Search Results (14)

Elucidating amyloid formation inside biomolecular condensates requires models that resolve (i) local, chemistry specific contacts controlling β registry and (ii) mesoscale phase behavior and cluster coalescence on microsecond timescales—capabilities beyond single resolution models. We present a hybrid united atom/coarse grained (UA–CG) force field coupling a PACE UA peptide model with the MARTINI CG framework. Cross resolution nonbonded parameters are first optimized against all atom side chain potentials of mean force to balance the relative strength between different types of interactions and then refined through universal parameter scaling by matching radius of gyration distributions for specific systems using. We applied this approach to simulate a recently reported model system comprising the LVFFAR₉ peptide that can co-assemble into amyloid fibrils via liquid–liquid phase separation. Our ten-microsecond simulations reveal rapid droplet formation populated by micelle like nanostructures with its inner core composed of LVFF clusters. The nanostructures can further fuse but the fusion is reaction-limited due to an electrostatic coalescence barrier. β structures emerge once clusters exceed ~10 peptides, and the LVFFAR₉ fraction modulates amyloid polymorphism, reversing parallel versus antiparallel registry at lower LVFFAR₉. These detailed insights generated from long simulations highlight the promise of our hybrid UA–CG strategy in investigating the molecular mechanism of condensate aging. Full article

The melting behavior of alkanes plays a critical role in a wide field of applications. While experimental studies have established the occurrence of premelting phenomena in both short- and long-chain alkanes, molecular-level insights remain limited. In this work, we employ coarse-grained molecular dynamics simulations to investigate the melting behavior of high-molecular-weight alkanes, with a particular focus on continuous premelting dynamics in the transition regime toward polymer-like systems. By simulating alkane chains of varying lengths and analyzing temperature-dependent structural changes, we identify a crossover from discrete phase transitions to a gradual premelting process beyond chain lengths of $N\approx 40$ coarse-grained beads. The extrapolation of melting temperatures to zero heating rate yields values that agree well with the experimental data for the longest simulated chains. Compared to previous simulation studies, the slower heating rates used here offer enhanced quantitative agreement. Overall, the results provide new molecular-level insights into the melting of long-chain alkanes and highlight the utility of coarse-grained models in capturing complex phase behavior. Full article

When flowing through the blood stream, drug carriers such as nanoparticles encounter hundreds of plasma proteins, forming a protein layer on the nanoparticle surface, known as the “protein corona”. Since the protein corona influences the size, shape, and surface properties of nanoparticles, it can modulate their circulating lifetime, cytotoxicity, and targeting efficiency. Therefore, understanding the mechanism of protein corona formation at the atomic scale is crucial, which has become possible due to advances in computer power and simulation methodologies. This review covers the following topics: (1) the structure, dynamics, and composition of protein corona on nanoparticles; (2) the effects of protein concentration and ionic strength on protein corona formation; (3) the effects of particle size, morphology, and surface properties on corona formation; (4) the interactions among lipids, membranes, and nanoparticles with the protein corona. For each topic, mesoscale, coarse-grained, and all-atom molecular dynamics simulations since 2020 are discussed. These simulations not only successfully reproduce experimental observations but also provide physical insights into the protein corona formation. In particular, these simulation findings can be applied to manipulate the formation of a protein corona that can target specific cells, aiding in the rational design of nanomedicines for drug delivery applications. Full article

In laser crack repair processes, laser parameters have significant influence on repair quality. Improper combination of laser process parameters may result in defects—such as porosity, ablation, and coarse grain size—in remelted zones. A trans-scale computational model is established by combining crystal plasticity finite elements and variable-node finite elements. The influence of microstructure characteristics such as grain size and porosity of the repair layer on the cumulative plastic slip (CPS) on the dominant slip system at the meso-scale and the J-integral at the macro-scale is studied to explore the effect of laser process parameters on repair quality. The results show that when the laser power is 1800 W and the heating time is 0.5 s, the grain size and porosity of the repaired specimen are the smallest. The J-integral of the repaired specimen is more than 8% smaller than that of the unrepaired specimen and about 3% smaller than that of the repaired specimen, with a laser power of 2000 W and a heating time of 1 s. Pores increase the CPS of the crystal around the pores, especially when a pore have sharp corners. Selecting appropriate laser process parameters can not only refine grain size but also reduce the volume fraction of pores and thus reduce the J-integral and eventually improve repair quality of repaired specimens. The study investigates the relationship of process parameter–microstructure–repair quality in the laser repair process and provides a method for studying the mechanical behavior of materials at macro and micro scales. Full article

Highly varying process conditions drive polymers into nonequilibrium molecular conformations. This has direct implications for the resulting structural and mechanical properties. This study rigorously investigated processing-property relations from a microscopic perspective. The corresponding models use a mesoscale molecular dynamics (MD) approach. Different loading conditions, including uniaxial and biaxial stretching, along with various cooling conditions, were employed to mimic process conditions on the micro-scale. The resulting intricate interplay between equi-biaxial stretching, orientation, and crystallization behavior in long polyethylene chains was reviewed. The study reveals notable effects depending on different cooling and biaxial stretching procedures. The findings emphasize the significance of considering distributions and directions of chain ordering. Local inspections of trajectories unveil that crystal growth predominantly occurs in regions devoid of entanglements. Full article

Polyacrylonitrile (PAN) is widely used as a raw material for the production of high-modulus carbon fibers, the internal structure of which is directly affected by the spinning of the precursor. Although PAN fibers have been studied for a long time, the formation of their internal structure has not been sufficiently investigated theoretically. This is due to the large number of stages in the process and the parameters controlling them. In this study, we present a mesoscale model describing the evolution of nascent PAN fibers during the coagulation. It is constructed within the framework of a mesoscale dynamic density functional theory. We use the model to study the influence of a combined solvent of dimethyl sulfoxide (DMSO, a good solvent) and water (a non-solvent) on the microstructure of the fibers. A porous structure of PAN is formed as a result of the microphase separation of the polymer and the residual combined solvent at a high water content in the system. The model shows that one of the possible ways to obtain the homogeneous fiber structure is to slow down the coagulation by increasing the amount of good solvent in the system. This result is in agreement with the existing experimental data and confirms the efficiency of the presented model. Full article

This study investigates the initial stage of the thermo-mechanical crystallization behavior for uni- and biaxially stretched polyethylene. The models are based on a mesoscale molecular dynamics approach. We take constraints that occur in real-life polymer processing into account, especially with respect to the blowing stage of the extrusion blow-molding process. For this purpose, we deform our systems using a wide range of stretching levels before they are quenched. We discuss the effects of the stretching procedures on the micro-mechanical state of the systems, characterized by entanglement behavior and nematic ordering of chain segments. For the cooling stage, we use two different approaches which allow for free or hindered shrinkage, respectively. During cooling, crystallization kinetics are monitored: We precisely evaluate how the interplay of chain length, temperature, local entanglements and orientation of chain segments influence crystallization behavior. Our models reveal that the main stretching direction dominates microscopic states of the different systems. We are able to show that crystallization mainly depends on the (dis-)entanglement behavior. Nematic ordering plays a secondary role. Full article

In this study, we investigate the thermo-mechanical relaxation and crystallization behavior of polyethylene using mesoscale molecular dynamics simulations. Our models specifically mimic constraints that occur in real-life polymer processing: After strong uniaxial stretching of the melt, we quench and release the polymer chains at different loading conditions. These conditions allow for free or hindered shrinkage, respectively. We present the shrinkage and swelling behavior as well as the crystallization kinetics over up to 600 ns simulation time. We are able to precisely evaluate how the interplay of chain length, temperature, local entanglements and orientation of chain segments influences crystallization and relaxation behavior. From our models, we determine the temperature dependent crystallization rate of polyethylene, including crystallization onset temperature. Full article

Surface segregation of the low molecular weight component of a polymeric mixture is a ubiquitous phenomenon that leads to degradation of industrial formulations. We report a simultaneous phase separation and surface migration phenomena in oligomer–polymer ( $OP$ ) and oligomer–gel ( $OG$ ) systems following a temperature quench that induces demixing of components. We compute equilibrium and time varying migrant (oligomer) density profiles and wetting layer thickness in these systems using coarse grained molecular dynamics (CGMD) and mesoscale hydrodynamics (MH) simulations. Such multiscale methods quantitatively describe the phenomena over a wide range of length and time scales. We show that surface migration in gel–oligomer systems is significantly reduced on account of network elasticity. Furthermore, the phase separation processes are significantly slowed in gels leading to the modification of the well known Lifshitz–Slyozov–Wagner (LSW) law $\ell \left(\tau \right)\sim {\tau }^{1/3}$ . Our work allows for rational design of polymer/gel–oligomer mixtures with predictable surface segregation characteristics that can be compared against experiments. Full article

This review covers the scope of multiscale computational fluid dynamics (CFD), laying the framework for studying hydrodynamics with and without chemical reactions in single and multiple phases regarded as continuum fluids. The molecular, coarse-grained particle, and meso-scale dynamics at the individual scale are excluded in this review. Scoping single-scale Eulerian CFD approaches, the necessity of multiscale CFD is highlighted. First, the Eulerian CFD theory, including the governing and turbulence equations, is described for single and multiple phases. The Reynolds-averaged Navier–Stokes (RANS)-based turbulence model such as the standard k-ε equation is briefly presented, which is commonly used for industrial flow conditions. Following the general CFD theories based on the first-principle laws, a multiscale CFD strategy interacting between micro- and macroscale domains is introduced. Next, the applications of single-scale CFD are presented for chemical and biological processes such as gas distributors, combustors, gas storage tanks, bioreactors, fuel cells, random- and structured-packing columns, gas-liquid bubble columns, and gas-solid and gas-liquid-solid fluidized beds. Several multiscale simulations coupled with Eulerian CFD are reported, focusing on the coupling strategy between two scales. Finally, challenges to multiscale CFD simulations are discussed. The need for experimental validation of CFD results is also presented to lay the groundwork for digital twins supported by CFD. This review culminates in conclusions and perspectives of multiscale CFD. Full article

A large number of low-resolution models have been proposed in the last decades to reduce the computational cost of molecular dynamics simulations for bio-nano systems, such as those involving the interactions of proteins with functionalized nanoparticles (NPs). For the proteins, “minimalist” models at the one-bead-per residue (Cα-based) level and with implicit solvent are well established. For the gold NPs, widely explored for biotechnological applications, mesoscale (MS) models treating the NP core with a single spheroidal object are commonly proposed. In this representation, the surface details (coating, roughness, etc.) are lost. These, however, and the specificity of the functionalization, have been shown to have fundamental roles for the interaction with proteins. We presented a mixed-resolution coarse-grained (CG) model for gold NPs in which the surface chemistry is reintroduced as superficial smaller beads. We compared molecular dynamics simulations of the amyloid β2-microglobulin represented at the minimalist level interacting with NPs represented with this model or at the MS level. Our finding highlights the importance of describing the surface of the NP at a finer level as the chemical-physical properties of the surface of the NP are crucial to correctly understand the protein-nanoparticle association. Full article

A multiscale molecular dynamics simulation study has been carried out in order to provide in-depth information on the adsorption of hemoglobin, myoglobin, and trypsin over citrate-capped AuNPs of 15 nm diameter. In particular, determinants for single proteins adsorption and simultaneous adsorption of the three types of proteins considered have been studied by Coarse-Grained and Meso-Scale molecular simulations, respectively. The results, discussed in the light of the controversial experimental data reported in the current experimental literature, have provided a detailed description of the (i) recognition process, (ii) number of proteins involved in the early stages of corona formation, (iii) protein competition for AuNP adsorption, (iv) interaction modalities between AuNP and protein binding sites, and (v) protein structural preservation and alteration. Full article

The physiological properties of biological soft matter are the product of collective interactions, which span many time and length scales. Recent computational modeling efforts have helped illuminate experiments that characterize the ways in which proteins modulate membrane physics. Linking these models across time and length scales in a multiscale model explains how atomistic information propagates to larger scales. This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes. Full article

Recent advances in molecular dynamics simulation methodologies and computational power have allowed accurate predictions of dendrimer size, shape, and interactions with bilayers and polyelectrolytes with modest computational effort. Atomistic and coarse-grained (CG) models show strong interactions of cationic dendrimers with lipid bilayers. The CG simulations with explicit lipid and water capture bilayer penetration and pore formation, showing that pore formation is enhanced at high dendrimer concentration, but suppressed at low temperature and high salt concentration, in agreement with experiments. Cationic linear polymers have also been simulated, but do not perforate membranes, evidently because by deforming into a pancake, the charges on a linear polymer achieve intimate contact with a single bilayer leaflet. The relatively rigid dendrimers, on the other hand, penetrate the bilayer, because only by interacting with both leaflets can they achieve a similar degree of contact between charged groups. Also, a “dendrimer-filled vesicle” structure for the dendrimer-membrane interaction is predicted by mesoscale thermodynamic simulations, in agreement with a picture derived from experimental observations. In simulations of complexes of dendrimer and polyelectrolyte, anionic linear chains wrap around the cationic dendrimer and penetrate inside it. Overall, these new results indicate that simulations can now provide predictions in excellent agreement with experimental observations, and provide atomic-scale insights into dendrimer structure and dynamics. Full article