Related papers: The entropic lock and key of the histone code
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein…
Transition metal ions play crucial roles in the structure and function of numerous proteins, contributing to essential biological processes such as catalysis, electron transfer, and oxygen binding. However, accurately modeling the…
Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction…
A theoretical analysis is presented for the excitation of single many-electron atoms and ions by twisted (or vortex) light. Special emphasis is put on excitations that can proceed via several electric and magnetic multipole channels. We…
Requiring stability of genetic code against translation errors, modelised by suitable mathematical operators in the crystal basis model of the genetic code, the main features of the organisation in multiplets of the mitochondrial and of the…
Despite more than half a century of studies in heavy-fermion compounds, a full understanding of the various possible magnetic ordering phenomena is still far from complete. Some heavy-fermion materials show so-called hidden-order phases,…
Recent progress has been made in the understanding of the physical properties of chromatin -- the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of…
We develop a linked cluster method to calculate the spectral weights of many-particle excitations at zero temperature. The dynamical structure factor is expressed as a sum of exclusive structure factors, each representing contributions from…
We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes and the vertical distance $d$…
Multisite protein modification is a ubiquitous mechanism utilized by cells to control protein functions. We have recently proposed a dynamical description of multisite protein modification which embodies all the essential features of the…
Understanding and quantifying entanglement entropy is crucial to characterize the quantum behaviors that drive phenomena in a variety of systems. Rare-earth spin complexes, with their unique magnetic properties, provide fertile ground for…
A representation of the genetic code as a six-dimensional Boolean hypercube is proposed. It is assumed here that this structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition.…
DNA exhibits remarkable potential as a data storage solution due to its impressive storage density and long-term stability, stemming from its inherent biomolecular structure. However, developing this novel medium comes with its own set of…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…
We discuss the transition strength between the disordered ground state and the basic low-lying triplet excitation for the Heisenberg chain with alternating exchange based on series expansions in the interdimer interaction up to tenth order.…
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need…
Gene regulation relies on the specificity of transcription factor (TF) - DNA interactions. In equilibrium, limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate…
ExpressInHost (https://gitlab.com/a.raguin/expressinhost) is a GTK/C++ based user friendly graphical interface that allows tuning the codon sequence of an mRNA for recombinant protein expression in a host microorganism. Heterologous gene…
A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is proposed, in which parameters are embedded into a low-cost, low-level (LL) ab initio theory and adjusted to obtain agreement…