Related papers: Off-lattice simulation of the solid phase DNA ampl…
Nanopore sequencing offers the ability for real-time analysis of long DNA sequences at a low cost, enabling new applications such as early detection of cancer. Due to the complex nature of nanopore measurements and the high cost of…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
The physical processes at the interface of a low-temperature plasma and a solid are extremely complex. They involve a huge number of elementary processes in the plasma, in the solid as well as charge, momentum and energy transfer across the…
We discuss some large effects of dynamical fermions. One is a cutoff effect, others concern the contribution of multi-pion states to correlation functions and are expected to survive the continuum limit. We then turn to the preparation for…
We discuss the emergence of p-wave superfluidity of identical atomic fermions in a two-dimensional optical lattice. The optical lattice potential manifests itself in an interplay between an increase in the density of states on the Fermi…
We present a comprehensive model for predicting the full performance of a second harmonic generationoptical parametric amplification system that aims at enhancing the temporal contrast of laser pulses. The model simultaneously takes into…
Structural changes in giant DNA induced by the addition of the flexible polymer PEG were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule…
Laser-plasma accelerators offer a compact means of producing high-energy electron beams, but their performance is fundamentally limited by dephasing between the accelerated electrons and the plasma wave. To overcome this limitation, we…
We investigate the phase separation in one-dimensional Fermi gases on optical lattices. The density distributions and the magnetization are calculated by means of density-matrix renormalization method. The phase separation between spin-up…
We investigate effects of optical lattice potential in one- and two-dimensional two-component trapped Fermi gases with population imbalances. Using the exact diagonalization and the density matrix renormalization group methods…
The phase diagram and the location of the critical endpoint (CEP) of lattice QCD with unimproved staggered fermions on a $N_t=4$ lattice was determined fifteen years ago with the multiparameter reweighting method by studying Fisher zeros.…
We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…
We report a project to study scalar particles by lattice QCD simulations. After a brief introduction of the current situation of lattice study of the sigma meson, we describe our numerical simulations of scalar mesons, $\sigma$ and…
We present an implementation of the linear density response function within the projector-augmented wave (PAW) method with applications to the linear optical and dielectric properties of both solids, surfaces, and interfaces. The response…
We have used molecular dynamics simulations for a comprehensive study of phase separation in a two-dimensional single component off-lattice model where particles interact through the Lennard-Jones potential. Via state-of-the-art methods we…
Synthetic data offers the promise of cheap and bountiful training data for settings where labeled real-world data is scarce. However, models trained on synthetic data significantly underperform when evaluated on real-world data. In this…
Simulated nucleotide sequences are widely used in theoretical and empirical molecular evolution studies. Conventional simulators generally use fixed parameter time-homogeneous Markov model for sequence evolution. In this work, we use the…
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…
A new x-ray amplification mechanism is considered in an interaction between a x-ray and an intense visible-light laser in a plasma. In normal circumstances, the x-ray amplification from this type of the physical processes is implausible…
The melting of a homopolymer double-stranded (ds) deoxyribonucleic acid (DNA) in the dilute limit is studied numerically in the presence of an attractive and impenetrable surface on a simple cubic lattice. The two strands of the DNA are…