Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics von Pasi, Marco, Maddocks, John H, Lavery, Richard

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Analyzing ion distributions around DNA von Lavery, Richard, Maddocks, John H, Pasi, Marco, Zakrzewska, Krystyna

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Sequence-Dependent Persistence Lengths of DNA von Mitchell, Jonathan S, Glowacki, Jaroslaw, Grandchamp, Alexandre E, Manning, Robert S, Maddocks, John H

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cgNA+web : A Visual Interface to the cgNA+ Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids von Sharma, Rahul, Patelli, Alessandro S., De Bruin, Lennart, Maddocks, John H.

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cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA von De Bruin, Lennart, Maddocks, John H

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Mechanics of two filaments in tight orthogonal contact von Grandgeorge, Paul, Baek, Changyeob, Singh, Harmeet, Johanns, Paul, Sano, Tomohiko G., Flynn, Alastair, Maddocks, John H., Reis, Pedro M.

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μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA von Pasi, Marco, Maddocks, John H, Beveridge, David, Bishop, Thomas C, Case, David A, Cheatham, 3rd, Thomas, Dans, Pablo D, Jayaram, B, Lankas, Filip, Laughton, Charles, Mitchell, Jonathan, Osman, Roman, Orozco, Modesto, Pérez, Alberto, Petkevičiūtė, Daiva, Spackova, Nada, Sponer, Jiri, Zakrzewska, Krystyna, Lavery, Richard

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systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA von Lavery, Richard, Zakrzewska, Krystyna, Beveridge, David, Bishop, Thomas C, Case, David A, Cheatham, Thomas III, Dixit, Surjit, Jayaram, B, Lankas, Filip, Laughton, Charles, Maddocks, John H, Michon, Alexis, Osman, Roman, Orozco, Modesto, Perez, Alberto, Singh, Tanya, Spackova, Nada, Sponer, Jiri

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Second-Order Comparison of Gaussian Random Functions and the Geometry of DNA Minicircles von Panaretos, Victor M., Kraus, David, Maddocks, John H.

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Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles von Lankaš, Filip, Lavery, Richard, Maddocks, John H.

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Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles von Pasi, Marco, Zakrzewska, Krystyna, Maddocks, John H, Lavery, Richard

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Helices von Chouaieb, Nadia, Goriely, Alain, Maddocks, John H.

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The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules von Dans, Pablo D, Balaceanu, Alexandra, Pasi, Marco, Patelli, Alessandro S, Petkevičiūtė, Daiva, Walther, Jürgen, Hospital, Adam, Bayarri, Genís, Lavery, Richard, Maddocks, John H, Orozco, Modesto

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Twist and stretch of helices explained via the Kirchhoff-Love rod model of elastic filaments von Ðuričković, Bojan, Goriely, Alain, Maddocks, John H

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Special issue: Multiscale simulations of DNA from electrons to nucleosomes von Maddocks, John H., Dans, Pablo D., Cheatham, Thomas H., Harris, Sarah, Laughton, Charles, Orozco, Modesto, Pollack, Lois, Olson, Wilma K.

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Global Curvature, Thickness, and the Ideal Shapes of Knots von Gonzalez, Oscar, Maddocks, John H.

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An open call for contributions to a special issue of Biophysical Reviews focused on multiscale simulations of DNA from electrons to nucleosomes von Olson, Wilma K., Maddocks, John H., Dans, Pablo D., Cheatham, Thomas H., Harris, Sarah, Laughton, Charlie, Orozco, Modesto, Pollack, Lois

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Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucl... von Dixit, Surjit B., Beveridge, David L., Case, David A., Cheatham, Thomas E., Giudice, Emmanuel, Lankas, Filip, Lavery, Richard, Maddocks, John H., Osman, Roman, Sklenar, Heinz, Thayer, Kelly M., Varnai, Péter

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Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles von Demurtas, Davide, Amzallag, Arnaud, Rawdon, Eric J, Maddocks, John H, Dubochet, Jacques, Stasiak, Andrzej

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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years? von da Rosa, Gabriela, Grille, Leandro, Calzada, Victoria, Ahmad, Katya, Arcon, Juan Pablo, Battistini, Federica, Bayarri, Genís, Bishop, Thomas, Carloni, Paolo, Cheatham III, Thomas, Collepardo-Guevara, Rosana, Czub, Jacek, Espinosa, Jorge R., Galindo-Murillo, Rodrigo, Harris, Sarah A., Hospital, Adam, Laughton, Charles, Maddocks, John H., Noy, Agnes, Orozco, Modesto, Pasi, Marco, Pérez, Alberto, Petkevičiūtė-Gerlach, Daiva, Sharma, Rahul, Sun, Ran, Dans, Pablo D.

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