[an error occurred while processing this directive]<meta name="keywords" content="Department of Computer Science, publications, by date, Peter Minary"></meta><meta name="description" content="Publications, by date, Department of Computer Science, Oxford, Peter Minary"></meta><title>Department of Computer Science, University of Oxford: Peter Minary : Publications
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			</style>[an error occurred while processing this directive]<div class="content-width"><ol class="breadcrumb text-uppercase"><li><a href="/">Home</a></li><li><a href="/aboutus/">About Us</a></li><li><a href="/people/">People</a></li><li><a href="/people/faculty.html">Faculty</a></li><li><a href="/people/Peter.Minary"><span itemprop="name">Peter Minary</span></a></li><li class="active">Publications</li></ol></div><!-- MOBILE NAVIGATION --><div class="content-width space-below mobile-menu-placeholder visible-xs visible-sm"></div><!-- COLUMNS --><div class="container-fluid content-width"><div class="row"><div class="col-xs-12 col-md-9 col-md-push-3" id="maincontent"><!-- CONTENT (Column 2) --><div class="page-title"><h1>Peter Minary : Publications
</h1></div><div role="toolbar" class="btn-toolbar"><div class="btn-group"><a href="/people/publications/date/Peter.Minary.html" aria-hidden="true" type="button" class="btn btn-oxford-blue"><span class="glyphicon glyphicon-sort-by-attributes"></span> By date</a><a href="/people/publications/title/Peter.Minary.html" aria-hidden="true" type="button" class="btn btn-default"><span class="glyphicon glyphicon-sort-by-attributes"></span> By title</a><a href="/people/publications/type/Peter.Minary.html" aria-hidden="true" type="button" class="btn btn-default"><span class="glyphicon glyphicon-sort-by-attributes"></span> By type</a><a href="/people/publications/bibtex/Peter.Minary.html" aria-hidden="true" type="button" class="btn btn-default"><span class="glyphicon glyphicon-file"></span> BibTex</a></div></div><p></p><ul class="list-unbulleted list-unbulleted-spaced"><li>
	
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	<p class="publicationTitle"> <strong>
            Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo </strong> </p>
	    <p class="publicationAuthors"> <em> Bernhard Knapp&#x201a; Samuel Demharter&#x201a; Charlotte M Deane and Peter Minary  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Bioinformatics</em>.
        
                Pages btv502.
            2015.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication9983-abstract.html">
			Details <span class="sr-only" > about <em> Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo  </em></span> </a> |
			<a href="/publications/publication9983.bib">
			BibTeX  <span class="sr-only" > data for <em> Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Training&#x2212;free atomistic prediction of nucleosome occupancy </strong> </p>
	    <p class="publicationAuthors"> <em> Peter Minary and Michael Levitt  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Proceedings of the National Academy of Sciences</em>.
        
            Vol. 111.
        
            No. 17.
        
                Pages 6293&#x2013;6298.
            2014.
        </p>
	
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            		href="/publications/publication9982-abstract.html">
			Details <span class="sr-only" > about <em> Training&#x2212;free atomistic prediction of nucleosome occupancy  </em></span> </a> |
			<a href="/publications/publication9982.bib">
			BibTeX  <span class="sr-only" > data for <em> Training&#x2212;free atomistic prediction of nucleosome occupancy  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Modeling and design by hierarchical natural moves </strong> </p>
	    <p class="publicationAuthors"> <em> Adelene YL Sim&#x201a; Michael Levitt and Peter Minary  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Proceedings of the National Academy of Sciences</em>.
        
            Vol. 109.
        
            No. 8.
        
                Pages 2890&#x2013;2895.
            2012.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7550-abstract.html">
			Details <span class="sr-only" > about <em> Modeling and design by hierarchical natural moves  </em></span> </a> |
			<a href="/publications/publication7550.bib">
			BibTeX  <span class="sr-only" > data for <em> Modeling and design by hierarchical natural moves  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Multiscale natural moves refine macromolecules using single&#x2212;particle electron microscopy projection images </strong> </p>
	    <p class="publicationAuthors"> <em> Junjie Zhang&#x201a; Peter Minary and Michael Levitt  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Proceedings of the National Academy of Sciences</em>.
        
            Vol. 109.
        
            No. 25.
        
                Pages 9845&#x2013;9850.
            2012.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7549-abstract.html">
			Details <span class="sr-only" > about <em> Multiscale natural moves refine macromolecules using single&#x2212;particle electron microscopy projection images  </em></span> </a> |
			<a href="/publications/publication7549.bib">
			BibTeX  <span class="sr-only" > data for <em> Multiscale natural moves refine macromolecules using single&#x2212;particle electron microscopy projection images  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Modeling nucleic acids </strong> </p>
	    <p class="publicationAuthors"> <em> Adelene YL Sim&#x201a; Peter Minary and Michael Levitt  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Current Opinion in Structural Biology</em>.
        2012.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7548-abstract.html">
			Details <span class="sr-only" > about <em> Modeling nucleic acids  </em></span> </a> |
			<a href="/publications/publication7548.bib">
			BibTeX  <span class="sr-only" > data for <em> Modeling nucleic acids  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm </strong> </p>
	    <p class="publicationAuthors"> <em> Peter Minary and Michael Levitt  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Journal of Computational Biology</em>.
        
            Vol. 17.
        
            No. 8.
        
                Pages 993&#x2013;1010.
            2010.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7551-abstract.html">
			Details <span class="sr-only" > about <em> Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm  </em></span> </a> |
			<a href="/publications/publication7551.bib">
			BibTeX  <span class="sr-only" > data for <em> Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Probing protein fold space with a simplified model </strong> </p>
	    <p class="publicationAuthors"> <em> Peter Minary and Michael Levitt  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Journal of molecular biology</em>.
        
            Vol. 375.
        
            No. 4.
        
                Pages 920.
            2008.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7553-abstract.html">
			Details <span class="sr-only" > about <em> Probing protein fold space with a simplified model  </em></span> </a> |
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			BibTeX  <span class="sr-only" > data for <em> Probing protein fold space with a simplified model  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Dynamical spatial warping: A novel method for the conformational sampling of biophysical structure </strong> </p>
	    <p class="publicationAuthors"> <em> Peter Minary&#x201a; Mark E Tuckerman and Glenn J Martyna  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>SIAM Journal on Scientific Computing</em>.
        
            Vol. 30.
        
            No. 4.
        
                Pages 2055&#x2013;2083.
            2008.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7552-abstract.html">
			Details <span class="sr-only" > about <em> Dynamical spatial warping: A novel method for the conformational sampling of biophysical structure  </em></span> </a> |
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			BibTeX  <span class="sr-only" > data for <em> Dynamical spatial warping: A novel method for the conformational sampling of biophysical structure  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Discussion of" EQUI&#x2212;energy sampler" by Kou&#x201a; Zhou and Wong </strong> </p>
	    <p class="publicationAuthors"> <em> P Minary and M Levitt  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Ann. Stat.</em>.
        
            Vol. 34.
        
            No. math. ST/0611221.
        
                Pages 1636&#x2013;1641.
            2006.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7554-abstract.html">
			Details <span class="sr-only" > about <em> Discussion of" EQUI&#x2212;energy sampler" by Kou&#x201a; Zhou and Wong  </em></span> </a> |
			<a href="/publications/publication7554.bib">
			BibTeX  <span class="sr-only" > data for <em> Discussion of" EQUI&#x2212;energy sampler" by Kou&#x201a; Zhou and Wong  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Reaction Mechanism of cis&#x2212;1&#x201a; 3&#x2212;Butadiene Addition to the Si (100)&#x2212;2<span style="font-family: serif"></span> 1 Surface </strong> </p>
	    <p class="publicationAuthors"> <em> Peter Minary and Mark E Tuckerman  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Journal of the American Chemical Society</em>.
        
            Vol. 127.
        
            No. 4.
        
                Pages 1110&#x2013;1111.
            2005.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7558-abstract.html">
			Details <span class="sr-only" > about <em> Reaction Mechanism of cis&#x2212;1&#x201a; 3&#x2212;Butadiene Addition to the Si (100)&#x2212;2<span style="font-family: serif"></span> 1 Surface  </em></span> </a> |
			<a href="/publications/publication7558.bib">
			BibTeX  <span class="sr-only" > data for <em> Reaction Mechanism of cis&#x2212;1&#x201a; 3&#x2212;Butadiene Addition to the Si (100)&#x2212;2<span style="font-family: serif"></span> 1 Surface  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Ab initio molecular dynamics: Concepts&#x201a; recent developments&#x201a; and future trends </strong> </p>
	    <p class="publicationAuthors"> <em> Radu Iftimie&#x201a; Peter Minary and Mark E Tuckerman  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Proceedings of the National Academy of Sciences of the United States of America</em>.
        
            Vol. 102.
        
            No. 19.
        
                Pages 6654&#x2013;6659.
            2005.
        </p>
	
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            		href="/publications/publication7555-abstract.html">
			Details <span class="sr-only" > about <em> Ab initio molecular dynamics: Concepts&#x201a; recent developments&#x201a; and future trends  </em></span> </a> |
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			BibTeX  <span class="sr-only" > data for <em> Ab initio molecular dynamics: Concepts&#x201a; recent developments&#x201a; and future trends  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Long range interactions on wires: A reciprocal space based formalism </strong> </p>
	    <p class="publicationAuthors"> <em> Peter Min&#xe1;ry&#x201a; Joseph A Morrone&#x201a; Dawn A Yarne&#x201a; Mark E Tuckerman and Glenn J Martyna  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>The Journal of chemical physics</em>.
        
            Vol. 121.
        
                Pages 11949.
            2004.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7559-abstract.html">
			Details <span class="sr-only" > about <em> Long range interactions on wires: A reciprocal space based formalism  </em></span> </a> |
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			BibTeX  <span class="sr-only" > data for <em> Long range interactions on wires: A reciprocal space based formalism  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Reaction Pathway of the [4+ 2] Diels&#x2212;Alder Adduct Formation on Si (100)&#x2212;2<span style="font-family: serif"></span> 1 </strong> </p>
	    <p class="publicationAuthors"> <em> Peter Minary and Mark E Tuckerman  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Journal of the American Chemical Society</em>.
        
            Vol. 126.
        
            No. 43.
        
                Pages 13920&#x2013;13921.
            2004.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7557-abstract.html">
			Details <span class="sr-only" > about <em> Reaction Pathway of the [4+ 2] Diels&#x2212;Alder Adduct Formation on Si (100)&#x2212;2<span style="font-family: serif"></span> 1  </em></span> </a> |
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			BibTeX  <span class="sr-only" > data for <em> Reaction Pathway of the [4+ 2] Diels&#x2212;Alder Adduct Formation on Si (100)&#x2212;2<span style="font-family: serif"></span> 1  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Long time molecular dynamics for enhanced conformational sampling in biomolecular systems </strong> </p>
	    <p class="publicationAuthors"> <em> P Minary&#x201a; ME Tuckerman and GJ Martyna  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Physical review letters</em>.
        
            Vol. 93.
        
            No. 15.
        
                Pages 150201.
            2004.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7556-abstract.html">
			Details <span class="sr-only" > about <em> Long time molecular dynamics for enhanced conformational sampling in biomolecular systems  </em></span> </a> |
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	<p class="publicationTitle"> <strong>
            Algorithms and novel applications based on the isokinetic ensemble. II. Ab initio molecular dynamics </strong> </p>
	    <p class="publicationAuthors"> <em> Peter Minary&#x201a; Glenn J Martyna and Mark E Tuckerman  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>The Journal of chemical physics</em>.
        
            Vol. 118.
        
                Pages 2527.
            2003.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7561-abstract.html">
			Details <span class="sr-only" > about <em> Algorithms and novel applications based on the isokinetic ensemble. II. Ab initio molecular dynamics  </em></span> </a> |
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	<p class="publicationTitle"> <strong>
            Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics </strong> </p>
	    <p class="publicationAuthors"> <em> Peter Minary&#x201a; Glenn J Martyna and Mark E Tuckerman  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>The Journal of chemical physics</em>.
        
            Vol. 118.
        
                Pages 2510.
            2003.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7560-abstract.html">
			Details <span class="sr-only" > about <em> Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics  </em></span> </a> |
			<a href="/publications/publication7560.bib">
			BibTeX  <span class="sr-only" > data for <em> Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            A new reciprocal space based treatment of long range forces on surfaces </strong> </p>
	    <p class="publicationAuthors"> <em> ME Tuckerman&#x201a; P Minary&#x201a; K Pihakari and GJ Martyna  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>J. Chem. Phys</em>.
        
            Vol. 116.
        
                Pages 5351.
            2002.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication7562-abstract.html">
			Details <span class="sr-only" > about <em> A new reciprocal space based treatment of long range forces on surfaces  </em></span> </a> |
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