Point-like Molecules Research Articles

The interplay of channel geometry and molecular features determines diffusion in lipidic cubic phases.

The transport behavior of inverse bicontinuous cubic phases is experimentally investigated as the combined outcome of solute molecular structure and geometrical details of the confining symmetry. Molecular diffusion is discussed in relation to curvature, bottlenecks, and interfacial properties of each cubic phase. Point-like molecules show faster diffusion across the double diamond (Pn3¯m) symmetry, while unfolded macromolecules display better performance inside the double primitive (Im3¯m) cubic phase. The former observation is in agreement with previous simulation work, whereas the latter indicates that dedicated theory needs to be developed for diffusing polymers. Furthermore, the effect of electrostatic interactions is assessed by a study of diffusion of nanoparticles and is rationalized via a combination of simulations and theoretical considerations as the result of a competition between water mobility and geometrical features of the channel.

Capturing Brownian dynamics with an on-lattice model of hard-sphere diffusion

Conventional master equation approaches approximate the diffusion of molecules in continuum space by the process of particles hopping on a spatial lattice. The hopping probability from one voxel (spatial lattice point) to its neighbor is usually considered to be constant throughout space. Such an assumption is only consistent with pointlike molecules and thus neglects volume-exclusion effects due to finite particle size. A few studies have attempted to introduce volume-exclusion effects by choosing the hopping probability from one voxel to a neighboring one to be a linear function of the number density. Here, we formulate an alternative master equation in which the hopping probability is equal to the fraction of available space in the neighboring voxel as estimated using scaled particle theory. This leads to the hopping probability being a nonlinear function of the number density. A mean-field approximation (mfa) leads to a partial differential equation of the advection-diffusion type. We show that the time evolution of the particle number density sampled using the stochastic simulation algorithm associated with the new master equation and the number density obtained by numerical integration of the mfa are in good agreement with each other. They are also distinctly different than the time evolution predicted by the conventional master equation and those with hopping probabilities which are linear functions of the number density. The results from the new lattice description are also shown to be in very good agreement with the lattice-free method of Brownian dynamics, even for highly crowded scenarios.

On the definition of the excess permittivity of a fluid mixture. II

In a previous work, an ideal fluid mixture is assumed to be a homogeneous linear and isotropic system that verifies the following conditions: (I) no interaction between molecules, (II) point-like molecules and (III) under fixed temperature and pressure conditions the number of molecules per unit volume is the same for both the individual components and the mixture. It was shown that for such ideal mixture the permittivity is the sum of the individual permittivities weighted with the mole fractions of the components. In this work it is shown that independently of the latter assumption the permittivity of the system can be expressed as the sum of the individual permittivities weighted with the volume fractions of the components.

Lipopolyamine-Mediated Single Nanoparticle Formation of Calf Thymus DNA Analyzed by Fluorescence Correlation Spectroscopy

The aim of this study is to analyze linear calf thymus DNA (ct DNA) nanoparticle formation with N4,N9-dioleoylspermine and N1-cholesteryl spermine carbamate. Fluorescence correlation spectroscopy (FCS) was used to determine the quality of ct DNA condensed by lipopolyamines. ct DNA was prelabeled with PicoGreen (PG) to allow fluorescence intensity fluctuation measurement and analysis. N4,N9-dioleoylspermine efficiently condensed ct DNA into point-like molecules with diffusion coefficient (D) = 1.8 x 10(-12) m2/s and particle number (PN) = 0.7 [at ammonium/phosphate (N/P) charge ratio = 1.0-1.5]. The determined PN values are close to the theoretical value of 0.6, providing evidence that the DNA conformation has been fully transformed, and thus a single nanoparticle has been detected. N1-cholesteryl spermine carbamate showed (slightly) poorer DNA condensation efficiency, even at higher N/P ratios (N/P = 1.5-2.5) with D = 1.3 x 10(-12) m2/s and PN value of 5.2. N4,N9-dioleoylspermine is a more efficient DNA-condensing agent than N1-cholesteryl spermine carbamate. FCS measurement using PG as the probe is a novel analytical method to detect single nanoparticles of condensed DNA in nonviral gene therapy formulation studies.

Nature of polarized excitons

The electromagnetic interaction energy of a molecular aggregate consisting of pointlike molecules in the presence of an electromagnetic field is derived. The corresponding Hamiltonian consists of three parts; H0 describes the aggregate in the absence of the electromagnetic field, H1 describes the interaction of the molecules with the external field, and H2 corresponds to the induced interaction between the molecules. Based on this Hamiltonian we derive a self-consistent equation of motion for a quasiparticle, which we refer to as a polarized exciton. The equation has the same form as the one in classical dipole theory. The polarized exciton model is based on a time-dependent perturbative treatment and corresponds to the assumption H0≫H1+H2. Our model is compared to standard exciton theory, which is based on the assumption H0≫H2≫H1. In particular the differences and similarities are illustrated for a direct example, a finite linear chain. We advocate the use of polarized excitons to fully account for the physics in these systems.

Energy transfer between finite-sized interacting molecules in a one-dimensional system

Abstract A theoretical model of electronic excitation energy transport between finite-size interacting molecules has been presented. To develop the model we have considered the respective finite-size particles distribution functions and their relation to the energy transfer process. Using appropriate averaging procedures, we calculated donor fluorescence decay profiles for one-dimensional molecular systems. A discussion of the results and a comparison with the findings of other authors are presented. It was shown that at a given concentration of interacting particles finite-size effects lead to significantly slower donor fluorescence decay profiles in comparison with point-like molecules considered in the Forster theory. We have also presented equations describing donor fluorescence decay profiles due to interaction with nearest-neighbor acceptor molecules.

Condensation of directed macromolecules

A liquid of point-like molecules and one-dimensional directed macromolecules (polymers) is constructed on a lattice from atoms with N colors and two spin orientations. Each site can be occupied by one and only one pair of atoms with the same color and opposite spin. Consequently, there is a competition between atoms with color α either belonging to a point-like molecule or to a macromolecule. Introducing a chemical potential for the point-like molecules we observe a second-order phase transition in the grand canonical ensemble where the density of macromolecules is the order parameter. The limit N→∞ can be solved exactly. In the macromolecular phase there are massless fluctuations because of a spontaneously broken symmetry.