相关论文: Facilitated diffusion of DNA-binding proteins: Eff…

A popular approach to protein design is to combine a generative model with a discriminative model for conditional sampling. The generative model samples plausible sequences while the discriminative model guides a search for sequences with…

A simple and efficient algorithm of the molecular-dynamics simulation of the hard disk system based on the Event-Driven method is developed. From the analysis of algorithm, the complexity is O(log N) per 1 event, and the constant…

Various bias-correction methods such as EXTRA, gradient tracking methods, and exact diffusion have been proposed recently to solve distributed {\em deterministic} optimization problems. These methods employ constant step-sizes and converge…

This work describes a new 1D hybrid approach for modeling atmospheric pressure discharges featuring complex chemistry. In this approach electrons are described fully kinetically using Particle-In-Cell/Monte-Carlo (PIC/MCC) scheme, whereas…

Pore-scale simulations accurately describe transport properties of fluids in the subsurface. These simulations enhance our understanding of applications such as assessing hydrogen storage efficiency and forecasting CO$_2$ sequestration…

The rapid development of AI highlights the pressing need for sustainable energy, a critical global challenge for decades. Nuclear fusion, generally seen as an ultimate solution, has been the focus of intensive research for nearly a century,…

Two separate algorithms for calculating the intermediate states, using cellular automata and the initial conditions in the rate matrix for the diffusion-collision model are introduced. They enable easy and fast calculations of the folding…

Strong experimental and theoretical evidence shows that transcription factors and other specific DNA-binding proteins find their sites using a two-mode search: alternating between 3D diffusion through the cell and 1D sliding along the DNA.…

The conformational landscape of proteins is crucial to understanding their functionality in complex biological processes. Traditional physics-based computational methods, such as molecular dynamics (MD) simulations, suffer from rare event…

We introduce a simplified technique for incorporating diffusive phenomena into lattice-gas molecular dynamics models. In this method, spatial interactions take place one dimension at a time, with a separate fractional timestep devoted to…

When addressing spatial biological questions using mathematical models, symmetries within the system are often exploited to simplify the problem by reducing its physical dimension. In a reduced-dimension model molecular movement is…

Spatial reaction-diffusion models have been employed to describe many emergent phenomena in biological systems. The modelling technique most commonly adopted in the literature implements systems of partial differential equations (PDEs),…

Aerosol injectors applied in single-particle diffractive imaging experiments demonstrated their potential in efficiently delivering nanoparticles with high density. Continuous optimization of injector design is crucial for achieving…

Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…

The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…

Bacteriophages infect cells by attaching to the outer membrane and injecting their DNA into the cell.The phage DNA is then transcribed by the cell's transcription machinery.A number of physical mechanisms by which DNA can be translocated…

This work presents a novel diffusion based dual-phase molecular communication system where the source leverages multiple cooperating nanomachines to improve the end-to-end reliability of communication. The Neyman-Pearson Likelihood Ratio…

Diffusive motion of regulatory enzymes on biopolymers with eventual capture at a reaction site is a common feature in cell biology. Using a lattice gas model we study the impact of diffusion and capture for a microtubule polymerase and a…

We present an investigation into diffusion models for molecular generation, with the aim of better understanding how their predictions compare to the results of physics-based calculations. The investigation into these models is driven by…

The need for improved engine efficiencies has motivated the development of high-pressure combustion systems, in which operating conditions achieve and exceed critical conditions. Associated with these conditions are large thermodynamic…