C. Hyeon

Kinetic model for the desensitization of G protein-coupled receptor

The paper develops a kinetic model to understand GPCR desensitization by integrating biochemical steps from ligand binding to receptor internalization, identifying three downregulation regimes based on phosphorylation, dephosphorylation, and beta-arrestin levels.

Glycolytic oscillations under periodic drivings

This study examines how periodic glucose injection affects glycolytic oscillations using a dynamical systems approach, revealing entrainment and chaotic behavior under specific driving conditions.

Moderate activity of RNA chaperone maximizes the yield of self-spliced pre-RNA in vivo

The paper uses a kinetic network model to show that optimal CYT-19 activity maximizes self-splicing yield of group I introns by balancing chaperone-mediated folding and self-splicing kinetics.

Dissecting the co-segregation probability from genome architecture mapping

This study derives a theoretical framework for co-segregation probability from genome architecture mapping and shows that normalization with many nuclear slices improves correlation with inter-locus distances.

TMAO Destabilizes RNA Secondary Structurevia Direct Hydrogen Bond Interactions

This study investigates how TMAO interacts with RNA hairpins using molecular dynamics simulations, revealing that TMAO destabilizes RNA via hydrogen bond interactions with solvent-exposed bases.

Location of the TEMPO moiety of TEMPO-PC in phosphatidylcholine bilayers is membrane phase-dependent

This study uses molecular dynamics simulations to show that the TEMPO moiety of TEMPO-PC partitions between aqueous and lipid phases depending on the membrane phase, affecting its positioning in phosphatidylcholine bilayers.

Extracting multi-way chromatin contacts from Hi-C data

This paper derives analytic expressions to predict multi-way chromatin contacts from Hi-C data, showing good correlation with experimental measurements.

Cost-precision trade-off relation determines the optimal morphogen gradient for accurate biological pattern formation

The paper shows that the optimal morphogen gradient length minimizes thermodynamic cost while ensuring precise boundary formation in development.

A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C

This paper introduces Multi-CD, a unified algorithm that infers chromatin domains at multiple scales from Hi-C data, revealing hierarchical structures and organizational principles across cell types.

Heterogeneous loop model to infer 3D chromosome structures from Hi-C

This paper introduces a heterogeneous loop model to infer 3D chromosome structures from Hi-C data and validates it against experimental measurements.

Interphase Human Chromosome Exhibits Out of Equilibrium Glassy Dynamics

The paper models human interphase chromosomes as a self-avoiding polymer to study their glassy dynamics and shows agreement between simulations and experimental data.

Architecture of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci

The paper uses a heteropolymer model with Hi-C data to study chromatin dynamics, finding that chromosome architecture determines spatiotemporal behavior and cell-to-cell variability.

Signaling Networks and Dynamics of Allosteric Transitions in Bacterial Chaperonin GroEL: Implications for Iterative Annealing of Misfolded Proteins

The paper introduces a method to analyze allostery in GroEL-GroES and shows that salt-bridge dynamics drive its allosteric transitions and function.

Molecular chaperones maximize the native state yield per unit time by driving substrates out of equilibrium

The paper develops a stochastic model to explain how molecular chaperones maximize native state production rates by driving substrates out of equilibrium, reconciling conflicting experimental results on ribozyme and protein folding.

Quantifying the Heat Dissipation from Molecular Motor’s Transport Properties in Nonequilibrium Steady States

The paper quantifies heat dissipation from molecular motors in nonequilibrium steady states and links it to transport properties like velocity and diffusivity.

Decoding Single Molecule Time Traces with Dynamic Disorder

This paper introduces VB-DCMM, an algorithm to analyze single molecule time trajectories with dynamic disorder, and applies it to H-DNA FRET data to reveal multiple internal states and kinetic paths.

Effects of dimethyl sulfoxide on surface water near phospholipid bilayers

This study uses molecular dynamics simulations to investigate how DMSO affects water structure and dynamics near phospholipid bilayers, revealing discrepancies between experimental and simulation results.