" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <span style="color: #f43e3e;">&#10033;</span> <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/46/81/46813d00e5a1ad9ce989c5811b85f7e4cabfafe5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/3269206.3271788"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

Heterohexameric Ring Arrangement of the Eukaryotic Proteasomal ATPases: Implications for Proteasome Structure and Assembly

Robert J. Tomko, Minoru Funakoshi, Kyle Schneider, Jimin Wang, Mark Hochstrasser
<span title="">2010</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/afqwz322bfdapd7r446dhqqbbm" style="color: black;">Molecular Cell</a> </i> &nbsp;
) and their cognate chaperones (Rpn14, Nas6, and Nas2).  ...  Finally, the ATPase ring structure casts light on alternative RP structural models and the mechanism of RP action.  ...  For the last lane (60*), the WCL was incubated for 10 min in DTT prior to gel loading. (B) Rpt3 and Rpt6 associate in doubly capped proteasomes (RP2CP).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.molcel.2010.02.035">doi:10.1016/j.molcel.2010.02.035</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20471945">pmid:20471945</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2879271/">pmcid:PMC2879271</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k77lfyywmvggpfk5cbodld342e">fatcat:k77lfyywmvggpfk5cbodld342e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110331202520/http://info.med.yale.edu/mbb/hochstrasser/Papers/20102.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e6/f2/e6f2583caecf001d85114c5f2392bb21643a832e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.molcel.2010.02.035"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879271" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods

Yu-Guo Tao, W. K. den Otter, J. T. Padding, J. K. G. Dhont, W. J. Briels
<span title="2005-06-22">2005</span> <i title="AIP Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hnc5ddfunnd3taca63uf5ggldm" style="color: black;">Journal of Chemical Physics</a> </i> &nbsp;
The model accounts for excluded volume interactions between rods, but neglects hydrodynamic interactions.  ...  Recently a microscopic theory for the dynamics of suspensions of long thin rigid rods was presented, confirming and expanding the well-known theory by Doi and Edwards ͓The Theory of Polymer Dynamics ͑Clarendon  ...  Excluded volume interactions are modeled with a pairwise interaction potential whose terms are proportional to the overlap volume of the corresponding pair of rods.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1063/1.1940031">doi:10.1063/1.1940031</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16035812">pmid:16035812</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qkfdfjytsrexfmokk532sawm3a">fatcat:qkfdfjytsrexfmokk532sawm3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922205729/https://pure.tue.nl/ws/files/3618086/905192617215107.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/90/17/9017c0d76a4369cdd2f485398f5ccc1b1f0ad0ff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1063/1.1940031"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

L. A. S. JOHNSON REVIEW No. 8. Multiple sequence alignment for phylogenetic purposes

David A. Morrison
<span title="">2006</span> <i title="CSIRO Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/l47flisgnvff3gpkmrvswzlkva" style="color: black;">Australian Systematic Botany</a> </i> &nbsp;
for pairwise alignment and use progressive similarity for the other three.  ...  to calculate interactively for each position in an editor.  ...  Two alternative alignments of part of the DNA polymerase A gene from 18 Leishmania and an Endotrypanum species (Kinetoplastida).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1071/sb06020">doi:10.1071/sb06020</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jphfjfnv3bf53fue2aadwq3xau">fatcat:jphfjfnv3bf53fue2aadwq3xau</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20081031195607/http://www.isu.edu/~kelchner/website/Readings_files/Morrison_ASB2006.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/da/28/da286b652d0f0ebabf032e66c245d122e9be5aa2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1071/sb06020"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Interactions and Dynamics in Charge-Stabilized Colloids

John C. Crocker, David G. Grier
<span title="">1998</span> <i title="Cambridge University Press (CUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4blfynd4h5govevt4qdogct6wi" style="color: black;">MRS bulletin</a> </i> &nbsp;
The most recent burst of activity has been driven by the development of new and quite general techniques for measuring colloidal and macromolecular interactions.  ...  The existence of colloidal suspensions as varied as milk, inks, and metallic sols attests to the efficacy of a variety of stabilizing mechanisms.  ...  The Rosetta stone for this problem is provided by the theories of simple liquids [46] and of stochastic processes [47] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1557/s0883769400029560">doi:10.1557/s0883769400029560</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e6vvd7wtdzbgndnybt3mcpo6wm">fatcat:e6vvd7wtdzbgndnybt3mcpo6wm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20111212120750/http://silver-colloids.com/Papers/Interactions.PDF" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/87/9c/879c74051a7b1bbf71a3d4a2a7822ca362e0189e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1557/s0883769400029560"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>
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