Gyration tensor based analysis of the shapes of polymer chains in an attractive spherical cage

Diffusion and Interaction Effects On Molecular Release Kinetics From Collapsed Microgels

The efficient transport of small molecules through dense hydrogel networks is crucial for various applications, including drug delivery, biosensing, catalysis, nanofiltration, water purification, and desalination. In dense polymer matrices, such as collapsed microgels, molecular transport follows the solution-diffusion principle: Molecules dissolve in the polymeric matrix and subsequently diffuse due to a concentration gradient. Employing dynamical density functional theory (DDFT), we investigate the nonequilibrium release kinetics of nonionic subnanometer-sized molecules from a microgel particle, using parameters derived from prior molecular simulations of a thermoresponsive hydrogel. The kinetics is primarily governed by the microgel radius and two intensive parameters: the diffusion coefficient and solvation free energy of the molecule. Our results reveal two limiting regimes: a diffusion-limited regime for large, slowly diffusing, and poorly soluble molecules within the hydrogel; and a reaction-limited regime for small, rapidly diffusing, and highly soluble molecules. These principles allow us to derive an analytical equation for release time, demonstrating excellent quantitative agreement with the DDFT results-a valuable and straightforward tool for predicting release kinetics from microgels.

State Transitions and Crystalline Structures of Single Polyethylene Rings: MD Simulations

This study investigates the structural changes of cyclic polyethylene (PE) single chains during cooling through molecular dynamics simulations. The influence of topological constraint on a ring is examined by comparing it with the results of its linear counterpart. A pseudo phase diagram of state transition for PE rings based on length and temperature is constructed, revealing a consistent chain-folding transition during cooling. The shape anisotropy of short crystallized cyclic chains exhibits oscillations with chain length, leading to a more pronounced odd-even effect in single cyclic chains compared with the linear ones. A honeycomb model is proposed to elucidate the odd-even effect of chain folding in crystalline structures of single linear and cyclic chains, and we discuss its potential to predict surface tension. Analyses of the tight folding model and the re-entry modes demonstrate that a cyclic chain possesses a shorter average crystalline stem length and a more compact folded structure than its linear counterpart. The findings highlight the impact of topological change on crystallization and the odd-even effect of chain length, providing valuable insights for understanding polymer crystallization with different topologies.

Unveiling the dynamic and thermodynamic interactions of hydrocortisone with β-cyclodextrin and its methylated derivatives through insights from molecular dynamics simulations

Cyclodextrins (CDs) can enhance the stability and bioavailability of pharmaceutical compounds by encapsulating them within their cavities. This study utilized molecular dynamics simulations to investigate the interaction mechanisms between hydrocortisone (HC) and various methylated CD derivatives. The results reveal that the loading of HC into CD cavities follows different mechanisms depending on the degree and position of methylation. Loading into βCD and 6-MeβCD was more complete, with the hydroxyl groups of HC facing the primary hydroxyl rim (PHR) and the ketone side facing the secondary hydroxyl rim (SHR). In contrast, 2,3-D-MeβCD and 2,6-D-MeβCD showed a different loading mechanism, with the ketone side facing the PHR and the hydroxyl groups facing the SHR. The root mean square fluctuation (RMSF) analysis demonstrated that methylation increases the flexibility of CD heavy atoms, with 3-MeβCD and 2,3-D-MeβCD exhibiting the highest flexibility. However, upon inclusion of HC, 3-MeβCD, 2,3-D-MeβCD, 2-MeβCD, and 6-MeβCD showed a significant reduction in flexibility, suggesting a more rigid structure that effectively retains HC within their cavities. The radial distribution function revealed a significant reduction in the number of water molecules within the innermost layer of the methylated CD cavities, particularly in TMeβCD, indicating a decrease in polarity. The presence of HC led to the release of high-energy water molecules, creating more favorable conditions for HC loading. Conformational analysis showed that methylation caused a partial decrease in the area of the PHR, a significant decrease in the area of the middle rim, and a notable decrease in the area of the SHR. The loading of HC increased the area of the PHR in most derivatives, with the most pronounced increase observed in 2,6-D-MeβCD and 6-MeβCD. The analysis of interaction energies and binding free energies demonstrated that the binding of HC to methylated CD derivatives is thermodynamically more favorable than to βCD, with the strongest association observed for 6-MeβCD, 2-MeβCD, and 2,3-D-MeβCD.

Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells

SARS-CoV-2 can re-structure chromatin organization and alter the epigenomic landscape of the host genome, but the mechanisms that produce such changes remain unclear. Here, we use polymer physics to investigate how the chromatin of the host genome is re-organized upon infection with SARS-CoV-2. We show that re-structuring of A/B compartments can be explained by a re-modulation of intra-compartment homo-typic affinities, which leads to the weakening of A-A interactions and the enhancement of A-B mixing. At the TAD level, re-arrangements are physically described by a reduction in the loop extrusion activity coupled with an alteration of chromatin phase-separation properties, resulting in more intermingling between different TADs and a spread in space of the TADs themselves. In addition, the architecture of loci relevant to the antiviral interferon response, such as DDX58 or IFIT, becomes more variable within the 3D single-molecule population of the infected model, suggesting that viral infection leads to a loss of chromatin structural specificity. Analysing the time trajectories of pairwise gene-enhancer and higher-order contacts reveals that this variability derives from increased fluctuations in the chromatin dynamics of infected cells. This suggests that SARS-CoV-2 alters gene regulation by impacting the stability of the contact network in time.

Programmable Colloids with Analogous Hypercoordination Complex Architectures

Colloidal molecule clusters (CMCs) are promising building blocks with molecule-like symmetry, offering exceptional synergistic properties for applications in plasmonics and catalysis. Traditional CMC fabrication has been limited to simple molecule-like structures utilizing isotropic particles. Here, we employ molecular dynamics simulation to investigate the co-assembly of anisotropic nanorods (NRs) and the stimulus-responsive polymer (SRP) via reversible adsorption. The results of the simulation show that it is possible to fabricate hypercoordination complex structures with high symmetry from the co-assembly of NRs and the SRP, even in analogy to the Th(BH4)4 structure. The coordination number of these CMCs can be precisely programmed by adjusting the shape and size of the ends of the NRs and the SRP cohesion energy. Furthermore, a finite-difference time-domain simulation indicates these hypercoordination structures exhibit significantly enhanced optical activity and plasmonic coupling effects. These findings introduce a new design approach for complex molecule-like structures utilizing anisotropic nanoparticles and may expand the applications of CMCs in photonics.

Self-assembly of rod-coil-rod block copolymers in a coil-selective solvent: coarse-grained simulation results

The solution self-assembly of amphiphilic polymers provides a versatile approach to design novel nanostructured materials. Multiblock polymers, particularly those composed of liquid crystalline and coil blocks, are of significant interest due to the potential display of nematic ordering in liquid crystalline domains, offering intriguing optical and mechanical properties. In this study, dissipative particle dynamics is used to investigate the solution self-assembly of rod-coil-rod copolymers in a coil-selective solvent. Extensive molecular simulations were conducted to elucidate the impact of polymer composition, concentration and flexibility on the self-assembly behavior. A quantitative analysis was performed to investigate how polymer conformations varied with changes in composition, concentration, and rigidity. Simulation results show that, at small rod compositions, rod-coil-rod polymers self-assemble into micelles at low concentrations, transitioning to network formation as concentration increases. An increase in rod composition leads to the formation of larger aggregates, resulting in cylindrical micelles and membranes. The results reported here also offer insights into the role of flexibility in shaping the self-assembly behavior of rod-coil-rod triblocks in selective solvents, thus, contributing to a comprehensive understanding of the factors governing the formation of diverse structures in the solution self-assembly of triblock copolymers.

Effect of solvent quality and sidechain architecture on conjugated polymer chain conformation in solution

Conjugated polymers (CPs) are solution-processible for various electronic applications, where solution aggregation and dynamics could impact the morphology in the solid state. Various solvents and solvent mixtures have been used to dissolve and process CPs, but few studies have quantified the effect of solvent quality on the solution behavior of CPs. Herein, we performed static light scattering and small-angle X-ray scattering combined with molecular dynamics (MD) simulation to investigate CP solution behaviors with solvents of varying quality, including poly(3-alkylthiophene) (P3ATs) with various sidechain lengths from -C4H9 to -C12H25, poly[bis(3-dodecyl-2-thienyl)-2,2'-dithiophene-5,5'-diyl] (PQT-12) and poly[2,5-bis(3-dodecylthiophen-2-yl)thieno[3,2-b]thiophene] (PBTTT-12). We found that chlorobenzene is a better solvent than toluene for various CPs, which was evident from the positive second virial coefficient A2 ranging from 0.3 to 4.7 × 10-3 cm3 mol g-2 towards P3ATs. For P3ATs in non-polar solvents, longer sidechains promote more positive A2, indicating a better polymer-solvent interaction, wherein A2 for toluene increases from -5.9 to 1.4 × 10-3 cm3 mol g-2, and in CB, A2 ranges from 1.0 to 4.7 × 10-3 cm3 mol g-2 when sidechain length increases from -C6H13 to -C12H25. Moreover, PQT-12 and PBTTT-12 have strong aggregation tendencies in all solutions, with an apparent positive A2 (∼0.5 × 10-3 cm3 mol g-2) due to multi-chain aggregates and peculiar chain folding. These solvent-dependent aggregation behaviors can be well correlated to spectroscopy measurement results. Our coarse-grained MD simulation results further suggested that CPs with long, dense, and branched sidechains can achieve enhanced polymer-solvent interaction, and thus enable overall better solution dispersion. This work provides quantitative insights into the solution behavior of conjugated polymers that can guide both the design and process of CPs toward next-generation organic electronics.

Parameterization of General Organic Polymers within the Open Force Field Framework

Polymer and chemically modified biopolymer systems present unique challenges to traditional molecular simulation preparation workflows. First, typical polymer and biomolecular input formats, such as Protein Data Bank (PDB) files, lack adequate chemical information needed for the parameterization of new chemistries. Second, polymers are typically too large for accurate partial charge generation methods. In this work, we employ direct chemical perception through the Open Force Field toolkit to create a flexible polymer simulation workflow for organic polymers, encompassing everything from biopolymers to soft materials. We propose and test a new input specification for monomer information that can, along with a 3D conformational geometry, parametrize and simulate most soft-material systems within the same workflow used for smaller ligands. The monomer format encompasses a subset of the SMIRKS substructure query language to uniquely identify chemical information and repeating charges in underspecified systems through matching atomic connectivity. This workflow is combined with several different approaches for automatic partial-charge generation for larger systems. As an initial proof of concept, a variety of diverse polymeric systems were parametrized with the Open Force Field toolkit, including functionalized proteins, DNA, homopolymers, cross-linked systems, and sugars. Additionally, shape properties and radial distribution functions were computed from molecular dynamics simulations of poly(ethylene glycol), polyacrylamide, and poly(N-isopropylacrylamide) homopolymers in aqueous solution and compared to previous simulation results in order to demonstrate a start-to-finish workflow for simulation and property prediction. We expect that these tools will greatly expedite the day-to-day computational research of soft-matter simulations and create a robust atomic-scale polymer specification in conjunction with existing polymer structural notations.

Exploring conformations of comb-like polymers with varying grafting density in dilute solutions

Comb-like polymers have shown potential as advanced materials for a diverse palette of applications due to the tunability of their polymer architecture. To date, however, it still remains a challenge to understand how the conformational properties of these polymers arise from the interplay of their architectural parameters. In this work, extensive simulations were performed using dissipative particle dynamics to investigate the effect of grafting density, backbone length, and sidechain length on the conformations of comb-like polymers immersed in a good solvent. To quantify the effect of these architectural parameters on polymer conformations, we computed the asphericity, radius of gyration, and backbone and sidechain end-to-end distances. Bond-bond correlation functions and effective Kuhn lengths were computed to quantify the topological stiffness induced by sidechain-sidechain interactions. Simulation results reveal that the effective Kuhn length increases as grafting density and sidechain length increase, in agreement with previous experimental and theoretical studies. This increase in stiffness results in comb-like polymers adopting extended conformations as grafting density and sidechain length increase. Simulation results regarding the radius of gyration of comb-like polymers as a function of grafting density are compared with scaling theory predictions based on a free energy proposed by Morozova and Lodge [ACS Macro Lett. 6, 1274-1279 (2017)] and scaling arguments by Tang et al. [Macromolecules 55, 8668-8675 (2022)].

Shock compression of semiflexible polymers

We employ molecular dynamics simulations to investigate the shock compression of linear semiflexible polymers. While the propagation velocity of a shock primarily depends on density, both chain rigidity and chain orientation significantly influence the shock width and the final temperature of the system. In general, the shock wave triggers molecular buckling in chains oriented perpendicular to the compression front. Following the passage of the front, the semiflexible chains buckle with a wavelength that decreases with the compression speed as λm ∼ up-0.2, and subsequent relaxation leads to a banana-like liquid crystal phase. In ordered systems with molecules oriented perpendicular to the compression front, the shock width increases by a factor of up to 10 compared to a similar isotropic system, resulting in enhanced shock energy absorption. These findings indicate that chain stiffness plays a critical role in the impact absorption properties of polymeric materials.

Multiscale modelling of chromatin 4D organization in SARS-CoV-2 infected cells

SARS-CoV-2 is able to re-structure chromatin organization and alters the epigenomic landscape of the host genome, though the mechanisms that produce such changes are still poorly understood. Here, we investigate with polymer physics chromatin re-organization of the host genome, in space and time upon SARS-CoV-2 viral infection. We show that re-structuring of A/B compartments is well explained by a re-modulation of intra-compartment homotypic affinities, which leads to the weakening of A-A interactions and enhances A-B mixing. At TAD level, re-arrangements are physically described by a general reduction of the loop extrusion activity coupled with an alteration of chromatin phase-separation properties, resulting in more intermingling between different TADs and spread in space of TADs themselves. In addition, the architecture of loci relevant to the antiviral interferon (IFN) response, such as DDX58 or IFIT, results more variable within the 3D single-molecule population of the infected model, suggesting that viral infection leads to a loss of chromatin structural specificity. Analysis of time trajectories of pairwise gene-enhancer and higher-order contacts reveals that such variability derives from a more fluctuating dynamics in infected case, suggesting that SARS-CoV-2 alters gene regulation by impacting the stability of the contact network in time. Overall, our study provides the first polymer-physics based 4D reconstruction of SARS-CoV-2 infected genome with mechanistic insights on the consequent gene mis-regulation.

Insights from molecular dynamics and DFT calculations into the interaction of 1,4-benzodiazepines with 2-hydroxypropyl-βCD in a theoretical study

This study delves into the interaction between benzodiazepine (BZD) drugs and 2-hydroxypropyl-β-cyclodextrin (2HPβCD), a cyclodextrin (CD) known to improve drug delivery and enhance therapeutic outcomes. We find that the 2HPβCD's atoms become more rigid in the presence of chlordiazepoxide (CDP), clonazepam (CLZ), and diazepam (DZM), whereas they become more flexible in the presence of nordazepam (NDM) and nitrazepam (NZP). We also investigated the structure of 2HPβCD and found that loading these drugs increases both the area and volume of the 2HPβCD cavity, making it more suitable for drug delivery. Moreover, this research found that all drugs exhibited negative values for the binding free energy, indicating thermodynamic favorability and improved solubility. The binding free energy order of the BZDs was consistent in both molecular dynamics and Monte Carlo methods, with CDP and DZM having the highest affinity for binding. We also analyzed the contribution of different interaction energies in binding between the carrier and the drugs and found that Van der Waals energy is the primary component. Our results indicate that the number of hydrogen bonds between 2HPβCD/water slightly decreases in the presence of BZDs, but the hydrogen bond's quality remains constant.

Phase behavior and dynamics in a colloid-polymer mixture under spherical confinement

From studies via molecular dynamics simulations, we report results on structure and dynamics in mixtures of active colloids and passive polymers that are confined inside a spherical container with a repulsive boundary. All interactions in the fully passive limit are chosen in such a way that in equilibrium coexistence between colloid-rich and polymer-rich phases occurs. For most part of the studies the chosen compositions give rise to Janus-like structure: nearly one side of the sphere is occupied by the colloids and the rest by the polymers. This partially wet situation mimics approximately a neutral wall in the fully passive scenario. Following the introduction of a velocity-aligning activity to the colloids, the shape of the polymer-rich domain changes to that of an ellipsoid, around the long axis of which the colloid-rich domain attains a macroscopic angular momentum. In the steady state, the orientation of this axis evolves via diffusion, magnitude of which depends upon the strength of activity, but only weakly.

Crumpling Defective Graphene Sheets

Upon crumpling, graphene sheets yield intriguing hierarchical structures with high resistance to compression and aggregation, garnering a great deal of attention in recent years for their remarkable potential in a variety of applications. Here, we aim to understand the effect of Stone-Wales (SW) defects, i.e., a typical topological defect of graphene, on the crumpling behavior of graphene sheets at a fundamental level. By employing atomistically informed coarse-grained molecular dynamics (CG-MD) simulations, we find that SW defects strongly influence the sheet conformation as manifested by the change in size scaling laws and weaken the self-adhesion of the sheet during the crumpling process. Remarkably, the analyses of the internal structures (i.e., local curvatures, stresses, and cross-section patterns) of crumpled graphene emphasize the enhanced mechanical heterogeneity and "glass-like" amorphous state elicited by SW defects. Our findings pave the way for understanding and exploring the tailored design of crumpled structure via defect engineering.

Coiling of semiflexible paramagnetic colloidal chains

Semiflexible filaments deform into a variety of configurations that dictate different phenomena manifesting at low Reynolds number. Harnessing the elasticity of these filaments to perform transport-related processes at the microfluidic scale requires structures that can be directly manipulated to attain controllable geometric features during their deformation. The configuration of semiflexible chains assembled from paramagnetic colloids can be readily controlled upon the application of external time-varying magnetic fields. In circularly rotating magnetic fields, these chains undergo coiling dynamics in which their ends close into loops that wrap inward, analogous to the curling of long nylon filaments under shear. The coiling is promising for the precise loading and targeted transport of small materials, however effective implementation requires an understanding of the role that field parameters and chain properties play on the coiling features. Here, we investigate the formation of coils in semiflexible paramagnetic chains using numerical simulations. We demonstrate that the size and shape of the initial coils are governed by the Mason and elastoviscous numbers, related to the field parameters and the chain bending stiffness. The size of the initial coil follows a nonmonotonic behavior with Mason number from which two regions are identified: (1) an elasticity-dependent nonlinear regime in which the coil size decreases with increasing field strength and for which loop shape tends to be circular, and (2) an elasticity-independent linear regime where the size increases with field strength and the shape become more elliptical. From the time scales associated to these regimes, we identify distinct coiling mechanisms for each case that relate the coiling dynamics to two other configurational dynamics of paramagnetic chains: wagging and folding behaviors.

The influence of molecular design on structure-property relationships of a supramolecular polymer prodrug

Supramolecular self-assemblies of hydrophilic macromolecules functionalized with hydrophobic, structure-directing components have long been used for drug delivery. In these systems, loading of poorly soluble compounds is typically achieved through physical encapsulation during or after formation of the supramolecular assembly, resulting in low encapsulation efficiencies and limited control over release kinetics, which are predominately governed by diffusion and carrier degradation. To overcome these limitations, amphiphilic prodrugs that leverage a hydrophobic drug as both the therapeutic and structure-directing component can be used to create supramolecular materials with higher loading and controlled-release kinetics using biodegradable or enzymatically cleavable linkers. Here, we report the design, synthesis, and characterization of a library of supramolecular polymer prodrugs based on poly(ethylene glycol) (PEG) and the proregenerative drug 1,4-dihydrophenonthrolin-4-one-3-carboxylic acid (DPCA). Structure-property relationships were elucidated through experimental characterization of prodrug behavior in both the wet and dry states using scattering techniques and electron microscopy and corroborated by coarse-grained modeling. Molecular architecture and the hydrophobic-to-hydrophilic ratio of PEG-DPCA conjugates strongly influenced their physical state in water, ranging from fully soluble to supramolecular spherical assemblies and nanofibers. Molecular design and supramolecular structure, in turn, were shown to dramatically alter hydrolytic and enzymatic release and cellular transport of DPCA. In addition to potentially expanding therapeutic options for DPCA through control of supramolecular assemblies, the design principles elaborated here may inform the development of other supramolecular prodrugs based on hydrophobic small-molecule compounds.

Unraveling the Role of Charge Patterning in the Micellar Structure of Sequence-Defined Amphiphilic Peptoid Oligomers by Molecular Dynamics Simulations

Electrostatic interactions play a significant role in regulating biological systems and have received increasing attention due to their usefulness in designing advanced stimulus-responsive materials. Polypeptoids are highly tunable N-substituted peptidomimetic polymers that lack backbone hydrogen bonding and chirality. Therefore, polypeptoids are suitable systems to study the effect of noncovalent interactions of substituents without complications of backbone intramolecular and intermolecular hydrogen bonding. In this study, all-atom molecular dynamics (MD) simulations were performed on micelles formed by a series of sequence-defined ionic polypeptoid block copolymers consisting of a hydrophobic segment and a hydrophilic segment in an aqueous solution. By combining the results from MD simulations and experimental small-angle neutron scattering data, further insights were gained into the internal structure of the formed polypeptoid micelles, which is not always directly accessible from experiments. In addition, information was gained into the physics of the noncovalent interactions responsible for the self-assembly of weakly charged polypeptoids in an aqueous solution. While the aggregation number is governed by electrostatic repulsion of the negatively charged carboxylate (COO^–) substituents on the polypeptoid chain within the micelle, MD simulations indicate that the position of the charge on singly charged chains mediates the shape of the micelle through the charge–dipole interactions between the COO^– substituent and the surrounding water. Therefore, the polypeptoid micelles formed from the single-charged series offer the possibility for tailorable micelle shapes. In contrast, the polypeptoid micelles formed from the triple-charged series are characterized by more pronounced electrostatic repulsion that competes with more significant charge–sodium interactions, making it difficult to predict the shape of the micelles. This work has helped further develop design principles for the shape and structure of self-assembled micelles by controlling the position of charged moieties on the backbone of polypeptoid block copolymers.

Temperature-Transferable Coarse-Grained Model for Poly(propylene oxide) to Study Thermo-Responsive Behavior of Triblock Copolymers

Thermo-responsive behavior of ethylene oxide (EO)-propylene oxide (PO) copolymers makes them suitable for many potential applications. Reproducing the origins of the tunable properties of EO-PO copolymers using coarse-grained (CG) models such as the MARTINI force field is critically important for building a better understanding of their behavior. In the present work, we have investigated the effects of coarse-graining on the water-polymer interaction across a temperature range. We compared the performance of different all-atom force fields to find the most appropriate one for the purpose of PO block parameterization in the MARTINI platform. We parameterized a CG temperature-dependent PO model based on the reproduction of the atomistic free energy of transfer of propylene oxide trimer from octane to water over a range of temperatures (20-60 °C) and compared the atomistic bond and angle distributions. Then, we used the model to study the effects of EO/PO ratio, molecular weight, and concentration on the thermo-responsive behavior of EO-PO copolymers in water. The results show an excellent agreement with experiments in different areas. Our temperature-dependent model reproduces (1) micellar phase above critical micelle temperature (CMT) and unimer phase below CMT for different Pluronics (a class of EO-PO triblock copolymers) spanning many EO/PO ratios and molecular weights; (2) spherical-to-rodlike micellar shape transition for Pluronics with 60 wt % of PO content or more; (3) diffusion coefficients for Pluronics with high PO content (P104 Pluronic with a PO mass of 3500 g mol^-1) across a broad range of temperatures; and (4) micelle core size and micelle diameter similar to experimental results. Overall, our model improves the temperature sensitivity of EO-PO copolymers of existing models significantly, particularly for copolymers that are dominated by PO agents.

Electrostatics Drive Oligomerization and Aggregation of Human Interferon Alpha-2a

Aggregation is a common phenomenon in the field of protein therapeutics and can lead to function loss or immunogenic patient responses. Two strategies are currently used to reduce aggregation: (1) finding a suitable formulation, which is labor-intensive and requires large protein quantities, or (2) engineering the protein, which requires extensive knowledge about the protein aggregation pathway. We present a biophysical characterization of the oligomerization and aggregation processes by Interferon alpha-2a (IFNα-2a), a protein drug with antiviral and immunomodulatory properties. This study combines experimental high throughput screening with detailed investigations by small-angle X-ray scattering and analytical ultracentrifugation. Metropolis Monte Carlo simulations are used to gain insight into the underlying intermolecular interactions. IFNα-2a forms soluble oligomers that are controlled by a fast pH and concentration-dependent equilibrium. Close to the isoelectric point of 6, IFNα-2a forms insoluble aggregates which can be prevented by adding salt. We show that monomer attraction is driven mainly by molecular anisotropic dipole–dipole interactions that increase with increasing pH. Repulsion is due to monopole–monopole interactions and depends on the charge of IFNα-2a. The study highlights how combining multiple methods helps to systematically dissect the molecular mechanisms driving oligomer formation and to design ultimately efficient strategies for preventing detrimental protein aggregation.

Quantitative analysis of neuronal mitochondrial movement reveals patterns resulting from neurotoxicity of rotenone and 6-hydroxydopamine

Alterations in mitochondrial dynamics, including their intracellular trafficking, are common early manifestations of neuronal degeneration. However, current methodologies used to study mitochondrial trafficking events rely on parameters that are primarily altered in later stages of neurodegeneration. Our objective was to establish a reliable applied statistical analysis to detect early alterations in neuronal mitochondrial trafficking. We propose a novel quantitative analysis of mitochondria trajectories based on innovative movement descriptors, including straightness, efficiency, anisotropy, and kurtosis. We evaluated time- and dose-dependent alterations in trajectory descriptors using biological data from differentiated SH-SY5Y cells treated with the mitochondrial toxicants 6-hydroxydopamine and rotenone. MitoTracker Red CMXRos-labelled mitochondria movement was analyzed by total internal reflection fluorescence microscopy followed by computational modelling to describe the process. Based on the aforementioned trajectory descriptors, this innovative analysis of mitochondria trajectories provides insights into mitochondrial movement characteristics and can be a consistent and sensitive method to detect alterations in mitochondrial trafficking occurring in the earliest time points of neurodegeneration.

Bottom-up coarse-grain modeling of plasticity and nanoscale shear bands in α-RDX

Computationally inexpensive particle-based coarse-grained (CG) models are essential for use in molecular dynamics (MD) simulations of mesoscopically slow cooperative phenomena, such as plastic deformations in solids. Molecular crystals possessing complex symmetry present enormous practical challenges for particle-based coarse-graining at molecularly resolved scales, when each molecule is in a single-site representation, and beyond. Presently, there is no published pairwise non-bonded single-site CG potential that is able to predict the space group and structure of a molecular crystal. In this paper, we present a successful coarse-graining at a molecular level from first principles of an energetic crystal, hexahydro-1,3,5-trinitro-s-triazine (RDX) in the alpha phase, using the force-matching-based multiscale coarse-graining (MSCG/FM) approach. The new MSCG/FM model, which implements an optimal pair decomposition of the crystal Helmholtz free energy potential in molecular center-of-mass coordinates, was obtained by force-matching atomistic MD simulations of liquid, amorphous, and crystalline states and in a wide range of pressures (up to 20 GPa). The MSCG/FM potentials for different pressures underwent top-down optimization to fine-tune the mechanical and thermodynamic properties, followed by consolidation into a transferable density-dependent model referred to as RDX-TC-DD (RDX True-Crystal Density-Dependent). The RDX-TC-DD model predicts accurately the crystal structure of α-RDX at room conditions and reproduces the atomistic reference system under isothermal (300 K) hydrostatic compression up to 20 GPa, in particular, the Pbca symmetry of α-RDX in the elastic regime. The RDX-TC-DD model was then used to simulate the plastic response of uniaxially ([100]) compressed α-RDX resulting in nanoscale shear banding, a key mechanism for plastic deformation and defect-free detonation initiation proposed for many molecular crystalline explosives. Additionally, a comparative analysis of the effect of core-softening of the RDX-TC-DD potential and the degree of molecular rigidity in the all-atom treatment suggests a stress-induced short-range softening of the effective intermolecular interaction as a fundamental cause of plastic instability in α-RDX. The reported RDX-TC-DD model and overall workflow to develop it open up possibilities to perform high quality simulation studies of molecular energetic materials under thermal and mechanical stimuli, including extreme conditions.

Armored Droplets as Soft Nanocarriers for Encapsulation and Release under Flow Conditions

Technical challenges in precision medicine and environmental remediation create an increasing demand for smart materials that can select and deliver a probe load to targets with high precision. In this context, soft nanomaterials have attracted considerable attention due to their ability to simultaneously adapt their morphology and functionality to complex ambients. Two major challenges are to precisely control this adaptability under dynamic conditions and provide predesigned functionalities that can be manipulated by external stimuli. Here, we report on the computational design of a distinctive class of soft nanocarriers, built from armored nanodroplets, able to selectively encapsulate or release a probe load under specific flow conditions. First, we describe in detail the mechanisms at play in the formation of pocket-like structures in armored nanodroplets and their stability under external flow. Then we use that knowledge to test the capacity of these pockets to yield flow-assisted encapsulation or expulsion of a probe load. Finally, the rheological properties of these nanocarriers are put into perspective with those of delivery systems employed in pharmaceutical and cosmetic technology.

Understanding the Role of Self-Adhesion in Crumpling Behaviors of Sheet Macromolecules

Understanding the crumpling behavior of two-dimensional (2D) macromolecular sheet materials is of fundamental importance in engineering and technological applications. Among the various properties of these sheets, interfacial adhesion critically contributes to the formation of crumpled structures. Here, we present a coarse-grained molecular dynamics (CG-MD) simulation study to explore the fundamental role of self-adhesion in the crumpling behaviors of macromolecular sheets having varying masses or sizes. By evaluating the potential energy evolution, our results show that the self-adhesion plays a dominant role in the crumpling behavior of the sheets compared to in-plane and out-of-plane stiffnesses. The macromolecular sheets with higher adhesion tend to form a self-folding planar structure at the quasi-equilibrium state of the crumpling and exhibit a lower packing efficiency as evaluated by the fractal dimension of the system. Notably, during the crumpling process, both the radius of gyration R_g and the hydrodynamic radius R_h of the macromolecular sheet can be quantitatively described by the power-law scaling relationships associated with adhesion. The evaluation of the shape descriptors indicates that the overall crumpling behavior of macromolecular sheets can be characterized by three regimes, i.e., the less bent, intermediate, and highly crumpled regimes, dominated by edge-bending, self-adhesion, and further compression, respectively. The internal structural analysis further reveals that the sheet transforms from the initially ordered state to the disordered glassy state upon crumpling, which can be facilitated by greater self-adhesion. Our study provides fundamental insights into the adhesion-dependent structural behavior of macromolecular sheets under crumpling, which is essential for establishing the structure-processing-property relationships for crumpled macromolecular sheets.

Molecular Dynamics Simulations of Nanostructures Formed by Hydrophobins and Oil in Seawater

Classical molecular dynamics simulations using the Martini coarse-grained force field were performed to study oil nanodroplets surrounded by fungal hydrophobin (HP) proteins in seawater. The class I EAS and the class II HFBII HPs were studied along with two model oils, namely, benzene and n-decane. Both HPs exhibit free energy minima at the oil-seawater interface, which is deeper in benzene compared to the n-decane systems. Larger constraint forces are required to keep both HPs within the n-decane phase compared to inside benzene, with HFBII being more affine to benzene compared to EAS. Smaller surface tensions are observed at benzene-seawater interfaces coated with HPs compared to their n-decane counterparts. In the latter the surface tension remains unchanged upon increases in the concentration of HPs, whereas in benzene systems adding more HPs lead to decreases in surface tension. EAS has a larger tendency to cluster together in the interface compared to HFBII, with both HPs having larger coordination numbers when surrounding benzene droplets compared to when they are around n-decane nanoblobs. The HP-oil nanostructures in seawater examined have radii of gyration ranging between 2 and 12 nm, where the n-decane structures are larger and have more irregular shapes compared to the benzene systems. The n-decane molecules within the nanostructures form a compact spherical core, with the HPs partially covering its surface and clustering together, conferring irregular shapes to the nanostructures. The EAS with n-decane structures are larger and have more irregular shapes compared to their HFBII counterparts. In contrast, in the HP-benzene structures both HPs tend to penetrate the oil part of the droplet. The HFBII-benzene structures having the larger oil/HP ratios examined tend to be more compact and spherical compared to their EAS counterparts; however, some of the HFBII-benzene systems that have smaller oil/HP ratios have a more elongated structure compared to their EAS counterparts. This simulation study provides insights into HP-oil nanostructures that are smaller than the oil droplets and gas bubbles recently studied in experiments and, thus, might be challenging to examine with experimental techniques.

Crowding-induced interactions of ring polymers

Macromolecular crowding and the presence of surfaces can significantly impact the spatial organization of biopolymers. While the importance of crowding-induced depletion interactions in biology has been recognized, much remains to be understood about the effect of crowding on biopolymers such as DNA plasmids. A fundamental problem highlighted by recent experiments is to characterize the impact of crowding on polymer-polymer and polymer-surface interactions. Motivated by the need for quantitative insight, we studied flexible ring polymers in crowded environments using Langevin dynamics simulations. The simulations demonstrated that crowding can lead to compaction of isolated ring polymers and enhanced interactions between two otherwise repulsive polymers. Using umbrella sampling, we determined the potential of mean force (PMF) between two ring polymers as a function of their separation distance at different volume fractions of crowding particles, φ. An effective attraction emerged at φ≈ 0.4, which is similar to the degree of crowding in cells. Analogous simulations showed that crowding can lead to strong adsorption of a ring polymer to a wall, with an effective attraction to the wall emerging at a smaller volume fraction of crowders (φ≈ 0.2). Our results reveal the magnitude of depletion interactions in a biologically-inspired model and highlight how crowding can be used to tune interactions in both cellular and cell-free systems.

Using nickel to fold discrete synthetic macromolecules into single-chain nanoparticles

Sequence-defined macromolecules were prepared with a thiolactone-based platform whereby ligand functionalities were introduced along the backbone enabling a nickel induced formation of single-chain nanoparticles.

Probing the potential of ureasil-poly(ethylene oxide) as a glyphosate scavenger in aqueous milieu: force-field parameterization and MD simulations

The intensive use of glyphosate in conventional agriculture and its high solubility in water have led to contamination of aqueous systems worldwide.

Designing Surface Charge Patterns for Shape Control of Deformable Nanoparticles

Designing reconfigurable materials based on deformable nanoparticles (NPs) hinges on an understanding of the energetically favored shapes these NPs can adopt. Using simulations, we show that hollow, deformable, patchy NPs tailored with surface charge patterns such as Janus patches, stripes, and polyhedrally distributed patches differently adapt their shape in response to changes in patterns and ionic strength, transforming into capsules, hemispheres, variably dimpled bowls, and polyhedra. The links between anisotropy in NP surface charge, shape, and the elastic energy density are discussed.

Kinetically-arrested single-polymer nanostructures from amphiphilic mikto-grafted bottlebrushes in solution: a simulation study

Solution self-assembly of molecular bottlebrushes offers a rich platform to create complex functional organic nanostructures. Recently, it has become evident that kinetics, not just thermodynamics, plays an important role in defining the self-assembled structures that can be formed. In this work, we present results from extensive molecular dynamics simulations that explore the self-assembly behavior of mikto-grafted bottlebrushes when the solvent quality for one of the side blocks is changed by a rapid quench. We have performed a systematic study of the effect of different structural parameters and the degree of incompatibility between side chains on the final self-assembled nanostructures in the low concentration limit. We found that kinetically-trapped complex nanostructures are prevalent as the number of macromonomers increases. We performed a quantitative analysis of the self-assembled morphologies by computing the radius of gyration tensor and relative shape anisotropy as the different relevant parameters were varied. Our results are summarized in terms of non-equilibrium morphology diagrams.

Phase behavior of AB/CD diblock copolymer blends via coarse-grained simulation

The phase diagram of equimolar blends of AB and CD diblock copolymers has been studied using dissipative particle dynamics. All unlike blocks interacted with the same χ, except for the B-C interaction, for which χ_BC < 0 in order to prevent macrophase separation. The BC interaction was able to prevent macrophase separation except for low volume fractions of B and C (φ_BC⪅ 0.1) and relatively equal fractions of A and D. For high φ_BC (φ_BC⪆ 0.92), a disordered state was obtained. For all microphase separated states the shapes/morphologies were described by the ratios of the eigenvalues of the radius of gyration tensor and their sphericity. These were used to classify the domains as forming sphere, cylinders, lamellae, or branched/gyroidal structures. For φ_BC < 0.5 the BC domains acted as an interfacial region which compatibilized the A and D domains, while for φ_BC > 0.5 the BC domain filled in the space between A and D domains. Several interesting structures were formed including a novel connected/branched spheres morphology, hierarchical lamellae, concentric spheres/cylinders, and a combination of cylinders/lamellae. Comparisons are made with the linear diblock and linear triblock phase diagrams.

Replica exchange molecular dynamics simulation of the coordination of Pt(ii)-Phenanthroline to amyloid-β

We report replica exchange molecular dynamics (REMD) simulations of the complex formed between amyloid-β peptides and platinum bound to a phenanthroline ligand, Pt(phen). After construction of an AMBER-style forcefield for the Pt complex, REMD simulation employing temperatures between 270 and 615 K was used to provide thorough sampling of the conformational freedom available to the peptide. We find that the full length peptide Aβ42, in particular, frequently adopts a compact conformation with a large proportion of α- and 3,10-helix content, with smaller amounts of β-strand in the C-terminal region of the peptide. Helical structures are more prevalent than in the metal-free peptide, while turn and strand conformations are markedly less common. Non-covalent interactions, including salt-bridges, hydrogen bonds, and π-stacking between aromatic residues and the phenanthroline ligand, are common, and markedly different from those seen in the amyloid-β peptides alone.

Hydration of diblock copolymer micelles: Effects of hydrophobicity and co-solvent

Diblock polymer micelles dispersed in an aqueous environment are being actively investigated for various applications, but there is only a qualitative understanding of the effect of the chemical structure on the micelle hydration and water dynamics as these properties are difficult to assess experimentally. Using all-atom molecular dynamics simulations, we investigate aqueous solutions of three comparable in size diblock copolymer micelles with core-forming blocks of different hydrophobicity: polybutadiene (PB), polycaprolactone (PCL), and polytetrahydrofuran (pTHF) with the same hydrophilic block, polyethylene oxide (PEO). We found that core-block hydrophobicity and ability to form hydrogen bonds with water strongly affect the water dynamics near the core: water molecules spend considerably less time in contact with the PB block than with PCL and pTHF blocks. We obtained polymer and solvent volume fraction profiles and determined that the interfacial width systematically increases with a decrease of core block hydrophobicity with water penetration into the core being negligible for PB-PEO and PCL-PEO micelles, while for pTHF-PEO micelles the interface is more diffuse and there is a noticeable penetration of water (17% by volume). For PCL-PEO micelles, which are commonly used in biomedical applications, we also investigated tetrahydrofuran (THF) penetration into the micelles from mixed THF:water solution at early stages of micelle dissolution. We found an inhomogeneous solvent distribution with a maximum of THF volume fraction in the interfacial core-corona region and partial exclusion from the PEO corona, which slows down micelle dissolution. These results can have important implications for micelle stability and use in biomedical applications.

Molecular Modeling of Complex Cross-Linked Networks of PEGDA Nanogels

Poly(ethylene glycol) (PEG)-based nanogels are attractive for biomedical applications due to their biocompatibility, versatile end group chemistry, and ability to sterically shield encapsulated drug molecules. The characteristics of a hydrogel network govern the encapsulation and efficient delivery of drug molecules for a target application. A molecular-level description of network topology can complement experimental investigations to understand its effects on the structural properties of these nanogels. In this work, atomistic molecular simulations of heterogeneous, nonideal PEG-diacrylate (PEGDA) nanogels are presented. The effects of cross-linking density and topological features on the structural properties of PEGDA nanogels were studied. The average functionality was controlled to systematically study the effect of cross-linking density on the radius of gyration, shape, and mesh size of the nanogels. For a given average functionality, the impact of distinct network topologies on the structural properties was also studied. The aspect ratios, based on the gyration tensor, were calculated to characterize the shapes of these nanogels for different topologies. Nanogel structures with higher cross-linking densities showed a globular shape, while structures with lower cross-linking density showed shape anisotropy. The distribution and connectivity of the cross-linked junctions played a key role in determining the size and shape anisotropy of PEGDA nanogels; the number of unreacted chain ends and their connectivity directly affected the anisotropy. The mesh size, denoted by the limiting "free volume element" present in the nanogel samples, does not show a significant change with increasing average functionality. This work provides insight into the structural properties of heterogeneous hydrogels that aid the design of nonideal nanogel networks for a targeted drug delivery application.

Aggregation Behavior of Model Asphaltenes Revealed from Large-Scale Coarse-Grained Molecular Simulations

Fully atomistic simulations of models of asphaltenes in simple solvents have allowed the study of trends in aggregation phenomena to understand the underlying role played by molecular structure. The detail included at this scale of molecular modeling is, however, at odds with the required spatial and temporal resolution needed to fully understand asphaltene aggregation. The computational cost required to explore the relevant scales can be reduced by employing coarse-grained (CG) models, which consist of lumping a few atoms into a single segment that is characterized by effective interactions. In this work, CG force fields developed via the statistical associating fluid theory (SAFT-γ) [ Müller , E. A. ; Jackson , G. Annu. Rev. Chem. Biomol. Eng. 5 , 2014 , 405 - 427 ] equation of state (EoS) provide a reliable pathway to link the molecular description with macroscopic thermophysical data. A recent modification of the SAFT-VR EoS [ Müller , E. A. ; Mejía , A. Langmuir 33 , 2017 , 11518 - 11529 ], which allows for the parameterization of homonuclear rings, is selected as the starting point to develop CG models for polycyclic aromatic hydrocarbons. The new aromatic-core models, along with others published for simpler organic molecules, are adopted for the construction of asphaltene models by combining different chemical moieties in a group-contribution fashion. We apply the procedure to two previously reported asphaltene models and perform molecular dynamics simulations to validate the coarse-grained representation against benchmark systems of 27 asphaltenes in a pure solvent (toluene or heptane) described in a fully atomistic fashion. An excellent match between both levels of description is observed for the cluster size, radii of gyration, and relative-shape-anisotropy-factor distributions. We exploit the advantages of the CG representation by simulating systems containing up to 2000 asphaltene molecules in an explicit solvent investigating the effect of asphaltene concentration, solvent composition, and temperature on aggregation. By studying large systems facilitated by the use of CG models, we observe stable continuous distributions of molecular aggregates at conditions away from the two-phase precipitation point. As a further example application, a widely accepted interpretation of cluster-size distributions in asphaltenic systems is challenged by performing system-size tests, reversibility checks, and a time-dependence analysis. The proposed coarse-graining procedure is seen to be general and predictive and, hence, can be applied to other asphaltenic molecular structures.

Physicochemical Response of Gelatin in a Coulombic Soup of Monovalent Salt: A Molecular Simulation and Experimental Study

The effect of salt on the static properties of aqueous solution of gelatin is studied by molecular dynamics simulation at pH = 1.2, 7, and 10. At the isoelectric point (pH = 7), a monotonic increase in size of the polymer is obtained with the addition of sodium chloride ions. In the positive polyelectrolyte regime (pH = 1.2), collapse of gelatin is observed with increase in salt concentration. In the negative polyelectrolyte regime, we observe an interesting collapse-reexpansion behavior. This is due to the screening of repulsion between the excess charges followed by the screening of attraction of oppositely charged ions as the salt concentration is increased. This mechanism is very different from the charge inversion mechanism which causes the reexpansion in the presence of multivalent ions. The location of salt concentration corresponding to the minimum size of the chain is comparable to the theoretical estimate. The shift in the peak of radial distribution function calculated between monomers and salt ions confirms this spatial reorganization. The predictions from the simulation are verified by dynamic light scattering(DLS) and small-angle X-ray scattering (SAXS) experiments. The size of the hydrodynamic "clusters" obtained from DLS confirms the simulation predictions. Persistence length of the gelatin is calculated from SAXS to get single chain statistics, which also agrees well with the simulation results.

Two-dimensional Monte Carlo simulations of coarse-grained poly(3-hexylthiophene) (P3HT) adsorbed on striped substrates

We investigate the structural phases of single poly(3-hexylthiophene) (P3HT) polymers that are adsorbed on a two-dimensional substrate with a striped pattern. We use a coarse-grained representation of the polymer and sophisticated Monte Carlo techniques such as a parallelized replica exchange scheme and local as well as non-local updates to the polymer's configuration. From peaks in the canonically derived observables, it is possible to obtain structural phase diagrams for varying substrate parameters. We find that the shape of the stripe pattern has a substantial effect on the obtained configurations of the polymer and can be tailored to promote either more stretched out or more compact configurations. In the compact phases, we observe different structural motifs, such as hairpins, double-hairpins, and interlocking "zipper" states.

Asphaltene Mesoscale Aggregation Behavior in Organic Solvents-A Brownian Dynamics Study

Significant advances have been achieved in understanding the main molecular mechanisms leading to asphaltene aggregation. However, the existing computational deficiency of molecular dynamics simulations did not allow full reproduction of the complex aggregation behavior of asphaltene in the past. In this work, we use the Brownian dynamics simulation to investigate asphaltene aggregation behavior on larger length and time scales that have not been previously accessed by molecular simulations. This enabled us to completely render the formation of clusters of asphaltene nanoaggregates and the resulting fractal or network of aggregates during the aggregation process. Asphaltene aggregation is studied at several volume fractions (ϕ = 1-7%) of asphaltene nanoaggregates in two solvents including heptane and heptol (i.e., a mixture of heptane and toluene). Our simulation results support the aggregation hierarchy proposed in the Yen-Mullins model (Mullins, Annu. Rev. Anal. Chem. 2011, 4, 393-418.) by demonstrating that asphaltene nanoaggregates form small clusters with an aggregation number of 7-8 and an average gyration radius of ∼4.0 nm capable of forming either fractal aggregates with a fractal dimension of 1.93-2.04 at low ϕ or percolating networks of aggregates at high ϕ. Percolating structures are observed at ϕ = 7% in both solvents. In heptol, the structures mainly percolate along two directions, whereas in heptane, they can percolate along three directions (i.e., x, y, and z). The self-diffusion coefficient ( D) significantly decreases as ϕ increases. Generally, D is larger in heptol than in heptane, but this difference diminishes as ϕ increases, approaching to almost the same value at ϕ = 7%.