ABSTRACT
We investigate the Belousov-Zhabotinsky (BZ) reaction in an attempt to establish a basis for computation using chemical oscillators coupled via inhibition. The system consists of BZ droplets suspended in oil. Interdrop coupling is governed by the non-polar communicator of inhibition, Br2. We consider a linear arrangement of three droplets to be a NOR gate, where the center droplet is the output and the other two are inputs. Oxidation spikes in the inputs, which we define to be TRUE, cause a delay in the next spike of the output, which we read to be FALSE. Conversely, when the inputs do not spike (FALSE) there is no delay in the output (TRUE), thus producing the behavior of a NOR gate. We are able to reliably produce NOR gates with this behavior in microfluidic experiment.
ABSTRACT
We have functionalized the sides of fd bacteriophage virions with oligonucleotides to induce DNA hybridization driven self-assembly of high aspect ratio filamentous particles. Potential impacts of this new structure range from an entirely new building block in DNA origami structures, inclusion of virions in DNA nanostructures and nanomachines, to a new means of adding thermotropic control to lyotropic liquid crystal systems. A protocol for producing the virions in bulk is reviewed. Thiolated oligonucleotides are attached to the viral capsid using a heterobifunctional chemical linker. A commonly used system is utilized, where a sticky, single-stranded DNA strand is connected to an inert double-stranded spacer to increase inter-particle connectivity. Solutions of fd virions carrying complementary strands are mixed, annealed, and their aggregation is studied using dynamic light scattering (DLS), fluorescence microscopy, and atomic force microscopy (AFM). Aggregation is clearly observed on cooling, with some degree of local order, and is reversible when temperature is cycled through the DNA hybridization transition.
Subject(s)
Bacteriophage M13/metabolism , DNA/chemistry , Virion/metabolism , Bacteriophage M13/isolation & purification , Capsid Proteins/chemistry , Capsid Proteins/metabolism , DNA/metabolism , Light , Microscopy, Atomic Force , Microscopy, Fluorescence , Nanostructures/chemistry , Nucleic Acid Conformation , Nucleic Acid Hybridization , Oligonucleotides/chemistry , Oligonucleotides/metabolism , Scattering, RadiationABSTRACT
We report on the construction of colloidal stars: 1 microm polystyrene beads grafted with a dense brush of 1 microm long and 10 nm wide charged semiflexible filamentous viruses. The pair interaction potentials of colloidal stars are measured using an experimental implementation of umbrella sampling, a technique originally developed in computer simulations in order to probe rare events. The influence of ionic strength and grafting density on the interaction is measured. Good agreements are found between the measured interactions and theoretical predictions based upon the osmotic pressure of counterions.
Subject(s)
Bacteriophage M13/chemistry , Capsid Proteins/chemistry , Colloids/chemistry , Polystyrenes/chemistry , Algorithms , Colloids/chemical synthesis , Computer Simulation , Fluorescence , Gold/chemistry , Microscopy, Electron, Transmission , Osmolar ConcentrationABSTRACT
Measurements of liquid-liquid phase transition temperatures (cloud points) of mixtures of a protein (lysozyme) and a polymer, poly(ethylene glycol) (PEG) show that the addition of low molecular weight PEG stabilizes the mixture whereas high molecular weight PEG was destabilizing. We demonstrate that this behavior is inconsistent with an entropic lysozyme-PEG depletion interaction and suggest that an energetic lysozyme-PEG attraction is responsible. In order to independently characterize the lysozyme-PEG interactions, light scattering experiments on the same mixtures were performed to measure second and third virial coefficients. These measurements indicate that PEG induces repulsion between lysozyme molecules, contrary to the depletion prediction. Furthermore, it is shown that third virial terms must be included in the mixture's free energy in order to qualitatively capture our data.
Subject(s)
Muramidase/chemistry , Polyethylene Glycols/chemistry , Light , Molecular Weight , Phase Transition , Scattering, RadiationABSTRACT
A method is presented for determining second virial coefficients (B(2)) of protein solutions from retention time measurements in size exclusion chromatography. We determine B(2) by analyzing the concentration dependence of the chromatographic partition coefficient. We show the ability of this method to track the evolution of B(2) from positive to negative values in lysozyme and bovine serum albumin solutions. Our size exclusion chromatography results agree quantitatively with data obtained by light scattering.
Subject(s)
Chromatography, Gel/methods , Flow Injection Analysis/methods , Muramidase/chemistry , Protein Interaction Mapping/methods , Serum Albumin, Bovine/chemistry , Algorithms , Macromolecular Substances , Muramidase/analysis , Protein Binding , Reproducibility of Results , Sensitivity and Specificity , Serum Albumin, Bovine/analysisABSTRACT
There is increasing evidence that entropy can induce microphase separation in binary fluid mixtures interacting through hard particle potentials. One such phase consists of alternating two-dimensional liquidlike layers of rods and spheres. We study the transition from a uniform miscible state to this ordered state using computer simulations, and compare results to experiments and theory. We conclude the following: (1) There is stable entropy driven microphase separation in mixtures of parallel rods and spheres. (2) Adding spheres smaller than the rod length decreases the total volume fraction needed for the formation of a layered phase, and therefore small spheres effectively stabilize the layered phase; the opposite is true for large spheres. (3) The degree of this stabilization increases with increasing rod length.
ABSTRACT
Aqueous suspensions of mixtures of the rodlike virus tobacco mosaic virus (TMV) with globular macromolecules such as polyethylene oxide (PEO) or bovine serum albumin (BSA) phase separate and exhibit rich and strikingly similar phase behavior. Isotropic, nematic, lamellar, and crystalline phases are observed as a function of the concentration of the constituents and ionic strength. The observed phase behavior is considered to arise from attractions between the two particles induced by the presence of BSA or PEO. For the TMV/BSA mixtures, the BSA adsorbs to the TMV and bridging of the BSA between TMV produces the attractions. For TMV/PEO mixtures, attractions are entropically driven via excluded volume effects known alternatively as the "depletion interaction" or "macromolecular crowding."
