Related papers: Interface-Driven Peptide Folding: Quantum Computat…

Protein folding is a central challenge in computational biology, with important applications in molecular biology, drug discovery and catalyst design. As a hard combinatorial optimisation problem, it has been studied as a potential target…

Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…

This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…

The evolution of drug-resistant microbial species is one of the major challenges to global health. The development of new antimicrobial treatments such as antimicrobial peptides needs to be accelerated to combat this threat. However, the…

Accurate prediction of protein active-site structures remains a central challenge in structural biology, particularly for short and flexible peptide fragments where conventional and simulation-based methods often fail. Here, we present a…

An adaptive modeling method (AMM) that couples a deep neural network potential and a classical force field is introduced to address the accuracy-efficiency dilemma faced by the molecular simulation community. The AMM simulated system is…

Anticancer peptides (ACPs) are a class of molecules that have gained significant attention in the field of cancer research and therapy. ACPs are short chains of amino acids, the building blocks of proteins, and they possess the ability to…

Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present PepFlow, the first…

Soluble alpha-amylases play an important role in the catabolism of polysaccharides. In this work, we show that the enzyme can interact with the lipid membrane and further alter its mechanical properties. Vesicle fluctuation spectroscopy is…

Amphiphilic molecules and their self-assembled structures have long been the target of extensive research due to their potential applications in fields ranging from materials design to biomedical and cosmetic applications. Increasing…

Therapeutic peptides show promise in targeting previously undruggable binding sites, with recent advancements in deep generative models enabling full-atom peptide co-design for specific protein receptors. However, the critical role of…

The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…

Space plasma simulations have seen an increase in the use of magnetohydrodynamic (MHD) with embedded Particle-in-Cell (PIC) models. This combined MHD-EPIC algorithm simulates some regions of interest using the kinetic PIC method while…

Motivated by recent experimental work on multicomponent lipid membranes supported by colloidal scaffolds, we report an exhaustive theoretical investigation of the equilibrium configurations of binary mixtures on curved substrates. Starting…

De novo therapeutic design is challenged by a vast chemical repertoire and multiple constraints, e.g., high broad-spectrum potency and low toxicity. We propose CLaSS (Controlled Latent attribute Space Sampling) - an efficient computational…

We conduct an extensive study on using near-term quantum computers for a task in the domain of computational biology. By constructing quantum models based on parameterised quantum circuits we perform sequence classification on a task…

Accounting for nuclear quantum effects (NQEs) can significantly alter material properties at finite temperatures. Atomic modeling using the path-integral molecular dynamics (PIMD) method can fully account for such effects, but requires…

Electrochemical interfaces are of fundamental importance in electrocatalysis, batteries, and metal corrosion. Finite-field methods are one of most reliable approaches for modeling electrochemical interfaces in complete cells under realistic…

We propose a new scalable platform for quantum computing (QC) -- an array of optically trapped symmetric-top molecules (STMs) of the alkaline earth monomethoxide (MOCH$_3$) family. Individual STMs form qubits, and the system is readily…

Quantum computers are special purpose machines that are expected to be particularly useful in simulating strongly correlated chemical systems. The quantum computer excels at treating a moderate number of orbitals within an active space in a…