More Like this

1. Quantum effects on the dynamics and properties of soft materials

   https://doi.org/10.1039/D6CC00073H  

   Garashchuk, Sophya; Jakowski, Jacek; Rassolov, Vitaly A (April 2026, Chemical Communications)

   The quantum effects of nuclear and electronic motion play an important role in the structure, dynamics, and function of soft materials, yet they are difficult to capture with conventional classical simulations or static electronic–structure methods. 

   more » « less
2. Fixation probability in evolutionary dynamics on switching temporal networks

   https://doi.org/10.1007/s00285-023-01987-5  

   Bhaumik, Jnanajyoti; Masuda, Naoki (November 2023, Journal of Mathematical Biology)

   Abstract Population structure has been known to substantially affect evolutionary dynamics. Networks that promote the spreading of fitter mutants are called amplifiers of selection, and those that suppress the spreading of fitter mutants are called suppressors of selection. Research in the past two decades has found various families of amplifiers while suppressors still remain somewhat elusive. It has also been discovered that most networks are amplifiers of selection under the birth-death updating combined with uniform initialization, which is a standard condition assumed widely in the literature. In the present study, we extend the birth-death processes to temporal (i.e., time-varying) networks. For the sake of tractability, we restrict ourselves to switching temporal networks, in which the network structure deterministically alternates between two static networks at constant time intervals or stochastically in a Markovian manner. We show that, in a majority of cases, switching networks are less amplifying than both of the two static networks constituting the switching networks. Furthermore, most small switching networks, i.e., networks on six nodes or less, are suppressors, which contrasts to the case of static networks. 

   more » « less
3. Dynamics in supramolecular nanomaterials

   https://doi.org/10.1039/d1sm00047k  

   Cho, Yukio; Christoff-Tempesta, Ty; Kaser, Samuel J.; Ortony, Julia H. (June 2021, Soft Matter)

   Self-assembly of amphiphilic small molecules in water leads to nanostructures with customizable structure–property relationships arising from their tunable chemistries. Characterization of these assemblies is generally limited to their static structures – e.g. their geometries and dimensions – but the implementation of tools that provide a deeper understanding of molecular motions has recently emerged. Here, we summarize recent reports showcasing dynamics characterization tools and their application to small molecule assemblies, and we go on to highlight supramolecular systems whose properties are substantially affected by their conformational, exchange, and water dynamics. This review illustrates the importance of considering dynamics in rational amphiphile design. 

   more » « less
4. Static three-dimensional structures determine fast dynamics between distal loci pairs in interphase chromosomes

   https://doi.org/10.1126/sciadv.adx1763  

   Shi, Guang; Shin, Sucheol; Thirumalai, D (August 2025, Science Advances)

   Live-cell imaging experiments have shown that the distal dynamics between enhancers and promoters are unexpectedly rapid and incompatible with standard polymer models. The discordance between the compact static chromatin organization and dynamics is a conundrum that violates the expected structure–function relationship. We developed a theory to predict chromatin dynamics by accurately determining three-dimensional (3D) structures from static Hi-C contact maps or fixed-cell imaging data. Using the calculated 3D coordinates, the theory accurately forecasts experimentally observed two-point chromatin dynamics. It predicts rapid enhancer–promoter interactions and uncovers a scaling relationship between two-point relaxation time and genomic separation, closely matching recent measurements. The theory predicts that cohesin depletion accelerates single-locus diffusion while significantly slowing relaxation dynamics within topologically associating domains. Our results demonstrate that chromatin dynamics can be reliably inferred from static structural data, reinforcing the notion that 3D chromatin structure governs dynamic behavior. This general framework offers powerful tools for exploring chromatin dynamics across diverse biological contexts. 

   more » « less
5. Fast sampling of protein conformational dynamics

   https://doi.org/10.1126/sciadv.aea4617  

   Sauer, Michael A; Mondal, Souvik; Neff, Brandon; Maiti, Sthitadhi; Heyden, Matthias (March 2026, Science Advances)

   Protein function often depends on dynamic transitions between conformations rather than just static structures. However, our current ability to characterize or predict such dynamics lags behind recent advances in protein structure prediction. Enhanced sampling methods can speed up molecular dynamics simulations to study protein conformational transitions but require prior knowledge of key collective motions involved. Here, we demonstrate for a series of proteins of varying complexity that the required information is encoded in anharmonic low-frequency vibrations. Using recently developed methods, we show that this information can be easily extracted from short dynamics simulations without requiring prior knowledge. Combined with enhanced sampling, we correctly predict conformational transitions in all test proteins and generate highly reproducible free energy landscapes. This allows for the rapid generation of accurate protein conformational ensembles, which is critical to unravel the complex relationship between protein sequence, structure, and dynamics. 

   more » « less