Correction for 'Development of a transferable coarse-grained model of polydimethylsiloxane' by Sonia Cambiaso , , 2022, https://doi.org/10.1039/d2sm00939k.
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Entropy-based methods for formulating bottom-up ultra-coarse-grained models.
J Chem Phys
January 2025
Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA.
Bottom-up coarse-grained (CG) modeling is an effective means of bypassing the limited spatiotemporal scales of conventional atomistic molecular dynamics while retaining essential information from the atomistic model. A central challenge in CG modeling is the trade-off between accuracy and efficiency, as the inclusion of often pivotal many-body interaction terms in the CG force-field renders simulation markedly slower than simple pairwise models. The Ultra Coarse-Graining (UCG) method incorporates many-body terms through discrete internal state variables that modulate the CG force-field according to, e.
View Article and Find Full Text PDFCryptochrome magnetoreception: Time course of photoactivation from non-equilibrium coarse-grained molecular dynamics.
Comput Struct Biotechnol J
December 2024
Department of Physics, University of Exeter, Stocker Rd., Exeter EX4 4QL, UK.
Magnetoreception, the ability to sense magnetic fields, is widespread in animals but remains poorly understood. The leading model links this ability in migratory birds to the photo-activation of the protein cryptochrome. Magnetic information is thought to induce structural changes in cryptochrome via a transient radical pair intermediate.
View Article and Find Full Text PDFRepresenting Structural Isomer Effects in a Coarse-Grain Model of Poly(Ether Ketone Ketone).
Polymers (Basel)
January 2025
Micron School of Material Science and Engineering, Boise State University, Boise, ID 83725, USA.
Carbon-fiber composites with thermoplastic matrices offer many processing and performance benefits in aerospace applications, but the long relaxation times of polymers make it difficult to predict how the structure of the matrix depends on its chemistry and how it was processed. Coarse-grained models of polymers can enable access to these long-time dynamics, but can have limited applicability outside the systems and state points that they are validated against. Here we develop and validate a minimal coarse-grained model of the aerospace thermoplastic poly(etherketoneketone) (PEKK).
View Article and Find Full Text PDFIdentifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations.
JACS Au
December 2024
Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
It has become increasingly evident that the conformational distributions of intrinsically disordered proteins or regions are strongly dependent on their amino acid compositions and sequence. To facilitate a systematic investigation of these sequence-ensemble relationships, we selected a set of 16 naturally occurring intrinsically disordered regions of identical length but with large differences in amino acid composition, hydrophobicity, and charge patterning. We probed their conformational ensembles with single-molecule Förster resonance energy transfer (FRET), complemented by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy as well as small-angle X-ray scattering (SAXS).
View Article and Find Full Text PDFComputational Characterization of the Structure, Energy, Strengths, and Fracture Resistances of Symmetric Tilt Grain Boundaries in Ice.
ACS Appl Mater Interfaces
January 2025
Department of Aerospace Engineering, Iowa State University, Ames, Iowa 50014, United States.
Using an interatomic potential that can capture the tetrahedral configuration of water molecules (HO) in ice without the need to explicitly track the motion of the O and H atoms, coarse-grained (CG) atomistic simulations are performed here to characterize the structures, energy, cohesive strengths, and fracture resistance of the grain boundaries (GBs) in polycrystalline ice resulting from water freezing. Taking the symmetric tilt grain boundaries (STGBs) with a tilting axis of ⟨0001⟩ as an example, several main findings from our simulations are (i) the GB energy, , exhibits a strong dependence on the GB misorientation angle, θ. The classical Read-Shockley model only predicts the - θ relation reasonably well when θ < 20° or θ > 45° but fails when 20° < θ < 45°; (ii) two "valleys" appear in the -θ landscape.
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