Related papers: Breathing dynamics based parameter sensitivity ana…
The Discrete NonLinear Schr\"odinger (DNLS) equation displays a parameter region characterized by the presence of localized excitations (breathers). While their formation is well understood and it is expected that the asymptotic…
A basic model of hydrogen bonds related to $\rm{H}_2\rm{O}$, which is adapted from the Jaynes--Cummings model, is suggested, and its different dynamic features are studied theoretically. In this model, the making and breaking of hydrogen…
Dynamical models of cognition play an increasingly important role in driving theoretical and experimental research in psychology. Therefore, parameter estimation, model analysis and comparison of dynamical models are of essential…
We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination…
This paper devotes to formulating several multiscale models to study the effect of pH-dependent ionic inhomogeneity on the electrical potential distributions and the graded elastic properties of a nanoscale DNA film and the related bending…
We study the temperature dependence of static and dynamic responses of Coulomb interacting particles in two-dimensional traps across the thermal crossover from an amorphous solid- to liquid-like behaviors. While static correlations, that…
The early planetesimal growth proceeds through a sequence of sticking collisions of dust agglomerates. Very uncertain is still the relative velocity regime in which growth rather than destruction can take place. The outcome of a collision…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could…
In the demanding biosensing environment, improving selection efficiency strategies has become an issue of great significance. DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, are representative of the…
Collective coordinate and direct numerical integration methods are applied to the analysis of a one-dimensional DNA model. A modification of the coupling constant in an extended region is found to be less selective towards the breather it…
The classical Hodgkin--Huxley (HH) model neglects the time-dependence of ion concentrations in spiking dynamics. The dynamics is therefore limited to a time scale of milliseconds, which is determined by the membrane capacitance multiplied…
Despite significant progress in static protein structure collection and prediction, the dynamic behavior of proteins, one of their most vital characteristics, has been largely overlooked in prior research. This oversight can be attributed…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
Motivated by bacterial chemotaxis and multi-species ecological interactions in heterogeneous environments, we study a general one-dimensional reaction-cross-diffusion system in the presence of spatial heterogeneity in both transport and…
Motivated by current interest in the dynamics of trapped quantum gases, we study the microcanonical dynamics of a trapped one-dimensional gas of classical particles interacting via a finite-range repulsive force of tunable strength. We…
When modeling longitudinal biomedical data, often dimensionality reduction as well as dynamic modeling in the resulting latent representation is needed. This can be achieved by artificial neural networks for dimension reduction, and…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
In this paper, a two-step strategy for parametric sensitivity analysis for such systems is proposed, exploiting advantages and synergies between two recently proposed sensitivity analysis methodologies for stochastic dynamics. The first…
DNA shape readout is an important mechanism of target site recognition by transcription factors, in addition to the sequence readout. Several models of transcription factor-DNA binding which consider DNA shape have been developed in recent…