Related papers: Multiscale Biomolecular Simulations in the Exascal…
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…
Rapid advancements in imaging techniques and analytical methods over the past decade have revolutionized our ability to comprehensively probe the biological world at multiple scales, pinpointing the type, quantity, location, and even…
Machine Learning (ML) models are trained using historical data to classify new, unseen data. However, traditional computing resources often struggle to handle the immense amount of data, commonly known as Big Data, within a reasonable time…
The present level of development of molecular force field methods is assessed from the point of view of simulation-based engineering, outlining the immediate perspective for further development and highlighting the newly emerging discipline…
Molecular dynamics (MD) simulations provide considerable benefits for the investigation and experimentation of systems at atomic level. Their usage is widespread into several research fields, but their system size and timescale are also…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
Recent advances in spatial omics technologies have revolutionized our ability to study biological systems with unprecedented resolution. By preserving the spatial context of molecular measurements, these methods enable comprehensive mapping…
We review the computation models for biofilm and bacteria cells, providing perspectives on biofilm's various properties and potential serving as engineering living materials (ELMs), considering the omnipresence of such biological matter.…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from…
The difficulty of simulating quantum systems, well-known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on…
Spectroscopy is a crucial laboratory technique for understanding quantum systems through their interactions with electromagnetic radiation. Particularly, spectroscopy is capable of revealing the physical structure of molecules, leading to…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
We present and discuss a framework for computer-aided multiscale analysis, which enables models at a "fine" (microscopic/stochastic) level of description to perform modeling tasks at a "coarse" (macroscopic, systems) level. These…
Quantum computing is an exciting field that uses quantum principles, such as quantum superposition and entanglement, to tackle complex computational problems. Superconducting quantum circuits, based on Josephson junctions, is one of the…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
One of the important challenges facing high resolution molecular dynamics calculations is to reproduce biological functions that occur in the macroscopic world and involve macroscopic variables. Some of these functions can be well described…
Digital quantum simulation uses the capabilities of quantum computers to determine the dynamics of quantum systems, which are beyond the computability of modern classical computers. A notoriously challenging task in this field is the…