Sampling rare conformational transitions with a quantum computer

Sampling a Rare Protein Transition Using Quantum Annealing

Simulating spontaneous structural rearrangements in macromolecules with classical molecular dynamics is an outstanding challenge. Conventional supercomputers can access time intervals of up to tens of μs, while many key events occur on exponentially longer time scales. Path sampling techniques have the advantage of focusing the computational power on barrier-crossing trajectories, but generating uncorrelated transition paths that explore diverse conformational regions remains a problem. We employ a hybrid path-sampling paradigm that addresses this issue by generating trial transition paths using a quantum annealing (QA) machine. We first employ a classical computer to perform an uncharted exploration of the conformational space. The data set generated in this exploration is then postprocessed using a path integral-based method to yield a coarse-grained network representation of the reactive kinetics. By resorting to a quantum annealer, quantum superposition can be exploited to encode all of the transition pathways in the initial quantum state, thus potentially solving the path exploration problem. Furthermore, each QA cycle yields a completely uncorrelated trial trajectory. We previously validated this scheme on a prototypically simple transition, which could be extensively characterized on a desktop computer. Here, we scale up in complexity and perform an all-atom simulation of a protein conformational transition that occurs on the millisecond time scale, obtaining results that match those of the Anton special-purpose supercomputer. Despite limitations due to the available quantum annealers, our study highlights how realistic biomolecular simulations provide potentially impactful new ground for applying, testing, and advancing quantum technologies.

Quantum computing for chemistry and physics applications from a Monte Carlo perspective

This Perspective focuses on the several overlaps between quantum algorithms and Monte Carlo methods in the domains of physics and chemistry. We will analyze the challenges and possibilities of integrating established quantum Monte Carlo solutions into quantum algorithms. These include refined energy estimators, parameter optimization, real and imaginary-time dynamics, and variational circuits. Conversely, we will review new ideas for utilizing quantum hardware to accelerate the sampling in statistical classical models, with applications in physics, chemistry, optimization, and machine learning. This review aims to be accessible to both communities and intends to foster further algorithmic developments at the intersection of quantum computing and Monte Carlo methods. Most of the works discussed in this Perspective have emerged within the last two years, indicating a rapidly growing interest in this promising area of research.

The Future of Drug Development with Quantum Computing

Novel medication development is a time-consuming and expensive multistage procedure. Recent technology developments have lowered timeframes, complexity, and cost dramatically. Current research projects are driven by AI and machine learning computational models. This chapter will introduce quantum computing (QC) to drug development issues and provide an in-depth discussion of how quantum computing may be used to solve various drug discovery problems. We will first discuss the fundamentals of QC, a review of known Hamiltonians, how to apply Hamiltonians to drug discovery challenges, and what the noisy intermediate-scale quantum (NISQ) era methods and their limitations are.We will further discuss how these NISQ era techniques can aid with specific drug discovery challenges, including protein folding, molecular docking, AI-/ML-based optimization, and novel modalities for small molecules and RNA secondary structures. Consequently, we will discuss the latest QC landscape's opportunities and challenges.

Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations

Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this limitation by collecting unbiased trajectories and capturing the relevant events. Moreover, the integration of machine learning can boost the sampling while simultaneously learning a quantitative representation of the mechanism. Still, the resulting trajectories are by construction non-Boltzmann-distributed, preventing the calculation of free energies and rates. We developed an algorithm to approximate the equilibrium path ensemble from machine-learning-guided path sampling data. At the same time, our algorithm provides efficient sampling, mechanism, free energy, and rates of rare molecular events at a very moderate computational cost. We tested the method on the folding of the mini-protein chignolin. Our algorithm is straightforward and data-efficient, opening the door to applications in many challenging molecular systems.