Microscopic Self-organization Research Articles

DNA self-organization controls valence in programmable colloid design

Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence-the number of interparticle bonds-is a prerequisite for the assembly of complex architectures. The assembly can be directed via solid "patchy" particles with prescribed geometries to make, for example, a colloidal diamond. We demonstrate here that the nanoscale ordering of individual molecular linkers can combine to program the structure of microscale assemblies. Specifically, we experimentally show that covering initially isotropic microdroplets with N mobile DNA linkers results in spontaneous and reversible self-organization of the DNA into Z(N) binding patches, selecting a predictable valence. We understand this valence thermodynamically, deriving a free energy functional for droplet-droplet adhesion that accurately predicts the equilibrium size of and molecular organization within patches, as well as the observed valence transitions with N Thus, microscopic self-organization can be programmed by choosing the molecular properties and concentration of binders. These results are widely applicable to the assembly of any particle with mobile linkers, such as functionalized liposomes or protein interactions in cell-cell adhesion.

Probing the microscopic nuclear matter self-organization processes in the neutron star crust

We investigate microscopic self-organization processes of nuclear matter in the outermost layers of neutron star crusts with the DYWAN model. In this framework a pure mean-field description of nuclear dynamics has been performed. Starting from initial crystalline lattices, which are expected in the most external regions, the system organizes itself in exotic structures. The present work focuses on the effects of both the initial lattice symmetries and the nuclear species on the morphology and on the evolution of those structures. The response of the system is analyzed when it is subjected to random fluctuations of the initial lattice.

Some theoretical problems in chemistry and physics

AbstractRecently the need for incorporating so‐called Jordan blocks in the theoretical formulation of dynamical processes in Nature has been confronted and challenged. In addition, quantum mechanics has evolved from the very theoretical to the highly technological prompting the establishment of the new field of quantum technology. Initial studies in an extended time‐irreversible picture seem to indicate a possible map of degenerate Jordan forms onto the description of complex natural phenomena. Jordan blocks appear logically in the generalized dynamical picture. A compelling interpretation is microscopic self‐organization (MSO). Not only have the manifestation of quantum thermal correlations, and the emergence of generic time scales been established, but the present viewpoint also appears to throw new light on the age‐old problem of quantum mechanics versus relativity. A simple resonance model is presented that bears out the problems and possibilities. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

MICROSCOPIC SELF-ORGANIZATION IN NETWORKS AND REGULAR LATTICE

We report our numerical studies on the microscopic self-organizations of a reaction system in three types of networks: a regular network, a small-world network, and a random network as well as on a regular lattice. Our simulation results show that the topology of the network has an important effect on the communication among reaction molecules, and plays an important role in microscopic self-organization. The correlation length among reacting molecules in a random or a small-world network is much shorter compared with that in the regular network. As a result, it is much easier to obtain a microscopic self-organization in a small-world or a random network. A phase transition from a stochastic state to a synchronized state was observed when the randomness of a small-world network was increased. We also demonstrate that good synchronization activities of enzymatic turnover cycles can be developed on a regular lattice when the correlation length created by the fast diffusion of regulatory particles is large enough.

Self-organization in living cells: networks of protein machines and nonequilibrium soft matter.

Microscopic self-organization phenomena inside a living cell should not represent merely a reduced copy of self-organization in macroscopic systems. A cell is populated by active protein machines that communicate via small molecules diffusing through the cytoplasm. Mutual synchronization of machine cycles can spontaneously develop in such networks - an effect which is similar to coherent laser generation. On the other hand, an interplay between reactions, diffusion and phase transitions in biological soft matter may lead to the formation of stationary or traveling nonequilibrium nanoscale structures.

Microscopic self-organization in networks.

We report our numerical studies on microscopic self-organization of a reaction system in three types of differently connected networks: a regular network, a small-world network, and a random network. Our simulation results show that the topology of the network has an important effect on the communication among reaction molecules, and plays an important role in microscopic self-organization. The correlation length among reacting molecules in a random or a small-world network is much shorter compared with that in a regular one. As a result, it is much easier to obtain microscopic self-organization in a small-world or a random network. We also observed a phase transition from a stochastic state to a synchronized state when we increased the randomness of a small-world network.

Microscopic Self-Organization in Biochemical Reactions: A Lattice Model

Microscopic Self-Organization in Biochemical Reactions: A Lattice Model

Challenges for (photo)electrocatalysis research

Semiconductor materials which allow electron transfer reactions via metal centered mechanisms have proven to be excellent electrocatalysts (e.g. substituted Chevrell-phases such as Mo 4Ru 2Se 8 for oxygen reduction, RuS 2 for oxygen evolution from water). They combine a high density of transition metal states (concentrated into small energy bands because of energy gaps) with the ability to induce coordination chemical interfacial mechanisms. A change of the electron number in the cluster, of the degree of substitution with foreign atoms, and of additional metal atoms introduced into channels besides the clusters allows far reaching conclusion on requirements for electrocatalysis during single and multi-electron transfer. A prominent additional property of catalysts of metal centered mechanisms is the ability to favor these compared to other electrochemical interfacial processes. This gives the catalysts a selective behavior with interesting possibilities for application (e.g. methanol fuel cell). At ambient temperature, technical catalysts do not match biological catalysts. The degree of order (decreasing entropy) which is reached during the process of electrocatalysis is recognized as an important quality factor. The most efficient way to build up temporary order is by dynamic self-organization in an open system. It requires the existence of autocatalytic processes. Mechanisms are discussed which may lead to an improvement of electrocatalysis via microscopic self-organization in (photo)electrochemistry and photosynthesis: the thermodynamic force of a reaction (e.g. photon energy, electrochemical potential) may induce a structural reorganization providing an optimized activation complex for charge separation (reaction center) or for multi-electron transfer during water oxidation (manganese complex of photosynthesis).

Self-organized electron transfer

As other energy fluxes can be largely enhanced under non-linear conditions which permit local entropy export, such as heat flow under the ordered Benard convection, this should also be possible on a microscopic scale for electron transfer. As a precondition an autocatalytic molecular loop must exist, which transfers a small fraction of the energy, which drives the reaction, through the surrounding medium to assist the electron transfer in a non-linear way. Such an autocatalytic side loop, which may be facilitated by transfer of phonon energy, leads to microscopic self-organization, ie to a temporary dissipative structure. It may significantly improve electron transfer through a non-equilibrium electron distribution and a decrease of the activation barrier. The problem is theoretically treated as a Kramers approach, a Brownian motion in a non-uniform force field, in which the friction term may become active ( eg through phonon assisted autocatalytic energy input leading to a dissipative activated complex). A formula for “self-organized” electron transfer is obtained which yields—for finite activation barriers—significantly higher rates than the Marcus formula. The derived new type of electron transfer mechanism is analyzed. It may help to explain how biological catalysts have evolved the ability of generating favourable energy barriers for multi-electron transfer near the thermodynamic overall potential

Microscopic Self-Organization of Enzymic Reactions in Small Volumes

Using an enzymic reaction with allosteric product activation as example, we show that allosterically regulated reactions in small volumes may develop strong microscopic correlations between individual molecular reaction events. Such correlations lead to coherent synchronous activity of the enzymic molecular population which is revealed in frequent periodic spiking of the reaction.

Microscopic self-organization in living cells: a study of time matching

Biochemical subsystems of a living cell may operate with only a few thousand enzyme molecules and their response can be triggered by the entrance of individual molecules of a certain species. This mode of operation is not described by classical chemical kinetics, which deals with large numbers of reacting molecules. Theoretical estimates for the characteristic times of enzymic reactions in small cells and cellular compartments show that any two macromolecules within a micrometer-size volume meet each other each second and that the transit time, required for a mediator molecule to meet a target enzyme, is comparable to the duration of a catalytic round for a single enzyme molecule. When these conditions are satisfied, an enzymic subsystem represents a coherent molecular network with persistent strong temporal correlations between the catalytic events of individual enzyme molecules.