Interfacial interactions between DNA and polysaccharide-coated magnetic nanoparticles: Insight from simulations and experiments.

In this work we examine the structural and energetic stability and the interactions between dextran-coated magnetic nanoparticles (MNPs) and a DNA oligonucleotide at ionic strength conditions that are relevant to physiological gene delivery processes. All-atom Molecular Dynamics simulations provided information at the atomic-level regarding the mechanisms responsible for the physical adsorption of Dextran on the magnetic surface and the conditions under which a successful DNA-Dextran complexation can be accomplished. Coulombic interactions were found to play the main role for the formation of the Dextran interfacial layer onto the magnetic surface while hydrogen bonding between the Dextran molecules enhanced the structural integrity of this layer.

Exploring the Origins of Association of Poly(acrylic acid) Polyelectrolyte with Lysozyme in Aqueous Environment through Molecular Simulations and Experiments.

This study provides a detailed picture of how a protein (lysozyme) complexes with a poly(acrylic acid) polyelectrolyte (PAA) in water at the atomic level using a combination of all-atom molecular dynamics simulations and experiments. The effect of PAA and temperature on the protein's structure is explored. The simulations reveal that a lysozyme's structure is relatively stable except from local conformational changes induced by the presence of PAA and temperature increase.

Therapeutic stapled peptides: Efficacy and molecular targets.

Peptide stapling, by employing a stable, preformed alpha-helical conformation, results in the production of peptides with improved membrane permeability and enhanced proteolytic stability, compared to the original peptides, and provides an effective solution to accelerate the rapid development of peptide drugs. Various reviews present peptide stapling chemistries, anchoring residues and one- or two-component cyclization, however, therapeutic stapled peptides have not been systematically summarized, especially focusing on various disease-related targets. This review highlights the latest advances in therapeutic peptide drug development facilitated by the application of stapling technology, including different stapling techniques, synthetic accessibility, applicability to biological targets, potential for solving biological problems, as well as the current status of development.

Varying the degree of oxidation of graphite: effect of oxidation time and oxidant mass.

In this work, we employ a fast and less toxic modified Hummers' method to develop graphene oxide (GO) with varying degrees of oxidation and investigate the effect of the latter on the structure and the thermal properties of the synthesized materials. Two different key parameters, the time of the oxidation reaction and the mass of the oxidation agent, were systematically altered in order to fine tune the oxidation degree. All graphene oxides were characterized by a plethora of experimental techniques, like X-ray diffraction (XRD), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) as well as infrared spectroscopy (IR) and X-ray photoelectron spectroscopy (XPS) for their structural, thermal and chemical identification.

Investigating the complexation propensity of self-assembling dipeptides with the anticancer peptide-drug Bortezomib: a computational study.

The investigation of potential self-assembled peptides as carriers for the delivery of anticancer drug Bortezomib is the topic of the present study. The self-assembly of Bortezomib in water is examined using all-atom molecular dynamics simulations and corresponding experimental results from FESEM experiments. In addition, a series of dipeptides with a similar chemical formula to Bortezomib with hydrogel-forming ability are being investigated for their propensity to bind to the drug molecule.

Structure of amino acid sequence-reversed wtRop protein: insights from atomistic molecular dynamics simulations.

This study aims to the investigation of the advantages of designing new proteins presume upon a 'bias' sequence of amino acids, based on the reversed sequence of parent proteins, such as the retro ones. The structural simplicity of wtRop offers a very attractive model system to study these aspects. The current work is based on all-atom Molecular Dynamics (MD) simulations and corresponding experimental evidence on two different types of reversed wtRop protein, one with a fully reversed sequence of amino acids (rRop) and another with a partially reversed sequence (prRop), where only the five residues of the loop region (30ASP-34GLN) were not reversed.

Morphology and Dynamics in Hydrated Graphene Oxide/Branched Poly(ethyleneimine) Nanocomposites: An In Silico Investigation.

Graphene oxide (GO)-branched poly(ethyleneimine) (BPEI) hydrated mixtures were studied by means of fully atomistic molecular dynamics simulations to assess the effects of the size of polymers and the composition on the morphology of the complexes, the energetics of the systems and the dynamics of water and ions within composites. The presence of cationic polymers of both generations hindered the formation of stacked GO conformations, leading to a disordered porous structure. The smaller polymer was found to be more efficient at separating the GO flakes due to its more efficient packing.

Self-Assembly of Phenylalanine-Leucine, Leucine-Phenylalanine, and Cyclo(-leucine-phenylalanine) Dipeptides through Simulations and Experiments.

For over two decades, peptide self-assembly has been the focus of attention and a great source of inspiration for biomedical and nanotechnological applications. The resulting peptide nanostructures and their properties are closely related to the information encoded within each peptide building block, their sequence, and their modes of self-organization. In this work.

The Role of Oxidation Pattern and Water Content in the Spatial Arrangement and Dynamics of Oxidized Graphene-Based Aqueous Dispersions.

In this work, we employ fully atomistic molecular dynamics simulations to elucidate the effects of the oxidation pattern and of the water content on the organization of graphene sheets in aqueous dispersions and on the dynamic properties of the different moieties at neutral pH conditions. Analysis of the results reveals the role of the oxidation motif (peripherally or fully oxidized flakes) in the tendency of the flakes to self-assemble and in the control of key structural characteristics, such as the interlayer distance between the sheets and the average size and the distribution of the formed aggregates. In certain cases, the results are compared to a pertinent experimental system, validating further the relevant computational models.

Dynamics of Polymer Chains in Poly(ethylene oxide)/Silica Nanocomposites via a Combined Computational and Experimental Approach.

The dynamics of polymer chains in poly(ethylene oxide)/silica (PEO/SiO) nanoparticle nanohybrids have been investigated via a combined computational and experimental approach involving atomistic molecular dynamics simulations and dielectric relaxation spectroscopy (DRS) measurements. The complementarity of the approaches allows us to study systems with different polymer molecular weights, nanoparticle radii, and compositions across a broad range of temperatures. We study the effects of spatial confinement, which is induced by the nanoparticles, and chain adsorption on the polymer's structure and dynamics.

Effects of the structure of lipid-based agents in their complexation with a single stranded mRNA fragment: a computational study.

In this work we employed fully atomistic molecular dynamics simulations, aiming towards a better understanding of the mechanisms associated with the formation and the stability of lipid-based RNA nanoassemblies, in an aqueous environment. We examined two groups of lipid-based complexation agents, differing in the degree of hydrophobicity and in the overall charge. The first group was comprised of cationic ionizable agents while the second included electrically neutral amphoteric phosphatidylcholine lipids.

Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments.

In the current work we study, via molecular simulations and experiments, the folding and stability of proteins from the tertiary motif of 4-α-helical bundles, a recurrent motif consisting of four amphipathic α-helices packed in a parallel or antiparallel fashion. The focus is on the role of the loop region in the structure and the properties of the wild-type Rop (wtRop) and RM6 proteins, exploring the key factors which can affect them, through all-atom molecular dynamics (MD) simulations and supporting by experimental findings. A detailed investigation of structural and conformational properties of wtRop and its RM6 loopless mutation is presented, which display different physical characteristics even in their native states.

Self-assembly of diphenylalanine peptides on graphene detailed atomistic simulations.

The self-assembly of diphenylalanine peptides (FF) on a graphene layer, in aqueous solution, is investigated, through all atom molecular dynamics simulations. Two interfacial systems are studied, with different concentrations of dipeptides and the results are compared with an aqueous solution of FF at room temperature. Corresponding length and time scales of the formed structures are quantified providing important insight into the adsorption mechanism of FF onto the graphene surface.

Complexation of single stranded RNA with an ionizable lipid: an all-atom molecular dynamics simulation study.

Complexation of a lipid-based ionizable cationic molecule (referred to as DML: see main text) with RNA in an aqueous medium was examined in detail by means of fully atomistic molecular dynamics simulations. The different stages of the DML-RNA association process were explored, while the structural characteristics of the final complex were described. The self-assembly process of the DML molecules was examined in the absence and in the presence of nucleotide sequences of different lengths.

Investigation of the properties of nanographene in polymer nanocomposites through molecular simulations: dynamics and anisotropic Brownian motion.

The dynamical behavior of nanographene sheets dispersed in polymer matrices is investigated through united-atom molecular dynamics simulations. The Brownian motion of the sheet and the anisotropy in its translational and orientational diffusion are the topics of the current study. Different polymer matrices and pristine and functionalized graphene constitute various nanocomposite systems.

Effect of macromolecular architecture on the self-assembly behavior of copolymers in a selective polymer host.

We present a detailed simulation study of the structural and dynamical behavior of star-shaped mikto-arm (polystyrene)8(poly(ethylene oxide))8, (PS)8(PEO)8, copolymers with eight arms of each type, versus that of a linear polystyrene-block-poly(ethylene oxide), PS-b-PEO, diblock, in a selective homopolymer host. Both copolymers are blended at the same weight fraction 33% with an oligomeric PEO host. We use atomistic molecular dynamics simulations to account for the molecular interactions present in the blends and to study quantitatively the dynamical and structural properties of these systems.

Dynamics and Structure of Monolayer Polymer Crystallites on Graphene.

Graphene-based nanostructured systems and van der Waals heterostructures comprise a material class of growing technological and scientific importance. Joining materials with vastly different properties, polymer/graphene heterosystems promise diverse applications in surface and nanotechnology, including photovoltaics or nanotribology. Fundamentally, molecular adsorbates are prototypical systems to study confinement-induced phase transitions exhibiting intricate dynamics, which require a comprehensive understanding of the dynamical and static properties on molecular time and length scales.

Collapse transitions in thermosensitive multi-block copolymers: a Monte Carlo study.

Monte Carlo simulations are performed on a simple cubic lattice to investigate the behavior of a single linear multiblock copolymer chain of various lengths N. The chain of type (AnBn)m consists of alternating A and B blocks, where A are solvophilic and B are solvophobic and N = 2nm. The conformations are classified in five cases of globule formation by the solvophobic blocks of the chain.

Dynamics of various polymer-graphene interfacial systems through atomistic molecular dynamics simulations.

The current work refers to a simulation study on hybrid polymer-graphene interfacial systems. We explore the effect of graphene on the mobility of polymers, by studying three well known and widely used polymers, polyethylene (PE), polystyrene (PS) and poly(methyl-methacrylate) (PMMA). Qualitative and quantitative differences in the dynamical properties of the polymer chains in particular at the polymer-graphene interface are detected.

Effect of solvent on the self-assembly of dialanine and diphenylalanine peptides.

Diphenylalanine (FF) is a very common peptide with many potential applications, both biological and technological, due to a large number of different nanostructures which it attains. The current work concerns a detailed study of the self-assembled structures of FF in two different solvents, an aqueous (H2O) and an organic (CH3OH) through simulations and experiments. Detailed atomistic molecular dynamics (MD) simulations of FF in both solvents have been performed, using an explicit solvent model.

Temperature-induced crystallization in concentrated suspensions of multiarm star polymers: a molecular dynamics study.

In this work, we study temperature-induced crystallization in dense suspensions of multiarm star polymers. This is a continuation of a previous study, which identified and studied the emergence of "glassy" amorphous states, in accordance with experimental observations. We performed molecular dynamics simulations on two types of star polymers: 128-arm stars and 64-arm stars dissolved in n-decane in the temperature range of 20-60 degrees C.