Interaction between the Polyelectrolytes Unfractionated Heparin and Universal Heparin Reversal Agents.

The interaction of unfractionated heparin (UFH) with universal heparin reversal agent 7 (UHRA-7) is investigated. UHRA-7 is composed of a hyperbranched polyglycerol core onto which an array of methylated tris(2-aminoethylamine) (Me-TREN) charged groups is grafted, which in turn are shielded with a layer of small chain poly(ethylene glycol) methyl ether (mPEG) chains. This system has previously been shown to be biocompatible and to be effective at neutralizing heparin.

3D Printed Cellulose Nanofiber Aerogel Scaffold with Hierarchical Porous Structures for Fast Solar-Driven Atmospheric Water Harvesting.

Hygroscopic salt-based composite sorbents are considered ideal candidates for solar-driven atmospheric water harvesting. The primary challenge for the sorbents lies in exposing more hygroscopically active sites to the surrounding air while preventing salt leakage. Herein, a hierarchically structured scaffold is constructed by integrating cellulose nanofiber and lithium chloride (LiCl) as building blocks through 3D printing combined with freeze-drying.

Geometric differences in the ribosome exit tunnel impact the escape of small nascent proteins.

The exit tunnel is the subcompartment of the ribosome that contains the nascent polypeptide chain and, as such, is involved in various vital functions, including regulation of translation and protein folding. As the geometry of the tunnel shows important differences across species, we focus on key geometrical features of eukaryote and prokaryote tunnels. We used a simple coarse-grained molecular dynamics model to study the role of the tunnel geometry in the post-translational escape of short proteins (short open reading frames [sORFs]) with lengths ranging from 6 to 56 amino acids.

Competing Effects of Hydration and Cation Complexation in Single-Chain Alginate.

Alginic acid, a naturally occurring anionic polyelectrolyte, forms strong physically cross-linked hydrogels in the presence of metal cations. The latter engage in electrostatic interactions that compete with intra- and intermolecular hydrogen bonds, determining the gel structure and properties of the system in aqueous media. In this study, we use all-atom molecular dynamics simulations to systematically analyze the interactions between alginic acid chains and Na and Ca counterions.

United-Atom Molecular Dynamics Study of the Mechanical and Thermomechanical Properties of an Industrial Epoxy.

Epoxy resins are the most commonly used adhesives in industry due to their versatility, low cost, low toxicity, low shrinkage, high strength, resistance to moisture, and effective electrical resistance. These diverse properties can be tailored based on the chemical structure of the curing agent and the conditions of the curing process. Molecular simulations of epoxy resins have gained attention in recent years as a means to navigate the vast choice of chemical agents and conditions that will give the required properties of the resin.

Revisiting Cation Complexation and Hydrogen Bonding of Single-Chain Polyguluronate Alginate.

Modifying the properties of bio-based materials has garnered increasing interest in recent years. In related applications, the ability of alginates to complex with metal ions has been shown to be effective in liquid-to-gel transitions, useful in the development of foodstuff and pharma products as well as biomaterials, among others. However, despite its ubiquitous use, alginate behavior as far as interactions with cations is not fully understood.

Expanding carbon capture capacity: uncovering additional CO adsorption sites in imine-linked porous organic cages.

With an increasing need to develop carbon capture technologies, research regarding the use of cage-based porous materials has garnered great interest. Typically, the study of gas adsorption in porous organic cages (POCs) has focused on the gas uptake inside the cage cavity. By using molecular dynamics simulation, this study reveals the presence of eight sites outside the cavity of a 15-crown-5 ether-substituted imine-linked POC which could enhance carbon dioxide adsorption capacity.

Negative Pressure within a Liquid-Fluid Interface Determines Its Thickness.

The density within the interface between two fluid phases at equilibrium gradually changes from that of one phase to that of the other. The main change in density, according to experimental measurements, practically occurs over a finite distance of O [1 nm]. If we assume that the average stress difference within the interface is on the order of magnitude of ambient pressure, then the Bakker equation implies that for a liquid with surface tensions, say ∼50 mN/m, we get an interface thickness of ∼500 nm.

Coarse-Grained Simulation of Protein-Imprinted Hydrogels.

The MARTINI force-field is adapted for acrylic functional monomers and used to simulate protein-imprinted polymers, including complexation in solution, cross-linking reaction, washing, and rebinding of the protein. A globally controlled grand canonical Monte Carlo simulation combined with molecular dynamics is used to achieve proper hydration and swelling of the gel. Two gel formulations are compared, one with only polar functional monomers and one with additional small number of charged monomers.

The Relation between α-Helical Conformation and Amyloidogenicity.

Amyloid fibrils are stable aggregates of misfolded proteins and polypeptides that are insoluble and resistant to protease activity. Abnormal formation of amyloid fibrils in vivo may lead to neurodegenerative disorders and other systemic amyloidosis, such as Alzheimer's, Parkinson's, and atherosclerosis. Because of their clinical importance, amyloids are under intense scientific research.

The selectivity of protein-imprinted gels and its relation to protein properties: A computer simulation study.

Polymer-based protein recognition systems have enormous potential within clinical and diagnostic fields due to their reusability, biocompatibility, ease of manufacturing, and potential specificity. Imprinted polymer matrices have been extensively studied and applied as a simple technique for creating artificial polymer-based recognition gels for a target molecule. Although this technique has been proven effective when targeting small molecules (such as drugs), imprinting of proteins have so far resulted in materials with limited selectivity due to the large molecular size of the protein and aqueous environment.

Sequence-dependent association of alginate with sodium and calcium counterions.

Molecular dynamics simulation is used to study in detail the binding of sodium and calcium ions to alginate chains, and its dependence on the content of guluronic (G) acid residues. Our previous studies showed that chains with different G content associate through different structural mechanisms due to differing degrees of rigidity of the ion-alginate chain complexes. Polymannuronate and polyguluronate chains form highly ordered structures due to their more rigid nature.

A closer look into the α-helix basin.

α-Helices are the most abundant structures found within proteins and play an important role in the determination of the global structure of proteins and their function. Representation of α-helical structures with the common (φ, ψ) dihedrals, as in Ramachandran maps, does not provide informative details regarding the helical structure apart for the abstract geometric meaning of the dihedrals. We present an alternative coordinate system that describes helical conformations in terms of residues per turn (ρ) and angle (ϑ) between backbone carbonyls relative to the helix direction through an approximate linear transformation between the two coordinates system (φ, ψ and ρ, ϑ).

Structural Characterization of Sodium Alginate and Calcium Alginate.

Alginate readily aggregates and forms a physical gel in the presence of cations. The association of the chains, and ultimately gel structure and mechanics, depends not only on ion type, but also on the sequence and composition of the alginate chain that ultimately determines its stiffness. Chain flexibility is generally believed to decrease with guluronic residue content, but it is also known that both polymannuronate and polyguluronate blocks are stiffer than heteropolymeric blocks.

Comparison of descriptors for predicting selectivity of protein-imprinted polymers.

Molecular imprinting is a technique that is used to create artificial receptors by the formation of a polymer network around a template molecule, creating a molecularly imprinted polymer. These artificial receptors may be used in applications that require molecular recognition, such as enantioseparations, biosensors, artificial catalysis, drug delivery and others. Small molecules, such as drugs, have been imprinted with high efficiency and, combined with the low cost of preparation, molecularly imprinted polymers have acquired commercial usage.

Cytosine derivatized bis(2,2'-bithienyl)methane molecularly imprinted polymer for selective recognition of 6-thioguanine, an antitumor drug.

A molecularly imprinted polymer (MIP) was designed and synthesized to serve as a functional material for selective recognition of 6-thioguanine (6TG), an antitumor drug. For that, the newly synthesized functional monomer, cytosine-bis(2,2'-bithienyl)-(4-carboxyphenyl)methane ester (Cyt-S4), revealed Watson-Crick type nucleobase pairing of 6TG. Formation of the Cyt-S4 and 6TG complex of the 2:1 stoichiometry was postulated based on the DFT calculations at the B3LYP/3-21G((⁎)) level and experimentally confirmed by fluorescence titration.

Conformational changes of globular proteins upon adsorption on a hydrophobic surface.

This paper presents a study of protein adsorption and denaturation using coarse-grained Monte Carlo simulations with simulated annealing. Intermolecular interactions are modeled using the Miyazawa-Jernigan (MJ) knowledge-based potential for an implicit solvent. Three different hydrophobicity scales are tested for adsorption of fibronectin on a hydrophobic surface.

Thermal stability limits of proteins in solution and adsorbed on a hydrophobic surface.

A coarse-grained Monte Carlo simulation is used to study thermal denaturation of small proteins in an infinitely dilute solution and adsorbed on a flat hydrophobic surface. Intermolecular interactions are modeled using the Miyazawa-Jernigan (MJ) knowledge-based potential for implicit solvent with the BULDG hydrophobicity scale. We analyze the thermal behavior of lysozyme for its prevalence of α-helices, fibronectin for its prevalence of β-sheets, and a short single helical peptide.

A brief review of coarse-grained and other computational studies of molecularly imprinted polymers.

Molecular imprinting is an established method for the creation of artificial recognition sites in synthetic materials through polymerization and cross-linking in the presence of template molecules. Removal of the templates leaves cavities that are complementary to the template molecules in size, shape, and functionality. In recent years, various theoretical and computational models have been developed as tools to aid in the design of molecularly imprinted polymers (MIPs) or to provide insight into the features that determine MIP performance.

Simulation of protein-imprinted polymers. 3. Imprinting selectivity.

Molecular imprinting has been extensively studied and applied as a simple technique for creating artificial polymer-based recognition gels for a target molecule. Although this technique is effective when targeting small molecules, attempts to extend it to larger templates, such as proteins, have, for the most part, failed to show similar success. Our group has developed a simple simulation model to study protein imprinting.

Simulation of protein-imprinted polymers. 2. Imprinting efficiency.

Molecular imprinting allows the creation of artificial recognition sites in synthetic materials through polymerization and cross-linking in the presence of template molecules. Removal of the templates leaves cavities that are complementary to the template molecules in size, shape, and functionality. Although this technique is effective when targeting small molecules, attempts to extend it to larger templates, such as proteins, have failed to show similar success.

Simulation of protein-imprinted polymers. 1. Imprinted pore properties.

Molecular imprinting is an established method for the creation of artificial recognition sites in synthetic materials through polymerization and cross-linking in the presence of template molecules. Removal of the templates leaves cavities that are complementary to the template molecules in size, shape, and functionality. Although this technique is effective when targeting small molecules, attempts to extend it to larger templates, such as proteins, have failed to show similar success.

Simulation of thin film membranes formed by interfacial polymerization.

Interfacial polymerization is widely used today for the production of ultrathin films for encapsulation, chemical separations, and desalination. Polyamide films, in particular, are employed in manufacturing of reverse osmosis and nanofiltration membranes. While these materials show excellent salt rejection, they have rather low water permeability, both properties that apparently stem from the rigid cross-linked structure.

Conformational behavior of polymers adsorbed on nanotubes.

The importance of hydrophobic interactions in determining polymer adsorption and wrapping of carbon nanotubes is still under debate. In this work, we concentrate on the effect of short-ranged weakly attractive hydrophobic interactions between polymers and nanotubes (modeled as an infinitely long and smooth cylindrical surface), neglecting all other interactions apart for chain flexibility. Using coarse-grained Monte Carlo simulation of such simplified systems, we find that uniform adsorption and wrapping of the nanotube occur for all degrees of chain flexibility for tubes with sufficiently large outer radii.

Phase behavior of physically cross-linked asymmetric random heteropolymers.

We study the phase behavior of physically cross-linked asymmetric copolymer networks where the composition of the minor component is small (<10%). The effects of the degree of cross-linking and monomer-monomer interactions on the microstructure of the network are considered. Two cases of cross-links are considered: (1) cross-linking of the majority component only, i.