Simulation Model for Hierarchical Self-Assembly of Soft Disklike Particles

Comparison of the Backbone Dynamics of Dehaloperoxidase-Hemoglobin Isoenzymes

Dehaloperoxidase (DHP) is a multifunctional hemeprotein with a functional switch generally regulated by the chemical class of the substrate. Its two isoforms, DHP-A and DHP-B, differ by only five amino acids and have an almost identical protein fold. However, the catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism ranges from 2- to 6-fold greater than that of DHP-A depending on the conditions. X-ray crystallography has shown that many substrates and ligands have nearly identical binding in the two isoenzymes, suggesting that the difference in catalytic efficiency could be due to differences in the conformational dynamics. We compared the backbone dynamics of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations. While the overall dynamics of the isoenzymes are similar, there are specific local differences in functional regions of each protein. In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational states likely coupled to a swinging motion of Tyr34. Moreover, Asn37 undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37 are adjacent to Tyr34 and Tyr38, it is possible that their dynamics modulate the formation and migration of the active tyrosyl radicals in DHP-A at pH 7. Another significant difference is that both distal and proximal histidines have a 15-18% smaller S2 value in DHP-B, thus their greater flexibility could account for the higher catalytic activity. The distal histidine grants substrate access to the distal pocket. The greater flexibility of the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut "push-pull"-type peroxidase mechanism.

Multiple 2D crystal structures in bilayered lamellae from direct self-assembly of 3D systems of soft Janus particles

Numerous crystals and Frank-Kasper phases in two-dimensional (2D) systems of soft particles have been presented by theoretical investigations. How to realize 2D crystals or Frank-kasper phases by direct self-assembly of...

Morphology of depletant-induced erythrocyte aggregates

Red blood cells suspended in quiescent plasma tend to aggregate into multicellular assemblages, including linearly stacked columnar rouleaux, which can reversibly form more complex clusters or branching networks. While these aggregates play an essential role in establishing hemorheological and pathological properties, the biophysics behind their self-assembly into dynamic mesoscopic structures remains under-explored. We employ coarse-grained molecular simulations to model low-hematocrit erythrocytes subject to short-range implicit depletion forces, and demonstrate not only that depletion interactions are sufficient to account for a sudden dispersion-aggregate transition, but also that the volume fraction of depletant macromolecules controls small aggregate morphology. We observe a sudden transition from a dispersion to a linear column rouleau, followed by a slow emergence of disorderly amorphous clusters of many short rouleaux at larger volume fractions. This work demonstrates how discocyte topology and short-range, non-specific, physical interactions are sufficient to self-assemble erythrocytes into various aggregate structures, with markedly different morphologies and biomedical consequences.

Kinetics-Controlled Amphiphile Self-Assembly Processes

Amphiphile self-assembly is an essential bottom-up approach of fabricating advanced functional materials. Self-assembled materials with desired structures are often obtained through thermodynamic control. Here, we demonstrate that the selection of kinetic pathways can lead to drastically different self-assembled structures, underlining the significance of kinetic control in self-assembly. By constructing kinetic network models from large-scale molecular dynamics simulations, we show that two largely similar amphiphiles, 1-[11-oxo-11-(pyren-1-ylmethoxy)-undecyl]pyridinium bromide (PYR) and 1-(11-((5a1,8a-dihydropyren-1-yl)methylamino)-11-oxoundecyl)pyridinium bromide (PYN), prefer distinct kinetic assembly pathways. While PYR prefers an incremental growth mechanism and forms a nanotube, PYN favors a hopping growth pathway leading to a vesicle. Such preference was found to originate from the subtle difference in the distributions of hydrophobic and hydrophilic groups in their chemical structures, which leads to different rates of the adhesion process among the aggregating micelles. Our results are in good agreement with experimental results, and accentuate the role of kinetics in the rational design of amphiphile self-assembly.

Control globular structure formation of a copolymer chain through inverse design

A copolymer chain in dilute solution can exhibit various globular structures with characteristic morphologies, which makes it a potentially useful candidate for artificial materials design. However, the chain has a huge conformation space and may not naturally form the globular structure we desire. An ideal way to control globular structure formation should be inverse design, i.e., starting from the target structure and finding out what kind of polymers can effectively generate it. To accomplish this, we propose an inverse design procedure, which is combined with Wang-Landau Monte Carlo to fully and precisely explore the huge conformation space of the chain. Starting from a desired target structure, all the geometrically possible sequences are exactly enumerated. Interestingly, reasonable interaction strengths are obtained and found to be not specified for only one sequence. Instead, they can be combined with many other sequences and also achieve a relatively high yield for target structure, although these sequences may be rather different. These results confirm the possibility of controlling globular structure formation of a copolymer chain through inverse design and pave the way for targeted materials design.

Supracolloidal helices from soft Janus particles by tuning the particle softness

Because of the unique architectures and promising potential applications of biomimetic helical structures in biotechnology and nanotechnology, the design and fabrication of these structures by experimentally realizable anisotropic colloidal particles remain one of the most challenging tasks in materials science. Here we show how soft Janus particles self-assemble into supracolloidal helices with distinctive structural characteristics, including single helices, double helices, and Bernal spirals, by appropriately tuning the particle softness. We further examine the kinetic mechanisms governing the formation of different helical structures by using particle-based dynamics simulations. Our results provide a new way for experimentally fabricating structure-controllable supracolloidal helices solely from the self-assembly of soft Janus particles.

GALAMOST: GPU-accelerated large-scale molecular simulation toolkit

GALAMOST [graphics processing unit (GPU)-accelerated large-scale molecular simulation toolkit] is a molecular simulation package designed to utilize the computational power of GPUs. Besides the common features of molecular dynamics (MD) packages, it is developed specially for the studies of self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by using some lately developed simulation techniques. To accelerate the simulations, GALAMOST contains a hybrid particle-field MD technique where particle–particle interactions are replaced by interactions of particles with density fields. Moreover, the numerical potential obtained by bottom-up coarse-graining methods can be implemented in simulations with GALAMOST. By combining these force fields and particle-density coupling method in GALAMOST, the simulations for polymers can be performed with very large system sizes over long simulation time. In addition, GALAMOST encompasses two specific models, that is, a soft anisotropic particle model and a chain-growth polymerization model, by which the hierarchical self-assembly of soft anisotropic particles and the problems related to polymerization can be studied, respectively. The optimized algorithms implemented on the GPU, package characteristics, and benchmarks of GALAMOST are reported in detail.

Hierarchical self-assembly of chiral fibres from achiral particles

We investigate, by molecular dynamics simulation, the behaviour of discotic particles in a solvent of Lennard-Jones spheres. When chromonic disc-sphere interactions are imposed on these systems, three regimes of self-assembly are observed. At moderate temperatures, numerous short threads of discs develop, but these threads remain isolated from one another. Quenching to low temperatures, alternatively, causes all of the discs to floc into a single extended aggregate which typically comprises several distinct sections and contains numerous packing defects. For a narrow temperature range between these regimes, however, defect-free chiral fibres are found to freely self-assemble. The spontaneous chirality of these fibres results from frustration between the hexagonal packing and interdigitation of neighbouring threads, the pitch being set by the particle shape. This demonstration of aggregate-wide chirality emerging owing to packing alone is pertinent to many biological and synthetic hierarchically self-assembling systems.