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The transport of polyelectrolytes confined by oppositely charged surfaces and driven by a constant electric field is of interest in studies of DNA separation according to size. Using molecular dynamics simulations that include the surface polarization effect, we find that the mobilities of the polyelectrolytes and their counterions change non-monotonically with the confinement surface charge density. For an optimum value of the confinement charge density, efficient separation of polyelectrolytes can be achieved over a wide range of polyelectrolyte charge due to the differential friction imparted by oppositely charged confinement on the polyelectrolyte chains. Furthermore, by altering the placement of the charged confinement counterions, enhanced polyelectrolyte separation can be achieved by utilizing the surface polarization effect due to dielectric mismatch between the media inside and outside the confinement. [ABSTRACT FROM AUTHOR]

In biological and synthetic materials, many important processes involve charges that are present in a medium with spatially varying dielectric permittivity. To accurately understand the role of electrostatic interactions in such systems, it is important to take into account the spatial dependence of the permittivity of the medium. However, due to the ensuing theoretical and computational challenges, this inhomogeneous dielectric response of the medium is often ignored or excessively simplified. We develop a variational formulation of electrostatics to accurately investigate systems that exhibit this inhomogeneous dielectric response. Our formulation is based on a true energy functional of the polarization charge density. The defining characteristic of a true energy functional is that at its minimum it evaluates to the actual value of the energy; this is a feature not found in many commonly used electrostatic functionals. We explore in detail the charged systems that exhibit sharp discontinuous change in dielectric permittivity, and we show that for this case our functional reduces to a functional of only the surface polarization charge density. We apply this reduced functional to study model problems for which analytical solutions are well known. We demonstrate, in addition, that the functional has many properties that make it ideal for use in molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

By combining molecular dynamics simulations and analytical arguments, we investigate the elastic properties of charged lipid bilayers. We show that electrostatic interactions between the head groups can lead to solidification of the lipid bilayer that would otherwise be in a liquid state if the charges were absent. All elastic parameters of the bilayer such as the bending rigidity κ and the two-dimensional bulk modulus λ and Young's modulus Y are found to depend on the values of the charges assigned to the lipid head groups. To extract κ and λ, we fit the molecular dynamics data to a standard elastic model for lipid bilayers. Moreover, we analytically obtain the dependence of the Young modulus Y on the relative strengths of electrostatic and van der Waals interactions in the zero temperature limit. [ABSTRACT FROM AUTHOR]

We investigate the equilibrium properties and the underlying dynamics of emulsions formed in asymmetric A-B copolymers in matrices of immiscible B and C molecular fluids using coarse-grained molecular dynamics simulations. The emulsions are generated by introducing net attractions among the A units of the copolymers and the C molecules. They coexist with an absorbed copolymer monolayer. We determine the interfacial properties as the emulsions are forming. In general, highly asymmetric copolymers self-assemble within the B-matrix phase into swollen micelles; the cores of which are composed of C-component material. Less asymmetric copolymers, however, after initially budding and eventually fissioning from the interfacial copolymer monolayer, generate emulsified “inverse swollen micelles” within the C-matrix phase. These stable inverse (crew-cut) swollen micelles, which form under the inward bending of the saturated or oversaturated interfaces toward the longer B-block due to the attraction between the A and C units, can encapsulate large amounts of B-matrix component in their cores. This monolayer collapse mechanism can be exploited to generate nanoreactors or containers that enhance the delivery of molecular components into immiscible molecular fluid environments. [ABSTRACT FROM AUTHOR]

The structure of soft matter systems at interfaces is of utmost importance in the fields of nanopatterning and self-assembly. It has been shown that lamellar and hexagonal patterns can form on interfaces, for a wide variety of systems. The asphericity of charged domains is considered here for different strengths of the electrostatics, determined by the interface media, relative to the short range van der Waals interactions between the molecular components. The phase behavior of the surface structure is explored by using molecular dynamics simulations, including some dynamical aspects of the interaction between neighboring domains, using the Lindemann criterion [F. Lindemann, Z. Phys. 11, 609 (1910)]. The charge ratio of the electrostatic components influences the shape of the domains, as well as the degree of local order in the interdomain structure. [ABSTRACT FROM AUTHOR]

Superparamagnetic nanoparticles incorporated into elastic media offer the possibility of creating actuators driven by external fields in a multitude of environments. Here, magnetoelastic membranes are studied through a combination of continuum mechanics and molecular dynamics simulations. We show how induced magnetic interactions affect the buckling and the configuration of magnetoelastic membranes in rapidly precessing magnetic fields. The field, in competition with the bending and stretching of the membrane, transmits forces and torques that drives the membrane to expand, contract, or twist. We identify critical field values that induce spontaneous symmetry breaking as well as field regimes where multiple membrane configurations may be observed. Our insights into buckling mechanisms provide the bases to develop soft, autonomous robotic systems that can be used at micro- and macroscopic length scales. [ABSTRACT FROM AUTHOR]

Membraneless organelles are aggregates of disordered proteins that form spontaneously to promote specific cellular functions in vivo. The possibility of synthesizing membraneless organelles out of cells will therefore enable fabrication of protein-based materials with functions inherent to biological matter. Since random copolymers contain various compositions and sequences of solvophobic and solvophilic groups, they are expected to function in nonbiological media similarly to a set of disordered proteins in membraneless organelles. Interestingly, the internal environment of these organelles has been noted to behave more like an organic solvent than like water. Therefore, an adsorbed layer of random copolymers that mimics the function of disordered proteins could, in principle, protect and enhance the proteins' enzymatic activity even in organic solvents, which are ideal when the products and/or the reactants have limited solubility in aqueous media. Here, we demonstrate via multiscale simulations that random copolymers efficiently incorporate proteins into different solvents with the potential to optimize their enzymatic activity. We investigate the key factors that govern the ability of random copolymers to encapsulate proteins, including the adsorption energy, copolymer average composition, and solvent selectivity. The adsorbed polymer chains have remarkably similar sequences, indicating that the proteins are able to select certain sequences that best reduce their exposure to the solvent. We also find that the protein surface coverage decreases when the fluctuation in the average distance between the protein adsorption sites increases. The results herein set the stage for computational design of random copolymers for stabilizing and delivering proteins across multiple media. [ABSTRACT FROM AUTHOR]

Controlling interactions between proteins and nanoparticles in electrolyte solutions is crucial for advancing biological sciences and biotechnology. The assembly of charged nanoparticles (NPs) and proteins in aqueous solutions can be directed by modifying the salt concentration. High concentrations of monovalent salt can induce the solubilization or crystallization of NPs and proteins. By using a multiscale coarse-grained molecular dynamics approach, we show that, due to ionic correlations in the electrolyte, NPs pairs at high monovalent salt concentrations interact via remarkably strong long-range attractions or repulsions, which can be split into three regimes depending on the surface charge densities of the NPs. NPs with zero-to-low surface charge densities interact via a long-range attraction that is stronger and has a similar range to the depletion attraction induced by polymers with radius of gyrations comparable to the NP diameter. On the other hand, moderately charged NPs with smooth surfaces as well as DNA-functionalized NPs with no possibility of hybridization between them interact via a strong repulsion of range and strength larger than the repulsion predicted by models that neglect ionic correlations, including the Derjaguin-Landau-Vervey-Overbeek (DLVO) model. Interactions between strongly charged NPs (>2 e/nm²), both types smooth and DNA-functionalized NPs, show an attractive potential well at intermediate-to-high salt concentrations, which demonstrates that electrolytes can induce aggregation of strongly charged NPs. Our work provides an improved understanding of the role of ionic correlations in NP assembly and design rules to utilize the salting-out process to crystallize NPs. [ABSTRACT FROM AUTHOR]

Directed crystallization of a large variety of nanoparticles, including proteins, via DNA hybridization kinetics has led to unique materials with a broad range of crystal symmetries. The nanoparticles are functionalized with DNA chains that link neighboring functionalized units. The shape of the nanoparticle, the DNA length, the sequence of the hybridizing DNA linker, and the grafting density determine the crystal symmetries and lattice spacing. By carefully selecting these parameters, one can, in principle, achieve all the symmetries found for both atomic and colloidal crystals of asymmetric shapes as well as new symmetries and can drive transitions between them. A scale-accurate coarse-grained model with explicit DNA chains provides the design parameters, including the degree of hybridization, to achieve specific crystal structures. The model also provides surface energy values to determine the shape of defect-free single crystals with macroscopic anisotropic properties, which has potential for the fabrication of materials with specific optical and mechanical properties. [ABSTRACT FROM AUTHOR]

ABSTRACT Self-assembled peptide amphiphile (PA) nanofibers are a class of supramolecular materials with promising applications in nanotechnology. Alignment of nanofibers, which is essential for biomaterials applications, is achieved at low salt concentrations in the PA nanofiber suspensions. Regardless of its importance, the effect of ion concentration on the properties of these nanostructures remains unexplored. Using atomistic molecular dynamics simulations, canonical PA nanostructures are investigated to elucidate the relationship between counterion condensation and morphological changes. Simulations reveal that nanofibers with the highest cross-section density have expanded radii. This expansion decreases the accessible volume for sodium counterions and diminishes the counterion translational entropy, while also reducing the total electrostatic potential. Interestingly, we show that the competition between these effects leads to a fraction of condensed counterions independent of the fiber radius. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017, 55, 901-906 [ABSTRACT FROM AUTHOR]

Surfaces formed by charged polymeric species are highly abundant in both synthetic and biological systems, for which maintaining an optimum contact distance and a pressure balance is paramount. Here we investigate interactions between surfaces of two same-charged and highly swollen polyelectrolyte gels, using extensive molecular dynamic simulations and minimal analytical methods. The external-pressure responses of the gels and the polymer-free ionic solvent layer separating two surfaces are considered. Simulations confirmed that the surfaces are held apart by osmotic pressure resulting from excess charges diffusing out of the network. At a threshold pressure, the counterion-induced osmotic pressure in the gel interiors becomes nearly equal to that in solvent gap, and the gels begin to deform. At the threshold pressure, the distance between surfaces is equivalent to the electrostatic screening length imposed by excess charges. Both the solvent layer and pressure dependence are well described by an analytical model based on the Poisson-Boltzmann solution for low and moderate electrostatic strengths. Scaling descriptions for the threshold pressure and critical distance compare well with the simulations. The threshold pressure decreases with increasing polymerization degree of network chains, similar to sparsely grafted polyelectrolyte brushes. As the electrostatic coupling strength is increased, the deviations from the analytical model also increase due to condensed counterions. Our results are of great importance for systems where charged gels or gel-like structures interact in various solvents, including systems encapsulated by gels and microgels in confinement. [ABSTRACT FROM AUTHOR]

The stability of colloidal suspensions is crucial in a wide variety of processes, including the fabrication of photonic materials and scaffolds for biological assemblies. The ionic strength of the electrolyte that suspends charged colloids is widely used to control the physical properties of colloidal suspensions. The extensively used two-body Derjaguin-Landau-Verwey-Overbeek (DLVO) approach allows for a quantitative analysis of the effective electrostatic forces between colloidal particles. DLVO relates the ionic double layers, which enclose the particles, to their effective electrostatic repulsion. Nevertheless, the double layer is distorted at high macroion volume fractions. Therefore, DLVO cannot describe the many-body effects that arise in concentrated suspensions. We show that this problem can be largely resolved by identifying effective point charges for the macroions using cell theory. This extrapolated point charge (EPC) method assigns effective point charges in a consistent way, taking into account the excluded volume of highly charged macroions at any concentration, and thereby naturally accounting for high volume fractions in both salt-free and added-salt conditions. We provide an analytical expression for the effective pair potential and validate the EPC method by comparing molecular dynamics simulations of macroions and monovalent microions that interact via Coulombic potentials to simulations of macroions interacting via the derived EPC effective potential. The simulations reproduce the macroion-macroion spatial correlation and the virial pressure obtained with the EPC model. Our findings provide a route to relate the physical properties such as pressure in systems of screened Coulomb particles to experimental measurements. [ABSTRACT FROM AUTHOR]

Interfacial liquid-liquid ion transport is of crucial importance to biotechnology and industrial separation processes including nuclear elements and rare earths. A water-in-oil microemulsion is formulated here with density and dimensions amenable to atomistic molecular dynamics simulation, facilitating convergent theoretical and experimental approaches to elucidate interfacial ion transport mechanisms. Lutetium(III) cations are transported from the 5 nm diameter water pools into the surrounding oil using an extractant (a lipophilic ligand). Changes in ion coordination sphere and interactions between the interfacial components are studied using a combination of synchrotron X-ray scattering, spectroscopy, and atomistic molecular dynamics simulations. Contrary to existing hypotheses, our model system shows no evidence of interfacial extractant monolayers, but rather ions are exchanged through water channels that penetrate the surfactant monolayer and connect to the oil-based extractant. Our results highlight the dynamic nature of the oil-water interface and show that lipophilic ion shuttles need not form flat monolayer structures to facilitate ion transport across the liquid-liquid interface. [ABSTRACT FROM AUTHOR]

Transport of ionic species in heterogeneous polymeric media is highly dependent on the charge distributions and interactions between mobile and immobile groups. Here we perform coarse-grained molecular dynamics simulations to study the ion dynamics in swollen polyelectrolyte gels under external electric fields. A nonlinear response of the ionic conductivity to an applied electric field, for field strengths that are comparable to the ionic coupling strength, is observed. This behavior correlates to a broadening of the ionic distribution around the polymer backbone under an increasing electric field. Also, we find that the weak-field ionic mobility in gels increases with density, which is opposite to the behavior of simple electrolytes. This relates to the mean coupling between charges that decreases in gels, but increases in simple electrolytes, with increasing density. These results provide more insights into the electric response of polyelectrolyte gels to support the development of applications that combine electric and mechanical properties of polyelectrolyte gels for energy storage, sensing, selective transport, and signal transfer. [ABSTRACT FROM AUTHOR]

We use molecular dynamics simulations to study the crystallizationof spherical nucleic-acid (SNA) gold nanoparticle conjugates, guidedby sequence-specific DNA hybridization events. Binary mixtures ofSNA gold nanoparticle conjugates (inorganic core diameter in the 8–15nm range) are shown to assemble into BCC, CsCl, AlB2, andCr3Si crystalline structures, depending upon particle stoichiometry,number of immobilized strands of DNA per particle, DNA sequence length,and hydrodynamic size ratio of the conjugates involved in crystallization.These data have been used to construct phase diagrams that are inexcellent agreement with experimental data from wet-laboratory studies. [ABSTRACT FROM AUTHOR]