相关论文: Selection of prebiotic oligonucleotides by cyclic …
Eukaryotic cells maintain their inner order by a hectic process of distillation of molecular factors taking place on the surface of their lipid membranes. To understand the properties of this molecular sorting process, a physical model of…
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 human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
We introduce a simple physical picture to explain the process of molecular sorting, whereby specific proteins are concentrated and distilled into submicrometric lipid vesicles in eukaryotic cells. To this purpose, we formulate a model based…
We design a system with a binary suspension of colloids and a surface that triggers the self-assembly of crystallites with a finite thickness. The proposed design allows controlling the number of layers forming the aggregate and constrains…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
Isologous diversification theory for cell differentiation is proposed, based on simulations of interacting cells with biochemical networks and cell division process following consumption of some chemicals. According to the simulations of…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
Usually, we expect large particles to sediment faster than small of the same material. Contrary to this intuition, we report a dynamical competition between sedimentation and phase ordering which leads to smaller particles settling faster…
The liquid-liquid phase separation of biomolecules is an important process for intracellular organization. Biomolecular sequence combinatorics leads to a large variety of proteins and nucleic acids which can interact to form a diversity of…
Reliable cell counting and segmentation of oligodendrocyte progenitor cells (OPCs) are critical image analysis steps that could potentially unlock mysteries regarding OPC function during pathology. We propose a saliency-based method to…
At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge {\it de novo} with relative ease. At early times of molecular evolution,…
Reduction of information entropy along with ever-increasing complexity are among the key signatures of living matter. Understanding the onset of such behavior in early prebiotic world is essential for solving the problem of origins of life.…
DNA-coated colloids can self-assemble into an incredible diversity of crystal structures, but applications of this technology are limited by poor understanding and control over the dynamical crystallization pathways. To address this…
A binary mixture of particles interacting with spherically-symmetric potentials leading to microsegregation is studied by theory and molecular dynamics (MD) simulations. We consider spherical particles with equal diameters and volume…
Molecular sorting is a fundamental process that allows eukaryotic cells to distill and concentrate specific chemical factors in appropriate cell membrane subregions, thus endowing them with different chemical identities and functional…
Active matter systems being in a non-equilibrium state, exhibit complex behaviors such as self-organization and giving rise to emergent phenomena. There are many examples of active particles with biological origins, including bacteria and…
This paper presents and tests a previously unrecognised mechanism for driving a replicating molecular system on the prebiotic earth. It is proposed that cell-free RNA replication in the primordial soup may have been driven by self-sustained…