Related papers: Mutation model for oligonucleotides fitting a Yule…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
In this paper, we study the stability of an Ordinary Differential Equation (ODE) usually referred to as Cyclic Feedback Loop, which typically models a biological network of molecules where each molecule regulates its successor in a cycle.…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
We probe small scalar coupling differences via the coherent interactions between two nuclear spin singlet states in organic molecules. We show that the spin-lock induced crossing (SLIC) technique enables the coherent transfer of singlet…
We investigate equilibrium properties of small world networks, in which both connectivity and spin variables are dynamic, using replicated transfer matrices within the replica symmetric approximation. Population dynamics techniques allow us…
Evolution consists of distinct stages: cosmological, biological, linguistic. Since biology verges on natural sciences and linguistics, we expect that it shares structures and features from both forms of knowledge. Indeed, in DNA we…
In several recent papers new gene-detection algorithms were proposed for detecting protein-coding regions without requiring learning dataset of already known genes. The fact that unsupervised gene-detection is possible closely connected to…
For neutral genealogy models in a finite, possibly non-constant population, there is a convenient ordered rearrangement of the particles, known as the lookdown representation, that greatly simplifies the analysis of the family trees. By…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
A theory is presented of the longitudinal dispersion of DNA under equilibrium confined in a nanochannel. Orientational fluctuations of the DNA chain build up to give rise to substantial fluctuations of the coil in the longitudinal direction…
The solution of non-linear evolution equations for dense nuclear gluon density has been suggested as one of the relevant mechanisms of pA and AA collisions at collider energies. Here we study a simple parameterization for the unintegrated…
A theory of systems with long-range correlations based on the consideration of binary N-step Markov chains is developed. In our model, the conditional probability that the i-th symbol in the chain equals zero (or unity) is a linear function…
There are currently no models readily available that provide nucleon-nucleon spin dependent scattering amplitudes at high energies ($s \geq 6$ $ GeV^2$). This work aims to provide a model for calculating these high energy scattering…
The first level of folding of DNA in eukaryotes is provided by the so called '10 nm chromatin fibre', where DNA wraps around histone proteins (approx. 10 nm in size) to form nucleosomes, which go on to create a zig zagging bead on a string…
Infinite-range spin-glass models with Levy-distributed interactions show a freezing transition similar to disordered spin systems on finite connectivity random graphs. It is shown that despite diverging moments of the local field…
The spin dynamics of stripes in high-temperature superconductors and related compounds is studied in the framework of a spin-wave theory for a simple spin-only model. The magnon dispersion relation and the magnetic structure factor are…
Gene sequences in the vicinity of splice sites are found to possess dinucleotide periodicities, especially RR and YY, with the period close to the pitch of nucleosome DNA. This confirms previously reported finding about preferential…
In reliable decision-making systems based on machine learning, models have to be robust to distributional shifts or provide the uncertainty of their predictions. In node-level problems of graph learning, distributional shifts can be…
Experiments in coherent nuclear and electron magnetic resonance, and optical spectroscopy correspond to control of quantum mechanical ensembles, guiding them from initial to final target states by unitary transformations. The control inputs…
Entanglement spectra (ES) for the critical SU(N) (2 <= N <= 4) spin chains and other integrable models of finite length are studied with the density matrix renormalization group method. For all models under investigation, the level spacings…