相关论文: Off-lattice simulation of the solid phase DNA ampl…

Many experimental studies of protein deposition on solid surfaces involve alternating adsorption/desorption steps. In this paper, we investigate the effect of a desorption step (separating two adsorption steps) on the kinetics, the…

Random sequential adsorption (RSA) models have been studied due to their relevance to deposition processes on surfaces. The depositing particles are represented by hard-core extended objects; they are not allowed to overlap. Numerical Monte…

We present technical details of an analysis of pseudo-scalar data from a QCD simulation with staggered fermions. The data were obtained close to the physical point with an inverse lattice spacing of about 3 GeV, and $N_f=2+1+1$. We compare…

The surrogate process approximation (SPA) is applied to model the nonequilibrium dynamics of a reaction coordinate (RC) associated with the unfolding and refolding processes of a deca-alanine peptide at 300 K. The RC dynamics, which…

Several stochastic simulation algorithms (SSAs) have been recently proposed for modelling reaction-diffusion processes in cellular and molecular biology. In this paper, two commonly used SSAs are studied. The first SSA is an on-lattice…

In this work we explore surrogate models to optimize plasma enhanced atomic layer deposition (PEALD) in high aspect ratio features. In plasma-based processes such as PEALD and atomic layer etching, surface recombination can dominate the…

We study pairs of interacting self-avoiding walks on the 3d simple cubic lattice. They have a common origin and are allowed to overlap only at the same monomer position along the chain. The latter overlaps are indeed favored by an energetic…

Our study aims at a better control and understanding of the transfer of a complex [DNA supercoiled plasmid - dodecyltrimethylammonium surfactant] layer from a liquid-vapour water interface onto a silicon surface without any additional…

We report Monte Carlo simulations of a simple off-lattice patchy-particle model for DNA `bricks'. We relate the parameters that characterise this model with the binding free energy of pairs of single-stranded DNA molecules. We verify that…

Tabular data is critical across diverse domains, yet high-quality datasets remain scarce due to privacy concerns and the cost of collection. Contemporary approaches adopt large language models (LLMs) for tabular augmentation, but exhibit…

We investigate the time-evolution and steady states of the stochastic susceptible-infected-recovered-susceptible(SIRS) epidemic model on one- and two- dimensional lattices. We compare the behavior of this system, obtained from computer…

This paper presents a two-phase protein folding optimization on a three-dimensional AB off-lattice model. The first phase is responsible for forming conformations with a good hydrophobic core or a set of compact hydrophobic amino acid…

We study a two-level dissipative non-equilibrium bosonic Rydberg system in an optical lattice, where multiple atoms can occupy a single site. The system is treated using two different approaches: solution of the master equation using a…

Due to their many potential applications, there is an increasing interest in studying hybrid systems composed of optically active media and plasmonic metamaterials. In this work we focus on a particular system which consists of an optically…

We consider an off-lattice liquid crystal pair potential in strictly two dimensions. The potential is purely repulsive and short-ranged. Nevertheless, by means of a single parameter in the potential, the system is shown to undergo a…

A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…

The spatial preferential attachment (SPA) is a model for complex networks. In the SPA model, nodes are embedded in a metric space, and each node has a sphere of influence whose size increases if the node gains an in-link, and otherwise…

Based on a newly developed contact-density chain-growth algorithm, we have simulated a nongrafted peptide in the vicinity of different attractive substrates. We analyzed the specificity of the peptide adsorption by focussing on the…

In massive multiple-input multiple-output (MIMO) downlink systems, the physical implementation of the base stations (BSs) requires the use of cheap and power-efficient power amplifiers (PAs) to avoid high hardware cost and high power…

Transformer models have achieved superior performance in various natural language processing tasks. However, the quadratic computational cost of the attention mechanism limits its practicality for long sequences. There are existing…