A Coarse-Grained Model of Stratum Corneum Lipids: Free Fatty Acids and Ceramide NS

Representing Structural Isomer Effects in a Coarse-Grain Model of Poly(Ether Ketone Ketone)

Carbon-fiber composites with thermoplastic matrices offer many processing and performance benefits in aerospace applications, but the long relaxation times of polymers make it difficult to predict how the structure of the matrix depends on its chemistry and how it was processed. Coarse-grained models of polymers can enable access to these long-time dynamics, but can have limited applicability outside the systems and state points that they are validated against. Here we develop and validate a minimal coarse-grained model of the aerospace thermoplastic poly(etherketoneketone) (PEKK). We use multistate iterative Boltzmann inversion to learn potentials with transferability across thermodynamic states relevant to PEKK processing. We introduce tabulated EKK angle potentials to represent the ratio of terephthalic (T) and isophthalic (I) acid precursor amounts, and validate against rheological experiments: The glass transition temperature is independent to T/I, but chain relaxation and melting temperature is. In sum we demonstrate a simple, validated model of PEKK that offers 15× performance speedups over united atom representations that enables studying thermoplastic processing-structure-property-performance relationships.

Molecular dynamics simulations of lipid composition and its impact on structural and dynamic properties of skin membrane

The stratum corneum (SC) plays the most important role in the absorption of topical and transdermal drugs. In this study, we developed a multi-layered SC model using coarse-grained molecular dynamics (CGMD) simulations of ceramides, cholesterol, and fatty acids in equimolar proportions, starting from two different initial configurations. In the first approach, all ceramide molecules were initially in the hairpin conformation, and the membrane bilayers were pre-formed. In the second approach, ceramide molecules were introduced in either the hairpin or splayed conformation, with the lipid molecules randomly oriented at the start of the simulation. The aim was to evaluate the effects of lipid chain length on the structural and dynamic properties of SC. By incorporating ceramides and fatty acids of different chain lengths, we simulated the SC membrane in healthy and diseased states. We calculated key structural properties including the thickness, normalized lipid area, lipid tail order parameters, and spatial ordering of the lipids from each system. The results showed that systems with higher ordering and structural integrity contained an equimolar ratio of ceramides (chain length of 24 carbon atoms), fatty acids with chain lengths ≥ of 20 carbon atoms, and cholesterol. In these systems, strong apolar interactions between the ceramide and fatty acid long acyl chains restricted the mobility of the lipid molecules, thereby maintaining a compact lipid headgroup region and high order in the lipid tail region. The simulations also revealed distinct flip-flop mechanisms for cholesterol and fatty acid within the multi-layered membrane. Cholesterol is mostly diffused through the tail-tail interface region of the membrane and could flip-flop in the same bilayer. In contrast, fatty acids flip-flopped between adjacent leaflets of two bilayers in which the tails crossed the thinner headgroup region of the membrane. To conclude, our SC model provides mechanistic insights into lipid mobility and is flexible in its design and composition of different lipids, enabling studies of varying skin conditions.

The phase behavior of skin-barrier lipids: A combined approach of experiments and simulations

Skin barrier function is localized in its outermost layer, the stratum corneum (SC), which is comprised of corneocyte cells embedded in an extracellular lipid matrix containing ceramides (CERs), cholesterol (CHOL), and free fatty acids (FFAs). The unique structure and composition of this lipid matrix are important for skin barrier function. In this study, experiments and molecular dynamics simulation were combined to investigate the structural properties and phase behavior of mixtures containing nonhydroxy sphingosine CER (CER NS), CHOL, and FFA. X-ray scattering for mixtures with varying CHOL levels revealed the presence of the 5.4 nm short periodicity phase in the presence of CHOL. Bilayers in coarse-grained multilayer simulations of the same compositions contained domains with thicknesses of approximately 5.3 and 5.8 nm that are associated with elevated levels, respectively, of CER sphingosine chains with CHOL, and CER acyl chains with FFA chains. The prevalence of the thicker domain increased with decreasing CHOL content. This might correspond to a phase with ∼5.8 nm spacing observed by x-rays (other details unknown) in mixtures with lower CHOL content. Scissoring and stretching frequencies from Fourier transform infrared spectroscopy (FTIR) also indicate interaction between FFA and CER acyl chains and little interaction between CER acyl and CER sphingosine chains, which requires CER molecules to adopt a predominantly extended conformation. In the simulated systems, neighbor preferences of extended CER chains align more closely with the FTIR observations than those of CERs with hairpin ceramide chains. Both FTIR and atomistic simulations of reverse mapped multilayer membranes detect a hexagonal to fluid phase transition between 65 and 80°C. These results demonstrate the utility of a collaborative experimental and simulation effort in gaining a more comprehensive understanding of SC lipid membranes.

The Sphingosine and Phytosphingosine Ceramide Ratio in Lipid Models Forming the Short Periodicity Phase: An Experimental and Molecular Simulation Study

The lipids located in the outermost layer of the skin, the stratum corneum (SC), play a crucial role in maintaining the skin barrier function. The primary components of the SC lipid matrix are ceramides (CERs), cholesterol (CHOL), and free fatty acids (FFAs). They form two crystalline lamellar phases: the long periodicity phase (LPP) and the short periodicity phase (SPP). In inflammatory skin conditions like atopic dermatitis and psoriasis, there are changes in the SC CER composition, such as an increased concentration of a sphingosine-based CER (CER NS) and a reduced concentration of a phytosphingosine-based CER (CER NP). In the present study, a lipid model was created exclusively forming the SPP, to examine whether alterations in the CER NS:CER NP molar ratio would affect the lipid organization. Experimental data were combined with molecular dynamics simulations of lipid models containing CER NS:CER NP at ratios of 1:2 (mimicking a healthy SC ratio) and 2:1 (observed in inflammatory skin diseases), mixed with CHOL and lignoceric acid as the FFA. The experimental findings show that the acyl chains of CER NS and CER NP and the FFA are in close proximity within the SPP unit cell, indicating that CER NS and CER NP adopt a linear conformation, similarly as observed for the LPP. Both the experiments and simulations indicate that the lamellar organization is the same for the two CER NS:CER NP ratios while the SPP NS:NP 1:2 model had a slightly denser hydrogen bonding network than the SPP NS:NP 2:1 model. The simulations show that this might be attributed to intermolecular hydrogen bonding with the additional hydroxide group on the headgroup of CER NP compared with CER NS.

Derived Coarse-Grained Potentials for Semicrystalline Polymers with a Blended Multistate Iterative Boltzmann Inversion Method

In this article, we employ the multistate iterative Boltzmann inversion (MS-IBI) method to develop coarse-grained potentials capable of representing molecular structure in both the amorphous and crystalline phases of semicrystalline polymers with improved accuracy while allowing for tunable control over the dynamics governing the α-relaxation process. A unique feature of this method is that the potentials are blended using the product of the target structural distributions, for example, the radial density function, for each phase and a weighting factor. To demonstrate this approach, a family of potentials for polyethylene is developed where the weighting factor of the crystalline phase ranges is varied from zero, incorporating information only from the amorphous phase, to unity, where the model is trained from only the crystalline phase. The most accurate representation of structural distributions was obtained when the crystalline phases is weighted at 50%. However, we show that when the crystalline phase is weighted at 90%, the model more accurately represents dynamics of the α-relaxation process, with realistic predicted values of activation energy and diffusion rates, with relatively minor impact on accuracy in structure.

[Research progress of coarse-grained molecular dynamics in drug carrier materials]

As one of the traditional computer simulation techniques, molecular simulation can intuitively display and quantify molecular structure and explain experimental phenomena from the microscopic molecular level. When the simulation system increases, the amount of calculation will also increase, which will cause a great burden on the simulation system. Coarse-grained molecular dynamics is a method of mesoscopic molecular simulation, which can simplify the molecular structure and improve computational efficiency, as a result, coarse-grained molecular dynamics is often used when simulating macromolecular systems such as drug carrier materials. In this article, we reviewed the recent research results of using coarse-grained molecular dynamics to simulate drug carriers, in order to provide a reference for future pharmaceutical preparation research and accelerate the entry of drug research into the era of precision drug design.

Using molecular simulation to understand the skin barrier

Skin's effectiveness as a barrier to permeation of water and other chemicals rests almost entirely in the outermost layer of the epidermis, the stratum corneum (SC), which consists of layers of corneocytes surrounded by highly organized lipid lamellae. As the only continuous path through the SC, transdermal permeation necessarily involves diffusion through these lipid layers. The role of the SC as a protective barrier is supported by its exceptional lipid composition consisting of ceramides (CERs), cholesterol (CHOL), and free fatty acids (FFAs) and the complete absence of phospholipids, which are present in most biological membranes. Molecular simulation, which provides molecular level detail of lipid configurations that can be connected with barrier function, has become a popular tool for studying SC lipid systems. We review this ever-increasing body of literature with the goals of (1) enabling the experimental skin community to understand, interpret and use the information generated from the simulations, (2) providing simulation experts with a solid background in the chemistry of SC lipids including the composition, structure and organization, and barrier function, and (3) presenting a state of the art picture of the field of SC lipid simulations, highlighting the difficulties and best practices for studying these systems, to encourage the generation of robust reproducible studies in the future. This review describes molecular simulation methodology and then critically examines results derived from simulations using atomistic and then coarse-grained models.

Multiscale Simulation of Ternary Stratum Corneum Lipid Mixtures: Effects of Cholesterol Composition

Molecular dynamics simulations of mixtures of the ceramide nonhydroxy-sphingosine (NS), cholesterol, and a free fatty acid are performed to gain molecular-level understanding of the structure of the lipids found in the stratum corneum layer of skin. A new coarse-grained force field for cholesterol was developed using the multistate iterative Boltzmann inversion (MS-IBI) method. The coarse-grained cholesterol force field is compatible with previously developed coarse-grained force fields for ceramide NS, free fatty acids, and water and validated against atomistic simulations of these lipids using the CHARMM force field. Self-assembly simulations of multilayer structures using these coarse-grained force fields are performed, revealing that a large fraction of the ceramides adopt extended conformations, which cannot occur in the single bilayer in water structures typically studied using molecular simulation. Cholesterol fluidizes the membrane by promoting packing defects, and an increase in cholesterol content is found to reduce the bilayer thickness due to an increase in interdigitation of the C₂₄ lipid tails, consistent with experimental observations. Using a reverse-mapping procedure, a self-assembled coarse-grained multilayer system is used to construct an equivalent structure with atomistic resolution. Simulations of this atomistic structure are found to closely agree with experimentally derived neutron scattering length density profiles. Significant interlayer hydrogen bonding is observed in the inner layers of the atomistic multilayer structure that are not found in the outer layers in contact with water or in equivalent bilayer structures. This work highlights the importance of simulating multilayer structures, as compared to the more commonly studied bilayer systems, to enable more appropriate comparisons with multilayer experimental membranes. These results also provide validation of the efficacy of the MS-IBI derived coarse-grained force fields and the framework for multiscale simulation.

Molecular Dynamics Simulations of Micelle Properties and Behaviors of Sodium Lauryl Ether Sulfate Penetrating Ceramide and Phospholipid Bilayers

Molecular dynamics (MD) simulations with the umbrella sampling (US) method were used to investigate the properties of micelles formed by sodium lauryl ether sulfate with two ether groups (SLE2S) and behaviors of corresponding surfactants transferring from micelles to ceramide and DMPC bilayer surfaces. Average micelle radii based on the Einstein-Smoluchowski and Stokes-Einstein relations showed excellent agreement with those measured by dynamic light scattering, while those obtained by evaluating the gyration radius or calculating the distance between the micelle sulfur atoms and center of mass overestimate the radii. As an SLE2S micelle was pulled down to the ceramide bilayer surface in a 400 ns constant-force steered MD (cf-SMD) simulation, the micelle was partially deformed on the bilayer surface, and several SLE2S surfactants easily were partitioned from the micelle into the ceramide bilayer. In contrast, a micelle was not deformed on the DMPC bilayer surface, and SLE2S surfactants were not transferred from the micelle to the DMPC bilayer. Potential of mean force (PMF) calculations revealed that the Gibbs free energy required for an SLE2S surfactant monomer to transfer from a micelle to bulk water can be compensated by decreased Gibbs free energy when an SLE2S monomer transfers into the ceramide bilayer from bulk water. In addition, micelle deformation on the ceramide bilayer surface can reduce the Gibbs free energy barrier required for a surfactant to escape the micelle and help the surfactant partition from the micelle into the ceramide bilayer. An SLE2S surfactant partitioning into the ceramide bilayer is attributed to hydrogen bonding and favorable interactions between the hydrophilic surfactant head and ceramide molecules, which are more dominant than the dehydration penalty during bilayer insertion. Such interactions between surfactant and lipid molecule heads are considerably reduced in DMPC bilayers owing to dielectric screening by water molecules deep inside the head/tail boundary between the DMPC bilayer. This computational work demonstrates the distinct behavior of SLE2S surfactant micelles on ceramide and DMPC bilayer surfaces in terms of variation in Gibbs free energy, which offers insight into designing surfactants used in transdermal drug delivery systems and cosmetics.

Development and application of coarse-grained MARTINI model of skin lipid ceramide [AP]

Stratum corneum (SC), the outermost layer of the skin, contains large variety of lipids, endowing them with the amphiphilic properties, needed to fulfil their key role in skin's barrier function. The individual role of lipid types in the barrier function is difficult to understand due to the immense heterogeneity and complexity of the lipid's organization within the SC. The lipid organization is being explored using both computational (molecular dynamics simulations) and experimental (neutron diffraction) techniques. Even though atomistic simulations provide unprecedented atomic level details, the major limitation is time and length scale that can be achieved with decent computational facility. Alternatively, coarse-grain (CG) models are currently being used to capture physics at bigger time and length scale without losing essential underlined structural information. In this study, a CG model of α-hydroxy phytosphingosines (CER[AP]) is developed based on philosophy of MARTINI force field. At first, the model is validated with various atomistic simulations and available experimental data. Later on, the model's compatibility with other major skin lipids, cholesterol, and free fatty acid (palmitic acid) is checked by simulating a mixture of lipid multilayer in presence and absence of water. The developed model of CER[AP] is able to predict key structural properties within the acceptable error limits. The phenomena of ceramide conformation transformation, cholesterol flip-flop, and specificity of lipid arrangement within the multilayered systems is observed during the simulation. This signifies the importance of model in capturing higher order structural transformations.

Coarse-graining of polyisoprene melts using inverse Monte Carlo and local density potentials

Bottom-up coarse-graining of polymers is commonly performed by matching structural order parameters such as distribution of bond lengths, bending and dihedral angles, and pair distribution functions. In this study, we introduce the distribution of nearest-neighbors as an additional order parameter in the concept of local density potentials. We describe how the inverse-Monte Carlo method provides a framework for forcefield development that is capable of overcoming challenges associated with the parameterization of interaction terms in polymer systems. The technique is applied on polyisoprene melts as a prototype system. We demonstrate that while different forcefields can be developed that perform equally in terms of matching target distributions, the inclusion of nearest-neighbors provides a straightforward route to match both thermodynamic and conformational properties. We find that several temperature state points can also be addressed, provided that the forcefield is refined accordingly. Finally, we examine both the single-particle and the collective dynamics of the coarse-grain models, demonstrating that all forcefields present a similar acceleration relative to the atomistic systems.

Coarse-grained molecular dynamics simulations of the effect of edge activators on the skin permeation behavior of transfersomes

Transfersomes (TRS) can provide sustained drug delivery and themselves are biocompatible, biodegradable and nontoxic. Edge activators (EAs) are key factors for increasing the deformability of TRS, and this active deformation mechanism is of commercial interest, especially at the molecular level. Accordingly, in this paper, the deformability of pure dipalmitoyl phosphatidylcholine (DPPC) vesicles, TRS with sodium cholate as an EA, and DPPC vesicles containing pogostone (POG) were compared via umbrella sampling technology. The DPPC conformation and membrane fluidity of these three types of bilayer systems were evaluated, and the changes in the membrane properties of vesicles caused by EAs were studied. EAs could increase the deformability of TRS by decreasing the deformation energy barrier due to their amphiphilic structures, which was similar to those of DPPC molecules. The membrane properties also changed via treatment with EAs including altering the tail chain angle, disturbing the ordered tail chain arrangement and prompting lateral diffusion of DPPC molecules. In addition, the impact of EAs on DPPC bilayers was further demonstrated to be concentration dependent. An ideal concentration was identified for the lowest amount of EA that offered a gel-liquid-crystalline phase transition of DPPC bilayers. Importantly, POG, a lipophobic transdermal drug, can also affect the skin permeation behavior of vesicles but had weaker effects than EA.

A Transferable, Multi-Resolution Coarse-Grained Model for Amorphous Silica Nanoparticles

Despite the ubiquity of nanoparticles in modern materials research, computational scientists are often forced to choose between simulations featuring detailed models of only a few nanoparticles or simplified models with many nanoparticles. Herein, we present a coarse-grained model for amorphous silica nanoparticles with parameters derived via potential matching to atomistic nanoparticle data, thus enabling large-scale simulations of realistic models of silica nanoparticles. Interaction parameters are optimized to match a range of nanoparticle diameters in order to increase transferability with nanoparticle size. Analytical functions are determined such that interaction parameters can be obtained for nanoparticles with arbitrary coarse-grained fidelity. The procedure is shown to be extensible to the derivation of cross-interaction parameters between coarse-grained nanoparticles and other moieties and validated for systems of grafted nanoparticles. The optimization procedure used is available as an open-source Python package and should be readily extensible to models of non-silica nanoparticles.

Assessing the transferability of common top-down and bottom-up coarse-grained molecular models for molecular mixtures

Assessing the performance of top-down and bottom-up coarse-graining approaches.

Mechanisms of lipid extraction from skin lipid bilayers by sebum triglycerides

Microsecond computations identify the pathways leading to the extraction of skin lipids by sebum triglycerides and the associated energetic costs.

Molecular dynamics simulations of stratum corneum lipid mixtures: A multiscale perspective

The lipid matrix of the stratum corneum (SC) layer of skin is essential for human survival; it acts as a barrier to prevent rapid dehydration while keeping potentially hazardous material outside the body. While the composition of the SC lipid matrix is known, the molecular-level details of its organization are difficult to infer experimentally, hindering the discovery of structure-property relationships. To this end, molecular dynamics simulations, which give molecular-level resolution, have begun to play an increasingly important role in understanding these relationships. However, most simulation studies of SC lipids have focused on preassembled bilayer configurations, which, owing to the slow dynamics of the lipids, may influence the final structure and hence the calculated properties. Self-assembled structures would avoid this dependence on the initial configuration, however, the size and length scales involved make self-assembly impractical to study with atomistic models. Here, we report on the development of coarse-grained models of SC lipids designed to study self-assembly. Building on previous work, we present the interactions between the headgroups of ceramide and free fatty acid developed using the multistate iterative Boltzmann inversion method. Validation of the new interactions is performed with simulations of preassembled bilayers and good agreement between the atomistic and coarse-grained models is found for structural properties. The self-assembly of mixtures of ceramide and free fatty acid is investigated and both bilayer and multilayer structures are found to form. This work therefore represents a necessary step in studying SC lipid systems on multiple time and length scales.