The emergence of interstellar molecular complexity explained by interacting networks

The Conformational Contribution to Molecular Complexity and Its Implications for Information Processing in Living Beings and Chemical Artificial Intelligence

This work highlights the relevant contribution of conformational stereoisomers to the complexity and functions of any molecular compound. Conformers have the same molecular and structural formulas but different orientations of the atoms in the three-dimensional space. Moving from one conformer to another is possible without breaking covalent bonds. The interconversion is usually feasible through the thermal energy available in ordinary conditions. The behavior of most biopolymers, such as enzymes, antibodies, RNA, and DNA, is understandable if we consider that each exists as an ensemble of conformers. Each conformational collection confers multi-functionality and adaptability to the single biopolymers. The conformational distribution of any biopolymer has the features of a fuzzy set. Hence, every compound that exists as an ensemble of conformers allows the molecular implementation of a fuzzy set. Since proteins, DNA, and RNA work as fuzzy sets, it is fair to say that life's logic is fuzzy. The power of processing fuzzy logic makes living beings capable of swift decisions in environments dominated by uncertainty and vagueness. These performances can be implemented in chemical robots, which are confined molecular assemblies mimicking unicellular organisms: they are supposed to help humans "colonise" the molecular world to defeat diseases in living beings and fight pollution in the environment.

Complex Networks and Interacting Particle Systems

Complex networks is a growing discipline aimed at understanding large interacting systems. One of its goals is to establish a relation between the interactions of a system and the networks structure that emerges. Taking a Lennard-Jones particle system as an example, we show that when interactions are governed by a potential, the notion of structure given by the physical arrangement of the interacting particles can be interpreted as a binary approximation to the interaction potential. This approximation simplifies the calculation of the partition function of the system and allows to study the stability of the interaction structure. We compare simulated results with those from the approximated partition function and show how the network and system perspective complement each other. With this, we draw a direct connection between the interactions of a molecular system and the network structure it forms and assess the degree to which it describes the system. We conclude by discussing the advantages and limitations of this method for weighted networks, as well as how this concept might be extended to more general systems.

Prebiotic Synthesis of ATP: A Terrestrial Volcanism-Dependent Pathway

Adenosine triphosphate (ATP) is a multifunctional small molecule, necessary for all modern Earth life, which must be a component of the last universal common ancestor (LUCA). However, the relatively complex structure of ATP causes doubts about its accessibility on prebiotic Earth. In this paper, based on previous studies on the synthesis of ATP components, a plausible prebiotic pathway yielding this key molecule is constructed, which relies on terrestrial volcanism to provide the required materials and suitable conditions.

Carrier Transport in Colloidal Quantum Dot Intermediate Band Solar Cell Materials Using Network Science

Colloidal quantum dots (CQDs) have been proposed to obtain intermediate band (IB) materials. The IB solar cell can absorb sub-band-gap photons via an isolated IB within the gap, generating extra electron-hole pairs that increase the current without degrading the voltage, as has been demonstrated experimentally for real cells. In this paper, we model the electron hopping transport (HT) as a network embedded in space and energy so that a node represents the first excited electron state localized in a CQD while a link encodes the Miller-Abrahams (MA) hopping rate for the electron to hop from one node (=state) to another, forming an "electron-HT network". Similarly, we model the hole-HT system as a network so that a node encodes the first hole state localized in a CQD while a link represents the MA hopping rate for the hole to hop between nodes, leading to a "hole-HT network". The associated network Laplacian matrices allow for studying carrier dynamics in both networks. Our simulations suggest that reducing both the carrier effective mass in the ligand and the inter-dot distance increases HT efficiency. We have found a design constraint: It is necessary for the average barrier height to be larger than the energetic disorder to not degrade intra-band absorption.

Organic Disordered Semiconductors as Networks Embedded in Space and Energy

Organic disordered semiconductors have a growing importance because of their low cost, mechanical flexibility, and multiple applications in thermoelectric devices, biosensors, and optoelectronic devices. Carrier transport consists of variable-range hopping between localized quantum states, which are disordered in both space and energy within the Gaussian disorder model. In this paper, we model an organic disordered semiconductor system as a network embedded in both space and energy so that a node represents a localized state while a link encodes the probability (or, equivalently, the Miller-Abrahams hopping rate) for carriers to hop between nodes. The associated network Laplacian matrix allows for the study of carrier dynamics using edge-centric random walks, in which links are activated by the corresponding carrier hopping rates. Our simulation work suggests that at room temperature the network exhibits a strong propensity for small-network nature, a beneficial property that in network science is related to the ease of exchanging information, particles, or energy in many different systems. However, this is not the case at low temperature. Our analysis suggests that there could be a parallelism between the well-known dependence of carrier mobility on temperature and the potential emergence of the small-world property with increasing temperature.