Related papers: How did prebiotic polymers become informational fo…

The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are…

In biology, ligand mediated transitions (LMT), where the binding of a molecular ligand onto the binding site of a receptor molecule leads to a well-defined change in the conformation of the receptor, are often referred to as 'the second…

A generalized autocatalytic model for chiral polymerization is investigated in detail. Apart from enantiomeric cross-inhibition, the model allows for the autogenic (non-catalytic) formation of left and right-handed monomers from a substrate…

In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…

We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…

The origin of life is yet a compelling scientific mystery that has sometimes been attributed to high-pressure impacts by small solar system bodies such as comets, meteoroids, asteroids, and transitional objects. High-pressure torsion (HPT)…

A core topic of research in prebiotic chemistry is the search for plausible synthetic routes that connect the building blocks of modern life such as sugars, nucleotides, amino acids, and lipids to "molecular food sources" that have likely…

The emergence of self-replication and information transmission in life's origin remains unexplained despite extensive research on the topic. A hypothesis explaining the transition from a simple organic world to a complex RNA world is…

We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…

In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…

Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing "replicator-first" and "metabolism-first"…

Biological cells with all of their surface structure and complex interior stripped away are essentially vesicles - membranes composed of lipid bilayers which form closed sacs. Vesicles are thought to be relevant as models of primitive…

This paper presents a speculative model of the cognitive mechanisms underlying the transition from episodic to mimetic (or memetic) culture with the arrival of Homo erectus, which Donald [1991] claims paved the way for the unique features…

A great number of biological organisms live in aqueous environments. Major evolutionary transitions, including the emergence of life itself, likely occurred in such environments. While the chemical aspects of the role of water in biology…

A universal feature of the biochemistry of any living system is that all the molecules and catalysts that are required for reactions of the system can be built up from an available food source by repeated application of reactions from…

Polymers with active segments constitute prospective future materials and are used as a model for some biological systems such as chromatin. The directions of the active forces are typically introduced with temporal or spatial correlations…

Based on the oligomer-world hypothesis we propose an abstract model where the molecular recognition among oligomers is described in the shape space. The origin of life in the oligomer world is regarded as the establishment of a metabolic…

In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using standard exact 3-dimensional lattice model we evolve sequences starting from random ones…

Helical motifs are ubiquitious in macromolecular systems. The mechanism of spontaneous emergence of helicity is unknown, especially in cases where torsional interactions are absent. Emergence of helical order needs coordinated organization…

Although it has been notoriously difficult to pin down precisely what it is that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique…