Hybrid Particle Field Research Articles

Phase Coexistence in Hamiltonian Hybrid Particle-Field Theory Using a Multi-Gaussian Approach.

This study introduces an implementation of multiple Gaussian filters within the Hamiltonian hybrid particle-field (HhPF) theory, aimed at capturing phase coexistence phenomena in mesoscopic molecular simulations. By employing a linear combination of two Gaussians, we demonstrate that HhPF can generate potentials with attractive and steric components analogous to Lennard-Jones (LJ) potentials, which are crucial for modeling phase coexistence. We compare the performance of this method with the multi-Gaussian core model (MGCM) in simulating liquid-gas coexistence for a single-component system across various densities and temperatures. Our results show that HhPF effectively captures detailed information on phase coexistence and interfacial phenomena, including microconfiguration transitions and increased interfacial fluctuations at higher temperatures. Notably, the phase boundaries obtained from HhPF simulations align more closely with those of LJ systems compared to the MGCM results. This work advances the hybrid particle-field methodology to address phase coexistence without requiring modifications to the equation of state or introducing additional interaction energy functional terms, offering a promising approach for mesoscale molecular simulations of complex systems.

Shape recognition and size measurement of particles in hybrid particle field based on interference technology

Shape recognition and size measurement of particles in hybrid particle field based on interference technology

Exploring the Molecular Dynamics of a Lipid-A Vesicle at the Atom Level: Morphology and Permeation Mechanism.

Lipid-A was previously shown to spontaneously aggregate into a vesicle via the hybrid particle field approach. We assess the validity of the proposed vesiculation mechanism by simulating the resulting lipid-A vesicle at the atom level. The spatial confinement imposed by the vesicle geometry on the conformation and packing of lipid-A induces significant heterogeneity of physical properties in the inner and outer leaflets. It also induces tighter molecular packing and lower acyl chain order compared to the lamellar arrangement. Around 5% of water molecules passively permeates the vesicle membrane inward and outward. The permeation is facilitated by interactions with water molecules that are transported across the membrane by a network of electrostatic interactions with the hydrogen bond donors/acceptors in the N-acetylglucosamine ring and upper region of the acyl chains of lipid-A. The permeation process takes place at low rates but still at higher frequencies than observed for the lamellar arrangement of lipid-A. These findings not only substantiate the proposed lipid-A vesiculation mechanism but also reveal the complex structural dynamics of an important nonlamellar arrangement of lipid-A.

On the equivalence of the hybrid particle-field and Gaussian core models.

Hybrid particle-field molecular dynamics is a molecular simulation strategy, wherein particles couple to a density field instead of through ordinary pair potentials. Traditionally considered a mean-field theory, a momentum and energy-conserving hybrid particle-field formalism has recently been introduced, which was demonstrated to approach the Gaussian Core model potential in the grid-converged limit. Here, we expand on and generalize the correspondence between the Hamiltonian hybrid particle-field method and particle-particle pair potentials. Using the spectral procedure suggested by Bore and Cascella, we establish compatibility to any local soft pair potential in the limit of infinitesimal grid spacing. Furthermore, we document how the mean-field regime often observed in hybrid particle-field simulations is due to the systems under consideration, and not an inherent property of the model. Considering the Gaussian filter form, in particular, we demonstrate the ability of the Hamiltonian hybrid particle-field model to recover all structural and dynamical properties of the Gaussian Core model, including solid phases, a first-order phase transition, and anomalous transport properties. We quantify the impact of the grid spacing on the correspondence, as well as the effect of the particle-field filtering length scale on the emergent particle-particle correlations.

Slip-Spring Hybrid Particle-Field Molecular Dynamics for Coarse-Graining Branched Polymer Melts: Polystyrene Melts as an Example.

The topology of chains significantly modifies the dynamical properties of polymer melts. Here, we extend a recently developed efficient simulation method, namely the slip-spring hybrid particle-field (SS-hPF) model, to study the structural and dynamical properties of branched polymer melts over large spatial-temporal scales. In the coarse-grained SS-hPF simulation of polymers, the bonded potentials are derived by iterative Boltzmann inversion from the underlying fine-grained model. The nonbonded potentials are computed from a density functional field instead of pairwise interactions used in standard molecular dynamics simulations, which increases the computational efficiency by a factor of 10-20. The entangled dynamics is lost due to the soft-core nature of density functional field interactions. It is recovered by a multichain slip-spring model that is rigorously parametrized from existing experimental or simulation data. To quantitatively predict the relaxation and diffusion of branched polymers, which are dominated by arm retraction rather than chain reptation, the slip-spring algorithm is augmented to improve the polymer dynamics near the branch point. Multiple dynamical observables, e.g., diffusion coefficients, arm relaxations, and tube survival probabilities, are characterized in an example coarse-grained model of symmetric and asymmetric star-shaped polystyrene melts. Consistent dynamical behaviors are identified and compared with theoretical predictions. With a single rescaling factor, the prediction of diffusion coefficients agrees well with the available experimental measurements. In this work, an efficient approach is provided to build chemistry-specific coarse-grained models for predicting the dynamics of branched polymers.

Atomistic hybrid particle-field molecular dynamics combined with slip-springs: Restoring entangled dynamics to simulations of polymer melts.

In hybrid particle-field (hPF) simulations (J. Chem. Phys., 2009 130, 214106), the entangled dynamics of polymer melts is lost due to chain crossability. Chains cross, because the field-treatment of the nonbonded interactions makes them effectively soft-core. We introduce a multi-chain slip-spring model (J. Chem. Phys., 2013 138, 104907) into the hPF scheme to mimic the topological constraints of entanglements. The structure of the polymer chains is consistent with that of regular molecular dynamics simulations and is not affected by the introduction of slip-springs. Although slight deviations are seen at short times, dynamical properties such as mean-square displacements and reorientational relaxation times are in good agreement with traditional molecular dynamics simulations and theoretical predictions at long times.

Generation of well relaxed all atom models of stereoregular polymers: a validation of hybrid particle-field molecular dynamics for polypropylene melts of different tacticities

ABSTRACT The tacticity of vinyl polymer chains strongly affects the physical properties of polymeric materials, as example the chain conformations and stiffness. In the present work we tested how the hybrid Particle-Field Molecular Dynamics (PF-MD) technique is capable to describe conformational differences of polymer chains as function of the tacticity. In particular, we focus on tacticity effect of atactic, isotactic, and syndiotactic polypropylene (PP) homopolymer melts. We found that PF-MD simulations exhibit dependence of Flory’s Characteristic Ratio from the fraction of racemo diads along the PP chains in qualitative agreement with Small Angle Neutron Scattering (SANS) experiments and theoretical previsions. Finally, we calculated and compared the packing length parameter on very high stereoregular syndiotactic PP systems with rheological measurements. A qualitative agreement between the calculated and experimental packing length is found.

Influence of Polymer Bidispersity on the Effective Particle–Particle Interactions in Polymer Nanocomposites

We investigate the role played by the bidispersity of polymer chains on the local structure and the potential of mean force (PMF) between silica nanoparticles (NPs) in a polystyrene melt. We use the hybrid particle-field molecular dynamics technique which allows to efficiently relax polymer nanocomposites even with high molecular weights.The NPs we investigate are either bare or grafted with polystyrene chains immersed in a melt of free polystyrene chains, whereas the grafted and the free polystyrene chains are either monodisperse or bidisperse. The two-body PMF shows that a bidisperse distribution of free polymer chains increases the strength of attraction between a pair of ungrafted NPs. If the NPs are grafted by polymer chains, the effective interaction crucially depends on bidispersity and grafting density of the polymer chains: for low grafting densities, the bidispersity of both free and grafted chains increases the repulsion between the NPs, whereas for high grafting densities we observe two different effects. An increase of bidispersity in free chains causes the rise of the repulsion between the NPs, while an increase of bidispersity in grafted chains promotes the rise of attraction. Additionally, a proper treatment of multi-body interactions improves the simpler two-body PMF calculations, in both unimodal and bimodal cases. We found that, by properly tuning the bidispersity of both free and grafted chains, we can control the structure of the composite materials, which can be confirmed by experimental observations. As a result, the hybrid particle-field approach is confirmed to be a valid tool for reproducing and predicting microscopic interactions, which determine the stability of the microscopic structure of the composite in a wide range of conditions.

Micellization of Pluronic P123 in Water/Ethanol/Turpentine Oil Mixed Solvents: Hybrid Particle-Field Molecular Dynamic Simulation.

The hybrid particle–field molecular dynamics simulation method (MD-SCF) was applied to study the self-assembly of Pluronic PEO20-PPO70-PEO20 (P123) in water/ethanol/turpentine oil- mixed solvents. In particular, the micellization process of P123 at low concentration (less than 20%) in water/ethanol/turpentine oil-mixed solvents was investigated. The aggregation number, radius of gyration, and radial density profiles were calculated and compared with experimental data to characterize the structures of the micelles self-assembled from P123 in the mixed solvent. This study confirms that the larger-sized micelles are formed in the presence of ethanol, in addition to the turpentine oil-swollen micelles. Furthermore, the spherical micelles and vesicles were both observed in the self-assembly of P123 in the water/ethanol/turpentine oil-mixed solvent. The results of this work aid the understanding of the influence of ethanol and oil on P123 micellization, which will help with the design of effective copolymer-based formulations.

Hybrid Particle-Field Model for Conformational Dynamics of Peptide Chains.

We propose the first model of a polypeptide chain based on a hybrid-particle field approach. The intramolecular potential is built on a two-bead coarse grain mapping for each amino acid. We employ a combined potential for the bending and the torsional degrees of freedom that ensures the stabilization of secondary structure elements in the conformational space of the polypeptide. The electrostatic dipoles associated with the peptide bonds of the main chain are reconstructed by a topological procedure. The intermolecular interactions comprising both the solute and the explicit solvent are treated by a density functional-based mean-field potential. Molecular dynamics simulations on a series of test systems show how the model here introduced is able to capture all the main features of polypeptides. In particular, homopolymers of different lengths yield a complex folding phase diagram, covering from the collapsed to swollen state. Moreover, simulations on models of a four-helix bundle and of an alpha + beta peptide evidence how the collapse of the hydrophobic core drives the appearance of both folded motifs and the stabilization of tertiary or quaternary assemblies. Finally, the polypeptide model is able to structurally respond to the environmental changes caused by the presence of a lipid bilayer.

Percolating Behavior of Nanoparticles in Block Copolymer Host: Hybrid Particle-Field Simulations

The hybrid particle–field method is extended to investigate self-assembly and percolating behavior of nanocomposites containing block copolymers and nanoparticles. The self-assembled nanostructures serve as templates to guide organization and distribution of nanoparticles. The percolation threshold of nanoparticles in the host of block copolymers is discussed in terms of composition of block copolymers, radius, and aspect ratio of nanoparticles. The simulated results demonstrate that the block copolymers have a synergistic or antagonistic effect on emergence of percolating network of nanoparticles, depending on the copolymer composition. There exists an optimal value of copolymer composition for lowering the percolation threshold of nanoparticles. In addition, regulating the geometrical shape of nanoparticles further lowers the percolation threshold of nanoparticles dispersed in the block copolymers. These simulated results provide useful guidelines for designing high-performance composite materials with ...

Toward Chemically Resolved Computer Simulations of Dynamics and Remodeling of Biological Membranes

Cellular membranes are fundamental constituents of living organisms. Apart from defining the boundaries of the cells, they are involved in a wide range of biological functions, associated with both their structural and the dynamical properties. Biomembranes can undergo large-scale transformations when subject to specific environmental changes, including gel-liquid phase transitions, change of aggregation structure, formation of microtubules, or rupture into vesicles. All of these processes are dependent on a delicate interplay between intermolecular forces, molecular crowding, and entropy, and their understanding requires approaches that are able to capture and rationalize the details of all of the involved interactions. Molecular dynamics-based computational models at atom-level resolution are, in principle, the best way to perform such investigations. Unfortunately, the relevant spatial and time dimensionalities involved in membrane remodeling phenomena would require computational costs that are today unaffordable on a routinely basis. Such hurdles can be removed by coarse-graining the representations of the individual molecular components of the systems. This procedure anyway reduces the possibility of describing the chemical variations in the lipid mixtures composing biological membranes. New hybrid particle field multiscale approaches offer today a promising alternative to the more traditional particle-based simulations methods. By combining chemically distinguishable molecular representations with mesoscale-based computationally affordable potentials, they appear as one of the most promising ways to keep an accurate description of the chemical complexity of biological membranes and, at the same time, cover the required scales to describe remodeling events.

Hybrid particle-field molecular dynamics simulation for polyelectrolyte systems.

To achieve simulations on large spatial and temporal scales with high molecular chemical specificity, a hybrid particle-field method was proposed recently. This method is developed by combining molecular dynamics and self-consistent field theory (MD-SCF). The MD-SCF method has been validated by successfully predicting the experimentally observable properties of several systems. Here we propose an efficient scheme for the inclusion of electrostatic interactions in the MD-SCF framework. In this scheme, charged molecules are interacting with the external fields that are self-consistently determined from the charge densities. This method is validated by comparing the structural properties of polyelectrolytes in solution obtained from the MD-SCF and particle-based simulations. Moreover, taking PMMA-b-PEO and LiCF3SO3 as examples, the enhancement of immiscibility between the ion-dissolving block and the inert block by doping lithium salts into the copolymer is examined by using the MD-SCF method. By employing GPU-acceleration, the high performance of the MD-SCF method with explicit treatment of electrostatics facilitates the simulation study of many problems involving polyelectrolytes.

Self-assembly of triton X-100 in water solutions: a multiscale simulation study linking mesoscale to atomistic models.

A multiscale scheme is proposed and validated for Triton X-100 (TX-100), which is a detergent widely employed in biology. The hybrid particle field formulation of the model allows simulations of large-scale systems. The coarse-grained (CG) model, accurately validated in a wide range of concentrations, shows a critical micelle concentration, shape transition in isotropic micellar phase, and appearance of hexagonal ordered phase in the experimental ranges reported in the literature. The fine resolution of the proposed CG model allows one to obtain, by a suitable reverse mapping procedure, atomistic models of micellar assemblies and of the hexagonal phase. In particular, atomistic models of the micelles give structures in good agreement with experimental pair distance distribution functions and hydrodynamic measurements. The picture emerging by detailed analysis of simulated systems is quite complex. Polydisperse mixtures of spherical-, oblate-, and prolate-shaped aggregates have been found. The shape and the micelle behavior are mainly dictated by the aggregation number (Nagg). Micelles with low Nagg values (∼40) are spherical, while those with high Nagg values (∼140 or larger) are characterized by prolate ellipsoidal shapes. For intermediate Nagg values (∼70), fluxional micelles alternating between oblate and prolate shapes are found. The proposed model opens the way to investigations of several mechanisms involving TX-100 assembly in protein and membrane biophysics.

A hybrid particle–field molecular dynamics approach: a route toward efficient coarse-grained models for biomembranes

This paper gives an overview of the coarse-grained models of phospholipids recently developed by the authors in the frame of a hybrid particle–field molecular dynamics technique. This technique employs a special class of coarse-grained models that are gaining popularity because they allow simulations of large scale systems and, at the same time, they provide sufficiently detailed chemistry for the mapping scheme adopted. The comparison of the computational costs of our approach with standard molecular dynamics simulations is a function of the system size and the number of processors employed in the parallel calculations. Due to the low amount of data exchange, the larger the number of processors, the better are the performances of the hybrid particle–field models. This feature makes these models very promising ones in the exploration of several problems in biophysics.

Long-Range Ordering of Symmetric Block Copolymer Domains by Chaining of Superparamagnetic Nanoparticles in External Magnetic Fields

A new method to achieve long-range orientational order in symmetric diblock copolymer nanodomains through the alignment and chaining of superparamagnetic nanoparticles in a magnetic field is investigated computationally and theoretically. The effects of nanoparticle size, volume fraction, and magnetization strength are explored using the hybrid particle field (HPF) technique for particles that selectively segregate into one domain of a symmetric diblock copolymer assembly. A critical selectivity of the particles for one nanodomain is observed, above which strong alignment results and below which comparatively disordered structures are formed. The 2D simulations reveal that, for a given nanoparticle volume fraction, only a nanoparticle size commensurate with the block copolymer domain spacing yields well-aligned nanostructures. Nanoparticles significantly larger than the domain spacing break the symmetry of the lamellar phase and result in poor alignment, while high defect densities are observed for smalle...

Effect of particle surface selectivity on composite nanostructures in nanoparticle/diblock copolymer mixture dilute solution

In this study the phase behavior of nanoparticle/diblock copolymer composites in dilute solution has been investigated by the hybrid particle-field (HPF) method. We focus on the influence of particle surface selectivity (i.e. hydrophobic and hydrophilic) on the distribution of nanoparticles in the micelles formed by the diblock copolymers. These two types of particle surface selectivity are simulated systematically. The different competition between the energy from enthalpy and the energy from entropy has been observed in the two kinds of composite systems. Our simulation results show that the particle surface selectivity is a crucial factor for determining the thermodynamic properties in the complex dilute solution, and the morphologies of micelles are controlled by the volume fraction of the nanoparticles. The change of particle distribution in various micelles enriches the composite microstructures that can be formed by nanoparticle and diblock copolymer.

Self-Consistent-Field and Hybrid Particle-Field Theory Simulation of Confined Copolymer and Nanoparticle Mixtures

In this paper, we used combined self-consistent-field and hybrid particle-field theory to explore the self-assembly behavior of diblock copolymer-nanoparticle mixtures confined between two concentric circular walls. The simulation reveals that the structural frustration, the loss of conformational entropy of the copolymer, and the radii of the two concentric circles have great influence on the morphologies of the system. We also discuss the underlying mechanism of controlling the self-assembly of such a system in terms of enthalpic interaction between particles and copolymers, steric repulsive interactions between particles, and the conformational entropy of copolymers, and a representative phase diagram in terms of block ratio and the particle volume fraction is constructed. This study suggests a route to help experimentalists better create high-performance nanodevices.