Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA
Drozdetski, Aleksander V, Tolokh, Igor S, Pollack, Lois, Baker, Nathan, Onufriev, Alexey V
Published in Physical review letters (08.07.2016)
Published in Physical review letters (08.07.2016)
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Journal Article
Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin
Tolokh, Igor S, Kinney, Nicholas Allen, Sharakhov, Igor V, Onufriev, Alexey V
Published in Epigenetics & chromatin (30.05.2023)
Published in Epigenetics & chromatin (30.05.2023)
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Journal Article
Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains
Tolokh, Igor S., Folescu, Dan E., Onufriev, Alexey V.
Published in The journal of physical chemistry. B (20.06.2024)
Published in The journal of physical chemistry. B (20.06.2024)
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Journal Article
Spermine Condenses DNA, but Not RNA Duplexes
Katz, Andrea M., Tolokh, Igor S., Pabit, Suzette A., Baker, Nathan, Onufriev, Alexey V., Pollack, Lois
Published in Biophysical journal (10.01.2017)
Published in Biophysical journal (10.01.2017)
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Journal Article
Location of a topologically associating domain at the nuclear periphery has no systematic causal effect on its genes transcription levels in drosophila nuclei
Tolokh, Igor S., Afanasyev, Alexander Y., Kim, Yoonjin, Sharakhov, Igor V., Onufriev, Alexey V.
Published in Biophysical journal (10.02.2023)
Published in Biophysical journal (10.02.2023)
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Journal Article
Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment
Bass, Lewis, Elder, Luke H., Folescu, Dan E., Forouzesh, Negin, Tolokh, Igor S., Karpatne, Anuj, Onufriev, Alexey V.
Published in Journal of chemical theory and computation (09.01.2024)
Published in Journal of chemical theory and computation (09.01.2024)
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Journal Article
Explicit ions/implicit water generalized Born model for nucleic acids
Tolokh, Igor S, Thomas, Dennis G, Onufriev, Alexey V
Published in The Journal of chemical physics (21.05.2018)
Published in The Journal of chemical physics (21.05.2018)
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Journal Article
Why double-stranded RNA resists condensation
Tolokh, Igor S, Pabit, Suzette A, Katz, Andrea M, Chen, Yujie, Drozdetski, Aleksander, Baker, Nathan, Pollack, Lois, Onufriev, Alexey V
Published in Nucleic acids research (15.09.2014)
Published in Nucleic acids research (15.09.2014)
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Journal Article
Accurate Evaluation of Charge Asymmetry in Aqueous Solvation
Mukhopadhyay, Abhishek, Tolokh, Igor S, Onufriev, Alexey V
Published in The journal of physical chemistry. B (21.05.2015)
Published in The journal of physical chemistry. B (21.05.2015)
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Journal Article
Introducing Charge Hydration Asymmetry into the Generalized Born Model
Mukhopadhyay, Abhishek, Aguilar, Boris H, Tolokh, Igor S, Onufriev, Alexey V
Published in Journal of chemical theory and computation (08.04.2014)
Published in Journal of chemical theory and computation (08.04.2014)
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Journal Article
Multi-shell model of ion-induced nucleic acid condensation
Tolokh, Igor S, Drozdetski, Aleksander V, Pollack, Lois, Baker, Nathan A, Onufriev, Alexey V
Published in The Journal of chemical physics (21.04.2016)
Published in The Journal of chemical physics (21.04.2016)
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Journal Article
Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations
Pabit, Suzette A, Katz, Andrea M, Tolokh, Igor S, Drozdetski, Aleksander, Baker, Nathan, Onufriev, Alexey V, Pollack, Lois
Published in The Journal of chemical physics (28.05.2016)
Published in The Journal of chemical physics (28.05.2016)
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Journal Article
Binding free energy and counterion release for adsorption of the antimicrobial peptide lactoferricin B on a POPG membrane
Tolokh, Igor S, Vivcharuk, Victor, Tomberli, Bruno, Gray, C G
Published in Physical review. E, Statistical, nonlinear, and soft matter physics (01.09.2009)
Published in Physical review. E, Statistical, nonlinear, and soft matter physics (01.09.2009)
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Journal Article
Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on a POPC membrane
Vivcharuk, Victor, Tomberli, Bruno, Tolokh, Igor S, Gray, C G
Published in Physical review. E, Statistical, nonlinear, and soft matter physics (01.03.2008)
Published in Physical review. E, Statistical, nonlinear, and soft matter physics (01.03.2008)
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Journal Article
Single-cell Hi-C: how modeling can augment experiment?
Mali, Samira, Tolokh, Igor S., Sharakhov, Igor V., Onufriev, Alexey V.
Published in Biophysical journal (11.02.2022)
Published in Biophysical journal (11.02.2022)
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Journal Article
3D architecture of Drosophila interphase chromatin is stabilized by relatively strong attractive interactions between highly-dynamic lamina-associated domains and nuclear envelope
Tolokh, Igor S., Kinney, Nicholas A., Sharakhov, Igor V., Onufriev, Alexey V.
Published in Biophysical journal (11.02.2022)
Published in Biophysical journal (11.02.2022)
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Journal Article
Non-Michaelis-Menten kinetics model for conductance of low-conductance potassium ion channels
Tolokh, Igor S, Tolokh, Illya I, Cho, Hee Cheol, D'Avanzo, Nazzareno, Backx, Peter H, Goldman, Saul, Gray, C G
Published in Physical review. E, Statistical, nonlinear, and soft matter physics (01.02.2005)
Published in Physical review. E, Statistical, nonlinear, and soft matter physics (01.02.2005)
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Journal Article