Related papers: Proteins Evolution Upon Point Mutations
With the help of lattice Monte Carlo modelling of heteropolymers, we show that the necessary condition for a protein to fold on short call is to proceed through partially folded intermediates. These elementary structures are formed at an…
Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the last few years fold-change detecting mechanisms, based on transcriptional networks, have been…
The effect of mutations on protein structures is usually rather localized and minor. Finding a mutation that can single-handedly change the fold and/or topology of a protein structure is a rare exception. The A31P mutant of the homodimeric…
Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds,…
Studying evolutionary correlations in alignments of homologous sequences by means of an inverse Potts model has proven useful to obtain residue-residue contact energies and to predict contacts in proteins. The quality of the results depend…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
In this work, we study the behavior of elementary electromagnetic sources, i.e., point-like electric charges and intrinsic magnetic dipoles, in the presence of homogeneous electromagnetic fields in a classical and covariant setting. We show…
Many crucial biological processes rely on networks of protein-protein interactions. Predicting the effect of amino acid mutations on protein-protein binding is vital in protein engineering and therapeutic discovery. However, the scarcity of…
We twice modify the Penna model for biological ageing. First we introduce back (good) mutations and a memory for them into the model. It allows us to observe an improvement of the species fitness over long time scales as well as punctuated…
The Weismann barrier, or the impossibility of inheritance of acquired traits, comprises a foundation of modern biology, and it has been a major obstacle in establishing the connection between evolution and ontogenesis. We propose the…
In this paper we study the effect of rare mutations, driven by a marked point process, on the evolutionary behavior of a population. We derive a Kolmogorov equation describing the expected values of the different frequencies and prove some…
We couple the issue of evolution in the laws of physics with that of violations of energy conservation. We define evolution in terms of time variables canonically dual to ``constants'' (such as $\Lambda$, the Planck mass or the…
We investigate the adiabatic orbital evolution of a point particle in the Kerr spacetime due to the emission of gravitational waves. In the case that the timescale of the orbital evolution is enough smaller than the typical timescale of…
For asexual organisms point mutations correspond to local displacements in the genotypic space, while other genotypic rearrangements represent long-range jumps. We investigate the spreading properties of an initially homogeneous population…
We show that in experimental atomic force microscopy studies of the lifetime distribution of mechanically stressed folded proteins the effects of externally applied fluctuations can not be distinguished from those of internally present…
The aim of this paper is to study the evolution of a material point of a body by itself, and not the body as a whole. To do this, we construct a groupoid encoding all the intrinsic properties of the particle and its characteristic…
Protein mutations can significantly influence protein solubility, which results in altered protein functions and leads to various diseases. Despite of tremendous effort, machine learning prediction of protein solubility changes upon…
Single-molecule force spectroscopy has opened a new field of research in molecular biophysics and biochemistry. Pulling experiments on individual proteins permit us to monitor conformational transitions with high temporal resolution and…
A gene's rate of sequence evolution is among the most fundamental evolutionary quantities in common use, but what determines evolutionary rates has remained unclear. Here, we show that the two most commonly used methods to disentangle the…
We construct center manifolds for a class of degenerate evolution equations including the steady Boltzmann equation and related kinetic models, establishing in the process existence and behavior of small-amplitude kinetic shock and boundary…