Jaewoon Jung

In molecular dynamics (MD) simulations, enforcing holonomic constraints on specific interatomic distances is crucial to extend the integration time step while maintaining numerical stability. While double‐precision arithmetic has traditionally been used to ensure numerical accuracy, there is a growing demand for single‐ and mixed‐precision calculations as GPU‐accelerated MD simulations become increasingly widespread. In this study, we present improvements to the constraint solvers through an analytical treatment for bonds involving a single hydrogen atom ( groups). For more complex groups with multiple hydrogens ( and ), we introduce two precision‐level implementation strategies: (1) a mixed‐precision approach, where variables are generally described in single‐precision while temporary coordinate updates are handled in double‐precision and (2) a pairwise arithmetic approach, where temporary coordinate variables are represented as pairs of single‐precision values to reduce rounding errors. These implementation strategies reduce velocity‐update errors compared with schemes using single precision for all variables. Energy drift analysis in microcanonical simulations confirms that these strategies maintain accuracy comparable to full double‐precision implementations. Performance benchmarks on GPUs with limited FP64 throughput (RTX 3080 and A6000 Ada) show that our proposed implementation strategies substantially reduce runtime compared with full double‐precision calculations. Conversely, on architectures with balanced FP32 and FP64 performance, such as CPUs or H100 GPUs, full double‐precision arithmetic remains the preferred choice for the constraint kernels evaluated in this study. Overall, these findings demonstrate that the proposed strategies provide an effective balance between numerical accuracy and computational performance on GPUs with limited FP64 throughput.

F ₁ -ATPase comprises the stator ring consisting of α ₃ β ₃ subunits and the rotor γ subunit. The γ subunit rotation mechanism has been extensively investigated by biochemical analyses, structural studies, single-molecule measurements, and computational studies. Recent cryoelectron microscopy (cryo-EM) structures of F ₁ -ATPase from the thermophilic bacterium Bacillus PS3 (TF ₁ ) provide us with further possibilities for a better understanding of the γ-rotation mechanisms. Using cryo-EM structures having the γ-rotation angles close to the binding dwell and catalytic dwell states, we investigate the relationships between the γ subunit rotation, conformational changes of the stator α ₃ β ₃ subunits, and the nucleotide-binding and release. We performed targeted molecular dynamics (MD) simulations with external forces on the α ₃ β ₃ subunits and observed 80° substep rotations of the γ subunit. Then, we optimized the most probable transition pathway through the mean-force string method simulations with 64 images. Finally, using umbrella sampling, we calculated the potential of mean forces along the minimum free energy pathway during the 80° substep rotation. Our MD simulations suggest that 80° substep rotation is divided into the first rotation, resting, and the second rotation. Notably, the first rotation is driven by the distortion of the stator α ₃ β ₃ subunits, and the second rotation is induced mainly by direct β/γ subunit interactions. This model, which we call the distortion–push mechanism, is consistent with the residue-level experimental analysis on F ₁ -ATPase and the atomic structures determined by X-ray crystallography and cryo-EM.

Despite advances in peptide and protein design, the rational design of membrane-spanning peptides that form conducting channels remains challenging due to our imperfect understanding of the sequence-to-structure relationships that drive membrane insertion, assembly, and conductance. Here, we describe the design and computational and experimental characterization of a series of coiled coil-based peptides that form transmembrane α-helical barrels with conductive channels. Through a combination of rational and computational design, we obtain barrels with 5 to 7 helices, as characterized in detergent micelles. In lipid bilayers, these peptide assemblies exhibit two conductance states with relative populations dependent on the applied potential: (i) low-conductance states that correlate with variations in the designed amino-acid sequences and modeled coiled-coil barrel geometries, indicating stable transmembrane α-helical barrels; and (ii) high-conductance states in which single channels change size in discrete steps. Notably, the high-conductance states are similar for all peptides in contrast to the low-conductance states. This indicates the formation of large, dynamic channels, as observed in natural barrel-stave peptide channels. These findings establish rational routes to design and tune functional membrane-spanning peptide channels with specific conductance and geometry.

In eukaryotic genomes, regulated access and communication between cis-regulatory elements (CREs) are necessary for enhancer-mediated transcription of genes. The molecular framework of the chromatin organization underlying such communication remains poorly understood. To better understand it, we develop a multiscale modeling pipeline to build near-atomistic models of the 200 kb Nanog gene locus in mouse embryonic stem cells comprising nucleosomes, transcription factors, co-activators, and RNA polymerase II–mediator complexes. By integrating diverse experimental data, including protein localization, genomic interaction frequencies, cryo-electron microscopy, and single-molecule fluorescence studies, our model offers novel insights into chromatin organization and its role in enhancer–promoter communication. The models equilibrated by high-performance molecular dynamics simulations span a scale of ∼350 nm, revealing an experimentally consistent local and global organization of chromatin and transcriptional machinery. Our models elucidate that the sequence-regulated chromatin accessibility facilitates the recruitment of transcription regulatory proteins exclusively at CREs, guided by the contrasting nucleosome organization compared to other regions. By constructing an experimentally consistent near-atomic model of chromatin in the cellular environment, our approach provides a robust framework for future studies on nuclear compartmentalization, chromatin organization, and transcription regulation.

We propose an accurate method for evaluating temperature and pressure in Langevin integration, based on the approach by Leimkuhler and Matthews (J. Chem. Phys. 138, 174102). This method improves the quality of configuration space than other Langevin dynamics methods. However, it encounters issues in pressure evaluation due to inaccuracies in momentum space. In particular, the conventional approach for calculating kinetic temperature using the full-time step momentum introduces errors proportional to the square of the time step (Δt2), leading to unreliable results when employing a large time step under isothermal–isobaric conditions. By calculating kinetic energy using the half-time step momentum in pressure evaluation, we can reduce the numerical errors. We performed molecular dynamics (MD) simulations using our refined pressure evaluation and improved accuracy and stability in the isothermal–isobaric MD simulations even with a long time step (Δt = 5 fs).

F ₁ -ATPase comprises the stator ring consisting of α₃β₃ subunits and the rotor γ subunit. The γ subunit rotation mechanism has been extensively investigated by biochemical analyses, structural studies, single-molecule measurements, and computational studies. Recent cryo-electron microscopy (cryo-EM) structures of F ₁ -ATPase from the thermophilic bacterium Bacillus PS3 (TF ₁ ) provide us with further possibilities for a better understanding of the γ-rotation mechanisms. Using cryo-EM structures having the γ-rotation angles close to the binding dwell and catalytic dwell states, we investigate the relationships between the γ subunit rotation, conformational changes of the stator α ₃ β ₃ subunits, and the nucleotide-binding and release. We performed targeted molecular dynamics (MD) simulations with external forces on the α₃β₃ subunits and observed 80° substep rotations of the γ subunit. Then, we optimized the most probable transition pathway through the mean-force string method simulations with 64 images. Finally, using umbrella sampling, we calculated the potential of mean forces along the minimum free energy pathway during the 80° substep rotation. Our MD simulations suggest that 80° substep rotation is divided into the first rotation, resting, and the second rotation. Notably, the first rotation is driven by the distortion of the stator α ₃ β ₃ subunits, and the second rotation is induced mainly by direct β/γ subunit interactions. This model, which we call the distortion-push mechanism, is consistent with the residue-level experimental analysis on F ₁ -ATPase and the atomic structures determined by X-ray crystallography and cryo-EM.

In eukaryotic genomes, regulated access and communication between cis-regulatory elements (CREs) are necessary for enhancer-mediated transcription of genes. The molecular framework of the chromatin organization underlying such communication remains poorly understood. To better understand it, we develop a multiscale modeling pipeline to build near-atomistic models of the 200 kb Nanog gene locus in mouse embryonic stem cells comprising nucleosomes, transcription factors, co-activators, and RNA polymerase II-Mediator complexes. By integrating diverse experimental data, including protein localization, genomic interaction frequencies, cryo-electron microscopy, and single-molecule fluorescence studies, our model offers novel insights into chromatin organization and its role in enhancer-promoter communication. The models equilibrated by high-performance molecular dynamics simulations span a scale of ∼350 nm, revealing an experimentally consistent local and global organization of chromatin and transcriptional machinery. Our models elucidate that the sequence-regulated chromatin accessibility facilitates the recruitment of transcription regulatory proteins exclusively at CREs, guided by the contrasting nucleosome organization compared to other regions. By constructing an experimentally consistent near-atomic model of chromatin in the cellular environment, our approach provides a robust framework for future studies on nuclear compartmentalization, chromatin organization, and transcription regulation.

Despite advances in peptide and protein design, the rational design of membrane-spanning peptides that form conducting channels remains challenging due to our imperfect understanding of the sequence-to-structure relationships that drive membrane insertion, assembly, and conductance. Here, we describe the design and computational and experimental characterization of a series of coiled coil-based peptides that form transmembrane α-helical barrels. Through a combination of rational and computational design, we obtain barrels with 5 to 7 helices, as characterized in detergent micelles. In lipid bilayers, these peptide assemblies exhibit two conductance states with relative populations dependent on the applied potential: (i) a low-conductance states that correlate with variations in the modeled coiled-coil barrel geometries, indicating stable transmembrane α-helical barrels; and (ii) high-conductance states in which single pores change size in discrete steps. Notably, the high-conductance states are similar for all peptides in contrast to the low-conductance states. This indicates the formation of large, dynamic pores through the recruitment and expulsion of peptides, as observed in natural barrel-stave peptide pores. These findings establish rational routes to design and tune functional membrane-spanning peptide channels with specific conductance and geometry.

GENeralized-Ensemble SImulation System (GENESIS) is a molecular dynamics (MD) software developed to simulate the conformational dynamics of a single biomolecule, as well as molecular interactions in large biomolecular assemblies and between multiple biomolecules in cellular environments. To achieve the latter purpose, the earlier versions of GENESIS emphasized high performance in atomistic MD simulations on massively parallel supercomputers, with or without graphics processing units (GPUs). Here, we implemented multiscale MD simulations that include atomistic, coarse-grained, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. They demonstrate high performance and are integrated with enhanced conformational sampling algorithms and free-energy calculations without using external programs except for the QM programs. In this article, we review new functions, molecular models, and other essential features in GENESIS version 2.1 and discuss ongoing developments for future releases.