sobolevnrm's nucleic_acids [at least 200 articles] Export

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	A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation [My Copy] Nucl. Acids Res., Vol. 37, No. 21. (1 November 2009), pp. 7137-7150. by Nikolay Korolev, Nikolay V. Berezhnoy, Khee D. Eom, James P. Tam, Lars Nordenskiold posted to nucleic_acids electrostatics beyond_mean_field by sobolevnrm on 2009-12-12 20:28:22 as
	Probing 3'-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: a model for "Chi" recognition complexes. [My Copy] Journal of molecular biology, Vol. 362, No. 1. (8 September 2006), pp. 26-43. by C. Jason Wong, Rachel L. Rice, Nathan A. Baker, Tao Ju, Timothy M. Lohman posted to nucleic_acids helicase by sobolevnrm on 2009-12-12 17:54:57 as
	Simulations of RNA Interactions with Monovalent Ions [My Copy] Vol. 469 (2009), pp. 411-432. by Alan A. Chen, Marcelo Marucho, Nathan A. Baker, Rohit V. Pappu posted to solvation review nucleic_acids electrostatics by sobolevnrm on 2009-12-12 02:50:01 as
	Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2514-2530. by Eva Fadrná, Nad’a Špačková, Joanna Sarzyñska, et al.Jaroslav Koča, Modesto Orozco, Thomas E. Cheatham, Tadeusz Kulinski, Jiří Šponer posted to nucleic_acids molecular_simulation molecular_dynamics by sobolevnrm on 2009-10-27 11:39:52 as along with 1 person qshao
	The impact of monovalent ion force field model in nucleic acids simulations [My Copy] Phys. Chem. Chem. Phys. (2009) by Agnes Noy, Ignacio Soteras, F. Javier Luque, Modesto Orozco posted to solvation review nucleic_acids electrostatics by sobolevnrm on 2009-10-17 01:34:55 as
	Assessing the performance of implicit solvation models at a nucleic acid surface [My Copy] Phys. Chem. Chem. Phys., Vol. 10, No. 32. (2008), pp. 4889-4902. by Feng Dong, Jason A. Wagoner, Nathan A. Baker posted to solvation nucleic_acids molecular_simulation electrostatics by sobolevnrm on 2009-10-16 13:35:01 as along with 3 people and 1 group onufriev simone jmccammon McCammon
	Correlation of RNA Secondary Structure Statistics with Thermodynamic Stability and Applications to Folding [My Copy] Journal of Molecular Biology, Vol. 391, No. 4. (28 August 2009), pp. 769-783. by Johnny C. Wu, David P. Gardner, Stuart Ozer, Robin R. Gutell, Pengyu Ren posted to structure nucleic_acids bioinformatics by sobolevnrm on 2009-08-13 13:27:38 as
	Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop. [My Copy] Journal of molecular biology, Vol. 390, No. 4. (24 July 2009), pp. 805-819. by Alan A. Chen, David E. Draper, Rohit V. Pappu posted to electrostatics nucleic_acids solvation by sobolevnrm on 2009-07-23 13:11:38 as
	The Influence of Monovalent Cation Size on the Stability of RNA Tertiary Structures [My Copy] Journal of Molecular Biology, Vol. 390, No. 4. (24 July 2009), pp. 791-804. by Dominic Lambert, Desirae Leipply, Ross Shiman, David E. Draper posted to electrostatics nucleic_acids solvation by sobolevnrm on 2009-07-23 13:11:26 as
	Imaging Surface Charges of Individual Biomolecules [My Copy] Nano Letters, Vol. 0, No. 0. (0000) by Carl Leung, Helen Kinns, Bart W. Hoogenboom, Stefan Howorka, Patrick Mesquida posted to electrostatics nanotech nucleic_acids single_molecule by sobolevnrm on 2009-06-30 12:49:01 as along with 2 people JohnnyP alexknight
	Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 27. (9 July 2009), pp. 9340-9347. by Phuong H. Nguyen, Philippe Derreumaux, Gerhard Stock posted to allostery nucleic_acids by sobolevnrm on 2009-06-30 12:48:45 as
	Nonspecific DNA-Protein Interaction: Why Proteins Can Diffuse along DNA [My Copy] Physical Review Letters, Vol. 102, No. 22. (2009), 228101. by Vincent Dahirel, Fabien Paillusson, Marie Jardat, Maria Barbi, Jean M. Victor posted to diffusion electrostatics nucleic_acids by sobolevnrm on 2009-06-15 00:13:53 as along with 7 people zeldin kumar_physics flbarroso edws jjray spm82 scratchmandoo
	Characterizing Structural Transitions Using Localized Free Energy Landscape Analysis [My Copy] PLoS ONE, Vol. 4, No. 5. (13 May 2009), e5525. by Nilesh K. Banavali, Alexander D. Mackerell posted to free_energy molecular_simulation nucleic_acids by sobolevnrm on 2009-05-13 12:12:15 as along with 1 person and 2 groups barry McCammon baker-group
	Electrical double layer, zeta potential, and electrophoretic charge of double-stranded DNA. [My Copy] Biopolymers, Vol. 16, No. 7. (July 1977), pp. 1415-1434. by J. A. Schellman posted to electrostatics nucleic_acids by sobolevnrm on 2009-05-13 12:10:57 as along with 1 person and 1 group onufriev baker-group
	Dynamical networks in tRNA:protein complexes [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6620-6625. by Anurag Sethi, John Eargle, Alexis A. Black, Zaida Luthey-Schulten posted to allostery graph_theory nucleic_acids protein-nucleic_acid_interactions by sobolevnrm on 2009-04-23 12:31:29 as along with 4 people and 2 groups anuragsethi jeargle AbnerCYH jmccammon McCammon baker-group
	Topological methods for exploring low-density states in biomolecular folding pathways [My Copy] The Journal of Chemical Physics, Vol. 130, No. 14. (2009), 144115. by Yuan Yao, Jian Sun, Xuhui Huang, et al.Gregory R. Bowman, Gurjeet Singh, Michael Lesnick, Leonidas J. Guibas, Vijay S. Pande, Gunnar Carlsson posted to clustering energy_landscapes nucleic_acids protein_folding by sobolevnrm on 2009-04-17 13:03:38 as along with 1 group baker-group
	The homology recognition well as an innate property of DNA structure [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 12. (24 March 2009), pp. 4683-4688. by Alexei A. Kornyshev, Aaron Wynveen posted to bioinformatics electrostatics nucleic_acids structure by sobolevnrm on 2009-03-28 16:13:22 as along with 1 group baker-group
	Structural properties of polymeric DNA from molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 130, No. 11. (2009), 115103. by Sudipta Samanta, Supti Mukherjee, Jaydeb Chakrabarti, Dhananjay Bhattacharyya posted to mechanics molecular_simulation nucleic_acids solvation by sobolevnrm on 2009-03-27 11:57:55 as along with 1 group baker-group
	Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity [My Copy] Quarterly Reviews of Biophysics, Vol. 11, No. 02. (1978), pp. 103-178. by Thomas M. Record, Charles F. Anderson, Timothy M. Lohman posted to electrostatics nucleic_acids review solvation by sobolevnrm on 2009-03-22 14:02:22 as along with 1 group baker-group
	Small Anion with Higher Valency Retards the Compaction of DNA in the Presence of Multivalent Cation [My Copy] Biophysical Journal, Vol. 96, No. 3. (04 February 2009), pp. 1068-1075. by Takuya Saito, Takafumi Iwaki, Kenichi Yoshikawa posted to electrostatics nucleic_acids solvation by sobolevnrm on 2009-03-20 11:48:02 as along with 1 group baker-group
	Mediating Role of Multivalent Cations in DNA Electrostatics: An Epsilon-Modified Poisson−Boltzmann Study of B-DNA−B-DNA Interactions in Mixture of NaCl and MgCl2 Solutions [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 7. (19 February 2009), pp. 2160-2169. by Sergei Gavryushov posted to electrostatics nucleic_acids solvation by sobolevnrm on 2009-03-19 12:11:42 as along with 1 group baker-group
	Molecular Dynamics Simulation of DNA-Functionalized Gold Nanoparticles [My Copy] The Journal of Physical Chemistry C, Vol. 113, No. 6. (12 February 2009), pp. 2316-2321. by One-Sun Lee, George C. Schatz posted to molecular_dynamics nanotech nucleic_acids by sobolevnrm on 2009-03-19 12:06:45 as along with 3 people and 1 group charlesvardeman georgwachter carlosjavierna baker-group
	Dynamics of Water and Ions Near DNA: Comparison of Simulation to Time-Resolved Stokes-Shift Experiments [My Copy] Journal of the American Chemical Society, Vol. 131, No. 5. (11 February 2009), pp. 1724-1735. by Sobhan Sen, Daniele Andreatta, Sergei Y. Ponomarev, David L. Beveridge, Mark A. Berg posted to electrostatics nucleic_acids solvation by sobolevnrm on 2009-03-18 11:28:01 as along with 2 people and 2 groups anuragsethi whitead Jiang Research Group baker-group
	RNA in motion [My Copy] Current Opinion in Chemical Biology, Vol. 12, No. 6. (December 2008), pp. 612-618. by K. Hall posted to nucleic_acids review by sobolevnrm on 2009-03-05 12:33:10 as along with 1 group baker-group
	Interaction of Cationic Lipid/DNA Complexes with Model Membranes As Determined by Neutron Reflectivity† [My Copy] Langmuir, Vol. 0, No. 0. (0000) by P. Callow, G. Fragneto, R. Cubitt, D. J. Barlow, M. J. Lawrence posted to biomembranes nucleic_acids by sobolevnrm on 2009-03-04 13:07:20 as along with 1 group baker-group
	Explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: lattice-sum versus reaction-field electrostatics [My Copy] Molecular Simulation, Vol. 34, No. 5. (April 2008), pp. 491-499. by Krautler, Vincent, Hunenberger, Philippe posted to electrostatics molecular_simulation nucleic_acids by sobolevnrm on 2009-03-04 13:06:29 as along with 1 person and 2 groups jmccammon baker-group McCammon
	Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme [My Copy] Biophys. J., Vol. 91, No. 2. (15 July 2006), pp. 626-638. by Maryna V. Krasovska, Jana Sefcikova, Kamila Reblova, Bohdan Schneider, Nils G. Walter, Jiri Sponer posted to electrostatics nucleic_acids solvation by sobolevnrm on 2009-03-04 13:05:51 as along with 1 person and 1 group onufriev baker-group
	DNA Attraction in Monovalent and Divalent Electrolytes [My Copy] Journal of the American Chemical Society, Vol. 130, No. 47. (26 November 2008), pp. 15754-15755. by Binquan Luan, Aleksei Aksimentiev posted to beyond_mean_field electrostatics molecular_dynamics nucleic_acids by sobolevnrm on 2009-02-06 11:51:49 as along with 1 group baker-group
	Molecular solvent model of cylindrical electric double layers: A systematic study by Monte Carlo simulations and density functional theory [My Copy] The Journal of Chemical Physics, Vol. 129, No. 15. (2008) by Teena Goel, Chandra N. Patra, Swapan K. Ghosh, Tulsi Mukherjee posted to beyond_mean_field electrostatics nucleic_acids statistical_mechanics by sobolevnrm on 2009-01-29 12:46:42 as along with 1 group baker-group
	RNA folding: thermodynamic and molecular descriptions of the roles of ions [My Copy] Biophys. J. (3 October 2008), biophysj.108.131813. by David E. Draper posted to electrostatics nucleic_acids review by sobolevnrm on 2009-01-29 12:46:09 as along with 1 person and 1 group dgront baker-group
	Remeasuring the Double Helix [My Copy] Science, Vol. 322, No. 5900. (17 October 2008), pp. 446-449. by Rebecca S. Mathew-Fenn, Rhiju Das, Pehr A. Harbury posted to mechanics nucleic_acids by sobolevnrm on 2009-01-28 13:10:33 as along with 6 people and 2 groups jbhiatt Elena_Zubova melting kshundyak marck samjlord baker-group moernerlab
	Packings of a charged line on a sphere [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 78, No. 6. (2008), 066603. by Silas Alben posted to electrostatics mathematics nucleic_acids statistical_mechanics by sobolevnrm on 2008-12-15 12:52:13 as
	Counterion-mediated electrostatic interactions between helical molecules [My Copy] Soft Matter (2009) by M. Kanduc, J. Dobnikar, R. Podgornik posted to electrostatics beyond_mean_field nucleic_acids statistical_mechanics by sobolevnrm on 2008-12-15 12:52:13 as
	A repulsive field: advances in the electrostatics of the ion atmosphere [My Copy] Current Opinion in Chemical Biology by Vincent B. Chu, Yu Bai, Jan Lipfert, Daniel Herschlag, Sebastian Doniach posted to electrostatics solvation nucleic_acids by sobolevnrm on 2008-12-15 12:52:13 as
	Critical Assessment of Nucleic Acid Electrostatics via Experimental and Computational Investigation of an Unfolded State Ensemble [My Copy] Journal of the American Chemical Society, Vol. 130, No. 37. (2008), 12334-12341. by Yu Bai, Vincent B. Chu, Jan Lipfert, Vijay S. Pande, Daniel Herschlag, Sebastian Doniach posted to electrostatics solvation nucleic_acids by sobolevnrm on 2008-12-15 12:52:10 as
	Electrostatic Interactions in a Peptide-RNA Complex [My Copy] Journal of Molecular Biology, Vol. 331, No. 1. (2003), 75-88. by C. García-García, D. E. Draper posted to electrostatics nucleic_acids by sobolevnrm on 2008-12-15 12:52:07 as
	Effects of Trimethylamine N-Oxide (TMAO) and Crowding Agents on the Stability of RNA Hairpins [My Copy] Journal of the American Chemical Society, Vol. 130, No. 23. (2008), 7364--7372. by David L. Pincus, Changbong Hyeon, D. Thirumalai posted to solvation nucleic_acids by sobolevnrm on 2008-12-15 12:52:06 as
	Assessing the performance of implicit solvation models at a nucleic acid surface [My Copy] Physical Chemistry Chemical Physics, Vol. 10 (2008), 4889-902. by F. Dong, J. A. Wagoner, N. A. Baker posted to electrostatics nonpolar solvation nucleic_acids by sobolevnrm on 2008-12-15 12:52:06 as
	Poisson-Boltzmann Theory for Membranes with Mobile Charged Lipids and the pH-Dependent Interaction of a DNA Molecule with a Membrane [My Copy] Biophys. J., Vol. 82, No. 1. (2002), 76--92. by Christian Fleck, Roland R. Netz, Hans H. von Grunberg posted to biomembranes electrostatics pka solvation nucleic_acids by sobolevnrm on 2008-12-15 12:52:06 as
	Liquid Crystalline Phase Behavior of High Molecular Weight DNA: A Comparative Study of the Influence of Metal Ions of Different Size, Charge and Binding Mode [My Copy] Biomacromolecules, Vol. 9, No. 7. (2008), 1860--1869. by Neethu Sundaresan, Cherumuttathu H. Suresh, Thresia Thomas, T. J. Thomas, C. K. S. Pillai posted to electrostatics solvation nucleic_acids by sobolevnrm on 2008-12-15 12:52:06 as
	Electrostatic Interactions Guide the Active Site Face of a Structure-Specific Ribonuclease to Its RNA Substrate [My Copy] Biochemistry, Vol. 47, No. 34. (2008), pp. 8912-8918. by Matthew J. Plantinga, Alexei V. Korennykh, Joseph A. Piccirilli, Carl C. Correll posted to electrostatics protein-nucleic_acid_interactions nucleic_acids by sobolevnrm on 2008-09-04 14:04:28 as
	Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA [My Copy] Nucleic Acids Research, Vol. 36, No. 12. (2008), pp. 4118-4127. by Isabelle Bonnet, Andreas Biebricher, Pierre L. Porte, et al.Claude Loverdo, Olivier Benichou, Raphael Voituriez, Christophe Escude, Wolfgang Wende, Alfred Pingoud, Pierre Desbiolles posted to diffusion protein-nucleic_acid_interactions nucleic_acids by sobolevnrm on 2008-09-02 12:34:08 as
	Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory [My Copy] The Journal of Chemical Physics, Vol. 128, No. 18. (2008) by Yoshiteru Yonetani, Yutaka Maruyama, Fumio Hirata, Hidetoshi Kono posted to electrostatics solvation beyond_mean_field integral_equation nucleic_acids statistical_mechanics by sobolevnrm on 2008-08-29 13:42:11 as
	Electrostatic Free Energy Landscapes for DNA Helix Bending [My Copy] Biophysical Journal, Vol. 94, No. 8. (2008) by Zhi-Jie Tan, Shi-Jie Chen posted to electrostatics beyond_mean_field nucleic_acids statistical_mechanics by sobolevnrm on 2008-08-29 13:42:09 as
	Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method [My Copy] Chemical Physics Letters, Vol. 454, No. 4-6. (2008) by Donghong Min, Hongzhi Li, Guohui Li, Bernd A. Berg, Marcia O. Fenley, Wei Yang posted to electrostatics beyond_mean_field molecular_simulation nucleic_acids statistical_mechanics by sobolevnrm on 2008-08-29 13:42:09 as
	Evaluation of Ion Binding to DNA Duplexes Using a Size-Modified Poisson-Boltzmann Theory [My Copy] Biophysical Journal, Vol. 93, No. 9. (2007) by Vincent B. Chu, Yu Bai, Jan Lipfert, Daniel Herschlag, Sebastian Doniach posted to electrostatics beyond_mean_field nucleic_acids statistical_mechanics by sobolevnrm on 2008-08-29 13:42:08 as
	Counterion-counterion correlation in the double layer around cylindrical polyions: Counterion size and valency effects [My Copy] Journal of Chemical Physics, Vol. 127 (2007) by J. Piñero, L. B. Bhuiyan, J. Reščič, V. Vlachy posted to electrostatics beyond_mean_field nucleic_acids statistical_mechanics by sobolevnrm on 2008-08-29 13:42:08 as
	Polymorphism of DNAâanionic liposome complexes reveals hierarchy of ion-mediated interactions [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 32. (2005) by H. Liang, D. Harries, G. C. L. Wong posted to biomembranes electrostatics beyond_mean_field statistical_mechanics nucleic_acids by sobolevnrm on 2008-08-29 13:42:03 as
	Monte Carlo simulation of an inhomogeneous dielectric continuum model for B-DNA [My Copy] Physical Chemistry Chemical Physics, Vol. 7, No. 19. (2005) by S. Grandison, R. Penfold, Vanden-Broeck posted to electrostatics solvation beyond_mean_field nucleic_acids statistical_mechanics by sobolevnrm on 2008-08-29 13:42:03 as
	Incomplete Ion Dissociation Underlies the Weakened Attraction between DNA Helices at High Spermidine Concentrations [My Copy] Biophysical Journal, Vol. 89, No. 3. (2005) by J. Yang, D. C. Rau posted to electrostatics beyond_mean_field nucleic_acids statistical_mechanics by sobolevnrm on 2008-08-29 13:42:03 as

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electrostatics	2020
solvation	1604
biomembranes	1512
statistical_mechanics	674
mathematics	623
bioinformatics	614
diffusion	528
molecular_dynamics	514
molecular_simulation	512
nucleic_acids	479
multiscale	409
quasiharmonic_models	338
structure	327
nanotech	286
allostery	269
review	210
beyond_mean_field	210
protein_folding	203
protein-protein_interactions	187
systems_biology	186
software	178
kinetics	170
protein-ligand_interactions	167
acetylcholinesterase	167
misc	151
biological_systems	150
experimental_methodology	147
thrombin	143
correlated_mutations	126
neuromuscular_junctions	121
pka	119
protein-nucleic_acid_interactions	116
sterols	113
drug_design	111
outer_hair_cells	104
database	97
metalloregulation	96
structure_prediction	91
cellular_mechanics	91
ontology	87
imaging	86
ccne	84
protein-membrane_interactions	83
quantum_mechanics	83
nonpolar	80
nerve_agents	78
nitric_oxide	74
career	71
visualization	69
emulsions	67
interfaces	57
ligand-membrane_interactions	57
nmr	52
cancer	51
protein_engineering	48
mechanics	44
free_energy	44
integral_equation	41
clustering	41
teaching	39
ion_channels	38
enhanced_sampling	37
ultrasound	33
perfluorocarbons	31
statistics	27
graph_theory	24
sccne	24
programming	23
informatics	22
helicase	22
pgdh	21
flexoelectric	20
ribosome	17
fluid_mechanics	17
molecular-simulation	15
quasiharmonic-models	15
drug_delivery	15
geometry	14
gating	13
toxicity	13
nanotechnology	13
statistical-mechanics	12
apbs	11
energy_landscapes	10
funding	10
pdb2pqr	9
molecular-dynamics	8
cytoskeleton	8
nikr	8
cholesterol	6
electrochemistry	6
protein-protein-interactions	5
protein-ligand-interactions	5
finite_element	5
protein-folding	4
single_molecule	4
nitric-oxide	4
docking	4
finite_differences	3
scattering	3
nucleic-acids	3
optimization	3
ligand-membrane-interactions	3
hydrodynamics	3
thermodynamics	3
integral-equation	3
quantum-mechanics	2
ethics	2
neuroscience	2
conformation	2
boundary_element	2
generalized_born	2
oxysterols	2
biodistribution	2
virus	2
salicylate	2
systems-biology	2
nanoparticles	2
computational_geometry	2
magnetism	2
protein-membrane-interactions	2
web	1
redox_potentials	1
protein-engineering	1
lipids	1
data_mining	1
protein-design	1
integral_equations	1
colloid-complex	1
red_blood_cell	1
hydrogen_bonds	1
mice	1
protein	1
systems	1
phosphatidylcholines	1
protein-allostery	1
text-mining	1
mutual-information	1
protein-nucleic-acid-interactions	1
text_mining	1
cheminformatics	1
melittin	1
fluorescence_quenching	1

sobolevnrm's nucleic_acids [at least 200 articles] Export

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