Related papers: Off-lattice simulation of the solid phase DNA ampl…
Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…
Spatially-structured light with tunable intensity, wavelength, and spatiotemporal profiles has demonstrated significant potentials for fundamental and applied science, including the ultrafast and high-field physics. Nevertheless, the…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
The successive projection algorithm (SPA) is a workhorse algorithm to learn the $r$ vertices of the convex hull of a set of $(r-1)$-dimensional data points, a.k.a. a latent simplex, which has numerous applications in data science. In this…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
Experiments show that the movement of eukaryotic cells is regulated by a process of phase separation of two competing enzymes on the cell membrane, that effectively amplifies shallow external gradients of chemical attractant. Notably, the…
We study an abstracted model of neuronal activity via numerical simulation, and report spatiotemporal pattern formation and critical like dynamics. A population of pulse coupled, discretised, relaxation oscillators is simulated over…
We investigate the large deviation behavior of the overlap probability density in the Sherrington--Kirkpatrick model from several analytical perspectives. First we analyze the spin glass phase using the coupled replica scheme. Here…
We developed an improved model in order to predict the RF behavior and the slow light properties of the SOA valid for any experimental conditions. It takes into account the dynamic saturation of the SOA, which can be fully characterized by…
DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating…
We examine quantum phases emerged by double degeneracy of $p$-orbital bands in attractive atomic Fermi gases loaded on a 1D optical lattice. Our numerical simulations by the density-matrix renormalization group predict the emergence of a…
The study and modelling of planar capacitors remain highly relevant due to their broad applications. However, their accurate modelling presents significant challenges due to intrinsic high-frequency effects, which include not only parasitic…
An optical lattice is a periodic light crystal constructed from the standing-wave interference patterns of laser beams. It can be used to store and manipulate quantum degenerate atoms and is an ideal platform for the quantum simulation of…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We report complex plasma experiments, assisted by numerical simulations, providing an alternative qualitative link between the macroscopic response of polycrystalline solid matter to small shearing forces and the possible underlying…
Theory of the optical parametric amplification at high-frequency pumping in crystals with a regular space modulation of the sign of nonlinear coupling coefficient of interacting waves is developed. By applying the matrix method, the theory…
Sparsity is a desirable attribute. It can lead to more efficient and more effective representations compared to the dense model. Meanwhile, learning sparse latent representations has been a challenging problem in the field of computer…
Using numerical simulations and analytical approximations we study a modified version of the two-dimensional lattice model [R. Piasecki,phys. stat. sol. (b) 209, 403 (1998)] for random pH:(1-p)L systems consisting of grains of high (low)…
We present results of an ultraviolet photoemission spectroscopy study of artificially synthesized poly(dA)-poly(dT) DNA molecules on $p$-type Si substrates. For comparison, we also present the electronic density of states (DOS) calculated…