Supramolecular chemistry offers an exciting opportunity to assemble materials with molecular precision. However, there remains an unmet need to turn molecular self-assembly into functional materials and devices. Harnessing the inherent properties of both disordered proteins and graphene oxide (GO), we report a disordered protein-GO co-assembling system that through a diffusion-reaction process and disorder-to-order transitions generates hierarchically organized materials that exhibit high stability and access to non-equilibrium on demand. We use experimental approaches and molecular dynamics simulations to describe the underlying molecular mechanism of formation and establish key rules for its design and regulation. Through rapid prototyping techniques, we demonstrate the system’s capacity to be controlled with spatio-temporal precision into well-defined capillary-like fluidic microstructures with a high level of biocompatibility and, importantly, the capacity to withstand flow. Our study presents an innovative approach to transform rational supramolecular design into functional engineering with potential widespread use in microfluidic systems and organ-on-a-chip platforms.

We report on combined experimental and theoretical investigations of the water/micelle interface of cationic, anionic, zwitterionic, and non-ionic surfactants using a new hydrophobic acid-base indicator 2,6dinitro-4-n-dodecylphenol. The indices of the so-called apparent ionization constant, app a pK , of the indicator fixed in the micellar pseudophase are determined by the spectrophotometric method. The data allows estimating the Stern layer's electrostatic potential of the ionic micelles . Molecular Dynamics modeling was used to locate the dye molecule and, in particular, its ionizing group OH  Owithin the micelles of the studied surfactants. The comparison of the  values estimated using 2,6-dinitro-4-ndodecylphenol with both our computer simulation and literature experimental results reveals obstacles in monitoring electrical interfacial potentials. In particular, the  values of the surfactant micelles with alkylammonium groups determined via 2,6-dinitro-4-n-dodecylphenol are overestimated. The reason is specific interactions of the indicator anion with the surfactant head groups. For anionic surfactants, however, this indicator is quite suitable, which is confirmed by the location of HA and Aequilibrium forms in the pseudophase.

Present experimental methods do not have sufficient resolution to investigate all processes in virus particles at atomistic details. We report the results of molecular dynamics simulations and analyze the connection between the number of ions inside an empty capsid of PCV2 virus and its stability. We compare the crystallographic structures of the capsids with unresolved N-termini and without them in realistic conditions (room temperature and aqueous solution) and show that the structure is preserved. We find that the chloride ions play a key role in the stability of the capsid. A low number of chloride ions results in loss of the native icosahedral symmetry, while an optimal number of chloride ions create a neutralizing layer next to the positively charged inner surface of the capsid. Understanding the dependence of the capsid stability on the distribution of the ions will help clarify the details of the viral life cycle that is ultimately connected to the role of packaged viral genome inside the capsid.

The all-atom model of an MS2 bacteriophage particle without its genome (the capsid) was built using high-resolution cryo-electron microscopy (EM) measurements for initial conformation. The structural characteristics of the capsid and the dynamics of the surrounding solution were examined using molecular dynamics simulation. The model demonstrates the overall preservation of the cryo-EM structure of the capsid at physiological conditions (room temperature and ions composition). The formation of a dense anion layer near the inner surface and a diffuse cation layer near the outer surface of the capsid was detected. The flow of water molecules and ions across the capsid through its pores were quantified, which was considerable for water and substantial for ions.

We present a set of novel all-atom potential models for sodium dodecyl sulfate (SDS), developed within the framework of the widely used OPLS-AA and General AMBER force fields. The choice of the parameters for the models is made by rigorously following the methodology of the used force fields to ensure full compatibility with the models for other compounds. For the GAFF model, extensive quantum-chemical computations are performed to obtain reliable Boltzmann-averaged atomic point charges, and the latter are compared with the single-conformation charges. For representation of the hydrocarbon tail, we use recently published improved parameters that correctly reproduce the properties of lipids and long alkanes. The models are validated on the basis of correct reproduction of the main properties of micelles (size, degree of counterion binding) as well as diffusion coefficient of the SDS monomer. As an extended test, a simulation of a micelle with a high aggregation number (382) and unnatural initial shape is performed, and a restructuring to the correct shape is observed. This proves the suitability of the developed models for simulations of concentrated SDS solutions containing large micelles and also emphasizes importance of hydrocarbon tail parameters for the micelle properties. Finally, the developed DS models are tested in combination with several common Na and water models. Their effect on the properties of SDS micelles is discussed, and suitable combinations are determined.

A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported. C 2015 AIP Publishing LLC. [http://dx

MS2 bacteriophage is often used as a model for evaluating pathogenic viruses’ behavior in aqueous solution. However, the questions of the virus surface’s hydrophilic/hydrophobic balance, the charge distribution, and the binding mechanism are open. Using the dynamic light scattering method and laser Doppler electrophoresis, the hydrodynamic diameter and the ζ-potential of the virus particles were measured at their concentration of 5 × 1011 particles per mL and ionic strength 0.03 M. The values were found to be 30 nm and −29 or −34 mV (by Smoluchowski or Ohshima approximations), respectively. The MS2 bacteriophage surface was also investigated using a series of acid–base indicator dyes of various charge type, size, and structure. Their spectral and acid–base properties (pK a ) are very sensitive to the microenvironment in aqueous solution, including containing nanoparticles. The electrostatic potential of the surface Ψ was estimated using the common formula: Ψ = 59 × (pK a i – pK a ) in mV at 25 °C. The Ψ values were −50 and +10 mV, respectively, which indicate the “mosaic” way of the charge distribution on the surface. These data are in good agreement with the obtained ζ-potential values and provide even more information about the virus surface. It was found that the surface of the MS2 virus is hydrophilic in solution in contrast to the commonly accepted hypothesis of the hydrophobicity of virus particles. No hydrophobic interactions between various molecular probes and the capsid were observed.

The problem of using surfactant micellar aqueous solutions as reaction media centers on estimating the polarity of the micellar pseudophase. The most popular approach is the utilization of solvatochromic dyes. Among the last, the strongest ones are the dipolar pyridinium N-phenolate dyes. The complication of such approach, however, consists in the nonuniform character of the environment of the indicator fixed in the micellar pseudophase. The aim of this study is to reveal the character of localization and orientation of the standard solvatochromic pyridinium N-phenolate dye, 4-(2,4,6-triphenylpyridinium-1-yl)-2,6-diphenylphenolate, the so-called Reichardt's dye, within the micellar pseudophase of an anionic (sodium n-dodecyl sulfate, SDS) and cationic (cetyltrimethylammonium bromide, CTAB) surfactants using MD simulations. The locus and hydration of the dye are found to be dependent on the surfactant nature. New approaches are proposed to quantitatively describe the state of the dye within the pseudophase. The results confirm the experimental data, which indicate the higher polarity of the interfacial region in the case of the SDS micelles. Because this dye is also used as an interfacial acid-base probe, the corresponding study is simultaneously performed for its protonated, i.e., cationic form. The neutral and protonated forms of the dye are found to be localized and hydrated in a different way in both SDS and CTAB micelles. This should be taken into account when using the Reichardt's dye as an acid-base indicator for estimating the electrical surface potential of micelles. The presented approach may be recommended to shed light upon the locus of other solvatochromic and acid-base indicators in micelles and micellar-like aggregates.