Related papers: Efficiency of DNA replication in the Polymerase Ch…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
We consider a single-species diffusion-limited annihilation reaction with reactants confined to a two-dimensional surface with one arbitrarily large dimension and the other comparable in size to interparticle distances. This situation could…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
The cage model for polymer reptation, proposed by Evans and Edwards, and its recent extension to model DNA electrophoresis, are studied by numerically exact computation of the drift velocities for polymers with a length L of up to 15…
A phenomenological model based on the three-dimensional theory of nonlinear elasticity is developed to describe the phenomenon of overstretching in the force-extension curve for dsDNA. By using the concept of a material with multiple…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
Diffusion through semipermeable structures arises in a wide range of processes in the physical and life sciences. Examples at the microscopic level range from artificial membranes for reverse osmosis to lipid bilayers regulating molecular…
Tracer-diffusion of small molecules through dense systems of chain polymers is studied within an athermal lattice model, where hard core interactions are taken into account by means of the site exclusion principle. An approximate mapping of…
Recently the physical characterization of a number of biological processes has proven indispensable for a full understanding of natural phenomena. One such example is the mechanical properties of transcription, which have been shown to have…
I develop a kinetic mechanism to explain chain folding in polymer crystallization which is based on the competition between the formation of stems, which is due to frequent occupations of trans states along the chains in the supercooled…
Diffusion models excel at modeling complex data distributions, including those of images, proteins, and small molecules. However, in many cases, our goal is to model parts of the distribution that maximize certain properties: for example,…
Cell reproduction involves replication of diverse molecule species, in contrast to simple replication system with fewer components. Here, we address why such diversity is sustained despite the efficiency of simple replication systems, using…
We propose a novel approach for modeling chemical reactions within the particle-based Fokker-Planck framework for gas flow simulations which conserves mass, momentum, and energy while retaining the performance advantages of the…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees…
A deterministic mathematical model for the polymerization of hyperbranched molecules accounting for substitution, cyclization, and shielding effect has been developed as a system of nonlinear population balances. The solution obtained by a…
Based on the theory of stochastic chemical kinetics, the inherent randomness and stochasticity of biochemical reaction networks can be accurately described by discrete-state continuous-time Markov chains. The analysis of such processes is,…
We discuss a problem of cyclization of a polymer molecule, which is an important example of reaction in a system showing strongly non-Markovian behavior on the timescales of interest. We show that the knowledge of the joint three-time…
This paper presents a probabilistic approach for DNA sequence analysis. A DNA sequence consists of an arrangement of the four nucleotides A, C, T and G and different representation schemes are presented according to a probability measure…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…