Publications
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2023. Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator. Frontiers in Microbiology. 13
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2023. Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling.. Nat Commun. 14(1):2594.
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2022. Design – a new way to look at old molecules. Journal of Integrative Bioinformatics. 19:20220020.
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2022. Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]. Living Journal of Computational Molecular Science. 4:1583.
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2022. Human Learning for Molecular Simulations: The Collective Variables Dashboard in VMD.. J Chem Theory Comput. 18(3):1945-1956.
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2021. Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom. Bio-protocol. 11:e4097.
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2020. Computer Simulations Provide Guidance for Molecular Medicine Through Insights on Dynamics and Mechanisms at the Atomic Scale. 7th International Conference on the Development of Biomedical Engineering in Vietnam (BME7).
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2020. Implicit Modeling of the Impact of Adsorption on Solid Surfaces for Protein Mechanics and Activity with a Coarse-Grained Representation. J Phys Chem B. 124:8516–8523.
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2020. Protein Interaction Energy Landscapes are Shaped by Functional and also Non-functional Partners.. J Mol Biol. 432(4):1183-1198.
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2020. Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics. 153
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2020. Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS.. Protein Sci. 29(1):237-246.
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2020. Water dynamics at electrified graphene interfaces: a jump model perspective. Phys Chem Chem Phys.
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2019. Amyloid-β (29–42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids. The Journal of Physical Chemistry B. 123:2687–2696.
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2019. Effect of Ions on Water Dynamics in Dilute and Concentrated Aqueous Salt Solutions. J Phys Chem B. 123:3312-3324.
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2019. Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates.. Proc Natl Acad Sci U S A. 116(51):26057-26065.
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2019. Interaction mechanism between the focused ultrasound and lipid membrane at the molecular level. The Journal of chemical physics. 150:215101.
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2019. Involvement of the GABAA receptor α subunit in the mode of action of etifoxine. Pharmacological research. 145:104250.
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2019. Molecular Graphics: Bridging Structural Biologists and Computer Scientists.. Structure. 27(11):1617-1623.
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2019. Nonequilibrium atomistic molecular dynamics simulation of tubular nanomotor propelled by bubble propulsion. The Journal of chemical physics. 151:024103.
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2019. The positioning of Chi sites allows the RecBCD pathway to suppress some genomic rearrangements. Nucleic Acids Res. 47:1836-1846.
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2019. Slow extension of the invading DNA strand in a D-loop formed by RecA-mediated homologous recombination may enhance recognition of DNA homology. J Biol Chem. 294:8606-8616.
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2019. Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. II. In Aqueous Solution.. J Phys Chem B. 123(31):6750-6756.
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2019. Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. I. In a Bilayer Mimicking a Neuronal Membrane.. J Phys Chem B. 123(17):3643-3648.
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2018. Applications to water transport systems: general discussion.. Faraday Discuss. 209:389-414.
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2018. Applications to water transport systems: general discussion.. Faraday Discuss. 209:389-414.