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Charge fluctuation effects on the shape of flexible polyampholytes with applications to intrinsically disordered proteins

The Journal of chemical physics, 2018-10, Vol.149 (16), p.163323-163323

2018

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Dynamics of an adenine-adenine RNA conformational switch from discrete path sampling

The Journal of chemical physics, 2019-03, Vol.150 (12), p.125101-125101

2019

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Exploring biomolecular energy landscapes

Chemical communications (Cambridge, England), 2017-06, Vol.53 (52), p.6974-6988

2017

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Intrinsically Disordered Energy Landscapes

Scientific reports, 2015-05, Vol.5 (1), p.10386-10386, Article 10386

2015

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Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants

The journal of physical chemistry letters, 2021-09, Vol.12 (37), p.9026-9032

2021

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Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch

The Journal of chemical physics, 2017-10, Vol.147 (15), p.152715-152715

2017

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On the Emergence of Orientational Order in Folded Proteins with Implications for Allostery

Symmetry (Basel), 2021-05, Vol.13 (5), p.770

2021

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Structure and Properties of DNA in Apolar Solvents

The journal of physical chemistry. B, 2014-07, Vol.118 (29), p.8540-8548

2014

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Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA

Journal of chemical theory and computation, 2018-07, Vol.14 (7), p.3763-3779

2018

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Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins

The journal of physical chemistry. B, 2019-04, Vol.123 (16), p.3462-3474

2019

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Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their aggregation propensities

Proceedings of the National Academy of Sciences - PNAS, 2020-08, Vol.117 (33), p.19926-19937

2020

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Differences in the free energies between the excited states of A β 40 and A β 42 monomers encode their aggregation propensities

Proceedings of the National Academy of Sciences - PNAS, 2020-08, Vol.117 (33), p.19926-19937

2020

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Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA−Protein Complexes

Journal of chemical theory and computation, 2024-02, Vol.20 (3), p.1398-1413

2024

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Energy Landscapes for Base-Flipping in a Model DNA Duplex

The journal of physical chemistry. B, 2022-04, Vol.126 (16), p.3012-3028

2022

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Lipase sensing by naphthalene diimide based fluorescent organic nanoparticles: a solvent induced manifestation of self-assembly

Soft matter, 2021-03, Vol.17 (8), p.217-218

2021

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Energy Landscape and Pathways for Transitions between Watson–Crick and Hoogsteen Base Pairing in DNA

The journal of physical chemistry letters, 2018-01, Vol.9 (1), p.229-241

2018

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Probing helical transitions in a DNA duplexElectronic supplementary information (ESI) available: Figure showing the diverse range of base-pairing interactions at the helix termini for the B-DNA ensemble, free energy disconnectivity graph coloured according to the number of native contacts, plot of slide vs. Zp for distinguishing between the B-DNA and A-DNA structures. See DOI: 10.1039/c6cp06309h

2016-12

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Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences

Journal of chemical theory and computation, 2024-04, Vol.20 (7), p.2934-2946

2024

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Blood Dots: Hemoglobin-Derived Carbon Dots as Hydrogen Peroxide Sensors and Pro-Drug Activators

ACS sustainable chemistry & engineering, 2018-04, Vol.6 (4), p.4661-4670

2018

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Impact of divalent ions on the conformations of single and double stranded DNA: A coarse-grained molecular dynamics study

Biophysical journal, 2023-02, Vol.122 (3), p.212a-212a

2023

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Morphological transformation of self-assemblies by tuning hydrophobic segment of small amphiphiles

Journal of colloid and interface science, 2019-03, Vol.539, p.414-424

2019

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Probing helical transitions in a DNA duplex

Physical chemistry chemical physics : PCCP, 2017, Vol.19 (1), p.878-892

2017

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Conformational fluctuations and phases in fused in sarcoma (FUS) low‐complexity domain

Biopolymers, 2024-03, Vol.115 (2), p.e23558-n/a

2024

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Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides

The journal of physical chemistry. B, 2021-06, Vol.125 (22), p.5809-5822

2021

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Conformational Energy Landscape of the Ritonavir Molecule

The journal of physical chemistry. B, 2016-05, Vol.120 (19), p.4331-4340

2016

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Charge fluctuation effects on the shape of flexible polyampholytes with applications to intrinsically disordered proteins

Dynamics of an adenine-adenine RNA conformational switch from discrete path sampling

Exploring biomolecular energy landscapes

Intrinsically Disordered Energy Landscapes

Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants

Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch

On the Emergence of Orientational Order in Folded Proteins with Implications for Allostery

Structure and Properties of DNA in Apolar Solvents

Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA

Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins

Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their aggregation propensities

Differences in the free energies between the excited states of A β 40 and A β 42 monomers encode their aggregation propensities

Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA−Protein Complexes

Energy Landscapes for Base-Flipping in a Model DNA Duplex

Lipase sensing by naphthalene diimide based fluorescent organic nanoparticles: a solvent induced manifestation of self-assembly

Energy Landscape and Pathways for Transitions between Watson–Crick and Hoogsteen Base Pairing in DNA

Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences

Blood Dots: Hemoglobin-Derived Carbon Dots as Hydrogen Peroxide Sensors and Pro-Drug Activators

Impact of divalent ions on the conformations of single and double stranded DNA: A coarse-grained molecular dynamics study

Morphological transformation of self-assemblies by tuning hydrophobic segment of small amphiphiles

Probing helical transitions in a DNA duplex

Conformational fluctuations and phases in fused in sarcoma (FUS) low‐complexity domain

Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides

Conformational Energy Landscape of the Ritonavir Molecule

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