Challenges and limits of mechanical stability in 3D direct laser writing

Direct laser writing is an effective technique for fabrication of complex 3D polymer networks using ultrashort laser pulses. Practically, it remains a challenge to design and fabricate high performance materials with different functions that possess a combination of high strength, substantial ductility, and tailored functionality, in particular for small feature sizes. To date, it is difficult to obtain a time-resolved microscopic picture of the printing process in operando. To close this gap, we herewith present a molecular dynamics simulation approach to model direct laser writing and investigate the effect of writing condition and aspect ratio on the mechanical properties of the printed polymer network. We show that writing conditions provide a possibility to tune the mechanical properties and an optimum writing condition can be applied to fabricate structures with improved mechanical properties. We reveal that beyond the writing parameters, aspect ratio plays an important role to tune the stiffness of the printed structures

Monte-Carlo Simulations of Soft Matter Using SIMONA: A Review of Recent Applications

Molecular simulations such as Molecular Dynamics (MD) and Monte Carlo (MC) have gained increasing importance in the explanation of various physicochemical and biochemical phenomena in soft matter and help elucidate processes that often cannot be understood by experimental techniques alone. While there is a large number of computational studies and developments in MD, MC simulations are less widely used, but they offer a powerful alternative approach to explore the potential energy surface of complex systems in a way that is not feasible for atomistic MD, which still remains fundamentally constrained by the femtosecond timestep, limiting investigations of many essential processes. This paper provides a review of the current developments of a MC based code, SIMONA, which is an efficient and versatile tool to perform large-scale conformational sampling of different kinds of (macro)molecules. We provide an overview of the approach, and an application to soft-matter problems, such as protocols for protein and polymer folding, physical vapor deposition of functional organic molecules and complex oligomer modeling. SIMONA offers solutions to different levels of programming expertise (basic, expert and developer level) through the usage of a designed Graphical Interface pre-processor, a convenient coding environment using XML and the development of new algorithms using Python/C++. We believe that the development of versatile codes which can be used in different fields, along with related protocols and data analysis, paves the way for wider use of MC methods

Tacticity dependence of single chain polymer folding

Precision polymerization techniques offer the exciting opportunity to manufacture single-chain nanoparticles (SCNPs) with intramolecular crosslinks placed in specific positions along the polymer chain. Earlier studies showed that synthetic polymer chains can fold into defined SCNP conformations through a reversible two-state process, similar to that observed for small peptides and proteins – yet far behind in its structural sophistication. While the natural structures of proteins arise from polypeptides of perfectly defined stereochemistry, the role of main-chain stereochemistry on SCNP folding remains largely unexplored. To investigate the effect of tacticity on SCNP architectures, the development of specific simulation strategies is critical to provide reliable data. Herein, we investigate the structural transitions of SCNPs of different stereochemistries, i.e. atactic, syndiotactic and isotactic of various lengths (L = 10 to L = 30) using all-atom Monte-Carlo simulations. The results indicate that structural transitions occur in syndiotactic polymers at lower temperature compared to atactic and isotactic polymer chains. The effect of main chain stereochemistry on the transition temperature was found to be especially pronounced for shorter polymer chains of length L = 10 to L = 20

Sampling of the conformational landscape of small proteins with Monte Carlo methods

Computer simulation provides an increasingly realistic picture of large-scale conformational change of proteins, but investigations remain fundamentally constrained by the femtosecond timestep of molecular dynamics simulations. For this reason, many biologically interesting questions cannot be addressed using accessible state-of-the-art computational resources. Here, we report the development of an all-atom Monte Carlo approach that permits the modelling of the large-scale conformational change of proteins using standard off-the-shelf computational hardware and standard all-atom force fields. We demonstrate extensive thermodynamic characterization of the folding process of the α-helical Trp-cage, the Villin headpiece and the β-sheet WW-domain. We fully characterize the free energy landscape, transition states, energy barriers between different states, and the per-residue stability of individual amino acids over a wide temperature range. We demonstrate that a state-of-the-art intramolecular force field can be combined with an implicit solvent model to obtain a high quality of the folded structures and also discuss limitations that still remain

Covalent Adaptable Microstructures via Combining Two‐Photon Laser Printing and Alkoxyamine Chemistry: Toward Living 3D Microstructures

Manufacturing programmable materials, whose mechanical properties can be adapted on demand, is highly desired for their application in areas ranging from robotics, to biomedicine, or microfluidics. Herein, the inclusion of dynamic and living bonds, such as alkoxyamines, in a printable formulation suitable for two-photon 3D laser printing is exploited. On one hand, taking advantage of the dynamic covalent character of alkoxyamines, the nitroxide exchange reaction is investigated. As a consequence, a reduction of the Young´s Modulus by 50%, is measured by nanoindentation. On the other hand, due to its “living” characteristic, the chain extension becomes possible via nitroxide mediated polymerization. In particular, living nitroxide mediated polymerization of styrene results not only in a dramatic increase of the volume (≈8 times) of the 3D printed microstructure but also an increase of the Young\u27s Modulus by two orders of magnitude (from 14 MPa to 2.7 GPa), while maintaining the shape including fine structural details. Thus, the approach introduces a new dimension by enabling to create microstructures with dynamically tunable size and mechanical properties

MOF‐Hosted Enzymes for Continuous Flow Catalysis in Aqueous and Organic Solvents

Fully exploiting the potential of enzymes in cell-free biocatalysis requires stabilization of the catalytically active proteins and their integration into efficient reactor systems. Although in recent years initial steps towards the immobilization of such biomolecules in metal-organic frameworks (MOFs) have been taken, these demonstrations have been limited to batch experiments and to aqueous conditions. Here we demonstrate a MOF-based continuous flow enzyme reactor system, with high productivity and stability, which is also suitable for organic solvents. Under aqueous conditions, the stability of the enzyme was increased 30-fold, and the space-time yield exceeded that obtained with other enzyme immobilization strategies by an order of magnitude. Importantly, the infiltration of the proteins into the MOF did not require additional functionalization, thus allowing for time- and cost-efficient fabrication of the biocatalysts using label-free enzymes

Tricationic Ionic Liquids: Structural and Dynamical Properties via Molecular Dynamics Simulations

Three imidazolium-based linear tricationic ionic liquids (LTILs) have been simulated to study their structural and dynamical properties and obtain a fundamental understanding of the molecular basis of the microscopic and macroscopic properties of their bulk liquid phase. The effects of temperature and alkyl chain length on the physiochemical, transport, and structural properties of these LTILs have been investigated. A nonpolarizable all-atom force field, which is a refined version of the Canongia Lopes and Paudua force field, was adopted for the simulations. Densities, mean square displacements, self-diffusivities, viscosities, electrical conductivities, and transference numbers have been presented for various ions from MD simulations. The detailed microscopic structures have been discussed in terms of radial distribution functions and spatial distribution functions. The results show that, similar to that in monocationic and dicationic ILs (MILs and DILs, respectively), the anions are mainly organized around the imidazolium rings. The diffusion coefficients of the studied LTILs are smaller than those of both MILs and DILs, with comparable viscosities. Unlike those of MILs and DILs, the diffusion coefficients of the cations and anions of the studied LTILs increase with an increase in the length of the alkyl chain between the rings for LTIL-1 and LTIL-2 but then decrease for LTIL-3, which is in a good agreement with the trend of viscosity data. The calculated transference numbers show that, similar to that in MILs and DILs, cations have a major role in carrying electric current in LTILs, but this role increases from MILs to LTILs

Evaluating the Effects of Geometry and Charge Flux in Force Field Modeling

We apply a model for analyzing the importance of conformational charge flux to 11 molecules with the R–(CH₂)_<i>n</i>–R structure (R = Cl, F, OH, SH, COOH, CONH₂, and NH₂ and <i>n</i> = 4–6). Atomic charges were obtained by fitting to results from density functional theory calculations using the HLY procedure, and their geometry dependence is decomposed into contributions from changes in bond lengths, bond angles, and torsional angles. The torsional degrees of freedom are the main contribution to the conformational dependence of atomic charges and molecular dipole moments, but indirect effects due to changes in bond distances and angles account for ∼15% of the variations. While the magnitude of charge flux and geometry effects have been found to be independent of the number of internal degrees of freedom, the nature of the R- group has a moderate influence. The indirect effects are comparable for all of the R-groups and are approximately one-half the magnitude of the corresponding effects in peptide models. However, the magnitudes are different, yet the relative importance of geometry and charge flux effects are completely similar to those of the peptide models, which suggests that modeling the charge flux effects for changes in bond lengths, bond angles, and torsional angles should be considered for developing improved force fields