相关论文: Coarse-Grained Simulation of DNA using LAMMPS

Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…

Deoxyribonucleic acid (DNA) has shown great promise in enabling computational applications, most notably in the fields of DNA digital data storage and DNA computing. Information is encoded as DNA strands, which will naturally bind in…

Large language models (LLMs) have revolutionized natural language processing and are increasingly applied to other sequential data types, including genetic sequences. However, adapting LLMs to genomics presents significant challenges.…

Short, partially complementary, single-stranded (ss)DNA strands can form nanostructures with a wide variety of shapes and mechanical properties. It is well known that semiflexible, linear dsDNA can undergo an isotropic to nematic (IN) phase…

In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…

Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes…

Large Genomic Foundation Models have recently achieved remarkable results and in-vivo translation capabilities. However these models quickly grow to over a few Billion of parameters and are expensive to run when compute is limited. To…

Coarse-grained simulations of conjugated polymers have become a popular way of investigating the device physics of organic photovoltaics. While UV-Vis spectroscopy remains one of key experimental methods for the interrogation of these…

Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…

With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…

Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the…

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to…

Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…

We establish, through coarse-grained computation, a connection between traditional, continuum numerical algorithms (initial value problems as well as fixed point algorithms) and atomistic simulations of the Larson model of micelle…

Molecular Dynamics is an important tool for computational biologists, chemists, and materials scientists, consuming a sizable amount of supercomputing resources. Many of the investigated systems contain charged particles, which can only be…

This dissertation explores how deep generative models can advance the analysis of challenging biological problems by integrating domain knowledge with deep learning. It focuses on two areas: DNA reaction kinetics and cryogenic electron…

Understanding the three-dimensional (3D) structure and stability of DNA is fundamental for its biological function and the design of novel drugs. In this study, we introduce an improved coarse-grained (CG) model, incorporating a more…

We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from…

Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…

LAMMPS is a widely popular classical Molecular Dynamics package. It was designed for materials modeling but it is well prepared for simulations in Soft Matter. The use packages like LAMMPS has advantages and disadvantages. The main…