Publications

Li, Z., Portillo-Ledesma, S., Janani, M., and Schlick, T. The influence of 10n and 10n + 5 linker lengths on chromatin fiber topologies explored by mesoscale modeling. Biophys. J. 125, 1-16 (2026)

Zeng, H. and Sun, X. Quantum dynamics in multistate harmonic models using tensor-train thermofield dynamics and semiclassical mapping dynamics. J. Chem. Phys. 163, 024131 (2025)

Li, Z., Zheng, L., Yang, Y., Wang, X., Sun, Z., and Zhang, J. Z. H. dMSGB-IE: Computational mutational scanning for (de)methylation thermodynamics. J. Chem. Phys. 163, 115101 (2025)

Zhang, J., Wan, Z., Gu, Q., Zhu, J., Zhong, J., He, X., and Yang, J. π–π Interactions Dictate the Growth of Aromatic Organic Aerosols. J. Phys. Chem. 129, 6071–6081 (2025)

Cao, J., Chen, Z., Li, H., Liu, C., He, Y., Zhang, H., Xu, L., Xiao, H., He, X., and Fang, G. Intelligent Design and Simulation of High-Entropy Alloys via Machine Learning and Multiobjective Optimization Algorithms. J. Chem. Theory Comput. 21, 7051–7061 (2025)

Zeng, Y., Liu, L., Xiong, D., Wan, Z., Bi, Z., Zeng, X., Wei, X., and He, X. Transfer Learning for Predicting ncRNA-Protein Interactions. J. Chem. Inf. Model. 65, 7956–7970 (2025)

Cao, J., Liu, C., Chen, Z., Li, H., Xu, L., Xiao, H., Wang, S., He, X., and Fang, G. Accelerated Discovery of Refractory High-Entropy Alloys via Interpretable Machine Learning. J. Phys. Chem. Lett. 16, 8806–8814 (2025)

Shi, Y., Li, Y., Zhai, J., Zhang, Y., Hu, B., Gu, Y.-C., Chen, X., Hu, L., and He, X. AI-driven advances in the design of RTP and TADF luminescent material. Chem. Phys. Rev. 6, 031309 (2025)

Wu, X., Zhang, X., Xia, W., Zhang, Y., Huang, K., Zhao, F., Ji, C., Wang, J., Zhou, B., and Zhang, J. Z. H. Discovery of novel Cytochrome bd oxidase inhibitors against Mycobacterium tuberculosis. Eur. J. Med. Chem. 298, 118010 (2025)

Newton, K., Yan, S., and Schlick, T. Conformational Analysis and Structure-Altering Mutations of the HIV-1 Frameshifting Element. Int. J. Mol. Sci. 26, 6297 (2025)

Portillo-Ledesma, S., Li, Z., and Schlick, T. Molecular dynamics simulations reveal subtle consequences of H3K9 and H3K27 tri-methylation on chromatin constituents. Biophys. J. 124, 4005-4017 (2025)

Schlick, T. and Grigoryev, S. Nucleosome Linker Length and Distribution as Major Players in Epigenetic Regulation: Insights from Cryo-Electron Microscopy and Modeling of Retina Cell Maturation. DNA Cell Biol. 44, 581-638 (2025)

Li, Z., Portillo-Ledesma, S., and Schlick, T. Chromatin higher-order folding as influenced by preferred values of linker DNA. Curr. Opin. Struct. Biol. 95, 103154 (2025)

Robledo, A. and Tuckerman, M. E. Efficient evaluation of path integrals for equilibrium and dynamical properties via contraction of closed and open chains. Mol. Phys. e2534674 (2025)

Hong, R. S., Mattei, A., Tuckerman, M. E., and Sheikh, A. Y. 3D conformation and crystal interaction insights into drug development challenges for HCV drug analogues via molecular simulations. Comm. Chem. 8, 229 (2025)

Kilgour, M., Tuckerman, M. E., and Rogal, J. Multi-type point cloud autoencoder: a complete equivariant embedding for molecule conformation and pose. Mach. Learn.: Sci. Technol. 6, 035055 (2025)

Chen, M. S., Robledo, A., Schäfer, C., Han, K. Y., Clementi, C., and Tuckerman, M. E. Machine learning-accelerated path integral molecular dynamics simulations of reactive organic electrolytes. J. Chem. Phys. 163, 144110 (2025)

Zhu, R., Zhang, Y., Zhu, T., and Xia, F. Coarse-Grained Simulation of Persistence Length and Twisting Dynamics of Micrometer-Scale Microtubules. J. Phys. Chem. Lett. 16, 7300–7306 (2025)

Gu, Y., Xia, S., Ouyang, Q., and Zhang, Y. Bioactivity Deep Learning for Complex Structure-Free Compound-Protein Interaction Prediction. J. Chem. Inf. Model. 65, 9910–9926 (2025)

Xu, Y., Bian, D., Ju, C.-W., Zhao, F., Xie, P., Wang, Y., Hu, W., Sun, Z., Zhang, J. Z. H., and Zhu, T. Pretrained E(3)-equivariant message-passing neural networks with multi-level representations for organic molecule spectra prediction. npj Comput. Mater. 11, 203 (2025)

Wu, X., Zhu, X., Fang, M., Qi, F., Yin, Z., Zhang, J. Z. H., Luo, S., Zhu, T., and Gao, Y. Insights into Binding Mechanisms of Potential Inhibitors Targeting PCSK9 Protein via Molecular Dynamics Simulation and Free Energy Calculation. Molecules 30, 2962 (2025)

Xiao, J., Zhang, Y., Li, B., Zhang, S., Gao, Y., Chen, W., Wang, H., Zhang, J. Z. H., and Zhu, T. A Deep Learning-Augmented Density Functional Framework for Reaction Modeling with Chemical Accuracy. JACS Au 5, 3892–3903 (2025)

Portillo-Ledesma, S., Hang, M., and Schlick, T. Regulation of genome architecture in Huntington’s disease. Biochemistry 64, 2100–2115 (2025)

Kable, B., Portillo-Ledesma, S., Popova, E. Y., Jentink, N., Swulius, M., Li, Z., Schlick, T., and Grigoryev, S. A. Compromised two-start zigzag chromatin folding in immature mouse retina cells driven by irregularly spaced nucleosomes with short DNA linkers. Nucleic Acids Res. 53, gkaf457 (2025)

Zeng, H., Kou, Y., and Sun, X. Physics-informed neural networks for quantum propagators in Wavepacket dynamics. Mol. Phys. e2501775 (2025)

Li, K., Xia, W., and Zhang, J. Z. H. Discovery of novel inhibitors of Aspergillus fumigatus DHODH via virtual screening, MD simulation, and in vitro activity assay. Molecules 30, 2607 (2025)

Feng, Y., Yan, X., Ma, M., Chen, R., Zhang, C., Cong, Y., Fang, B., Chen, C., Dai, L., Li, H., Jiang, H., Sun, H., Wei, H., Guo, R., Gao, B., Zhang, J. Z. H., and Zhang, L. Aqualigase: A star enzyme for one-step peptide bond dehydration condensation in a nature aqueous phase. ACS Catal. 15, 11594–11607 (2025)

Tang, S., Chen, D., Shen, H., Yuan, Z., Wei, H., Feng, Y., Li, L., Dong, J., and Zhang, L. Discovery of two novel ACE inhibitory peptides from soybeans: Stability, molecular interactions, and in vivo antihypertensive effects. Int. J. Biol. Macromol. 308, 142247 (2025)

Gu, J., Xiao, J., Wu, X., Zhu, X., Chen, H., Zhang, J. Z. H., Zhu, T., Gao, Y., and Yin, Z. Interaction of magnesium ion and acetate anion in bulk water: Toward high-level machine learning potential. Chin. J. Chem. Phys. 38, 95–101 (2025)

Geng, C., Zeng, J., Deng, X., Xia, F., and Xu, X. Molecular dynamics investigation into the stability of KRas and CRaf multimeric complexes. J. Phys. Chem. B 129, 3306–3316 (2025)

Wang, H., Zhang, H., Zhai, J., Liu, Y., Song, B., He, X., Ge, Y., and Li, D. Breaking hydrogen bond network enhances oxygenic photosynthesis of photosystem II. Fundamental Research (2025)

Pan, X., Gu, Y., Zhou, W., and Zhang, Y. Enhancing transthyretin binding affinity prediction with a consensus model: Insights from the Tox24 challenge. Chem. Res. Toxicol. 38, 900–908 (2025)

Kelly, T., Xia, S., Lu, J., and Zhang, Y. Unified deep learning of molecular and protein language representations with T5ProtChem. J. Chem. Inf. Model. 65, 3990–3998 (2025)

Chen, E. A. and Zhang, Y. Can deep learning blind docking methods be used to predict allosteric compounds? J. Chem. Inf. Model. 65, 3737–3748 (2025)

Pan, X., Zhang, X., Xia, S., and Zhang, Y. Fast and accurate prediction of tautomer ratios in aqueous solution via a Siamese neural network. J. Chem. Theory Comput. 21, 3132–3141 (2025)

Hou, D., Zhang, S., Ma, M., Lin, H., Wan, Z., Zhao, H., Zhou, R., He, X., Wei, X., Ju, D., and Zeng, X. A hyperbolic discrete diffusion 3D RNA inverse folding model for functional RNA design. J. Chem. Inf. Model. 65, 6568–6584 (2025)

Liu, J., Zhou, X., and He, X. Structure making and breaking effects of ions on the anomalous diffusion of water revealed by machine learning potentials. Phys. Chem. Chem. Phys. 27, 12438-12452 (2025)

Li, J., Tang, W., Zhu, J., Yang, J., and He, X. Hydroxymethanesulfonate formation accelerated at the air-water interface by synergistic enthalpy-entropy effects. Nat. Commun. 16, 5187 (2025)

Chen, S., Zhu, J., Li, J., Guo, P., Yang, J., and He, X. Entropy-driven difference in interfacial water reactivity between slab and nanodroplet. Nat. Commun. 16, 5250 (2025)

Li, Y., Xiong, D., Zhu, J., Mou, Y., Yang, J., and He, X. Dynamic mechanism of short peptide additive regulating solvation microenvironment of zinc ions. Batter. Supercaps e202400735 (2025)

Xiong, D., Ming, Y., Li, Y., Li, S., Chen, K., Liu, J., Duan, L., Li, H., Li, M., and He, X. EvoNB: A protein language model-based workflow for nanobody mutation prediction and optimization. J. Pharm. Anal. 15, 101260 (2025)

Chen, S., Zhang, Z.-H., Li, Y., Chen, Y., Yang, J., He, X., and Zhang, L. Implications of weaving pattern on the material properties of two-dimensional molecularly woven fabrics. Matter 8, 102050 (2025)

Chen, Z., Meng, Z., He, T., Li, H., Cao, J., Xu, L., Xiao, H., Zhang, Y., He, X., and Fang, G. Crystal structure prediction meets artificial intelligence. J. Phys. Chem. Lett. 16, 2581–2591 (2025)

Wang, L., Xue, Y., Wang, J.-N., Mo, Y., Mei, Y. Rational enzyme evolution by facilitating correlated motion along the reaction. J. Phys. Chem. B 129, 5591–5600 (2025)

Fu, Y., Mei, Y., and Liu, C. An iterative and automatic collective variable optimization scheme via unsupervised feature selection with CUR matrix decomposition. J. Chem. Phys. 162, 174101 (2025)

Akter, M., Lyu, X., Lu, J., Wang, X., Phonesavanh, T., Wang, H., Yu, H., and Kang, J. Role of Noncanonical Histone H2A Variant, H2A.Z, to Maintain Proper Centromeric Transcription and Chromosome Segregation. J. Biol. Chem. 301, 108464 (2025)

Liu, Z. and Sun, X. Direct All-Atom Nonadiabatic Semiclassical Simulations for Electronic Absorption Spectroscopy of Organic Photovoltaic Non-Fullerene Acceptor in Solution. J. Phys. Chem. Lett. 16, 4463–4473 (2025)

Huang, J., He, Y., Gan, Z., Wang, J., and Zhang, J. Z. H. Optimization of Nanobody Caplacizumab via Computational Design. Phys. Chem. Chem. Phys. 27, 9076-9086 (2025)

Xue, R., Zhang, M., Zhang, C., Zhang, J. Z. H., Xu, H., Wang, R., and Zhang, L. Molecular Simulations Guiding Recombinant Mussel Protein with Enhanced Applicable Properties for Adhesive Materials. Int. J. Biol. Macromol. 307, 141988 (2025)

Zhang, C., Huang, K., and Zhang, J. Z. H. Protein Solvation: Site-Specific Hydrophilicity, Hydrophobicity, Counter Ions, and Interaction Entropy. J. Chem. Phys. 162, 114103 (2025)