- DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study
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Research Article | published 28 Jan 2025 PLOS Computational Biology
- Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates
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Research Article | published 13 Jan 2025 PLOS Computational Biology
- Model supports asymmetric regulation across the intercellular junction for collective cell polarization
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Research Article | published 17 Dec 2024 PLOS Computational Biology
- AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis
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Research Article | published 14 Nov 2024 PLOS Computational Biology
- Mechanical stress and anionic lipids synergistically stabilize an atypical structure of the angiotensin II type 1 receptor (AT1)
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Research Article | published 13 Nov 2024 PLOS Computational Biology
- A mechanistic model of in vitro plasma activation to evaluate therapeutic kallikrein-kinin system inhibitors
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Research Article | published 04 Nov 2024 PLOS Computational Biology
- IsRNAcirc: 3D structure prediction of circular RNAs based on coarse-grained molecular dynamics simulation
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Research Article | published 28 Oct 2024 PLOS Computational Biology
- Alternate conformational trajectories in ribosome translocation
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Research Article | published 14 Aug 2024 PLOS Computational Biology
- Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force
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Research Article | published 07 Aug 2024 PLOS Computational Biology
- Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM
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Research Article | published 08 Jul 2024 PLOS Computational Biology
- Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
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Education | published 20 Jun 2024 PLOS Computational Biology
- Computational design of Periplasmic binding protein biosensors guided by molecular dynamics
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Research Article | published 17 Jun 2024 PLOS Computational Biology
- Systematic evaluation of lecithin:cholesterol acyltransferase binding sites in apolipoproteins via peptide based nanodiscs: regulatory role of charged residues at positions 4 and 7
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Research Article | published 28 May 2024 PLOS Computational Biology
- Transferable deep generative modeling of intrinsically disordered protein conformations
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Methods | published 23 May 2024 PLOS Computational Biology
- MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface
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Software | published 24 Apr 2024 PLOS Computational Biology
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