An official website of the United States government
We develop a physical and computational model for performing fully coupled, grain-resolved direct numerical simulations of cohesive sediment, based on the immersed boundary method. The model distributes the cohesive forces over a thin shell surrounding each particle, thereby allowing for the spatial and temporal resolution of the cohesive forces during particle–particle interactions. The influence of the cohesive forces is captured by a single dimensionless parameter in the form of a cohesion number, which represents the ratio of cohesive and gravitational forces acting on a particle. We test and validate the cohesive force model for binary particle interactions in the drafting–kissing–tumbling (DKT) configuration. Cohesive sediment grains can remain attached to each other during the tumbling phase following the initial collision, thereby giving rise to the formation of flocs. The DKT simulations demonstrate that cohesive particle pairs settle in a preferred orientation, with particles of very different sizes preferentially aligning themselves in the vertical direction, so that the smaller particle is drafted in the wake of the larger one. This preferred orientation of cohesive particle pairs is found to remain influential for systems of higher complexity. To this end, we perform large simulations of 1261 polydisperse settling particles starting from rest. These simulations reproduce several earlier experimental observations by other authors, such as the accelerated settling of sand and silt particles due to particle bonding, the stratification of cohesive sediment deposits, and the consolidation process of the deposit. They identify three characteristic phases of the polydisperse settling process, viz. (i) initial stir-up phase with limited flocculation, (ii) enhanced settling phase characterized by increased flocculation, and (iii) consolidation phase. The simulations demonstrate that cohesive forces accelerate the overall settling process primarily because smaller grains attach to larger ones and settle in their wakes. For the present cohesive number values, we observe that settling can be accelerated by up to 29 %. We propose physically based parametrization of classical hindered settling functions introduced by earlier authors, in order to account for cohesive forces. An investigation of the energy budget shows that, even though the work of the collision forces is much smaller than that of the hydrodynamic drag forces, it can substantially modify the relevant energy conversion processes.
more »
« less
This content will become publicly available on March 1, 2026
The role of biomolecular building blocks on the cohesion of biomatter plastics
Unaltered biological matter (biomatter) can be harnessed to fabricate cohesive, sustainable bioplastics. However, controlling the material properties of these bioplastics is challenging, as the contributions of different macromolecular building blocks to processability and performance are unknown. To deconvolute the roles of different classes of biomolecules, we developed experimental and computational methods to construct and analyze biomatter analogs composed of carbohydrates, proteins, and lipids. These analogs are intended to improve fundamental understanding of biomatter plastics. Spectroscopic analyses of biomatter analogs suggest that cohesion depends on protein aggregation during thermomechanical processing. Molecular dynamics simulations confirm that alterations to protein conformation and hydrogen bonding are likely the primary mechanisms underlying the formation of a cohesive, proteinaceous matrix. Simulations also corroborate experimental measurements highlighting the importance of hydrogen bonding and self-assembly between specific, small-molecule constituents. These conclusions may enable the engineering of next-generation biomatter plastics with improved performance.
more »
« less
- PAR ID:
- 10627367
- Publisher / Repository:
- CellPress
- Date Published:
- Journal Name:
- Matter
- Volume:
- 8
- Issue:
- 3
- ISSN:
- 2590-2385
- Page Range / eLocation ID:
- 101941
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Protein–protein and protein–water hydrogen bonding interactions play essential roles in the way a protein passes through the transition state during folding or unfolding, but the large number of these interactions in molecular dynamics (MD) simulations makes them difficult to analyze. Here, we introduce a state space representation and associated “rarity” measure to identify and quantify transition state passage (transit) events. Applying this representation to a long MD simulation trajectory that captured multiple folding and unfolding events of the GTT WW domain, a small protein often used as a model for the folding process, we identified three transition categories: Highway (faster), Meander (slower), and Ambiguous (intermediate). We developed data sonification and visualization tools to analyze hydrogen bond dynamics before, during, and after these transition events. By means of these tools, we were able to identify characteristic hydrogen bonding patterns associated with “Highway” versus “Meander” versus “Ambiguous” transitions and to design algorithms that can identify these same folding pathways and critical protein–water interactions directly from the data. Highly cooperative hydrogen bonding can either slow down or speed up transit. Furthermore, an analysis of protein–water hydrogen bond dynamics at the surface of WW domain shows an increase in hydrogen bond lifetime from folded to unfolded conformations with Ambiguous transitions as an outlier. In summary, hydrogen bond dynamics provide a direct window into the heterogeneity of transits, which can vary widely in duration (by a factor of 10) due to a complex energy landscape.more » « less
-
Polyethylene glycol (PEG) is one of the environmentally benign solvent options for green chemistry. It readily absorbs water when exposed to the atmosphere. The Molecular Dynamics (MD) simulations of PEG200, a commercial mixture of low molecular weight polyethyelene glycol oligomers, as well as di-, tetra-, and hexaethylene glycol are presented to study the effect of added water impurities up to a weight fraction of 0.020, which covers the typical range of water impurities due to water absorption from the atmosphere. Each system was simulated a total of four times using different combinations of two force fields for the water (SPC/E and TIP4P/2005) and two force fields for the PEG and oligomer (OPLS-AA and modified OPLS-AA). The observed trends in the effects of water addition were qualitatively quite robust with respect to these force field combinations and showed that the water does not aggregate but forms hydrogen bonds at most between two water molecules. In general, the added water causes overall either no or very small and nuanced effects in the simulation results. Specifically, the obtained water RDFs are mostly identical regardless of the water content. The added water reduces oligomer hydrogen bonding interactions overall as it competes and forms hydrogen bonds with the oligomers. The loss of intramolecular oligomer hydrogen bonding is in part compensated by oligomers switching from inter- to intramolecular hydrogen bonding. The interplay of the competing hydrogen bonding interactions leads to the presence of shallow extrema with respect to the water weight fraction dependencies for densities, viscosities, and self-diffusion coefficients, in contrast to experimental measurements, which show monotonous dependencies. However, these trends are very small in magnitude and thus confirm the experimentally observed insensitivity of these physical properties to the presence of water impurities.more » « less
-
Reguera, Gemma (Ed.)ABSTRACT With the rising demand for sustainable renewable resources, microorganisms capable of producing bioproducts such as bioplastics are attractive. While many bioproduction systems are well-studied in model organisms, investigating non-model organisms is essential to expand the field and utilize metabolically versatile strains. This investigation centers onRhodopseudomonas palustrisTIE-1, a purple non-sulfur bacterium capable of producing bioplastics. To increase bioplastic production, genes encoding the putative regulatory protein PhaR and the depolymerase PhaZ of the polyhydroxyalkanoate (PHA) biosynthesis pathway were deleted. Genes associated with pathways that might compete with PHA production, specifically those linked to glycogen production and nitrogen fixation, were deleted. Additionally, RuBisCO form I and II genes were integrated into TIE-1’s genome by a phage integration system, developed in this study. Our results show that deletion ofphaRincreases PHA production when TIE-1 is grown photoheterotrophically with butyrate and ammonium chloride (NH4Cl). Mutants unable to produce glycogen or fix nitrogen show increased PHA production under photoautotrophic growth with hydrogen and NH4Cl. The most significant increase in PHA production was observed when RuBisCO form I and form I & II genes were overexpressed, five times under photoheterotrophy with butyrate, two times with hydrogen and NH4Cl, and two times under photoelectrotrophic growth with N2. In summary, inserting copies of RuBisCO genes into the TIE-1 genome is a more effective strategy than deleting competing pathways to increase PHA production in TIE-1. The successful use of the phage integration system opens numerous opportunities for synthetic biology in TIE-1.IMPORTANCEOur planet has been burdened by pollution resulting from the extensive use of petroleum-derived plastics for the last few decades. Since the discovery of biodegradable plastic alternatives, concerted efforts have been made to enhance their bioproduction. The versatile microorganismRhodopseudomonas palustrisTIE-1 (TIE-1) stands out as a promising candidate for bioplastic synthesis, owing to its ability to use multiple electron sources, fix the greenhouse gas CO2, and use light as an energy source. Two categories of strains were meticulously designed from the TIE-1 wild-type to augment the production of polyhydroxyalkanoate (PHA), one such bioplastic produced. The first group includes mutants carrying a deletion of thephaRorphaZgenes in the PHA pathway, and those lacking potential competitive carbon and energy sinks to the PHA pathway (namely, glycogen biosynthesis and nitrogen fixation). The second group comprises TIE-1 strains that overexpress RuBisCO form I or form I & II genes inserted via a phage integration system. By studying numerous metabolic mutants and overexpression strains, we conclude that genetic modifications in the environmental microbe TIE-1 can improve PHA production. When combined with other approaches (such as reactor design, use of microbial consortia, and different feedstocks), genetic and metabolic manipulations of purple nonsulfur bacteria like TIE-1 are essential for replacing petroleum-derived plastics with biodegradable plastics like PHA.more » « less
-
This work reveals the influence of pendant hydrogen bonding strength and distribution on self-assembly and the resulting thermomechanical properties of A-AB-A triblock copolymers. Reversible addition-fragmentation chain transfer polymerization afforded a library of A-AB-A acrylic triblock copolymers, wherein the A unit contained cytosine acrylate (CyA) or post-functionalized ureido cytosine acrylate (UCyA) and the B unit consisted of n-butyl acrylate (nBA). Differential scanning calorimetry revealed two glass transition temperatures, suggesting microphase-separation in the A-AB-A triblock copolymers. Thermomechanical and morphological analysis revealed the effects of hydrogen bonding distribution and strength on the self-assembly and microphase-separated morphology. Dynamic mechanical analysis showed multiple tan delta (δ) transitions that correlated to chain relaxation and hydrogen bonding dissociation, further confirming the microphase-separated structure. In addition, UCyA triblock copolymers possessed an extended modulus plateau versus temperature compared to the CyA analogs due to the stronger association of quadruple hydrogen bonding. CyA triblock copolymers exhibited a cylindrical microphase-separated morphology according to small-angle X-ray scattering. In contrast, UCyA triblock copolymers lacked long-range ordering due to hydrogen bonding induced phase mixing. The incorporation of UCyA into the soft central block resulted in improved tensile strength, extensibility, and toughness compared to the AB random copolymer and A-B-A triblock copolymer comparisons. This study provides insight into the structure-property relationships of A-AB-A supramolecular triblock copolymers that result from tunable association strengths.more » « less
