Entanglement-Stabilized Nanoporous Polymer Films Made by Mechanical Deformation.

We present a new simulation-guided process to create nanoporous materials, which does not require specific chemical treatment and solely relies on mechanical deformation of pure highly entangled homopolymer films. Starting from fully equilibrated freestanding thick polymer melt films, we apply a simple "biaxial expansion" deformation. Upon expansion holes form, which are prevented from growing and coalescing beyond a characteristic size due to the entanglement structure of the melt. We investigate the local morphology, the void formation upon expansion, and their stabilization. The dependence of the average void (pore) size and void fraction (porosity) on the total strain and subsequent relaxation is investigated. Furthermore, the stabilization of the porous structure of the thin expanded films through cooling below the glass transition temperature Tg is discussed.

Multiscale Simulations of Self-Assembling Peptides: Surface and Core Hydrophobicity Determine Fibril Stability and Amyloid Aggregation.

Assemblies of peptides and proteins through specific intermolecular interactions set the basis for macroscopic materials found in nature. Peptides provide easily tunable hydrogen-bonding interactions, which can lead to the formation of ordered structures such as highly stable ß-sheets that can form amyloid-like supramolecular peptide nanofibrils (PNFs). PNFs are of special interest, as they could be considered as mimics of various fibrillar structures found in nature. In their ability to serve as supramolecular scaffolds, they could mimic certain features of the extracellular matrix to provide stability, interact with pathogens such as virions, and transduce signals between the outside and inside of cells. Many PNFs have been reported that reveal rich bioactivities. PNFs supporting neuronal cell growth or lentiviral gene transduction have been studied systematically, and their material properties were correlated to bioactivities. However, the impact of the structure of PNFs, their dynamics, and stabilities on their unique functions is still elusive. Herein, we provide a microscopic view of the self-assembled PNFs to unravel how the amino acid sequence of self-assembling peptides affects their secondary structure and dynamic properties of the peptides within supramolecular fibrils. Based on sequence truncation, amino acid substitution, and sequence reordering, we demonstrate that peptide-peptide aggregation propensity is critical to form bioactive ß-sheet-rich structures. In contrast to previous studies, a very high peptide aggregation propensity reduces bioactivity due to intermolecular misalignment and instabilities that emerge when fibrils are in close proximity to other fibrils in solution. Our multiscale simulation approach correlates changes in biological activity back to single amino acid modifications. Understanding these relationships could lead to future material discoveries where the molecular sequence predictably determines the macroscopic properties and biological activity. In addition, our studies may provide new insights into naturally occurring amyloid fibrils in neurodegenerative diseases.

Peptide Amphiphiles as Biodegradable Adjuvants for Efficient Retroviral Gene Delivery.

Retroviral gene delivery is the key technique for in vitro and ex vivo gene therapy. However, inefficient virion-cell attachment resulting in low gene transduction efficacy remains a major challenge in clinical applications. Adjuvants for ex vivo therapy settings need to increase transduction efficiency while being easily removed or degraded post-transduction to prevent the risk of venous embolism after infusing the transduced cells back to the bloodstream of patients, yet no such peptide system have been reported thus far. In this study, peptide amphiphiles (PAs) with a hydrophobic fatty acid and a hydrophilic peptide moiety that reveal enhanced viral transduction efficiency are introduced. The PAs form ß-sheet-rich fibrils that assemble into positively charged aggregates, promoting virus adhesion to the cell membrane. The block-type amphiphilic sequence arrangement in the PAs ensures efficient cell-virus interaction and biodegradability. Good biodegradability is observed for fibrils forming small aggregates and it is shown that via molecular dynamics simulations, the fibril-fibril interactions of PAs are governed by fibril surface hydrophobicity. These findings establish PAs as additives in retroviral gene transfer, rivalling commercially available transduction enhancers in efficiency and degradability with promising translational options in clinical gene therapy applications.

Chilling alcohol on the computer: isothermal compressibility and the formation of hydrogen-bond clusters in liquid propan-1-ol.

Molecular dynamics simulations have been performed to compute the isothermal compressibility [Formula: see text] of liquid propan-1-ol in the temperature range [Formula: see text] K. A change in behaviour, from normal (high T) to anomalous (low T), has been identified for [Formula: see text] at [Formula: see text] K. The average number of hydrogen bonds (H-bond) per molecule turns to saturation in the same temperature interval, suggesting the formation of a relatively rigid network. Indeed, simulation results show a strong tendency to form H-bond clusters with distinct boundaries, with the average largest size and width of the size distribution growing upon decreasing temperature, in agreement with previous theoretical and experimental studies. These results also emphasise a connection between the behaviour of [Formula: see text] and the formation of nanometric structures.

Glass transition temperature of (ultra-)thin polymer films.

The glass transition temperature of confined and free-standing polymer films of varying thickness is studied by extended molecular dynamics simulations of bead-spring chains. The results are connected to the statistical properties of the polymers in the films, where the chain lengths range from short, unentangled to highly entangled. For confined films, perfect scaling of the thickness-dependent end-to-end distance and radius of gyrations normalized to their bulk values in the directions parallel and perpendicular to the surfaces is obtained. In particular, the reduced end-to-end distance in the perpendicular direction is very well described by an extended Silberberg model. For bulk polymer melts, the relation between the chain length and Tg follows the Fox-Flory equation. For films, no further confinement induced chain length effect is observed. Tg decreases and is well described by Keddie's formula, where the reduction is more pronounced for free-standing films. It is shown that Tg begins to deviate from bulk Tg at the characteristic film thickness, where the average bond orientation becomes anisotropic and the entanglement density decreases.

Determining glass transition in all-atom acrylic polymeric melt simulations using machine learning.

The functionality of many polymeric materials depends on their glass transition temperatures (Tg). In computer simulations, Tg is often calculated from the gradual change in macroscopic properties. Precise determination of this change depends on the fitting protocols. We previously proposed a robust data-driven approach to determine Tg from the molecular dynamics simulation data of a coarse-grained semiflexible polymer model. In contrast to the global macroscopic properties, our method relies on high-resolution microscopic details. Here, we demonstrate the generality of our approach by using various dimensionality reduction and clustering methods and apply it to an atomistic model of acrylic polymers. Our study reveals the explicit contribution of the side chain and backbone residues in influencing the determination of the glass transition temperature.

Smart Polymers for Soft Materials: From Solution Processing to Organic Solids.

Polymeric materials are ubiquitous in our everyday life, where they find a broad range of uses-spanning across common household items to advanced materials for modern technologies. In the context of the latter, so called "smart polymers" have received a lot of attention. These systems are soluble in water below their lower critical solution temperature Tℓ and often exhibit counterintuitive solvation behavior in mixed solvents. A polymer is known as smart-responsive when a slight change in external stimuli can significantly change its structure, functionm and stability. The interplay of different interactions, especially hydrogen bonds, can also be used for the design of lightweight high-performance organic solids with tunable properties. Here, a general scheme for establishing a structure-property relationship is a challenge using the conventional simulation techniques and also in standard experiments. From the theoretical side, a broad range of all-atom, multiscale, generic, and analytical techniques have been developed linking monomer level interaction details with macroscopic material properties. In this review, we briefly summarize the recent developments in the field of smart polymers, together with complementary experiments. For this purpose, we will specifically discuss the following: (1) the solution processing of responsive polymers and (2) their use in organic solids, with a goal to provide a microscopic understanding that may be used as a guiding tool for future experiments and/or simulations regarding designing advanced functional materials.

Stabilizing α-Helicity of a Polypeptide in Aqueous Urea: Dipole Orientation or Hydrogen Bonding?

We propose a mechanism for α-helix folding of polyalanine in aqueous urea that reconciles experimental and simulation studies. Over 15 µs long, all-atom simulations reveal that, upon dehydrating the protein's first solvation shell, a delicate balance between localized urea-residue dipole interactions and hydrogen bonds dictates polypeptide solvation properties and structure. Our work clarifies the experimentally observed tendency of these alanine-rich systems to form secondary structures at low and intermediate urea concentrations. Moreover, it is consistent with the commonly accepted hydrogen-bond-induced helix unfolding, dominant at high urea concentrations. These results establish a structure-property relationship highlighting the importance of microscopic dipole-dipole orientations/interactions for the operational understanding of macroscopic protein solvation.

Molecular Simulation Strategies for Understanding the Degradation Mechanisms of Acrylic Polymers.

Acrylic polymers, commonly used in paints, can degrade over time by several different chemical and physical mechanisms, depending on structure and exposure conditions. While exposure to UV light and temperature results in irreversible chemical damage, acrylic paint surfaces in museums can also accumulate pollutants, such as volatile organic compounds (VOCs) and moisture, that affect their material properties and stability. In this work, we studied the effects of different degradation mechanisms and agents on properties of acrylic polymers found in artists' acrylic paints for the first time using atomistic molecular dynamics simulations. Through the use of enhanced sampling methods, we investigated how pollutants are absorbed into thin acrylic polymer films from the environment around the glass transition temperature. Our simulations suggest that the absorption of VOCs is favorable (-4 to -7 kJ/mol depending on VOCs), and the pollutants can easily diffuse and be emitted back into the environment slightly above glass transition temperature when the polymer is soft. However, typical environmental fluctuations in temperature (<16 °C) can lead for these acrylic polymers to transition to glassy state, in which case the trapped pollutants act as plasticizers and cause a loss of mechanical stability in the material. This type of degradation results in disruption of polymer morphology, which we investigate through calculation of structural and mechanical properties. In addition, we also investigate the effects of chemical damage, such as backbone bond scission and side-chain cross-linking reactions on polymer properties.

Data-Driven Identification and Analysis of the Glass Transition in Polymer Melts.

Understanding the nature of glass transition, as well as the precise estimation of the glass transition temperature for polymeric materials, remains open questions in both experimental and theoretical polymer sciences. We propose a data-driven approach, which utilizes the high-resolution details accessible through the molecular dynamics simulation and considers the structural information on individual chains. It clearly identifies the glass transition temperature of polymer melts of weakly semiflexible chains. By combining principal component analysis and clustering, we identify the glass transition temperature in the asymptotic limit even from relatively short time trajectories, which just reach into the Rouse-like monomer displacement regime. We demonstrate that fluctuations captured by the principal component analysis reflect the change in a chain's behavior: from conformational rearrangement above to small fluctuations below the glass transition temperature. Our approach is straightforward to apply and should be applicable to other polymeric glass-forming liquids.

Free Standing Dry and Stable Nanoporous Polymer Films Made through Mechanical Deformation.

A new straight forward approach to create nanoporous polymer membranes with well defined average pore diameters is presented. The method is based on fast mechanical deformation of highly entangled polymer films at high temperatures and a subsequent quench far below the glass transition temperature Tg . The process is first designed generally by simulation and then verified for the example of polystyrene films. The methodology does not need any chemical processing, supporting substrate, or self assembly process and is solely based on polymer inherent entanglement effects. Pore diameters are of the order of ten polymer reptation tube diameters. The resulting membranes are stable over months at ambient conditions and display remarkable elastic properties.

Virtual Screening for Organic Solar Cells and Light Emitting Diodes.

The field of organic semiconductors is multifaceted and the potentially suitable molecular compounds are very diverse. Representative examples include discotic liquid crystals, dye-sensitized solar cells, conjugated polymers, and graphene-based low-dimensional materials. This huge variety not only represents enormous challenges for synthesis but also for theory, which aims at a comprehensive understanding and structuring of the plethora of possible compounds. Eventually computational methods should point to new, better materials, which have not yet been synthesized. In this perspective, it is shown that the answer to this question rests upon the delicate balance between computational efficiency and accuracy of the methods used in the virtual screening. To illustrate the fundamentals of virtual screening, chemical design of non-fullerene acceptors, thermally activated delayed fluorescence emitters, and nanographenes are discussed.

FAIR data enabling new horizons for materials research.

The prosperity and lifestyle of our society are very much governed by achievements in condensed matter physics, chemistry and materials science, because new products for sectors such as energy, the environment, health, mobility and information technology (IT) rely largely on improved or even new materials. Examples include solid-state lighting, touchscreens, batteries, implants, drug delivery and many more. The enormous amount of research data produced every day in these fields represents a gold mine of the twenty-first century. This gold mine is, however, of little value if these data are not comprehensively characterized and made available. How can we refine this feedstock; that is, turn data into knowledge and value? For this, a FAIR (findable, accessible, interoperable and reusable) data infrastructure is a must. Only then can data be readily shared and explored using data analytics and artificial intelligence (AI) methods. Making data 'findable and AI ready' (a forward-looking interpretation of the acronym) will change the way in which science is carried out today. In this Perspective, we discuss how we can prepare to make this happen for the field of materials science.

Mesoscopic Modeling of a Highly-Ordered Sanidic Polymer Mesophase and Comparison With Experimental Data.

Board-shaped polymers form sanidic mesophases: assemblies of parallel lamellae of stacked polymer backbones separated by disordered side chains. Sanidics vary significantly with respect to polymer order inside their lamellae, making them "stepping stones" toward the crystalline state. Therefore, they are potentially interesting for studying crystallization and technological applications. Building on earlier mesoscopic models of the most disordered sanidics Σd, we focus on the other extreme, near-crystalline order, and develop a generic model that captures a highly ordered Σr mesophase. Polymers are described by generic hindered-rotation chains. Anisotropic nonbonded potentials, with strengths comparable to the thermal energy, mimic board-like monomer shapes. Lamellae equilibrated with Monte Carlo simulations, for a broad range of model parameters, have intralamellar order typical for Σr mesophases: periodically stacked polymers that are mutually registered along their backbones. Our mesophase shows registration on both monomer and chain levels. We calculate scattering patterns and compare with data published for highly ordered sanidic mesophases of two different polymers: polyesters and polypeptoids. Most of the generic structural features that were identified in these experiments are present in our model. However, our mesophase has correlations between chains located in different lamellae and is therefore closer to the crystalline state than the experimental samples.

The Effects of Proline Isomerization on the Solvation Behavior of Elastin-Like Polypeptides in Water-Ethanol Mixtures.

Elastin-like polypeptides (ELPs) are well-known proline-rich stimulus-responsive polymers. They have broad applications ranging from drug delivery to green chemistry. Recently, the authors have shown that the cis/trans proline isomerization can be used to regulate their conformational behavior while keeping the lower critical solution temperature (LCST) unchanged in pure water. In aqueous ethanol mixtures, ELPs typically exhibit an expanded-collapsed-expanded transition known as the co-non-solvency phenomenon. Since it is unclear how proline isomerization affects the solvation behavior of ELPs in aqueous ethanol mixtures, an all-atom insight on single ELPs has been provided to address this question. It is found that if all proline residues are in the cis state, the peptides only experience a collapsed-expanded transition as ethanol concentration increases, i.e., the initial collapse vanishes because cis isomers prefer the compact structures in pure water. The data from the authors also suggest that proline isomerization does not change the shift in solvation free energy of an ELP with given sequence, but it varies the affinity of the peptide to both the solvent and cosolvent molecules.

Active Topological Glass Confined within a Spherical Cavity.

We study active topological glass under spherical confinement, allowing us to exceed the chain lengths simulated previously and determine the critical exponents of the arrested conformations. We find a previously unresolved "tank-treading" dynamic mode of active segments along the ring contour. This mode can enhance active-passive phase separation in the state of active topological glass when both diffusional and conformational relaxation of the rings are significantly suppressed. Within the observational time, we see no systematic trends in the positioning of the separated active domains within the confining sphere. The arrested state exhibits coherent stochastic rotations. We discuss possible connections of the conformational and dynamic features of the system to chromosomes enclosed in the nucleus of a living cell.

From adaptive resolution to molecular dynamics of open systems.

ABSTRACT: We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on discussing its basic principles and presenting its current numerical and theoretical developments. Examples of applications to systems of interest to soft matter, chemical physics, and condensed matter illustrate the method's advantages and limitations in its practical use and thus settle the challenge for further future numerical and theoretical developments.

Acrylic Paints: An Atomistic View of Polymer Structure and Effects of Environmental Pollutants.

Most of the artwork and cultural heritage objects are stored in museums under conditions that are difficult to monitor. While advanced technologies aim to control and prevent the degradation of cultural heritage objects in line with preventive conservation measures, there is much to be learned in terms of the physical processes that lead to the degradation of the synthetic polymers that form the basis of acrylic paints largely used in contemporary art. In museums, stored objects are often exposed to temperature and relative humidity fluctuations as well as airborne pollutants such as volatile organic compounds (VOCs). The glass transition of acrylic paints is below room temperature; while low temperatures may cause cracking, at high temperatures the sticky surface of the paint becomes vulnerable to pollutants. Here we develop fully atomistic models to understand the structure of two types of acrylic copolymers and their interactions with VOCs and water. The structure and properties of acrylic copolymers are slighlty modified by incorporation of a monomer with a longer side chain. With favorable solvation free energies, once absorbed, VOCs and water interact with the polymer side chains to form hydrogen bonds. The cagelike structure of the polymers prevents the VOCs and water to diffuse freely below the glass transition temperature. In addition, our model forms the foundation for developing mesoscopic and continuum models that will allow us to access longer time and length scales to further our understanding of the degradation of artwork.