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Many-Body Neural Network-Based Force Field for Structure-Based Coarse-Graining of Water
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OpenMSCG: A Software Tool for Bottom-Up Coarse-Graining
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Chemical Potential of a Flexible Polymer Liquid in a Coarse-Grained Representation
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Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin’s Regulation on Actin Filaments
Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experimental work suggests that cofilin also forms functionally distinct oligomers through thiol post-translational modification (PTM) that encourages actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. Here, we also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol post-translational modification cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.
Molecular Dynamics Simulations of Ion-Containing Polymers Using Generic Coarse-Grained Models
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Entanglements via Slip Springs with Soft, Coarse-Grained Models for Systems Having Explicit Liquid–Vapor Interfaces
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Coarse-Grained Modeling of Polymer Cleavage within a Porous Catalytic Support
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Coarse-Grained Water Model Development for Accurate Dynamics and Structure Prediction
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Active learning a coarse-grained neural network model for bulk water from sparse training data
Active learning scheme to train neural network potentials for molecular simulations.
United atom and coarse grained models for crosslinked polydimethylsiloxane with applications to the rheology of silicone fluids
Particle-based models of crosslinked PDMS were developed at multiple resolutions for direct numerical simulations of silicone rheological properties and behavior.
A three-point velocity estimation method for two-dimensional coarse-grained imaging data
Time delay and velocity estimation methods have been widely studied subjects in the context of signal processing, with applications in many different fields of physics. The velocity of waves or coherent fluctuation structures is commonly estimated as the distance between two measurement points divided by the time lag that maximizes the cross correlation function between the measured signals, but this is demonstrated to result in erroneous estimates for two spatial dimensions. We present an improved method to accurately estimate both components of the velocity vector, relying on three non-aligned measurement points. We introduce a stochastic process describing the fluctuations as a superposition of uncorrelated pulses moving in two dimensions. Using this model, we show that the three-point velocity estimation method, using time delays calculated through cross correlations, yields the exact velocity components when all pulses have the same velocity. The two- and three-point methods are tested on synthetic data generated from realizations of such processes for which the underlying velocity components are known. The results reveal the superiority of the three-point technique. Finally, we demonstrate the applicability of the velocity estimation on gas puff imaging data of strongly intermittent plasma fluctuations due to the radial motion of coherent, blob-like structures at the boundary of the Alcator C-Mod tokamak.
Systematic time-coarse-graining for driven quantum systems
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