Related papers: How did prebiotic polymers become informational fo…
We define a lattice model for the interaction of a polymer with water. We solve the model in a suitable approximation. In the case of a non-polar homopolymer, for reasonable values of the parameters, the polymer is found in a non-compact…
Volatiles are compounds with low sublimation temperatures, and they make up most of the condensible mass in typical planet-forming environments. They consist of relatively small, often hydrogenated, molecules based on the abundant elements…
Holographic functional methods are introduced as probes of discrete time-stepped maps that lead to chaotic behavior. The methods provide continuous time interpolation between the time steps, thereby revealing the maps to be…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
The origin of life is shrouded in mystery, with few surviving clues, obscured by evolutionary competition. Previous reviews have touched on the complementary approaches of top-down and bottom-up synthetic biology to augment our…
Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple…
Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
Here, we provide an overview of theoretical approaches to semiflexible polymers and their networks. Such semiflexible polymers have large bending rigidities that can compete with the entropic tendency of a chain to crumple up into a random…
We study analytically and numerically a model metabolic cycle composed of an arbitrary number of species of catalytically active particles. Each species converts a substrate into a product, the latter being used as the substrate by the next…
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…
We present a simple mathematical model that captures the evolutionary capabilities of a prebiotic compartment or protocell. In the model the protocell contains an autocatalytic set whose chemical dynamics is coupled to the growth-division…
Chemically fueled supramolecular systems can exhibit complex, time-dependent behaviors reminiscent of living matter when maintained far from equilibrium by continuous energy or fuel consumption. Here, we introduce a minimal…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…
We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…